Index: /issm/branches/trunk-jpl-ad2-integrated/AUTHORS =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/AUTHORS (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/AUTHORS (revision 18231) @@ -0,0 +1,27 @@ +Ice Sheet System Model is a JPL/UCI collaboration to develop a massively-parallelized +multi-purpose finite element framework dedicated to ice sheet modeling + +Project Scientist: + Eric Rignot + +Project Manager: + Eric Larour + +Current core developers: + * Eric Larour + * Helene Seroussi + * Mathieu Morlighem + +Contributors: + We thank the following contributors for their help in making ISSM better! + + Robert Crippen, Jet Propulsion Laboratory. robbert.crippen@jpl.nasa.gov + HoleFiller routines to plug incomplete datasets. See HoleFiller module in src/m/matlab/utils + + Point Inclusion in Polygon Test (pnpoly.c used in Utils/Arguscontourtomesh/IsInPoly.c) + W. Randolph Franklin (WRF) + http://www.ecse.rpi.edu/Homepages/wrf/Research/Short_Notes/pnpoly.html + + DACE: A Matlab Kriging toolbox, Søren N.Lophaen, Hans Bruun Nielsen and Jacob + Søndergaard (Technical University of Denmark) + http://www2.imm.dtu.dk/~hbn/dace/ Index: /issm/branches/trunk-jpl-ad2-integrated/Makefile.am =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/Makefile.am (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/Makefile.am (revision 18231) @@ -0,0 +1,5 @@ +EXTRA_DIST = reconf scripts test m4 examples cron etc doc packages contributors.txt +SUBDIRS = src +bin_SCRIPTS= README.rtf + +ACLOCAL_AMFLAGS = -I m4 Index: /issm/branches/trunk-jpl-ad2-integrated/README =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/README (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/README (revision 18231) @@ -0,0 +1,61 @@ +------------------------------------------------------------------------------ + +ISSM +Ice Sheet System Modeling: a framework for modeling ice flow on ice sheet/ice shelf +systems using Finite Elemenent Analysis, and parallel technologies. + +------------------------------------------------------------------------------ + +Jet Propulsion Laboratory + +Eric Larour (Project Manager) +Mathieu Morlighem (Core Developer, Anisotropic Meshing, Control Methods) +Helene Seroussi (Core Develper Coupling 2D-3D, Multi-model, full-Stokes) +Nicole Schlegel (Developer, Atmospheric Forcing) +Chris Borstad (Developer, Rifting/Faulting/Crack Propagation) +Feras Habbal (Developer, Solver Technologies) +Daria Halkides (Analyst, Atmospheric Forcing) +Ala Khazendar (Analyst, Ice Sheet Processes) + +Email: issm@jpl.nasa.gov + +------------------------------------------------------------------------------ + +Website: http://issm.jpl.nasa.gov/ for additional information. + +------------------------------------------------------------------------------ + +License + +ISSM is California Institute of Technology Copyright, Distributed under BSD Three Clause License. + + +Copyright (c) 2002-2011, California Institute of Technology. +All rights reserved. Based on Government Sponsored Research under contracts +NAS7-1407 and/or NAS7-03001. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. +2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. +3. Neither the name of the California Institute of Technology (Caltech), + its operating division the Jet Propulsion Laboratory (JPL), the National + Aeronautics and Space Administration (NASA), nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE CALIFORNIA INSTITUTE OF TECHNOLOGY BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +------------------------------------------------------------------------------ Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-arm-linux.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-arm-linux.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-arm-linux.sh (revision 18231) @@ -0,0 +1,14 @@ +#!/bin/sh + +./configure \ + --prefix=$ISSM_DIR\ + --libdir=$ISSM_DIR/../mobile/android/ISSM_APP/libs/armeabi\ + --build="i386-apple-darwin10.8.0"\ + --host="arm-linux-androideabi"\ + --enable-shared\ + --with-android=jni\ + --with-android-ndk=$ISSM_DIR/externalpackages/android/android-ndk/install\ + --without-fortran\ + --without-wrappers\ + --without-kriging\ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-discover.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-discover.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-discover.sh (revision 18231) @@ -0,0 +1,26 @@ +#!/bin/csh + +#PETSc 3.2 +#MPI /usr/local/intel/mpi/4.0.3.008/lib64/ + +./configure \ + --prefix=$ISSM_DIR \ + --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \ + --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mkl-dir="/usr/local/intel/mkl/10.1.2.024/lib/64/" \ + --with-mpi-include="/usr/local/intel/mpi/4.0.3.008/include64/" \ + --with-mpi-libflags="-L/usr/local/intel/mpi/4.0.3.008/lib64/ -lmpi -lmpiif" \ + --with-petsc-arch=$ISSM_ARCH \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-scalapack-dir="/usr/local/intel/mkl/10.1.2.024/lib/64/" \ + --with-blacs-dir="/usr/local/intel/mkl/10.1.2.024/lib/64/" \ + --with-blas-lapack-dir="/usr/local/intel/mkl/10.1.2.024/lib/64/" \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-O3 -xS -DMPICH_IGNORE_CXX_SEEK" \ + --with-vendor=intel-discover + Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-greenplanet.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-greenplanet.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-greenplanet.sh (revision 18231) @@ -0,0 +1,25 @@ +#!/bin/sh + +#PETSc 3.2 +#MPI /sopt/mpi/openmpi-1.5.4_psm/intel + +./configure \ + --prefix=$ISSM_DIR \ + --with-wrappers=no \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ + --with-mpi-include="/sopt/mpi/openmpi-1.5.4_psm/intel/include/" \ + --with-mpi-libflags="-L/sopt/mpi/openmpi-1.5.4_psm/intel/lib/ -lmpi -lmpi_f77" \ + --with-petsc-arch=$ISSM_ARCH \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-mkl-dir=/opt/intel/mkl/10.2.4.032/ \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-O3" \ + --with-vendor=intel-linux Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-hoffman2.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-hoffman2.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-hoffman2.sh (revision 18231) @@ -0,0 +1,18 @@ +#!/bin/csh + +./configure \ + --prefix=$ISSM_DIR \ + --with-wrappers=no \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include=/u/local/intel/11.1/openmpi/1.4.5/include \ + --with-mpi-libflags="-L/u/local/intel/11.1/openmpi/1.4.5/include -lmpi" \ + --with-petsc-arch=$ISSM_ARCH \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-O3 -L/u/local/intel/11.1/openmpi/1.4.5/lib -lmpi -lmpi_f77 -lmpi_cxx" Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-ios-linux.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-ios-linux.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-ios-linux.sh (revision 18231) @@ -0,0 +1,28 @@ +#!/bin/sh + +export DEVROOT="/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/" +export SDKROOT="$DEVROOT/SDKs/iPhoneOS6.0.sdk/" +export CC=$DEVROOT/usr/bin/gcc +export LD=$DEVROOT/usr/bin/ld +export CPP=$DEVROOT/usr/bin/cpp +export CXX=$DEVROOT/usr/bin/g++ +export CXXFLAGS="-O -arch armv7 -isysroot $SDKROOT" +export CFLAGS="-O -arch armv7 -isysroot $SDKROOT" +export AR=$DEVROOT/usr/bin/ar +export AS=$DEVROOT/usr/bin/as +export LDFLAGS="-lstdc++ -arch armv7 -isysroot $SDKROOT" +export LIBTOOL=$DEVROOT/usr/bin/libtool +export STRIP=$DEVROOT/usr/bin/strip +export RANLIB=$DEVROOT/usr/bin/ranlib + +./configure \ + --prefix=$ISSM_DIR \ + --build="i386-apple-darwin10.8.0" \ + --host="arm-apple-darwin10" \ + --enable-shared \ + --with-ios=yes \ + --without-fortran \ + --without-wrappers \ + --without-kriging \ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-acenet.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-acenet.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-acenet.sh (revision 18231) @@ -0,0 +1,17 @@ +#!/bin/bash + +./configure \ + --prefix=/home/klemorza/issm/trunk-jpl \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include=$OPENMPI/include \ + --with-mpi-libflags="-L$OPENMPI/lib -lmpi" \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-cxxoptflags="-O2" \ + --with-numthreads=32 \ + --with-serial=no \ + --with-modules=no \ + --enable-debugging CC=mpicc CXX=mpiCC F77=mpif77 Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-ad.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-ad.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-ad.sh (revision 18231) @@ -0,0 +1,20 @@ +#!/bin/sh + +./configure \ + --prefix=$ISSM_DIR \ + --without-wrappers\ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install\ + --without-thermal \ + --without-control \ + --without-hydrology \ + --without-stressbalance \ + --without-balanced \ + --without-responses \ + --without-slope \ + --without-rifts \ + --without-steadystate \ + --without-transient \ + --without-3d \ + --without-groundingline \ + --without-kriging \ + --with-adolc-dir=$ISSM_DIR/externalpackages/adolc/install Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-cloud.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-cloud.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-cloud.sh (revision 18231) @@ -0,0 +1,20 @@ +#!/bin/sh + +#External packages versions: +#petsc 3.1 or 3.2 +#mpich 1.4 + +./configure \ + --prefix=$ISSM_DIR \ + --without-wrappers \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/petsc/src/externalpackages/metis-5.0.2-p3 \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib/ -lmpich -lmpl " \ + --with-petsc-arch=$ISSM_ARCH \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-cxxoptflags=" -O2 -fpermissive" Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-cmake.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-cmake.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-cmake.sh (revision 18231) @@ -0,0 +1,2 @@ +rm $ISSM_DIR/CMakeCache.txt +cmake -D GSL_DIR=${GSL_DIR} ${ISSM_DIR} Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-larsen-ad.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-larsen-ad.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-larsen-ad.sh (revision 18231) @@ -0,0 +1,11 @@ +#!/bin/sh + +./configure \ + --prefix=$ISSM_DIR \ + --without-kriging \ + --without-kml \ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ + --with-adolc-dir=$ISSM_DIR/externalpackages/adolc/install \ + --with-adolc-version=3 \ + --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-larsen-gia.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-larsen-gia.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-larsen-gia.sh (revision 18231) @@ -0,0 +1,32 @@ +#!/bin/sh + +#External packages versions: +#petsc 3.4 +#mpich 3.0 + +./configure \ + --prefix=$ISSM_DIR \ + --with-matlab-dir=$ISSM_DIR/externalpackages/matlab/install \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/lib/python2.7/site-packages/numpy/core/include/numpy\ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib/ -lmpich -lmpl " \ + --with-petsc-arch=$ISSM_ARCH \ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ + --with-shapelib-dir="$ISSM_DIR/externalpackages/shapelib/install" \ + --with-math77-dir="$ISSM_DIR/externalpackages/math77/install" \ + --with-gia="yes"\ + --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.6/ -lgfortran" \ + --with-graphics-lib="/usr/lib/x86_64-linux-gnu/libX11.so" \ + --with-cxxoptflags="-march=opteron -O2" \ + --with-numthreads=16 \ + --enable-debugging Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-larsen.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-larsen.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-larsen.sh (revision 18231) @@ -0,0 +1,28 @@ +#!/bin/sh + +#External packages versions: +#petsc 3.4 +#mpich 3.0 + +./configure \ + --prefix=$ISSM_DIR \ + --with-matlab-dir=$ISSM_DIR/externalpackages/matlab/install \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/lib/python2.7/site-packages/numpy/core/include/numpy\ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-boost-dir=$ISSM_DIR/externalpackages/boost/install/ \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib/ -lmpich -lmpl " \ + --with-petsc-arch=$ISSM_ARCH \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ + --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.6/ -lgfortran" \ + --with-graphics-lib="/usr/lib/x86_64-linux-gnu/libX11.so" \ + --with-cxxoptflags="-march=opteron -O2" \ + --with-numthreads=16 \ + --enable-debugging Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-murdo-ad.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-murdo-ad.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-murdo-ad.sh (revision 18231) @@ -0,0 +1,10 @@ +#!/bin/sh + +./configure \ + --prefix=$ISSM_DIR \ + --without-kriging \ + --without-kml \ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ + --with-adolc-dir=$ISSM_DIR/externalpackages/adolc/install \ + --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-murdo-nopetsc.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-murdo-nopetsc.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-murdo-nopetsc.sh (revision 18231) @@ -0,0 +1,16 @@ +#!/bin/sh +./configure \ + --prefix=$ISSM_DIR\ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib/ -lmpich" \ + --with-graphics-lib="/usr/lib/x86_64-linux-gnu/libX11.so" \ + --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install\ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-numthreads=18 \ + --enable-debugging Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-murdo.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-murdo.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-murdo.sh (revision 18231) @@ -0,0 +1,26 @@ +#!/bin/sh + +#petsc 3.2 +#mpich 1.4 + +./configure \ + --prefix=$ISSM_DIR \ + --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib/ -lmpich" \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/lib/python2.7/site-packages/numpy/core/include/numpy\ + --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ + --with-petsc-arch=$ISSM_ARCH \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ + --with-graphics-lib="/usr/lib/x86_64-linux-gnu/libX11.so" \ + --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\ + --with-numthreads=18 \ + --enable-debugging + #--with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-pleiades-ampi-gcc.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-pleiades-ampi-gcc.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-pleiades-ampi-gcc.sh (revision 18231) @@ -0,0 +1,22 @@ +#!/bin/csh +./configure \ + --prefix=$ISSM_DIR \ + --without-kriging \ + --with-wrappers=no \ + --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib/ -lmpich -lmpl " \ + --with-adolc-dir="$ISSM_DIR/externalpackages/adolc/install"\ + --with-ampi-dir="$ISSM_DIR/externalpackages/adjoinablempi/install"\ + --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-blas-lapack-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-gsl-dir="$ISSM_DIR/externalpackages/gsl/install" \ + --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-hypre-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-graphics-lib="/usr/lib64/libX11.so" \ + --with-cxxoptflags=" -O3 -march=corei7-avx" \ + --with-vendor="intel-pleiades-gcc" \ + CFLAGS="-O3 -march=corei7-avx" \ + CXXFLAGS="-O3 -march=corei7-avx" \ + FFLAGS="-O3 -march=corei7-avx" Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-pleiades-ampi.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-pleiades-ampi.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-pleiades-ampi.sh (revision 18231) @@ -0,0 +1,19 @@ +#!/bin/csh +./configure \ + --prefix=$ISSM_DIR \ + --without-kriging \ + --with-wrappers=no \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-mpi-include="/nasa/sgi/mpt/2.06rp16/include" \ + --with-mpi-libflags="-L/nasa/sgi/mpt/2.06rp16/ -lmpi -lmpi++" \ + --with-adolc-dir="$ISSM_DIR/externalpackages/adolc/install"\ + --with-ampi-dir="$ISSM_DIR/externalpackages/adjoinablempi/install"\ + --with-mkl-dir="/nasa/intel/Compiler/2013.1.117/composer_xe_2013.1.117/mkl/lib/intel64" \ + --with-gsl-dir="$ISSM_DIR/externalpackages/gsl/install" \ + --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-hypre-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-graphics-lib="/usr/lib64/libX11.so" \ + --with-cxxoptflags="-O3" \ + --with-vendor="intel-pleiades" Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-pleiades-gcc-4.4.4.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-pleiades-gcc-4.4.4.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-pleiades-gcc-4.4.4.sh (revision 18231) @@ -0,0 +1,17 @@ +#!/bin/csh +./configure \ + --prefix=$ISSM_DIR \ + --without-kriging \ + --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \ + --with-petsc-arch=$ISSM_ARCH \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \ + --with-mpi-include="/nasa/mvapich2/1.4.1/gcc.sles11/include"\ + --with-mpi-libflags=" -L/nasa/mvapich2/1.4.1/gcc.sles11/lib -lmpichcxx -lmpich -lpthread -lrdmacm -libverbs -libumad -lrt" \ + --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-hypre-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-graphics-lib="/usr/lib64/libX11.so" \ + --with-cxxoptflags="-g -O2" \ + --with-vendor="intel-pleiades-gcc" Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-pleiades-gcc-4.7.0.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-pleiades-gcc-4.7.0.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-pleiades-gcc-4.7.0.sh (revision 18231) @@ -0,0 +1,18 @@ +#!/bin/csh +./configure \ + --prefix=$ISSM_DIR \ + --without-kriging \ + --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \ + --with-petsc-arch=$ISSM_ARCH \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \ + --with-mpi-include="/nasa/mvapich2/1.6.sles11/gcc/include" \ + --with-mpi-libflags="-L/nasa/mvapich2/1.6.sles11/gcc/lib -lmpich -lopa -lpthread -lrdmacm -libverbs -libumad -ldl -lrt" \ + --with-blas-lapack-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-hypre-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-graphics-lib="/usr/lib64/libX11.so" \ + --with-cxxoptflags="-g -O2" \ + --with-vendor="intel-pleiades-gcc" Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-pleiades-intel2012.0.032-mpt.2.06rp16.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-pleiades-intel2012.0.032-mpt.2.06rp16.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-pleiades-intel2012.0.032-mpt.2.06rp16.sh (revision 18231) @@ -0,0 +1,18 @@ +#!/bin/csh +./configure \ + --prefix=$ISSM_DIR \ + --without-kriging \ + --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \ + --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-petsc-arch=$ISSM_ARCH \ + --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \ + --with-mpi-include="/nasa/sgi/mpt/2.06rp16/include" \ + --with-mpi-libflags="-L/nasa/sgi/mpt/2.06rp16/ -lmpi" \ + --with-mkl-dir="/nasa/intel/Compiler/2012.0.032/composer_xe_2011_sp1/mkl/lib/intel64"\ + --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-hypre-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-graphics-lib="/usr/lib64/libX11.so" \ + --with-cxxoptflags="-g -O2" \ + --with-vendor="intel-pleiades" Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-skylla.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-skylla.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-skylla.sh (revision 18231) @@ -0,0 +1,23 @@ +#!/bin/sh + +#External packages versions: +#petsc 3.4 +#mpich 3.0 + +./configure \ + --prefix=$ISSM_DIR \ + --with-matlab-dir=$ISSM_DIR/externalpackages/matlab/install \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib/ -lmpich -lmpl " \ + --with-petsc-arch=$ISSM_ARCH \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-tao-dir=$ISSM_DIR/externalpackages/tao/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.2/ -lgfortran" \ + --with-graphics-lib="/usr/lib64/libX11.so.6" \ + --with-cxxoptflags="-g -O2" \ + --with-numthreads=8 Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-ubuntu64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-ubuntu64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-linux64-ubuntu64.sh (revision 18231) @@ -0,0 +1,25 @@ +#!/bin/sh + +./configure \ + --prefix=$ISSM_DIR \ + --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include="/usr/lib/mpich/include" \ + --with-mpi-libflags="-L/usr/lib/mpich/lib -lmpich -lmpl -ldl" \ + --with-petsc-arch=$ISSM_ARCH \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ + --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\ + --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.7/ -lgfortran"\ + --with-numthreads=8 \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --enable-debugging + + Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-macosx64-ad.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-macosx64-ad.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-macosx64-ad.sh (revision 18231) @@ -0,0 +1,18 @@ +#!/bin/sh + +./configure \ + --prefix=$ISSM_DIR \ + --without-wrappers\ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install\ + --without-thermal \ + --without-control \ + --without-hydrology \ + --without-stressbalance \ + --without-balanced \ + --without-responses \ + --without-slope \ + --without-rifts \ + --without-steadystate \ + --without-transient \ + --without-3d \ + --without-groundingline Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-macosx64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-macosx64.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/sh + +#petsc 3.4 +#mpich 3.0.4 + +./configure \ + --prefix=$ISSM_DIR \ + --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ + --with-mpi-libflags=" $ISSM_DIR/externalpackages/mpich/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich/install/lib/libmpl.a " \ + --with-petsc-arch=$ISSM_ARCH \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ + --with-fortran-lib="/usr/lib/gcc/i686-apple-darwin10/4.2.1/x86_64/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ + --with-numthreads=8 Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-pleiades-petsc3.4.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-pleiades-petsc3.4.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-pleiades-petsc3.4.sh (revision 18231) @@ -0,0 +1,20 @@ +#!/bin/csh + +./configure \ + --prefix=$ISSM_DIR \ + --with-wrappers=no \ + --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \ + --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-tao-dir="$ISSM_DIR/externalpackages/tao/install" \ + --with-mpi-include="/nasa/sgi/mpt/2.06rp16/include" \ + --with-mpi-libflags="-L/nasa/sgi/mpt/2.06rp16/ -lmpi" \ + --with-mkl-dir="/nasa/intel/Compiler/2013.1.117/composer_xe_2013.1.117/mkl/lib/intel64" \ + --with-gsl-dir="$ISSM_DIR/externalpackages/gsl/install" \ + --with-dakota-dir="$ISSM_DIR/externalpackages/dakota/install" \ + --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-hypre-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-graphics-lib="/usr/lib64/libX11.so" \ + --with-cxxoptflags="-O3" \ + --with-vendor="intel-pleiades" Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-pleiades-petscdev.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-pleiades-petscdev.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-pleiades-petscdev.sh (revision 18231) @@ -0,0 +1,25 @@ +#!/bin/csh + +./configure \ + --prefix=$ISSM_DIR \ + --with-wrappers=no \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/petsc/src/externalpackages/metis-5.0.2-p3 \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ + --with-mpi-include=/nasa/sgi/mpt/2.04/include \ + --with-mpi-libflags="-L/nasa/sgi/mpt/2.04/lib/ -lmpi -lpthread -lgfortran" \ + --with-petsc-arch=$ISSM_ARCH \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-mkl-dir=/nasa/intel/mkl/10.0.011/lib/64/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-spai-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-hypre-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-superlu-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-spooles-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-pastix-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-O3" \ + --with-vendor=intel-pleiades Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-win7-32.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-win7-32.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-win7-32.sh (revision 18231) @@ -0,0 +1,15 @@ +#!/bin/sh + +#get configure.sh to pick up the win7 Visual Studio compiler +./configure --prefix=$ISSM_DIR \ + --disable-static \ + --with-vendor=intel-win7-32 \ + --with-matlab-dir=""$ISSM_DIR/externalpackages/matlab/install"" \ + --with-blas-lapack-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \ + --with-metis-dir="$ISSM_DIR/externalpackages/metis/install" \ + --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-petsc-arch=$ISSM_ARCH \ + --with-mpi-libdir="$ISSM_DIR/externalpackages/petsc/install/lib" \ + --with-mpi-libflags="-Wl,libpetsc.lib" \ + --with-mpi-include="$ISSM_DIR/externalpackages/petsc/install/include/mpiuni" Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-win7-64-parallel.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-win7-64-parallel.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-win7-64-parallel.sh (revision 18231) @@ -0,0 +1,17 @@ +#!/bin/sh + +#Dos style path needed for the windows sdk 7.1 cl compiler: +ISSM_DIR_WIN=`cygpath -m "$ISSM_DIR"` + +#get configure.sh to pick up the win7 Visual Studio compiler +./configure --prefix=$ISSM_DIR \ + --with-vendor=intel-win7-64 \ + --with-matlab-dir="C:/MATLAB/R2012b/"\ + --with-triangle-dir="$ISSM_DIR_WIN/externalpackages/triangle/install" \ + --with-metis-dir="$ISSM_DIR_WIN/externalpackages/metis/install" \ + --with-petsc-dir="$ISSM_DIR_WIN/externalpackages/petsc/install" \ + --with-petsc-arch=$ISSM_ARCH \ + --with-blas-lapack-dir="$ISSM_DIR/externalpackages/petsc/install/lib" \ + --with-mpi-include="C:/MPICH2/include" \ + --with-mpi-libflags="-LC:/MPICH2/lib mpi.lib" + Index: /issm/branches/trunk-jpl-ad2-integrated/configs/config-win7-64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/config-win7-64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/config-win7-64.sh (revision 18231) @@ -0,0 +1,15 @@ +#!/bin/sh + +#get configure.sh to pick up the win7 Visual Studio compiler +./configure --prefix=$ISSM_DIR \ + --disable-static \ + --with-vendor=intel-win7-64 \ + --with-matlab-dir=""$ISSM_DIR/externalpackages/matlab/install"" \ + --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \ + --with-metis-dir="$ISSM_DIR/externalpackages/metis/install" \ + --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-petsc-arch=$ISSM_ARCH \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/lib/ \ + --with-mpi-libflags-dir="$ISSM_DIR/externalpackages/petsc/install/lib" \ + --with-mpi-libflagss="-Wl,libpetsc.lib" \ + --with-mpi-include-dir="$ISSM_DIR/externalpackages/petsc/install/include/mpiuni" Index: /issm/branches/trunk-jpl-ad2-integrated/configs/configure.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configs/configure.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configs/configure.sh (revision 18231) @@ -0,0 +1,19 @@ +#!/bin/sh + +#Default configuration script +#petsc 3.4 +#mpich 1.4 + +./configure \ + --prefix=$ISSM_DIR \ + --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \ + --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \ + --with-mpi-include="$ISSM_DIR/externalpackages/mpich/install/include" \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib/ -lmpich" \ + --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-petsc-arch="$ISSM_ARCH" \ + --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-blas-lapack-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install/" \ + --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install/" \ + --with-numthreads=2 Index: /issm/branches/trunk-jpl-ad2-integrated/configure.ac =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/configure.ac (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/configure.ac (revision 18231) @@ -0,0 +1,48 @@ +# Process this file with autoconf to produce a configure script. + +#AUTOCONF +AC_INIT([Ice Sheet System Model (ISSM)],[4.7],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure +AC_CONFIG_AUX_DIR([./aux-config]) #Put config files in aux-config +AC_CONFIG_MACRO_DIR([m4]) #m4 macros are located in m4 +m4_include([m4/issm_options.m4]) +AC_CANONICAL_TARGET #Determine the system type + +#Compilers +AC_PROG_CC([icc cccl cl icl gcc]) +AC_PROG_CPP +AC_PROG_CXX([icpc cccl cl icl g++]) +AC_PROG_F77([ifort g77 gfortran]) + +#Libraries and linking +AC_F77_LIBRARY_LDFLAGS +AC_PATH_XTRA #figure out X library and include paths + +#AUTOMAKE +#Initialize automake and declare foreign so that we don't need a ChangeLog, INSTALL, etc +AM_INIT_AUTOMAKE([foreign]) +AC_CONFIG_HEADERS([./config.h]) #Config file must be config.h +AM_SILENT_RULES([yes]) #Do not show compilation command by default +AM_PROG_CC_C_O +AM_PROG_AR + +#Libtool +LT_INIT + +#Run issm_options.m4 +ISSM_OPTIONS + +#List all Makefiles +AC_CONFIG_FILES([ + Makefile + src/Makefile + src/c/Makefile + src/wrappers/Makefile + src/wrappers/python/Makefile + src/wrappers/matlab/Makefile + src/mobile/Makefile + src/mobile/native/Makefile + src/m/Makefile + ]) + +#End of configure.ac +AC_OUTPUT Index: /issm/branches/trunk-jpl-ad2-integrated/etc/environment.csh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/etc/environment.csh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/etc/environment.csh (revision 18231) @@ -0,0 +1,103 @@ +#ISSM_DIR should have been defined already in your shell settings file (.bashrc, .cshrc, etc ...) + +#Load ISSM scripts +setenv PATH {$PATH}:{$ISSM_DIR}/scripts + +#MATLAB +set MATLAB_DIR="$ISSM_DIR/externalpackages/matlab/install" +if (-d MATLAB_DIR) then + setenv MATLAB_DIR {$MATLAB_DIR} + setenv PATH {$MATLAB_DIR}/bin:{$PATH} + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$MATLAB_DIR}/bin/glnxa64 +endif + +#MPI +set MPI_DIR="$ISSM_DIR/externalpackages/mpich/install" +if (-d $MPI_DIR) then + setenv MPI_DIR {$MPI_DIR} + setenv PATH {$MPI_DIR}/bin:{$PATH} + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$MPI_DIR/lib + setenv MANPATH {$MANPATH}:$MPI_DIR/man +endif + +#PETSC +set PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" +if (-d $PETSC_DIR) then + setenv PETSC_DIR {$PETSC_DIR} + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$PETSC_DIR/lib +endif + +#SLEPC +set SLEPC_DIR="$ISSM_DIR/externalpackages/slepc/install" +if (-d $SLEPC_DIR) then + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$SLEPC_DIR/lib +endif + +#PETSC +set TAO_DIR="$ISSM_DIR/externalpackages/tao/install" +if (-d $TAO_DIR) then + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$TAO_DIR/lib +endif + +#Dakota +set DAKOTA_DIR="$ISSM_DIR/externalpackages/dakota/install" +if (-d $DAKOTA_DIR) then + setenv PATH {$PATH}:{$DAKOTA_DIR}/bin + setenv MANPATH {$MANPATH}:{$MPI_DIR}/man:{$DAKOTA_DIR}/docs/man:{$DAKOTA_DIR}/docs/man-ref +endif + +#Doxygen +set DOXYGEN_DIR="$ISSM_DIR/externalpackages/doxygen/install" +if (-d $DOXYGEN_DIR) then + setenv MANPATH {$MANPATH}:{$DOXYGEN_DIR}/man + setenv PATH {$PATH}:{$DOXYGEN_DIR}/bin +endif + +#AUTOTOOLS +set AUTOTOOLS_DIR="$ISSM_DIR/externalpackages/autotools/install" +if (-d $AUTOTOOLS_DIR) then + setenv PATH {$AUTOTOOLS_DIR}/bin:{$PATH} +endif + +#SSH +set SSH_DIR="$ISSM_DIR/externalpackages/ssh" +if (-d $SSH_DIR) then + setenv PATH {$PATH}:{$SSH_DIR} +endif + +#VALGRIND +set VALGRIND_DIR="$ISSM_DIR/externalpackages/valgrind/install/bin" +if (-d $VALGRIND_DIR) then + setenv PATH {$PATH}:{$VALGRIND_DIR} +endif + +#MERCURIAL +set MERCURIAL_DIR="$ISSM_DIR/externalpackages/mercurial/install" +if (-d $MERCURIAL_DIR) then + setenv PYTHONPATH {$MERCURIAL_DIR}/mercurial/pure/ + setenv PATH {$PATH}:{$MERCURIAL_DIR} +endif + +#GSL +set GSL_DIR="$ISSM_DIR/externalpackages/gsl/install" +if (-d $GSL_DIR) then + setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$GSL_DIR}/lib +endif + +#CMAKE +set CMAKE_DIR="$ISSM_DIR/externalpackages/cmake/install" +if (-d $CMAKE_DIR) then + setenv PATH {$CMAKE_DIR}/bin:{$PATH} +endif + +#YAMS +set YAMS_DIR="$ISSM_DIR/externalpackages/yams/install" +if (-d $YAMS_DIR) then + setenv PATH {$PATH}:{$YAMS_DIR}/bin +endif + +#SHELL2JUNIT +set SHELL2JUNIT_DIR="$ISSM_DIR/externalpackages/shell2junit" +if (-d $SHELL2JUNIT_DIR) then + setenv PATH {$PATH}:{$SHELL2JUNIT_DIR}/install +endif Index: /issm/branches/trunk-jpl-ad2-integrated/etc/environment.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/etc/environment.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/etc/environment.sh (revision 18231) @@ -0,0 +1,307 @@ +#ISSM_DIR and ISSM_ARCH should have been defined already in your shell settings file (.bashrc, .cshrc, etc ...) + +pathprepend(){ #{{{ + if [ -d "$1" ] && [[ ":$PATH:" != *":$1:"* ]]; then + name=$1 + if [[ "$ISSM_ARCH" == "cygwin-intel" ]]; then + #export path using the cygwin convention + name=`cygpath -u $1` + fi + export PATH="$name:$PATH" + fi +} #}}} +pathappend(){ #{{{ + if [ -d "$1" ] && [[ ":$PATH:" != *":$1:"* ]]; then + name=$1 + if [[ "$ISSM_ARCH" == "cygwin-intel" ]]; then + #export path in cygwin convention + name=`cygpath -u $1` + fi + export PATH="$PATH:$name" + fi +} #}}} +libpathprepend(){ #{{{ + if [ -d "$1" ] && [[ ":$LD_LIBRARY_PATH:" != *":$1:"* ]]; then + export LD_LIBRARY_PATH="$1:$LD_LIBRARY_PATH" + fi + if [ -d "$1" ] && [[ ":$LD_RUN_PATH:" != *":$1:"* ]]; then + export LD_RUN_PATH="$1:$LD_RUN_PATH" + fi +} #}}} +libpathappend(){ #{{{ + if [ -d "$1" ] && [[ ":$LD_LIBRARY_PATH:" != *":$1:"* ]]; then + export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$1" + fi + if [ -d "$1" ] && [[ ":$LD_RUN_PATH:" != *":$1:"* ]]; then + export LD_RUN_PATH="$LD_RUN_PATH:$1" + fi +} #}}} +dylibpathprepend(){ #{{{ + if [ -d "$1" ] && [[ ":$DYLD_LIBRARY_PATH:" != *":$1:"* ]]; then + export DYLD_LIBRARY_PATH="$1:$DYLD_LIBRARY_PATH" + fi + if [ -d "$1" ] && [[ ":$LD_RUN_PATH:" != *":$1:"* ]]; then + export LD_RUN_PATH="$1:$LD_RUN_PATH" + fi +} #}}} +dylibpathappend(){ #{{{ + if [ -d "$1" ] && [[ ":$DYLD_LIBRARY_PATH:" != *":$1:"* ]]; then + export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$1" + fi + if [ -d "$1" ] && [[ ":$LD_RUN_PATH:" != *":$1:"* ]]; then + export LD_RUN_PATH="$LD_RUN_PATH:$1" + fi +} #}}} + +#FIXME: during installation packages are installed one by one but environment.sh was sourced +#before so new packages are NOT in the path. +#may resource environment.sh with: +#if [ -z $(echo "$PATH" | grep "$MATLAB_DIR") ]; then export $PATH...; fi + +#Windows compilers: +if [[ "$ISSM_ARCH" == "cygwin-intel" ]]; then + source $ISSM_DIR/externalpackages/windows/windows_environment.sh +fi + +#Load ISSM scripts +pathappend "$ISSM_DIR/scripts" + +MATLAB_DIR="$ISSM_DIR/externalpackages/matlab/install" +export MATLAB_DIR +pathprepend "$MATLAB_DIR/bin" #take precedence over /usr/local/bin/matlab +libpathappend "$MATLAB_DIR/lib" + +#legacy mpich2 (To be removed) +MPI_DIR="$ISSM_DIR/externalpackages/mpich2/install" +if [ -d "$MPI_DIR" ]; then + export MPI_DIR + pathprepend "$MPI_DIR/bin" + libpathappend "$MPI_DIR/lib" +fi + +MPI_DIR="$ISSM_DIR/externalpackages/mpich/install" +if [ -d "$MPI_DIR" ]; then + export MPI_DIR + pathprepend "$MPI_DIR/bin" + libpathappend "$MPI_DIR/lib" +fi + +export MPI_INC_DIR="$MPI_DIR/include" + +PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" +export PETSC_DIR +libpathappend "$PETSC_DIR/lib" + +SLEPC_DIR="$ISSM_DIR/externalpackages/slepc/install" +libpathappend "$SLEPC_DIR/lib" + +TAO_DIR="$ISSM_DIR/externalpackages/tao/install" +libpathappend "$TAO_DIR/lib" + +DAKOTA_DIR="$ISSM_DIR/externalpackages/dakota/install" +pathappend "$DAKOTA_DIR/bin" +libpathappend "$DAKOTA_DIR/lib" +dylibpathprepend "$DAKOTA_DIR/lib" + +DOXYGEN_DIR="$ISSM_DIR/externalpackages/doxygen/install" +pathprepend "$DOXYGEN_DIR/bin" + +AUTOTOOLS_DIR="$ISSM_DIR/externalpackages/autotools/install" +pathprepend "$AUTOTOOLS_DIR/bin" + +SDK_DIR="C:/MicrosoftVisualStudio 9.0/Microsoft Visual C++ 2008 Express Edition with SP1 - ENU" +pathappend "$SDK_DIR" + +SSH_DIR="$ISSM_DIR/externalpackages/ssh" +pathappend "$SSH_DIR" + +VALGRIND_DIR="$ISSM_DIR/externalpackages/valgrind/install" +pathprepend "$VALGRIND_DIR/bin" + +CPPCHECK_DIR="$ISSM_DIR/externalpackages/cppcheck/install" +pathappend "$CPPCHECK_DIR/bin" + +GDAL_DIR="$ISSM_DIR/externalpackages/gdal/install" +pathprepend "$GDAL_DIR/bin" +libpathappend "$GDAL_DIR/lib" + +PROJ4_DIR="$ISSM_DIR/externalpackages/proj.4/install" +dylibpathprepend "$PROJ4_DIR/lib" +libpathprepend "$PROJ4_DIR/lib" + +MERCURIAL_DIR="$ISSM_DIR/externalpackages/mercurial/install" +if [ -d "$MERCURIAL_DIR" ]; then + export PYTHONPATH="$PYTHONPATH:$MERCURIAL_DIR/mercurial/pure/" + pathappend "$MERCURIAL_DIR" +fi + +BOOST_DIR="$ISSM_DIR/externalpackages/boost/install" +BOOSTROOT="$ISSM_DIR/externalpackages/boost/install" +if [ -d "$BOOST_DIR" ]; then + export BOOSTROOT + export BOOST_DIR + libpathappend "$BOOST_DIR/lib" + dylibpathappend "$BOOST_DIR/lib" + pathappend "$BOOST_DIR/bin" +fi + +XERCESROOT="$ISSM_DIR/externalpackages/xerces/install" +XERCESCROOT="$ISSM_DIR/externalpackages/xerces/src" +if [ -d "$XERCESROOT" ]; then + export XERCESROOT + export XERCESCROOT +fi + +XAIF_DIR="$ISSM_DIR/externalpackages/xaifbooster/xaifBooster" +XAIFBOOSTERROOT="$ISSM_DIR/externalpackages/xaifbooster/" +XAIFBOOSTER_HOME="$ISSM_DIR/externalpackages/xaifbooster/xaifBooster" +PLATFORM="x86-Linux" +if [ -d "$XAIF_DIR" ]; then + export XAIFBOOSTERROOT + export XAIFBOOSTER_HOME + export XAIF_DIR + export PLATFORM +fi + +ANGELROOT="$ISSM_DIR/externalpackages/angel/angel" +if [ -d "$ANGELROOT" ]; then + export ANGELROOT +fi + +OPENANALYSISROOT="$ISSM_DIR/externalpackages/openanalysis/install" +if [ -d "$OPENANALYSISROOT" ]; then + export OPENANALYSISROOT + libpathappend "$OPENANALYSISROOT/lib" +fi + +JVM_DIR="/usr/local/gcc/4.3.2/lib64/gcj-4.3.2-9/" +libpathappend "$JVM_DIR" + +BBFTP_DIR="$ISSM_DIR/externalpackages/bbftp/install" +pathappend "$BBFTP_DIR/bin" + +ADIC_DIR="$ISSM_DIR/externalpackages/adic/install" +pathappend "$ADIC_DIR/bin" +libpathappend "$ADIC_DIR/lib" + +COLPACK_DIR="$ISSM_DIR/externalpackages/colpack/install" +libpathappend "$COLPACK_DIR/lib" + +ECLIPSE_DIR="$ISSM_DIR/externalpackages/eclipse/install" +pathappend "$ECLIPSE_DIR" + +APPSCAN_DIR="$ISSM_DIR/externalpackages/appscan/install" +pathappend "$APPSCAN_DIR/bin" + +RATS_DIR="$ISSM_DIR/externalpackages/rats/install" +pathappend "$RATS_DIR/bin" + +DYSON_DIR="$ISSM_DIR/externalpackages/dyson/" +pathappend "$DYSON_DIR" + +CMAKE_DIR="$ISSM_DIR/externalpackages/cmake/install" +pathprepend "$CMAKE_DIR/bin" + +SHAPELIB_DIR="$ISSM_DIR/externalpackages/shapelib/install" +pathappend "$SHAPELIB_DIR/exec" + +CCCL_DIR="$ISSM_DIR/externalpackages/cccl/install" +pathappend "$CCCL_DIR/bin" + +PACKAGEMAKER_DIR="$ISSM_DIR/externalpackages/packagemaker/install" +pathappend "$PACKAGEMAKER_DIR" + +#android-dev-dir +export ANDROID_DIR="$ISSM_DIR/externalpackages/android" + +export ANDROID_NDK_DIR="$ANDROID_DIR/android-ndk/install" +pathappend "$ANDROID_NDK_DIR/arm-linux-android-install/bin" + +export ANDROID_SDK_DIR="$ANDROID_DIR/android-sdk/install" +pathappend "$ANDROID_SDK_DIR/" + +GSL_DIR="$ISSM_DIR/externalpackages/gsl/install" +libpathappend "$GSL_DIR/lib" + +GMAKE_DIR="$ISSM_DIR/externalpackages/gmake/install" +pathprepend "$GMAKE_DIR/bin" + +PYTHON_DIR="$ISSM_DIR/externalpackages/python/install" +if [ -d "$PYTHON_DIR" ]; then + export PYTHONPATH="$PYTHONPATH:$ISSM_DIR/lib" + pathprepend "$PYTHON_DIR/bin" + libpathprepend "$PYTHON_DIR/lib" + libpathprepend "$ISSM_DIR/lib" +fi + +MODELE_DIR="$ISSM_DIR/externalpackages/modelE/install" +pathappend "$MODELE_DIR/src/exec" + +GIT_DIR="$ISSM_DIR/externalpackages/git/install" +pathprepend "$GIT_DIR/bin" + +NCVIEW_DIR="$ISSM_DIR/externalpackages/ncview/install" +pathappend "$NCVIEW_DIR" + +TCLX_DIR="$ISSM_DIR/externalpackages/tclx/install/lib/tclx8.4" +libpathappend "$TCLX_DIR" + +ASPELL_DIR="$ISSM_DIR/externalpackages/aspell/install" +pathappend "$ASPELL_DIR/bin" + +HDF5_DIR="$ISSM_DIR/externalpackages/hdf5/install" +dylibpathappend "$HDF5_DIR/lib" +libpathappend "$HDF5_DIR/lib" +if [ -d "$HDF5_DIR" ]; then + export LIBRARY_PATH="$LIBRARY_PATH:$HDF5_DIR/lib" + export C_INCLUDE_PATH="$C_INCLUDE_PATH:$HDF5_DIR/include" +fi + +NETCDF_DIR="$ISSM_DIR/externalpackages/netcdf/install" +pathappend "$NETCDF_DIR/bin" +dylibpathappend "$NETCDF_DIR/lib" +libpathappend "$NETCDF_DIR/lib" +if [ -d "$NETCDF_DIR" ]; then + export LIBRARY_PATH="$LIBRARY_PATH:$NETCDF_DIR/lib" + dylibpathappend "$NETCDF_DIR/lib" + libpathappend "$NETCDF_DIR/lib" + export C_INCLUDE_PATH="$C_INCLUDE_PATH:$NETCDF_DIR/include" +fi + +NETCDF_CXX_DIR="$ISSM_DIR/externalpackages/netcdf-cxx/install" +libpathappend "$NETCDF_CXX_DIR/lib" + +SVN_DIR="$ISSM_DIR/externalpackages/svn/install" +pathprepend "$SVN_DIR/bin" +libpathappend "$SVN_DIR/lib" + +APR_DIR="$ISSM_DIR/externalpackages/apr/install" +pathappend "$APR_DIR/bin" +libpathappend "$APR_DIR/lib" + +APR_UTIL_DIR="$ISSM_DIR/externalpackages/apr-util/install" +pathappend "$APR_UTIL_DIR/bin:$PATH" +libpathappend "$APR_UTIL_DIR/lib" + +SQLITE_DIR="$ISSM_DIR/externalpackages/sqlite/install" +pathappend "$SQLITE_DIR/bin" +libpathappend "$SQLITE_DIR/lib" + +YAMS_DIR="$ISSM_DIR/externalpackages/yams/install" +pathappend "$YAMS_DIR" + +SWIG_DIR="$ISSM_DIR/externalpackages/swig/install" +pathappend "$SWIG_DIR" + +#AUX-CONFIG +pathappend "$ISSM_DIR/aux-config" + +#INISHELL +pathappend "$ISSM_DIR/externalpackages/inishell/install" + +#SHELL2JUNIT +pathappend "$ISSM_DIR/externalpackages/shell2junit/install" + +#EXPAT +libpathprepend "$ISSM_DIR/externalpackages/expat/install" +dylibpathprepend "$ISSM_DIR/externalpackages/expat/install" Index: /issm/branches/trunk-jpl-ad2-integrated/examples/Data/Download.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/Data/Download.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/Data/Download.sh (revision 18231) @@ -0,0 +1,25 @@ +#!/bin/bash + +echo "Downloading Square shelf dataset" +$ISSM_DIR/scripts/DownloadExternalPackage2.py 'http://issm.jpl.nasa.gov/files/workshop2014/SquareShelf.nc' 'SquareShelf.nc' + +echo "Downloading SeaRISE dataset - Antarctica" +$ISSM_DIR/scripts/DownloadExternalPackage2.py 'http://websrv.cs.umt.edu/isis/images/c/cc/Antarctica_5km_withshelves_v0.75.nc' 'Antarctica_5km_withshelves_v0.75.nc' + +echo "Downloading InSAR Antarctic velocities" +$ISSM_DIR/scripts/DownloadExternalPackage2.py 'ftp://sidads.colorado.edu/pub/DATASETS/nsidc0484_MEASURES_antarc_vel_V01/900m/antarctica_ice_velocity.nc' 'Antarctica_ice_velocity.nc' + +echo "Downloading PIG errors" +$ISSM_DIR/scripts/DownloadExternalPackage2.py 'http://issm.jpl.nasa.gov/files/workshop2014/CrossOvers2009.mat' 'CrossOvers2009.mat' + +echo "Downloading SeaRISE dataset - Greenland" +$ISSM_DIR/scripts/DownloadExternalPackage2.py 'http://websrv.cs.umt.edu/isis/images/e/e9/Greenland_5km_dev1.2.nc' 'Greenland_5km_dev1.2.nc' + +echo "Downloading Jason Box's SMB" +$ISSM_DIR/scripts/DownloadExternalPackage2.py 'http://issm.jpl.nasa.gov/files/workshop2014/Box_Greenland_SMB_monthly_1840-2012_5km_ver20140421.nc' 'Box_Greenland_SMB_monthly_1840-2012_5km_ver20140421.nc' + +echo "Downloading IceBridge Jakobshavn bedrock" +$ISSM_DIR/scripts/DownloadExternalPackage2.py 'https://data.cresis.ku.edu/data/grids/old_versions/Jakobshavn_2008_2011_Composite.zip' 'Jakobshavn_2008_2011_Composite.zip' +unzip Jakobshavn_2008_2011_Composite.zip +mv Jakobshavn_2008_2011_Composite/grids/Jakobshavn_2008_2011_Composite_XYZGrid.txt . +rm -rf Jakobshavn_2008_2011_Composite Jakobshavn_2008_2011_Composite.zip Index: /issm/branches/trunk-jpl-ad2-integrated/examples/Greenland/DomainOutline.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/Greenland/DomainOutline.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/Greenland/DomainOutline.exp (revision 18231) @@ -0,0 +1,733 @@ +## Name:DomainOutline +## Icon:0 +# Points Count Value +727 1.000000 +# X pos Y pos +47662.8073760000 -2621047.2585999998 +39869.9055420000 -2638077.6292949999 +26037.5047870000 -2644088.3483640002 +24868.5695120000 -2659115.1460360000 +25647.8596950000 -2674141.9437079998 +16880.8451320000 -2687666.0616130000 +515.7512810000 -2685662.4885900002 +-7666.7956450000 -2672639.2639410002 +-22083.6640370000 -2677147.3032430001 +-30071.3884170000 -2690170.5278920000 +-44683.0793550000 -2694678.5671930001 +-41760.7411680000 -2709705.3648660001 +-37669.4677050000 -2724231.2692820001 +-44488.2568100000 -2738757.1736989999 +-55787.9644690000 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+41818.1310010000 -2586610.8472679998 +30810.6571600000 -2599133.1786610000 +44253.4128240000 -2608650.1505200001 +47662.8073760000 -2621047.2585999998 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/Greenland/Greenland.par =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/Greenland/Greenland.par (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/Greenland/Greenland.par (revision 18231) @@ -0,0 +1,82 @@ +%Name and hemisphere +md.miscellaneous.name='SeaRISEgreenland'; +md.mesh.hemisphere='n'; + +disp(' Loading SeaRISE data from NetCDF'); +ncdata='../Data/Greenland_5km_dev1.2.nc'; +x1 = ncread(ncdata,'x1'); +y1 = ncread(ncdata,'y1'); +usrf = ncread(ncdata,'usrf')'; +topg = ncread(ncdata,'topg')'; +velx = ncread(ncdata,'surfvelx')'; +vely = ncread(ncdata,'surfvely')'; +temp = ncread(ncdata,'airtemp2m')'; +smb = ncread(ncdata,'smb')'; +gflux = ncread(ncdata,'bheatflx')'; + +disp(' Interpolating surface and bedrock'); +md.geometry.base = InterpFromGridToMesh(x1,y1,topg,md.mesh.x,md.mesh.y,0); +md.geometry.surface = InterpFromGridToMesh(x1,y1,usrf,md.mesh.x,md.mesh.y,0); + +disp(' Constructing thickness'); +md.geometry.thickness=md.geometry.surface-md.geometry.base; + +%Set min thickness to 1 meter +pos0=find(md.geometry.thickness<=0); +md.geometry.thickness(pos0)=1; +md.geometry.surface=md.geometry.thickness+md.geometry.base; + +disp(' Interpolating velocities '); +md.inversion.vx_obs = InterpFromGridToMesh(x1,y1,velx,md.mesh.x,md.mesh.y,0); +md.inversion.vy_obs = InterpFromGridToMesh(x1,y1,vely,md.mesh.x,md.mesh.y,0); +md.inversion.vel_obs = sqrt(md.inversion.vx_obs.^2+md.inversion.vy_obs.^2); +md.initialization.vx = md.inversion.vx_obs; +md.initialization.vy = md.inversion.vy_obs; +md.initialization.vz = zeros(md.mesh.numberofvertices,1); +md.initialization.vel= md.inversion.vel_obs; + +disp(' Interpolating temperatures'); +md.initialization.temperature=InterpFromGridToMesh(x1,y1,temp,md.mesh.x,md.mesh.y,0)+273.15; + +disp(' Interpolating surface mass balance'); +md.surfaceforcings.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); +md.surfaceforcings.mass_balance=md.surfaceforcings.mass_balance*md.materials.rho_water/md.materials.rho_ice; + +disp(' Construct basal friction parameters'); +md.friction.coefficient=30*ones(md.mesh.numberofvertices,1); +pos=find(md.mask.groundedice_levelset<0); +md.friction.coefficient(pos)=0; %no friction applied on floating ice +md.friction.p=ones(md.mesh.numberofelements,1); +md.friction.q=ones(md.mesh.numberofelements,1); + +disp(' Construct ice rheological properties'); +md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); +md.materials.rheology_B=paterson(md.initialization.temperature); +md.friction.q=ones(md.mesh.numberofelements,1); +md.friction.p=ones(md.mesh.numberofelements,1); + +disp(' Set other boundary conditions'); +md.mask.ice_levelset(md.mesh.vertexonboundary==1)=0; +md.basalforcings.floatingice_melting_rate = zeros(md.mesh.numberofvertices,1); +md.basalforcings.groundedice_melting_rate = zeros(md.mesh.numberofvertices,1); +md.thermal.spctemperature = [md.initialization.temperature;1]; %impose observed temperature on surface +md.masstransport.spcthickness = NaN*ones(md.mesh.numberofvertices,1); + +disp(' Set geothermal heat flux'); +md.basalforcings.geothermalflux=InterpFromGridToMesh(x1,y1,gflux,md.mesh.x,md.mesh.y,0); + +disp(' Set Pressure'); +md.initialization.pressure=md.materials.rho_ice*md.constants.g*md.geometry.thickness; + +disp(' Single point constraint for continental model'); +%Set at least one vertex to velocity 0 so as to not get a singular problem (point on the wet peninsula) +md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6); +md.stressbalance.spcvx = NaN*ones(md.mesh.numberofvertices,1); +md.stressbalance.spcvy = NaN*ones(md.mesh.numberofvertices,1); +md.stressbalance.spcvz = NaN*ones(md.mesh.numberofvertices,1); +location = 1.0e+06 *[.32011 -2.2039]; +[dist pos]=min(sqrt((md.mesh.x - location(1)).^2 + (md.mesh.y - location(2)).^2)); +md.stressbalance.spcvx(pos) = 0; +md.stressbalance.spcvy(pos) = 0; +md.stressbalance.spcvz(pos) = 0; + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/Greenland/Jak_grounded.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/Greenland/Jak_grounded.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/Greenland/Jak_grounded.exp (revision 18231) @@ -0,0 +1,19 @@ +## Name:Jak_grouded +## Icon:0 +# Points Count Value +13 1.000000 +# X pos Y pos +-414397.6663804040 -2243466.6708395295 +-421486.9037621063 -2215731.3059818177 +-342860.8164377716 -2178965.8223332223 +-275835.2993744044 -2209281.2211311869 +-226210.6377024883 -2262816.9253914217 +-228144.0660793162 -2295067.3496445753 +-333193.6745536321 -2328607.7908678548 +-379595.9555975018 -2325382.7484425395 +-422775.8560133249 -2285392.2223686292 +-427287.1888925899 -2265396.9593316740 +-411819.7618779668 -2254431.8150856020 +-413108.7141291854 -2243466.6708395295 +-414397.6663804040 -2243466.6708395295 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/Greenland/Jak_outline.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/Greenland/Jak_outline.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/Greenland/Jak_outline.exp (revision 18231) @@ -0,0 +1,17 @@ +## Name:Jak +## Icon:0 +# Points Count Value +11 1.000000 +# X pos Y pos +-421561.7247949215 -2216716.3488182197 +-386019.6416099078 -2203459.4896082953 +-351446.8879663036 -2185999.2360147359 +-289086.6874689616 -2214129.6445821370 +-255160.1535196303 -2282353.9688088228 +-340138.0433165266 -2317597.8140254519 +-383306.1449952667 -2302506.6581698526 +-416391.9672407377 -2279120.5885137189 +-448056.7322601135 -2246463.4475331730 +-429126.8716234095 -2231167.6696134652 +-421561.7247949215 -2216716.3488182197 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/Greenland/runme.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/Greenland/runme.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/Greenland/runme.m (revision 18231) @@ -0,0 +1,272 @@ +clear all; +steps=[1]; + +%Location of SeaRISE dataset +ncdata='../Data/Greenland_5km_dev1.2.nc'; + +if any(steps==1) + disp(' Step 1: Mesh creation'); + + %Generate initial uniform mesh (resolution = 20000 m) + md=triangle(model,'./DomainOutline.exp',20000); + + % Get velocities (Note: You can use ncdisp('file') to see an ncdump) + x1 = ncread(ncdata,'x1'); + y1 = ncread(ncdata,'y1'); + velx = ncread(ncdata,'surfvelx'); + vely = ncread(ncdata,'surfvely'); + vx = InterpFromGridToMesh(x1,y1,velx',md.mesh.x,md.mesh.y,0); + vy = InterpFromGridToMesh(x1,y1,vely',md.mesh.x,md.mesh.y,0); + vel = sqrt(vx.^2+vy.^2); + + %Mesh Greenland + md=bamg(md,'hmax',400000,'hmin',5000,'gradation',1.7,'field',vel,'err',8); + + %convert x,y coordinates (Polar stereo) to lat/lon + [md.mesh.lat,md.mesh.long]=xy2ll(md.mesh.x,md.mesh.y,+1,39,71); + + save ./Models/Greenland.Mesh_generation md; + + plotmodel (md,'data','mesh'); +end + +if any(steps==2) + disp(' Step 2: Parameterization'); + md = loadmodel('./Models/Greenland.Mesh_generation'); + + md = setmask(md,'',''); + md = parameterize(md,'./Greenland.par'); + md = setflowequation(md,'SSA','all'); + + save ./Models/Greenland.Parameterization md; +end + +if any(steps==3) + disp(' Step 3: Control method friction'); + md = loadmodel('./Models/Greenland.Parameterization'); + + %Control general + md.inversion.iscontrol=1; + md.inversion.nsteps=30; + md.inversion.step_threshold=0.99*ones(md.inversion.nsteps,1); + md.inversion.maxiter_per_step=5*ones(md.inversion.nsteps,1); + + %Cost functions + md.inversion.cost_functions=[101 103 501]; + md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,3); + md.inversion.cost_functions_coefficients(:,1)=350; + md.inversion.cost_functions_coefficients(:,2)=0.6; + md.inversion.cost_functions_coefficients(:,3)=2e-6; + + %Controls + md.inversion.control_parameters={'FrictionCoefficient'}; + md.inversion.gradient_scaling(1:md.inversion.nsteps)=50; + md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); + md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); + + %Additional parameters + md.stressbalance.restol=0.01; md.stressbalance.reltol=0.1; + md.stressbalance.abstol=NaN; + + %Go solve + md.cluster=generic('name',oshostname,'np',2); + md.toolkits=toolkits; + md.verbose=verbose('solution',true,'control',true); + md=solve(md,StressbalanceSolutionEnum); + + %Update model friction fields accordingly + md.friction.coefficient=md.results.StressbalanceSolution.FrictionCoefficient; + + save ./Models/Greenland.Control_drag md; +end + +if any(steps==4) + disp(' Step 4: Transient run'); + md = loadmodel('./Models/Greenland.Control_drag'); + + %Set surface mass balance + x1 = ncread(ncdata,'x1'); + y1 = ncread(ncdata,'y1'); + smb = ncread(ncdata,'smb'); + smb = InterpFromGridToMesh(x1,y1,smb',md.mesh.x,md.mesh.y,0); + smb = smb*md.materials.rho_freshwater/md.materials.rho_ice; + smb = [smb smb smb-1.0]; + md.surfaceforcings.mass_balance = [smb;1 10 20]; + + %Set transient options, run for 20 years, saving every timestep + md.timestepping.time_step=0.2; + md.timestepping.final_time=20; + md.settings.output_frequency=1; + + %Additional options + md.inversion.iscontrol=0; + md.transient.requested_outputs={'IceVolume','TotalSmb', ... + 'SurfaceforcingsMassBalance'}; + md.verbose=verbose('solution',true,'module',true,'convergence',true); + + %Go solve + md.cluster=generic('name',oshostname,'np',2); + md=solve(md,TransientSolutionEnum); + + save ./Models/Greenland.Transient md; +end + +if any(steps==5) + disp(' Step 5: Plotting'); + md = loadmodel('./Models/Greenland.Transient'); + %md = loadmodel('./Models/Greenland.HistoricTransient'); + + %Planview plots + plotmodel(md,'data',md.results.TransientSolution(end).Vel,'caxis',[1e-1 6000],... + 'log', 10, 'title', 'Velocity (m/y)','gridded',1, ... + 'data', md.results.TransientSolution(1).SurfaceforcingsMassBalance, ... + 'title', 'Surface mass balance (m/y)', 'gridded',1,... + 'data',md.results.TransientSolution(end).Thickness,... + 'title','Thickness (m)', 'gridded',1, ... + 'data',md.results.TransientSolution(end).Surface, ... + 'title', 'Surface (m)', 'gridded',1); + + %Line Plots + figure + + %Plot surface mass balance + surfmb=[]; for i=1:100; surfmb=[surfmb ... + md.results.TransientSolution(i).SurfaceforcingsMassBalance]; end + subplot(3,1,1); plot([0.2:0.2:20],mean(surfmb)); title('Mean Surface mass balance'); + + %Plot velocity + vel=[]; for i=1:100; vel=[vel md.results.TransientSolution(i).Vel]; end + subplot(3,1,2); plot([0.2:0.2:20],mean(vel)); title('Mean Velocity'); + + %Plot Volume + volume=[]; for i=1:100; volume=[volume md.results.TransientSolution(i).IceVolume]; end + subplot(3,1,3); plot([0.2:0.2:20],volume); title('Ice Volume'); + xlabel('years') +end + +if any(steps==6) + disp(' Step 6: Historical Relaxation run'); + md = loadmodel('./Models/Greenland.Control_drag'); + + ncbox='../Data/Box_Greenland_SMB_monthly_1840-2012_5km_ver20140421.nc'; + + %convert mesh x,y into the Box projection + [md.mesh.lat,md.mesh.long] = xy2ll(md.mesh.x,md.mesh.y,+1,39,71); + [xi,yi]= ll2xy(md.mesh.lat,md.mesh.long,+1,45,70); + + %Set surface mass balance + lat = ncread(ncbox,'lat'); + lon = ncread(ncbox,'lon'); + smbbox = ncread(ncbox,'SMB'); + [x1 y1]=ll2xy(lat,lon,+1,45,70); + + %surface mass balance + smbmean = mean(mean(smbbox,3),4); + save -v7.3 smbbox smbbox x1 y1; + clear smbbox + + %Interpolate and set surface mass balance + index = BamgTriangulate(x1(:),y1(:)); + smb_mo = InterpFromMeshToMesh2d(index,x1(:),y1(:),smbmean(:),xi,yi); + smb = smb_mo*12/1000*md.materials.rho_freshwater/md.materials.rho_ice; + md.surfaceforcings.mass_balance = [smb;1 ]; + + %Set transient options, run for 20 years, saving every timestep + md.timestepping.time_step=0.2; + md.timestepping.final_time=200; + md.settings.output_frequency=1; + + %Additional options + md.inversion.iscontrol=0; + md.transient.requested_outputs={'IceVolume','TotalSmb', ... + 'SurfaceforcingsMassBalance'}; + md.verbose=verbose('solution',true,'module',true); + + %Go solve + md.cluster=generic('name',oshostname,'np',2); + md=solve(md,TransientSolutionEnum); + + save ./Models/Greenland.HistoricTransient md; +end + +if any(steps==7) + disp(' Step 7: Box Transient run'); + md = loadmodel('./Models/Greenland.HistoricTransient'); + + %load past transient results + md.geometry.base=md.results.TransientSolution(end).Base; + md.geometry.thickness=md.results.TransientSolution(end).Thickness; + md.geometry.surface=md.geometry.base+md.geometry.thickness; + md.initialization.vx=(md.results.TransientSolution(end).Vx); + md.initialization.vy=(md.results.TransientSolution(end).Vy); + md.results=[]; + + %convert mesh x,y into the Box projection + [md.mesh.lat,md.mesh.long] = xy2ll(md.mesh.x,md.mesh.y,+1,39,71); + [xi,yi]= ll2xy(md.mesh.lat,md.mesh.long,+1,45,70); + + %Set surface mass balance + load smbbox + index = BamgTriangulate(x1(:),y1(:)); + + %Set years to run + years_of_simulation = 2003:2012; + + %initialize surface mass balance matrix + smb = nan*ones(md.mesh.numberofvertices,length(years_of_simulation)*12); + + %Interpolate and set surface mass balance + for year=years_of_simulation + for month=1:12 + smb_mo = griddata(double(x1),double(y1),... + double(squeeze(smbbox(:,:,month,year-1839))),xi,yi,'nearest'); + smb(:,(year-years_of_simulation(1))*12+month) = smb_mo; + end + end + md.surfaceforcings.mass_balance = ... + [smb*12/1000*md.materials.rho_freshwater/md.materials.rho_ice; ... + [1/24:1/12:length(years_of_simulation)]]; + + %Set transient options, monthly timestep, saving every month + md.timestepping.time_step=1/12; + md.timestepping.final_time=length(years_of_simulation); + md.settings.output_frequency=1; + + %Additional options + md.inversion.iscontrol=0; + md.transient.requested_outputs={'IceVolume','TotalSmb', ... + 'SurfaceforcingsMassBalance'}; + md.verbose=verbose('solution',true,'module',true); + + %Go solve + md.cluster=generic('name',oshostname,'np',2); + md=solve(md,TransientSolutionEnum); + + save ./Models/Greenland.BoxTransient md; +end + +if any(steps==8) + disp(' Step 8: Plot Box Transient'); + md = loadmodel('./Models/Greenland.BoxTransient'); + + %Set years run + years_of_simulation = 2003:2012; + t = [years_of_simulation(1):1/12:years_of_simulation(end)+11/12]; + + %Line Plots + figure + + %Plot surface mass balance + surfmb=[]; for i=1:length(t); surfmb=[surfmb ... + md.results.TransientSolution(i).TotalSmb]; end + subplot(3,1,1); plot(t,surfmb); title('Total Surface mass balance'); + + %Plot velocity + vel=[]; for i=1:length(t); vel=[vel md.results.TransientSolution(i).Vel]; end + subplot(3,1,2); plot(t,max(vel)); title('Max Velocity'); + + %Plot Volume + volume=[]; for i=1:length(t); volume=[volume md.results.TransientSolution(i).IceVolume]; end + subplot(3,1,3); plot(t,volume); title('Ice Volume'); + xlabel('years') +end Index: /issm/branches/trunk-jpl-ad2-integrated/examples/ISMIP/CheatyIsmipA.par =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/ISMIP/CheatyIsmipA.par (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/ISMIP/CheatyIsmipA.par (revision 18231) @@ -0,0 +1,52 @@ +%Parameterization for ISMIP A experiment + +%Set the Simulation generic name #md.miscellaneous +%-> + +%Geometry +disp(' Constructing Geometry'); + +%Define the geometry of the simulation #md.geometry +%surface is [-x*tan(0.5*pi/180)] #md.mesh +%-> +md.geometry.surface=-md.mesh.x*tan(0.5*pi/180.); +%base is [surface-1000+500*sin(x*2*pi/L).*sin(y*2*pi/L)] +%L is the size of the side of the square #max(md.mesh.x)-min(md.mesh.x) +%-> +L=max(md.mesh.x)-min(md.mesh.x); +md.geometry.base=md.geometry.surface-1000.0+500.0*sin(md.mesh.x*2.0*pi/L).*sin(md.mesh.y*2.0*pi/L); +%thickness is the difference between surface and base #md.geometry +%-> +md.geometry.thickness=md.geometry.surface-md.geometry.base; +%plot the geometry to check it out +%-> +plotmodel(md,'data',md.geometry.thickness); + +disp(' Defining friction parameters'); + +%These parameters will not be used but need to be fixed #md.friction +%one friciton coefficient per node (md.mesh.numberofvertices,1) +%-> +md.friction.coefficient=200.0*ones(md.mesh.numberofvertices,1); +%one friciton exponent (p,q) per element +%-> +md.friction.p=ones(md.mesh.numberofelements,1); +%-> +md.friction.q=ones(md.mesh.numberofelements,1); + +disp(' Construct ice rheological properties'); + +%The rheology parameters sit in the material section #md.materials +%B has one value per vertex +%-> +md.materials.rheology_B=6.8067e7*ones(md.mesh.numberofvertices,1); +%n has one value per element +%-> +md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); + +disp(' Set boundary conditions'); + +%Set the default boundary conditions for an ice-sheet +% #help SetIceSheetBC +%-> +md=SetIceSheetBC(md); Index: /issm/branches/trunk-jpl-ad2-integrated/examples/ISMIP/CheatyIsmipF.par =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/ISMIP/CheatyIsmipF.par (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/ISMIP/CheatyIsmipF.par (revision 18231) @@ -0,0 +1,66 @@ +%Parameterization for ISMIP F experiment + +%Set the Simulation generic name #md.miscellaneous +%-> + +%Geometry +disp(' Constructing Geometry'); + +%Define the geometry of the simulation #md.geometry +%surface is [-x*tan(3.0*pi/180)] #md.mesh +%-> +md.geometry.surface=md.mesh.x*tan(3.0*pi/180.0); +%base is [surface-1000+100*exp(-((x-L/2).^2+(y-L/2).^2)/(10000.^2))] +%L is the size of the side of the square #max(md.mesh.x)-min(md.mesh.x) +%-> +L=max(md.mesh.x)-min(md.mesh.x); +%-> +md.geometry.base=md.geometry.surface-1000.0+100.0*exp(-((md.mesh.x-L/2.0).^2.0+(md.mesh.y-L/2.0).^2.0)/(10000.^2.0)); +%thickness is the difference between surface and base #md.geometry +%-> +md.geometry.thickness=md.geometry.surface-md.geometry.base; +%plot the geometry to check it out +%-> +plotmodel(md,'data',md.geometry.thickness); + +disp(' Defining friction parameters'); + +%These parameters will not be used but need to be fixed #md.friction +%one friciton coefficient per node (md.mesh.numberofvertices,1) +%conversion form year to seconds with #md.constants.yts +%-> +md.friction.coefficient=sqrt(md.constants.yts/(1000*2.140373*10^-7))*ones(md.mesh.numberofvertices,1); +%one friciton exponent (p,q) per element +%-> +md.friction.p=ones(md.mesh.numberofelements,1); +%-> +md.friction.q=zeros(md.mesh.numberofelements,1); + +disp(' Construct ice rheological properties'); + +%The rheology parameters sit in the material section #md.materials +%B has one value per vertex +%-> +md.materials.rheology_B=(1/(2.140373*10^-7/md.constants.yts))*ones(md.mesh.numberofvertices,1); +%n has one value per element +%-> +md.materials.rheology_n=1*ones(md.mesh.numberofelements,1); + +disp(' Set boundary conditions'); + +%Set the default boundary conditions for an ice-sheet +% #help SetIceSheetBC +%-> +md=SetIceSheetBC(md); + +disp(' Initializing velocity and pressure'); + +%initialize the velocity and pressurefields of #md.initialization +%-> +md.initialization.vx=zeros(md.mesh.numberofvertices,1); +%-> +md.initialization.vy=zeros(md.mesh.numberofvertices,1); +%-> +md.initialization.vz=zeros(md.mesh.numberofvertices,1); +%-> +md.initialization.pressure=zeros(md.mesh.numberofvertices,1); Index: /issm/branches/trunk-jpl-ad2-integrated/examples/ISMIP/CheatyRunme.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/ISMIP/CheatyRunme.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/ISMIP/CheatyRunme.m (revision 18231) @@ -0,0 +1,229 @@ +%wich steps to perform steps are from 1 to 8 +%step 7 is specific to ISMIPA +%step 8 is specific to ISMIPF + +steps=[1:7]; + +% parameter file to be used, choose between CheatyIsmipA.par or CheatyIsmipF.par +ParamFile='CheatyIsmipF.par' + +%Run Steps + +% {{{ Mesh Generation #1 +if any(steps==1) + + %initialize md as a new model #help model + %-> + md=model(); + % generate a squaremesh #help squaremesh + % Side is 80 km long with 20 points + %-> + if(ParamFile=='CheatyIsmipA.par'), + md=squaremesh(md,80000,80000,20,20); + elseif(ParamFile=='CheatyIsmipF.par'), + md=squaremesh(md,100000,100000,30,30); + end + % plot the given mesh #plotdoc + %-> + plotmodel(md,'data','mesh') + % save the given model + %-> + save ./Models/ISMIP.Mesh_generation md; +end +% }}} + +% {{{ Masks #2 +if any(steps==2) + + % load the preceding step #help loadmodel + % path is given by the organizer with the name of the given step + %-> + md = loadmodel('./Models/ISMIP.Mesh_generation'); + % set the mask #help setmask + % all MISMIP nodes are grounded + %-> + md=setmask(md,'',''); + % plot the given mask #md.mask to locate the field + %-> + plotmodel(md,'data',md.mask.groundedice_levelset); + % save the given model + %-> + save ./Models/ISMIP.SetMask md; +end +% }}} + +% {{{ Parameterization #3 +if any(steps==3) + + % load the preceding step #help loadmodel + % path is given by the organizer with the name of the given step + %-> + md = loadmodel('./Models/ISMIP.SetMask'); + % parametrize the model # help parameterize + % you will need to fil-up the parameter file defined by the + % ParamFile variable + %-> + md=parameterize(md,ParamFile); + % save the given model + %-> + save ./Models/ISMIP.Parameterization md; +end +% }}} + +% {{{ Extrusion #4 +if any(steps==4) + + % load the preceding step #help loadmodel + % path is given by the organizer with the name of the given step + %-> + md = loadmodel('./Models/ISMIP.Parameterization'); + % vertically extrude the preceding mesh #help extrude + % only 5 layers exponent 1 + %-> + md=extrude(md,9,1); + % plot the 3D geometry #plotdoc + %-> + plotmodel(md,'data',md.geometry.base) + % save the given model + %-> + save ./Models/ISMIP.Extrusion md; +end +% }}} + +% {{{ Set the flow computing method #5 +if any(steps==5) + + % load the preceding step #help loadmodel + % path is given by the organizer with the name of the given step + %-> + md = loadmodel('./Models/ISMIP.Extrusion'); + % set the approximation for the flow computation #help setflowequation + % We will be using the Higher Order Model (HO) + %-> + md=setflowequation(md,'HO','all'); + % save the given model + %-> + save ./Models/ISMIP.SetFlow md; +end +% }}} + +% {{{ Set Boundary Conditions #6 +if any(steps==6) + + % load the preceding step #help loadmodel + % path is given by the organizer with the name of the given step + %-> + md = loadmodel('./Models/ISMIP.SetFlow'); + % dirichlet boundary condition are known as SPCs + % ice frozen to the base, no velocity #md.stressbalance + % SPCs are initialized at NaN one value per vertex + %-> + md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1); + %-> + md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1); + %-> + md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1); + % extract the nodenumbers at the base #md.mesh.vertexonbase + %-> + basalnodes=find(md.mesh.vertexonbase); + % set the sliding to zero on the bed + %-> + md.stressbalance.spcvx(basalnodes)=0.0; + %-> + md.stressbalance.spcvy(basalnodes)=0.0; + % periodic boundaries have to be fixed on the sides + % create tabs with the side of the domain + % for x + % create maxX #help find + %-> + maxX=find(md.mesh.x==max(md.mesh.x)); + % create minX + %-> + minX=find(md.mesh.x==min(md.mesh.x)); + % for y, max X and minX should be excluded + % create maxY + %-> + maxY=find(md.mesh.y==max(md.mesh.y) & md.mesh.x~=max(md.mesh.x) & md.mesh.x~=min(md.mesh.x)); + % create minY + %-> + minY=find(md.mesh.y==min(md.mesh.y) & md.mesh.x~=max(md.mesh.x) & md.mesh.x~=min(md.mesh.x)); + % set the node that should be paired together + % #md.stressbalance.vertex_pairing + %-> + md.stressbalance.vertex_pairing=[minX,maxX;minY,maxY]; + if (ParamFile=='CheatyIsmipF.par') + % if we are dealing with IsmipF the solution is in + % masstransport + md.masstransport.vertex_pairing=md.stressbalance.vertex_pairing; + end + % save the given model + %-> + save ./Models/ISMIP.BoundaryCondition md; +end +% }}} + +% {{{ Solving #7 +if any(steps==7) + % load the preceding step #help loadmodel + % path is given by the organizer with the name of the given step + %-> + md = loadmodel('./Models/ISMIP.BoundaryCondition'); + % Set cluster #md.cluster + % generic parameters #help generic + % set only the name and number of process + %-> + md.cluster=generic('name',oshostname(),'np',2); + % Set which control message you want to see #help verbose + %-> + md.verbose=verbose('convergence',true); + % Solve #help solve + % we are solving a StressBalanc + %-> + md=solve(md,StressbalanceSolutionEnum()); + % save the given model + %-> + save ./Models/ISMIP.StressBalance md; + % plot the surface velocities #plotdoc + %-> + plotmodel(md,'data',md.results.StressbalanceSolution.Vel) +end +% }}} + +% {{{ Solving #8 +if any(steps==8) + % load the preceding step #help loadmodel + % path is given by the organizer with the name of the given step + %-> + md = loadmodel('./Models/ISMIP.BoundaryCondition'); + % Set cluster #md.cluster + % generic parameters #help generic + % set only the name and number of process + %-> + md.cluster=generic('name',oshostname(),'np',2); + % Set which control message you want to see #help verbose + %-> + md.verbose=verbose('convergence',true); + % set the transient model to ignore the thermal model + % #md.transient + %-> + md.transient.isthermal=0; + % define the timestepping scheme + % everything here should be provided in years #md.timestepping + % give the length of the time_step (4 years) + %-> + md.timestepping.time_step=4; + % give final_time (20*4 years time_steps) + %-> + md.timestepping.final_time=4*20; + % Solve #help solve + % we are solving a TransientSolution + %-> + md=solve(md,TransientSolutionEnum); + % save the given model + %-> + save ./Models/ISMIP.Transient md; + % plot the surface velocities #plotdoc + %-> + plotmodel(md,'data',md.results.TransientSolution(20).Vel) +end +% }}} Index: /issm/branches/trunk-jpl-ad2-integrated/examples/ISMIP/IsmipA.par =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/ISMIP/IsmipA.par (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/ISMIP/IsmipA.par (revision 18231) @@ -0,0 +1,52 @@ +%Parameterization for ISMIP A experiment + +%Set the Simulation generic name #md.miscellaneous +%-> + +%Geometry +disp(' Constructing Geometry'); + +%Define the geometry of the simulation #md.geometry +%surface is [-x*tan(0.5*pi/180)] #md.mesh +%-> + +%base is [surface-1000+500*sin(x*2*pi/L).*sin(y*2*pi/L)] +%L is the size of the side of the square #max(md.mesh.x)-min(md.mesh.x) +%-> + +%-> + +%thickness is the difference between surface and base #md.geometry +%-> + +%plot the geometry to check it out +%-> + + +disp(' Defining friction parameters'); + +%These parameters will not be used but need to be fixed #md.friction +%one friciton coefficient per node (md.mesh.numberofvertices,1) +%-> + +%one friciton exponent (p,q) per element +%-> + +%-> + + +disp(' Construct ice rheological properties'); + +%The rheology parameters sit in the material section #md.materials +%B has one value per vertex +%-> + +%n has one value per element +%-> + + +disp(' Set boundary conditions'); + +%Set the default boundary conditions for an ice-sheet +% #help SetIceSheetBC +%-> Index: /issm/branches/trunk-jpl-ad2-integrated/examples/ISMIP/IsmipF.par =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/ISMIP/IsmipF.par (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/ISMIP/IsmipF.par (revision 18231) @@ -0,0 +1,64 @@ +%Parameterization for ISMIP F experiment + +%Set the Simulation generic name #md.miscellaneous +%-> + +%Geometry +disp(' Constructing Geometry'); + +%Define the geometry of the simulation #md.geometry +%surface is [-x*tan(3.0*pi/180)] #md.mesh +%-> + +%base is [surface-1000+100*exp(-((x-L/2).^2+(y-L/2).^2)/(0.1*L^2))] +%L is the size of the side of the square #max(md.mesh.x)-min(md.mesh.x) +%-> + +%-> + +%thickness is the difference between surface and base #md.geometry +%-> + +%plot the geometry to check it out +%-> + + +disp(' Defining friction parameters'); + +%These parameters will not be used but need to be fixed #md.friction +%one friciton coefficient per node (md.mesh.numberofvertices,1) +%conversion form year to seconds with #md.constants.yts +%-> + +%one friciton exponent (p,q) per element +%-> + +%-> + + +disp(' Construct ice rheological properties'); + +%The rheology parameters sit in the material section #md.materials +%B has one value per vertex +%-> + +%n has one value per element +%-> + + +disp(' Set boundary conditions'); + +%Set the default boundary conditions for an ice-sheet +% #help SetIceSheetBC +%-> + +disp(' Initializing velocity and pressure'); + +%initialize the velocity and pressurefields of #md.initialization +%-> + +%-> + +%-> + +%-> Index: /issm/branches/trunk-jpl-ad2-integrated/examples/ISMIP/runme.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/ISMIP/runme.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/ISMIP/runme.m (revision 18231) @@ -0,0 +1,224 @@ +%wich steps to perform steps are from 1 to 8 +%step 7 is specific to ISMIPA +%step 8 is specific to ISMIPF + +steps=[1]; + +% parameter file to be used, choose between IsmipA.par or IsmipF.par +ParamFile='IsmipA.par' + +%Run Steps + +% {{{ Mesh Generation #1 +if any(steps==1) + + %initialize md as a new model #help model + %-> + + % generate a squaremesh #help squaremesh + % Side is 80 km long with 20 points + %-> + + % plot the given mesh #plotdoc + %-> + + % save the given model + %-> + +end +% }}} + +% {{{ Masks #2 +if any(steps==2) + + % load the preceding step #help loadmodel + % path is given by the organizer with the name of the given step + %-> + + % set the mask #help setmask + % all MISMIP nodes are grounded + %-> + + % plot the given mask #md.mask to locate the field + %-> + + % save the given model + %-> + +end +% }}} + +% {{{ Parameterization #3 +if any(steps==3) + + % load the preceding step #help loadmodel + % path is given by the organizer with the name of the given step + %-> + + % parametrize the model # help parameterize + % you will need to fil-up the parameter file (given by the + % ParamFile variable) + %-> + + % save the given model + %-> + +end +% }}} + +% {{{ Extrusion #4 +if any(steps==4) + + % load the preceding step #help loadmodel + % path is given by the organizer with the name of the given step + %-> + + % vertically extrude the preceding mesh #help extrude + % only 5 layers exponent 1 + %-> + + % plot the 3D geometry #plotdoc + %-> + + % save the given model + %-> + +end +% }}} + +% {{{ Set the flow computing method #5 + +if any(steps==5) + + % load the preceding step #help loadmodel + % path is given by the organizer with the name of the given step + %-> + + % set the approximation for the flow computation #help setflowequation + % We will be using the Higher Order Model (HO) + %-> + + % save the given model + %-> + +end +% }}} + +% {{{ Set Boundary Conditions #6 +if any(steps==6) + + % load the preceding step #help loadmodel + % path is given by the organizer with the name of the given step + %-> + + % dirichlet boundary condition are known as SPCs + % ice frozen to the base, no velocity #md.stressbalance + % SPCs are initialized at NaN one value per vertex + %-> + + %-> + + %-> + + % extract the nodenumbers at the base #md.mesh.vertexonbase + %-> + + % set the sliding to zero on the bed (Vx and Vy) + %-> + + %-> + + % periodic boundaries have to be fixed on the sides + % create tabs with the side of the domain + % for x + % create maxX #help find + %-> + + % create minX + %-> + + % for y, max X and minX should be excluded + % create maxY + %-> + + % create minY + %-> + + % set the node that should be paired together + % #md.stressbalance.vertex_pairing + %-> + + if (ParamFile=='IsmipF.par') + % if we are dealing with IsmipF the solution is in masstransport + md.masstransport.vertex_pairing=md.stressbalance.vertex_pairing; + end + % save the given model + %-> + +end +% }}} + +% {{{ Solving #7 +if any(steps==7) + % load the preceding step #help loadmodel + % path is given by the organizer with the name of the given step + %-> + + % Set cluster #md.cluster + % generic parameters #help generic + % set only the name and number of process + %-> + + % Set which control message you want to see #help verbose + %-> + + % Solve #help solve + % we are solving a StressBalanc + %-> + + % save the given model + %-> + + % plot the surface velocities #plotdoc + %-> +end +% }}} + +% {{{ Solving #8 +if any(steps==8) + % load the preceding step #help loadmodel + % path is given by the organizer with the name of the given step + %-> + + % Set cluster #md.cluster + % generic parameters #help generic + % set only the name and number of process + %-> + + % Set which control message you want to see #help verbose + %-> + + % set the transient model to ignore the thermal model + % #md.transient + %-> + + % define the timestepping scheme + % everything here should be provided in years #md.timestepping + % give the length of the time_step (4 years) + %-> + + % give final_time (20*4 years time_steps) + %-> + + % Solve #help solve + % we are solving a TransientSolution + %-> + + % save the given model + %-> + + % plot the surface velocities #plotdoc + %-> + +end +% }}} Index: /issm/branches/trunk-jpl-ad2-integrated/examples/IceflowModels/Contour.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/IceflowModels/Contour.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/IceflowModels/Contour.exp (revision 18231) @@ -0,0 +1,11 @@ +## Name:Contour +## Icon:0 +# Points Count Value +5 1.000000 +# X pos Y pos +260815.7808871837 745919.4159004869 +712422.3484428506 757574.3645213632 +640499.8210173184 195805.8409951325 +342774.0098139530 279721.4710654409 +260815.7808871837 745919.4159004869 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/IceflowModels/EISMINT.par =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/IceflowModels/EISMINT.par (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/IceflowModels/EISMINT.par (revision 18231) @@ -0,0 +1,53 @@ +disp(' creating thickness'); +hmin=0.01; +hmax=2756.7; +radius=sqrt((md.mesh.x).^2+(md.mesh.y).^2); +radiusmax=max(radius); +radius(find(radius>(1.-10^-9)*radiusmax))=radiusmax; %eliminate roundoff issues in next statement +md.geometry.thickness=hmin*ones(size(md.mesh.x,1),1)+hmax*(4.*((1./2.)^(4./3.)*ones(size(md.mesh.x,1),1)-((radius)./(2.*radiusmax)).^(4./3.))).^(3./8.); +md.geometry.base=0.*md.geometry.thickness; +md.geometry.surface=md.geometry.base+md.geometry.thickness; + +disp(' creating drag'); +md.friction.coefficient=20.*ones(md.mesh.numberofvertices,1); +md.friction.coefficient(find(md.mask.groundedice_levelset<0.))=0.; +md.friction.p=ones(md.mesh.numberofelements,1); +md.friction.q=ones(md.mesh.numberofelements,1); + +disp(' creating temperatures'); +tmin=238.15; %K +st=1.67*10^-2/1000.; %k/m +md.initialization.temperature=tmin+st*radius; +md.basalforcings.geothermalflux=4.2*10^-2*ones(md.mesh.numberofvertices,1); + +disp(' creating flow law parameter'); +md.materials.rheology_B=6.81*10^7*ones(md.mesh.numberofvertices,1); %to have the same B as the analytical solution +md.materials.rheology_n=3.*ones(md.mesh.numberofelements,1); + +disp(' creating surface mass balance'); +smb_max=0.5; %m/yr +sb=10^-2/1000.; %m/yr/m +rel=450.*1000.; %m +md.surfaceforcings.mass_balance=min(smb_max,sb*(rel-radius)); + +disp(' creating velocities'); +constant=0.3; +md.inversion.vx_obs=constant/2.*md.mesh.x.*(md.geometry.thickness).^-1; +md.inversion.vy_obs=constant/2.*md.mesh.y.*(md.geometry.thickness).^-1; +md.inversion.vel_obs=sqrt((md.inversion.vx_obs).^2+(md.inversion.vy_obs).^2); +md.initialization.vx=zeros(md.mesh.numberofvertices,1); +md.initialization.vy=zeros(md.mesh.numberofvertices,1); +md.initialization.vz=zeros(md.mesh.numberofvertices,1); +md.initialization.pressure=zeros(md.mesh.numberofvertices,1); + +%Deal with boundary conditions: +disp(' boundary conditions for stressbalance model:'); +md=SetMarineIceSheetBC(md,'./RoundFront.exp'); + +radius=sqrt((md.mesh.x).^2+(md.mesh.y).^2); +pos=find(radius==min(radius)); +md.mesh.x(pos)=0.; md.mesh.y(pos)=0.; %the closest node to the center is changed to be exactly at the center + +md.stressbalance.spcvx(pos)=0.; +md.stressbalance.spcvy(pos)=0.; +md.stressbalance.spcvz(pos)=0.; Index: /issm/branches/trunk-jpl-ad2-integrated/examples/IceflowModels/RoundFront.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/IceflowModels/RoundFront.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/IceflowModels/RoundFront.exp (revision 18231) @@ -0,0 +1,47 @@ +## Name: +## Icon:0 +# Points Count Value +41 1 +# X pos Y pos +1000000.000000 0.000000 +987688.340595 156434.465040 +951056.516295 309016.994375 +891006.524188 453990.499740 +809016.994375 587785.252292 +707106.781187 707106.781187 +587785.252292 809016.994375 +453990.499740 891006.524188 +309016.994375 951056.516295 +156434.465040 987688.340595 +0.000000 1000000.000000 +-156434.465040 987688.340595 +-309016.994375 951056.516295 +-453990.499740 891006.524188 +-587785.252292 809016.994375 +-707106.781187 707106.781187 +-809016.994375 587785.252292 +-891006.524188 453990.499740 +-951056.516295 309016.994375 +-987688.340595 156434.465040 +-1000000.000000 0.000000 +-987688.340595 -156434.465040 +-951056.516295 -309016.994375 +-891006.524188 -453990.499740 +-809016.994375 -587785.252292 +-707106.781187 -707106.781187 +-587785.252292 -809016.994375 +-453990.499740 -891006.524188 +-309016.994375 -951056.516295 +-156434.465040 -987688.340595 +-0.000000 -1000000.000000 +156434.465040 -987688.340595 +309016.994375 -951056.516295 +453990.499740 -891006.524188 +587785.252292 -809016.994375 +707106.781187 -707106.781187 +809016.994375 -587785.252292 +891006.524188 -453990.499740 +951056.516295 -309016.994375 +987688.340595 -156434.465040 +1000000.000000 0.000000 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/IceflowModels/Square.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/IceflowModels/Square.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/IceflowModels/Square.exp (revision 18231) @@ -0,0 +1,10 @@ +## Name:domainoutline +## Icon:0 +# Points Count Value +5 1. +# X pos Y pos +0 0 +1000000 0 +1000000 1000000 +0 1000000 +0 0 Index: /issm/branches/trunk-jpl-ad2-integrated/examples/IceflowModels/SquareFront.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/IceflowModels/SquareFront.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/IceflowModels/SquareFront.exp (revision 18231) @@ -0,0 +1,10 @@ +## Name:icefront +## Icon:0 +# Points Count Value +5 1. +# X pos Y pos +-1000 900000 +-1000 1100000 +1100000 1100000 +1100000 900000 +-1000 900000 Index: /issm/branches/trunk-jpl-ad2-integrated/examples/IceflowModels/SquareShelf.par =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/IceflowModels/SquareShelf.par (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/IceflowModels/SquareShelf.par (revision 18231) @@ -0,0 +1,55 @@ +%Start defining model parameters here + +%Geometry +hmin=300; +hmax=1000; +ymin=min(md.mesh.y); +ymax=max(md.mesh.y); +xmin=min(md.mesh.x); +xmax=max(md.mesh.x); +md.geometry.thickness=hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin)+0.1*(hmin-hmax)*(md.mesh.x-xmin)/(xmax-xmin); +md.geometry.base=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; +md.geometry.surface=md.geometry.base+md.geometry.thickness; + +%Initial velocity and pressure +x = transpose(ncread('../Data/SquareShelf.nc','x')); +y = transpose(ncread('../Data/SquareShelf.nc','y')); +vx = transpose(ncread('../Data/SquareShelf.nc','vx')); +vy = transpose(ncread('../Data/SquareShelf.nc','vy')); +index = transpose(ncread('../Data/SquareShelf.nc','index')); +md.initialization.vx=InterpFromMeshToMesh2d(index,x,y,vx,md.mesh.x,md.mesh.y); +md.initialization.vy=InterpFromMeshToMesh2d(index,x,y,vy,md.mesh.x,md.mesh.y); +clear vx vy x y index; +md.initialization.vz=zeros(md.mesh.numberofvertices,1); +md.initialization.pressure=zeros(md.mesh.numberofvertices,1); + +%Materials +md.initialization.temperature=(273-20)*ones(md.mesh.numberofvertices,1); +md.materials.rheology_B=paterson(md.initialization.temperature); +md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); + +%Friction +md.friction.coefficient=20*ones(md.mesh.numberofvertices,1); +md.friction.coefficient(find(md.mask.groundedice_levelset<0.))=0.; +md.friction.p=ones(md.mesh.numberofelements,1); +md.friction.q=ones(md.mesh.numberofelements,1); + +%Numerical parameters +md.stressbalance.viscosity_overshoot=0.3; +md.masstransport.stabilization=1; +md.thermal.stabilization=1; +md.settings.waitonlock=30; +md.verbose=verbose(0); +md.stressbalance.restol=0.10; +md.steadystate.reltol=0.02; +md.stressbalance.reltol=0.02; +md.stressbalance.abstol=NaN; +md.timestepping.time_step=1; +md.timestepping.final_time=3; + +%Boundary conditions: +md=SetIceShelfBC(md,'./SquareFront.exp'); + +%Change name so that no test have the same name +A=dbstack; +if (length(A)>2), md.miscellaneous.name=A(3).file(1:end-2); end Index: /issm/branches/trunk-jpl-ad2-integrated/examples/IceflowModels/eismint.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/IceflowModels/eismint.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/IceflowModels/eismint.m (revision 18231) @@ -0,0 +1,51 @@ +md=model(); + +%Create mesh with roundmesh +md=roundmesh(md,750000,30000); + +%Set mask +md=setmask(md,'',''); + +%Parameterize model +md=parameterize(md,'EISMINT.par'); + +%We extrude the model to have a 3d model +md=extrude(md,10,1); + +%Set ice flow approximation +md=setflowequation(md,'SIA','all'); + +%Create boundary conditions: zero velocity on the bed +pos=find(md.mesh.vertexonbase); +md.stressbalance.spcvx(pos)=0; +md.stressbalance.spcvy(pos)=0; +md.stressbalance.spcvz(pos)=0; + +%Go Solve +md.cluster=generic('np',2); +md.verbose.convergence=1; +md=solve(md,StressbalanceSolutionEnum()); +vel=DepthAverage(md,sqrt(md.results.StressbalanceSolution.Vx.^2+md.results.StressbalanceSolution.Vy.^2)); + +%Calculate analytical velocity +constant=0.3; +vx_obs=constant/2*md.mesh.x.*(md.geometry.thickness).^-1; +vy_obs=constant/2*md.mesh.y.*(md.geometry.thickness).^-1; +vel_obs=sqrt(vx_obs.^2+vy_obs.^2); +vel_obs=project2d(md,vel_obs,1); + +plotmodel(md,... + 'data',vel ,'view',2,'caxis',[0 200],'title','Modelled velocity',... + 'data',vel_obs,'view',2,'caxis',[0 200],'title','Analytical velocity',... + 'data',abs(vel-vel_obs)./(vel_obs+eps)*100,'caxis',[0 30],'view',2,'title','Relative misfit (%)'); + +subplot(2,2,4) +hold on; +plot(sqrt((md.mesh.x2d).^2+(md.mesh.y2d).^2),vel,'r.'); +plot(sqrt((md.mesh.x2d).^2+(md.mesh.y2d).^2),vel_obs,'b.'); +title('Analytical vs calculated velocity'); +xlabel('distance to the center of the icesheet [m]'); +ylabel('velocity (m/yr)'); +legend('calculated velocity','exact velocity'); +axis([0 750000 0 200]); +hold off; Index: /issm/branches/trunk-jpl-ad2-integrated/examples/IceflowModels/runme.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/IceflowModels/runme.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/IceflowModels/runme.m (revision 18231) @@ -0,0 +1,8 @@ +md=triangle(model(),'Square.exp',80000.); +md=setmask(md,'all',''); +md=parameterize(md,'SquareShelf.par'); +md=extrude(md,3,1); +%Set flow equation +md=setflowequation(md,'HO','Contour.exp','fill','SSA','coupling','tiling'); +%Solve +md=solve(md,StressbalanceSolutionEnum); Index: /issm/branches/trunk-jpl-ad2-integrated/examples/Inversion/DomainOutline.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/Inversion/DomainOutline.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/Inversion/DomainOutline.exp (revision 18231) @@ -0,0 +1,10 @@ +## Name:DomainOutline +## Icon:0 +# Points Count Value +5 1.000000 +# X pos Y pos +0 0 +1000000 0 +1000000 1000000 +0 1000000 +0 0 Index: /issm/branches/trunk-jpl-ad2-integrated/examples/Inversion/Front.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/Inversion/Front.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/Inversion/Front.exp (revision 18231) @@ -0,0 +1,10 @@ +## Name:icefront +## Icon:0 +# Points Count Value +5 1. +# X pos Y pos +-1000 900000 +-1000 1100000 +1100000 1100000 +1100000 900000 +-1000 900000 Index: /issm/branches/trunk-jpl-ad2-integrated/examples/Inversion/Square.par =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/Inversion/Square.par (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/Inversion/Square.par (revision 18231) @@ -0,0 +1,24 @@ +%Start defining model parameters here + +disp(' creating thickness'); +hmin = 300; +hmax = 1000; +ymin = min(md.mesh.y); +ymax = max(md.mesh.y); +md.geometry.thickness = hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin); +md.geometry.base = -md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; +md.geometry.surface = md.geometry.base+md.geometry.thickness; + +disp(' creating drag'); +md.friction.coefficient=200*ones(md.mesh.numberofvertices,1); +md.friction.coefficient(find(md.mask.groundedice_levelset<0.))=0.; +md.friction.p = ones(md.mesh.numberofelements,1); +md.friction.q = ones(md.mesh.numberofelements,1); + +disp(' creating flow law paramter'); +md.materials.rheology_B=1.8*10^8*ones(md.mesh.numberofvertices,1); +md.materials.rheology_B(find(md.mesh.x400000 & md.mesh.x<600000))=10; + + md = solve(md,StressbalanceSolutionEnum); + plotmodel(md,'data',md.friction.coefficient,'caxis',[0 100],'figure',1); + plotmodel(md,'data',md.results.StressbalanceSolution.Vel,'figure',2); + save model1 md +end +if step==2 + %Modify rheology, now constant + loadmodel('model1.mat'); + md.friction.coefficient(:)=50; + + %results of previous run are taken as observations + md.inversion=m1qn3inversion(); + md.inversion.vx_obs = md.results.StressbalanceSolution.Vx; + md.inversion.vy_obs = md.results.StressbalanceSolution.Vy; + md.inversion.vel_obs = md.results.StressbalanceSolution.Vel; + + md = solve(md,StressbalanceSolutionEnum); + plotmodel(md,'data',md.friction.coefficient,'caxis',[0 100],'figure',1); + plotmodel(md,'data',md.results.StressbalanceSolution.Vel,'figure',2); + save model2 md +end +if step==3 + %invert for ice rigidity + loadmodel('model2.mat'); + + %Set up inversion parameters + maxsteps = 20; + md.inversion.iscontrol = 1; + md.inversion.control_parameters = {'FrictionCoefficient'}; + md.inversion.maxsteps = maxsteps; + md.inversion.dxmin=10^-6; + md.inversion.cost_functions = [103 501]; + md.inversion.cost_functions_coefficients = ones(md.mesh.numberofvertices,2); + md.inversion.cost_functions_coefficients(:,2)=0; + md.inversion.min_parameters = 10^-5*ones(md.mesh.numberofvertices,1); + md.inversion.max_parameters = 100*ones(md.mesh.numberofvertices,1); + + %Go solve! + md.verbose=verbose(0); + md=solve(md,StressbalanceSolutionEnum); + plotmodel(md,'data',md.results.StressbalanceSolution.FrictionCoefficient,'caxis',[0 100],'figure',1); + plotmodel(md,'data',md.results.StressbalanceSolution.Vel,'figure',2); +end Index: /issm/branches/trunk-jpl-ad2-integrated/examples/Jakobshavn/Domain.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/Jakobshavn/Domain.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/Jakobshavn/Domain.exp (revision 18231) @@ -0,0 +1,34 @@ +## Name:JksOutline +## Icon:0 +# Points Count Value +28 1.000000 +# X pos Y pos +-442320.3882147236 -2277080.6549030584 +-415649.3149820761 -2315476.9356749961 +-356259.6577274340 -2351834.4758754564 +-309585.2795717255 -2384114.5349311619 +-279812.9187561168 -2353193.6362587260 +-274850.8586214480 -2287953.9379578433 +-294854.1635456266 -2263149.2609987380 +-309585.2795753506 -2232228.3623235333 +-348041.2456311518 -2191113.7607873622 +-376728.1557929466 -2197909.5626934194 +-391614.3362011510 -2203685.9943137392 +-417355.0231571503 -2206404.3150757281 +-420122.3381705935 -2211830.0535394503 +-421889.2049176788 -2218344.8015625700 +-420705.1891998384 -2226200.5387845989 +-425774.4833068820 -2230306.5097973733 +-429242.2244052034 -2235353.9400299159 +-427025.7933000360 -2240741.0910965428 +-431045.5636035603 -2255158.9014255330 +-424708.0734753361 -2261343.7626088522 +-423137.8820362946 -2268466.9593191240 +-428054.2739333302 -2272589.0010017036 +-432362.3262468725 -2272393.9161962867 +-435068.8255516959 -2273140.2906106352 +-437641.3726878429 -2272612.1952726739 +-439529.7800752302 -2272929.1351353633 +-442475.4525940326 -2275381.7044264446 +-442320.3882147236 -2277080.6549030584 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/Jakobshavn/Front.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/Jakobshavn/Front.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/Jakobshavn/Front.exp (revision 18231) @@ -0,0 +1,15 @@ +## Name:Front +## Icon:0 +# Points Count Value +9 1.000000 +# X pos Y pos +-443691.7204476296 -2241744.0087129781 +-444020.9148401438 -2244124.0631026439 +-443856.3176438867 -2245205.9060070375 +-441551.9568962874 -2244773.1688452801 +-440399.7765224879 -2243474.9573600078 +-439905.9849337166 -2240662.1658085845 +-441387.3597000304 -2238065.7428380400 +-443856.3176438867 -2237633.0056762826 +-443691.7204476296 -2241744.0087129781 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/Jakobshavn/Jks.par =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/Jakobshavn/Jks.par (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/Jakobshavn/Jks.par (revision 18231) @@ -0,0 +1,61 @@ + +%Name and hemisphere +md.mesh.hemisphere='n'; +md.miscellaneous.name='Jakobshavn'; + +%Load SeaRISE dataset +disp(' Loading SeaRISE data from NetCDF'); +ncdata = '../Data/Greenland_5km_dev1.2.nc'; +x1 = ncread(ncdata,'x1'); +y1 = ncread(ncdata,'y1'); +thk = ncread(ncdata,'thk')'; +topg = ncread(ncdata,'topg')'; +velx = ncread(ncdata,'surfvelx')'; +vely = ncread(ncdata,'surfvely')'; +temp = ncread(ncdata,'airtemp2m')'; +smb = ncread(ncdata,'smb')'; + +disp(' Interpolating thicknesses'); +md.geometry.thickness=InterpFromGridToMesh(x1,y1,thk,md.mesh.x,md.mesh.y,0); +pos0=find(md.geometry.thickness<=10); +md.geometry.thickness(pos0)=10; + +disp(' Interpolating bedrock topography'); +md.geometry.base = InterpFromGridToMesh(x1,y1,topg,md.mesh.x,md.mesh.y,0); + +disp(' Constructing surface elevation'); +md.geometry.surface=md.geometry.thickness+md.geometry.base; + +disp(' Interpolating velocities'); +md.inversion.vx_obs = InterpFromGridToMesh(x1,y1,velx,md.mesh.x,md.mesh.y,0); +md.inversion.vy_obs = InterpFromGridToMesh(x1,y1,vely,md.mesh.x,md.mesh.y,0); +md.inversion.vel_obs = sqrt(md.inversion.vx_obs.^2+md.inversion.vy_obs.^2); +md.initialization.vx = md.inversion.vx_obs; +md.initialization.vy = md.inversion.vy_obs; +md.initialization.vel= md.inversion.vel_obs; + +disp(' Interpolating temperatures'); +md.initialization.temperature=InterpFromGridToMesh(x1,y1,temp,md.mesh.x,md.mesh.y,0)+273.15; %convert to Kelvin + +disp(' Interpolating surface mass balance'); +md.surfaceforcings.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); +md.surfaceforcings.mass_balance=md.surfaceforcings.mass_balance*md.materials.rho_water/md.materials.rho_ice; + +disp(' Construct basal friction parameters'); +md.friction.coefficient=30*ones(md.mesh.numberofvertices,1); +md.friction.coefficient(find(md.mask.groundedice_levelset<0.))=0.; +md.friction.p=ones(md.mesh.numberofelements,1); +md.friction.q=ones(md.mesh.numberofelements,1); + +disp(' Construct ice rheological properties'); +md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); +md.materials.rheology_B=paterson(md.initialization.temperature); +md.damage.D=zeros(md.mesh.numberofvertices,1); +%Reduce viscosity along the shear margins +weakb=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,'WeakB.exp','node',2); +pos=find(weakb);md.materials.rheology_B(pos)=.3*md.materials.rheology_B(pos); + +disp(' Set other boundary conditions'); +md=SetMarineIceSheetBC(md,'./Front.exp'); +md.basalforcings.floatingice_melting_rate=zeros(md.mesh.numberofvertices,1); +md.basalforcings.groundedice_melting_rate=zeros(md.mesh.numberofvertices,1); Index: /issm/branches/trunk-jpl-ad2-integrated/examples/Jakobshavn/WeakB.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/Jakobshavn/WeakB.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/Jakobshavn/WeakB.exp (revision 18231) @@ -0,0 +1,60 @@ +## Name:WeakB +## Icon:0 +# Points Count Value +24 1.000000 +# X pos Y pos +-441022.7144520371 -2238435.7116546673 +-441639.8422268176 -2239053.0142011684 +-439171.3311276956 -2240699.1543251718 +-437319.9478033541 -2241727.9919026736 +-435879.9829955329 -2241933.7594181742 +-432382.9256051101 -2242756.8294801759 +-430942.9607972889 -2242962.5969956759 +-429708.7052477279 -2243991.4345731782 +-428680.1589564271 -2245020.2721506800 +-427651.6126651262 -2246049.1097281822 +-425800.2293407847 -2247077.9473056840 +-424565.9737912237 -2247695.2498521851 +-419341.0001274022 -2251604.8326466926 +-416049.6519952395 -2253868.2753171972 +-416049.6519952395 -2252222.1351931938 +-418312.4538361013 -2249341.3899761885 +-423331.7182416627 -2245843.3422126817 +-425594.5200825246 -2245226.0396661805 +-426623.0663738254 -2244402.9696041788 +-427445.9034068661 -2243991.4345731782 +-428885.8682146872 -2242756.8294801759 +-431148.6700555491 -2241522.2243871735 +-436497.1107703134 -2239670.3167476696 +-441022.7144520371 -2238435.7116546673 + +## Name:WeakB +## Icon:0 +# Points Count Value +24 1.000000 +# X pos Y pos +-442668.3885181184 -2245226.0396661805 +-440405.5866772566 -2245843.3422126817 +-438759.9126111752 -2246049.1097281822 +-437525.6570616142 -2246460.6447591828 +-435879.9829955329 -2246872.1797901839 +-434028.5996711914 -2248106.7848831862 +-431354.3793138092 -2249547.1574916886 +-430120.1237642482 -2249341.3899761885 +-429297.2867312076 -2250164.4600381902 +-427857.3219233864 -2249958.6925226897 +-426623.0663738254 -2250164.4600381902 +-424771.6830494839 -2250575.9950691909 +-423537.4274999229 -2250781.7625846914 +-422714.5904668822 -2251399.0651311926 +-415226.8149621988 -2259629.7657512082 +-419135.2908691420 -2259218.2307202076 +-422838.0575178250 -2255720.1829567007 +-424977.3923077441 -2252016.3676776937 +-426623.0663738254 -2251810.6001621932 +-428268.7404399067 -2251399.0651311926 +-429708.7052477279 -2251399.0651311926 +-431560.0885720694 -2251399.0651311926 +-443902.6440676794 -2246460.6447591828 +-442668.3885181184 -2245226.0396661805 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/Jakobshavn/runme.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/Jakobshavn/runme.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/Jakobshavn/runme.m (revision 18231) @@ -0,0 +1,90 @@ +steps=[4]; + +if any(steps==1) + disp(' Step 1: Mesh creation'); + md=triangle(model,'Domain.exp',2000); + + %Get observed velocity field on mesh nodes + ncdata='../Data/Greenland_5km_dev1.2.nc'; + if ~exist(ncdata,'file'), + error('File Greenland_5km_dev1.2.nc not downloaded in Data Directory. Please cd ../Data and run the download script.'); + end + x1 = ncread(ncdata,'x1'); + y1 = ncread(ncdata,'y1'); + velx = ncread(ncdata,'surfvelx'); + vely = ncread(ncdata,'surfvely'); + vx = InterpFromGridToMesh(x1,y1,velx',md.mesh.x,md.mesh.y,0); + vy = InterpFromGridToMesh(x1,y1,vely',md.mesh.x,md.mesh.y,0); + vel = sqrt(vx.^2+vy.^2); + + %refine mesh using surface velocities as metric + md=bamg(md,'hmin',1200,'hmax',15000,'field',vel,'err',5); + [md.mesh.lat,md.mesh.long] = xy2ll(md.mesh.x,md.mesh.y,+1,39,71); + + save JksMesh.mdl md +end +if any(steps==2) + disp(' Step 2: Parameterization'); + md=loadmodel('JksMesh.mdl'); + + md=setmask(md,'',''); + md=parameterize(md,'Jks.par'); + + %zones of shear margin softening + weakb=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,'WeakB.exp','node',2); + pos=find(weakb); + md.materials.rheology_B(pos)=.3*md.materials.rheology_B(pos); + + save JksPar.mdl md +end +if any(steps==3) + disp(' Step 3: Control method friction'); + md=loadmodel('JksPar.mdl'); + + md=setflowequation(md,'SSA','all'); + + %Control general + md.inversion.iscontrol=1; + md.inversion.nsteps=20; + md.inversion.step_threshold=0.99*ones(md.inversion.nsteps,1); + md.inversion.maxiter_per_step=5*ones(md.inversion.nsteps,1); + md.verbose=verbose('solution',true,'control',true); + + %Cost functions + md.inversion.cost_functions=[101 103]; + md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); + md.inversion.cost_functions_coefficients(:,1)=40; + md.inversion.cost_functions_coefficients(:,2)=1; + + %Controls + md.inversion.control_parameters={'FrictionCoefficient'}; + md.inversion.gradient_scaling(1:md.inversion.nsteps)=30; + md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); + md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); + + %Additional parameters + md.stressbalance.restol=0.01; + md.stressbalance.reltol=0.1; + md.stressbalance.abstol=NaN; + + %Go solve + md.cluster=generic('name',oshostname,'np',4); + md=solve(md,StressbalanceSolutionEnum); + + save JksControl.mdl md +end +if any(steps==4) + disp(' Plotting') + md=loadmodel('JksControl.mdl'); + + plotmodel(md,'unit#all','km','axis#all','equal',... + 'FontSize#all',12,... + 'data',md.inversion.vel_obs,'title','Observed velocity',... + 'data',md.results.StressbalanceSolution.Vel,'title','Modeled Velocity',... + 'colorbar#1','off','colorbar#2','on','colorbartitle#2','[m/yr]',... + 'caxis#1-2',[0,7000],... + 'data',md.geometry.base,'title','Base elevation',... + 'data',md.results.StressbalanceSolution.FrictionCoefficient,... + 'title','Friction Coefficient',... + 'colorbar#3','on','colorbartitle#3','[m]','colorbar#4','on'); +end Index: /issm/branches/trunk-jpl-ad2-integrated/examples/Mesh/Square.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/Mesh/Square.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/Mesh/Square.exp (revision 18231) @@ -0,0 +1,10 @@ +## Name:Square +## Icon:0 +# Points Count Value +5 1. +# X pos Y pos +0 0 +1 0 +1 1 +0 1 +0 0 Index: /issm/branches/trunk-jpl-ad2-integrated/examples/Mesh/circles.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/Mesh/circles.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/Mesh/circles.m (revision 18231) @@ -0,0 +1,7 @@ +function vel=circles(x,y), + +u=4*x-2; v=4*y-2; + +vel=tanh(30*(u.^2+v.^2-0.25)) ... + +tanh(30*((u-0.75).^2+(v-0.75).^2-0.25)) +tanh(30*((u-0.75).^2+(v+0.75).^2-0.25)) ... + +tanh(30*((u+0.75).^2+(v-0.75).^2-0.25)) +tanh(30*((u+0.75).^2+(v+0.75).^2-0.25)) ; Index: /issm/branches/trunk-jpl-ad2-integrated/examples/Mesh/shock.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/Mesh/shock.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/Mesh/shock.m (revision 18231) @@ -0,0 +1,3 @@ +function vel=shock(x,y), + +vel=exp(-(sqrt((x+0.1).^2+(y+0.1).^2)-0.75).^2*10^6)+((x+0.1).^2+(y+0.1).^2)/2; Index: /issm/branches/trunk-jpl-ad2-integrated/examples/Pig/CheatSheet.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/Pig/CheatSheet.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/Pig/CheatSheet.m (revision 18231) @@ -0,0 +1,18 @@ +if perform(org,'ModelHO') + % Load Model + mdHO = loadmodel('./Models/PIG.Control_drag'); + md.inversion.iscontrol=0; + + disp(' Extruding mesh') + number_of_layers=3; + md=extrude(md,number_of_layers,0.9); + + disp(' Using HO Ice Flow Model') + md=setflowequation(md, 'HO', 'all'); + + % Solve + md=solve(md,StressbalanceSolutionEnum); + + % Save Model + save ./Models/PIG.ModelHO md; +end Index: /issm/branches/trunk-jpl-ad2-integrated/examples/Pig/DomainOutline.bkp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/Pig/DomainOutline.bkp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/Pig/DomainOutline.bkp (revision 18231) @@ -0,0 +1,120 @@ +## Name: +## Icon:0 +# Points Count Value +114 25000.000000 +# X pos Y pos +-1712113.0179281300 -349656.0205056490 +-1711509.1917759699 -349354.1074295690 +-1709240.6586108401 -349354.1074295690 +-1707080.1508345299 -348922.0058743060 +-1705459.7700022999 -347193.5996532570 +-1703083.2114483600 -345249.1426545770 +-1701138.7544496800 -344168.8887664210 +-1698438.1197292900 -343952.8379887900 +-1698006.0181740201 -341900.3556012940 +-1693793.0280102200 -340279.9747690600 +-1691092.3932898301 -339631.8224361670 +-1688391.7585694401 -339415.7716585360 +-1686447.3015707601 -340063.9239914290 +-1683530.6160727399 -341036.1524907690 +-1682558.3875734000 -343304.6856558960 +-1682134.7209454600 -344182.1487658350 +-1682126.2860181299 -345681.2442098390 +-1681072.0444963200 -345932.4393879640 +-1680634.4718407800 -346682.5639403050 +-1680571.9614614199 -348557.8753211580 +-1677446.4424933300 -348370.3441830730 +-1675508.6207331200 -349495.5310115840 +-1676616.9911885399 -353567.0975933760 +-1672991.8601872099 -353799.6175753630 +-1668839.1631938200 -353999.1991486380 +-1667132.2298986400 -355121.4651541420 +-1666069.5534494901 -357496.8595698890 +-1662944.0344814099 -358309.4945015920 +-1660756.1712037399 -358747.0671571240 +-1657922.9836098100 -361682.8074238540 +-1656579.2228470000 -364003.8487410000 +-1653004.8841628900 -364748.0635758530 +-1653442.4568184200 -361622.5446077650 +-1651129.5727820301 -355684.0585683980 +-1648929.2928810001 -350845.9692010000 +-1646260.7698359799 -347802.2804785470 +-1644571.8968503401 -341785.6704672340 +-1643503.3064999001 -340869.0986596620 +-1643190.7546030900 -336680.9032424240 +-1642690.6715682000 -335243.1645171040 +-1641913.0916588283 -332341.0814454452 +-1640683.9739821283 -330436.6112348017 +-1637816.0327364956 -328532.1410241582 +-1635241.2508976001 -328652.8685499910 +-1631765.4107996500 -327017.1790921330 +-1625934.5618617306 -322342.6128395668 +-1620608.3852626982 -320438.1426289233 +-1616101.6204481323 -320438.1426289233 +-1611594.8556335662 -320914.2601815842 +-1607907.5026034669 -321866.4952869060 +-1602991.0318966676 -324723.2006028712 +-1599713.3847588014 -327579.9059188365 +-1593977.5022675355 -328532.1410241582 +-1590699.8551296694 -334721.6692087495 +-1589259.8391499999 -338300.0840570000 +-1588627.0898328500 -343572.9950327750 +-1588056.6000060199 -345432.3563530700 +-1586993.9235568701 -347432.6884926460 +-1589259.8391499999 -349315.9832070000 +-1585493.6744521901 -352996.1122558430 +-1585118.6121760199 -354496.3613605250 +-1585861.9157163899 -356240.3342513760 +-1586368.8197632500 -358747.0671571240 +-1587889.0972700799 -360996.6006787950 +-1586681.3716600600 -363935.4286441500 +-1585806.2263489999 -365748.2296456410 +-1586743.8820394201 -368373.6655788350 +-1586056.2678664399 -370123.9562009640 +-1585493.6744521901 -371124.1222707520 +-1586243.7990045301 -373562.0270658610 +-1428620.2472997301 -364425.2597226670 +-1414257.6683934701 -327460.5482541260 +-1412220.4351378100 -325972.8942023180 +-1404515.9240538401 -296165.1737279960 +-1387984.9332285200 -267002.0106682320 +-1375329.9306695000 -287124.5773036880 +-1374139.7661228001 -286331.1342725540 +-1347030.4625590600 -322432.7921891520 +-1351262.1587251101 -326267.7668396330 +-1381809.7154237600 -297174.8556980530 +-1381677.4749185799 -295852.4506461620 +-1382481.1222932001 -294804.4361498400 +-1398663.5713381099 -316073.2308695170 +-1409694.4697897099 -363328.2128408530 +-1202495.3746585899 -351317.7619567180 +-1191463.4809399999 -350233.9748030000 +-1232161.1083569999 -292094.5070650000 +-1231243.1167609999 -288422.5406810000 +-1360067.9373810000 -107884.1934940000 +-1423274.3497420000 -81217.9259650000 +-1402446.7987670000 -45916.9921070000 +-1478343.8065599999 60338.8188030000 +-1513291.7310790000 4210.3339700000 +-1523175.9925589999 11976.5394190000 +-1503760.4789370000 36334.1837800000 +-1528509.5619775900 63667.6809196406 +-1623055.4918765700 62841.1506965373 +-1648011.3012850001 32874.5178730000 +-1638219.3909290000 20634.6299280000 +-1650153.2816760000 31038.5346810000 +-1725734.5897359999 -61372.6193030000 +-1719614.6457630000 -69022.5492690000 +-1759088.2843859999 -114004.1374660000 +-1755416.3180020000 -117064.1094530000 +-1761230.2647760001 -126856.0198080000 +-1758170.2927900001 -130527.9861920000 +-1762148.2563720001 -135423.9413700000 +-1764902.2311590000 -131445.9777880000 +-1769798.1863370000 -134199.9525750000 +-1775000.1387139999 -131445.9777880000 +-1794277.9622269999 -153477.7760890000 +-1712576.7101950001 -225081.1205660000 +-1729939.5891459100 -335652.4567604720 +-1712113.0179281300 -349656.0205056490 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/Pig/DomainOutline.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/Pig/DomainOutline.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/Pig/DomainOutline.exp (revision 18231) @@ -0,0 +1,101 @@ +## Name: +## Icon:0 +# Points Count Value +95 25000.000000 +# X pos Y pos +-1712113.0179281300 -349656.0205056490 +-1711509.1917759699 -349354.1074295690 +-1709240.6586108401 -349354.1074295690 +-1707080.1508345299 -348922.0058743060 +-1705459.7700022999 -347193.5996532570 +-1703083.2114483600 -345249.1426545770 +-1701138.7544496800 -344168.8887664210 +-1698438.1197292900 -343952.8379887900 +-1698006.0181740201 -341900.3556012940 +-1693793.0280102200 -340279.9747690600 +-1691092.3932898301 -339631.8224361670 +-1688391.7585694401 -339415.7716585360 +-1686447.3015707601 -340063.9239914290 +-1683530.6160727399 -341036.1524907690 +-1682558.3875734000 -343304.6856558960 +-1682134.7209454600 -344182.1487658350 +-1682126.2860181299 -345681.2442098390 +-1681072.0444963200 -345932.4393879640 +-1680634.4718407800 -346682.5639403050 +-1680571.9614614199 -348557.8753211580 +-1677446.4424933300 -348370.3441830730 +-1675508.6207331200 -349495.5310115840 +-1676616.9911885399 -353567.0975933760 +-1672991.8601872099 -353799.6175753630 +-1668839.1631938200 -353999.1991486380 +-1667132.2298986400 -355121.4651541420 +-1666069.5534494901 -357496.8595698890 +-1662944.0344814099 -358309.4945015920 +-1660756.1712037399 -358747.0671571240 +-1657922.9836098100 -361682.8074238540 +-1656579.2228470000 -364003.8487410000 +-1653004.8841628900 -364748.0635758530 +-1653442.4568184200 -361622.5446077650 +-1651129.5727820301 -355684.0585683980 +-1648929.2928810001 -350845.9692010000 +-1646260.7698359799 -347802.2804785470 +-1644571.8968503401 -341785.6704672340 +-1643503.3064999001 -340869.0986596620 +-1643190.7546030900 -336680.9032424240 +-1642690.6715682000 -335243.1645171040 +-1641913.0916588283 -332341.0814454452 +-1640683.9739821283 -330436.6112348017 +-1637816.0327364956 -328532.1410241582 +-1635241.2508976001 -328652.8685499910 +-1631765.4107996500 -327017.1790921330 +-1625934.5618617306 -322342.6128395668 +-1620608.3852626982 -320438.1426289233 +-1616101.6204481323 -320438.1426289233 +-1611594.8556335662 -320914.2601815842 +-1607907.5026034669 -321866.4952869060 +-1602991.0318966676 -324723.2006028712 +-1599713.3847588014 -327579.9059188365 +-1593977.5022675355 -328532.1410241582 +-1590699.8551296694 -334721.6692087495 +-1589259.8391499999 -338300.0840570000 +-1588627.0898328500 -343572.9950327750 +-1588056.6000060199 -345432.3563530700 +-1586993.9235568701 -347432.6884926460 +-1589259.8391499999 -349315.9832070000 +-1585493.6744521901 -352996.1122558430 +-1585118.6121760199 -354496.3613605250 +-1585861.9157163899 -356240.3342513760 +-1586368.8197632500 -358747.0671571240 +-1587889.0972700799 -360996.6006787950 +-1586681.3716600600 -363935.4286441500 +-1585806.2263489999 -365748.2296456410 +-1586743.8820394201 -368373.6655788350 +-1586056.2678664399 -370123.9562009640 +-1585493.6744521901 -371124.1222707520 +-1586243.7990045301 -373562.0270658610 +-1414257.6683934701 -327460.5482541260 +-1412220.4351378100 -325972.8942023180 +-1404515.9240538401 -296165.1737279960 +-1387984.9332285200 -267002.0106682320 +-1360067.9373810000 -107884.1934940000 +-1423274.3497420000 -81217.9259650000 +-1402446.7987670000 -45916.9921070000 +-1478343.8065599999 60338.8188030000 +-1503760.4789370000 36334.1837800000 +-1528509.5619775900 63667.6809196406 +-1623055.4918765700 62841.1506965373 +-1725734.5897359999 -61372.6193030000 +-1719614.6457630000 -69022.5492690000 +-1759088.2843859999 -114004.1374660000 +-1755416.3180020000 -117064.1094530000 +-1761230.2647760001 -126856.0198080000 +-1758170.2927900001 -130527.9861920000 +-1762148.2563720001 -135423.9413700000 +-1764902.2311590000 -131445.9777880000 +-1769798.1863370000 -134199.9525750000 +-1775000.1387139999 -131445.9777880000 +-1794277.9622269999 -153477.7760890000 +-1712576.7101950001 -225081.1205660000 +-1729939.5891459100 -335652.4567604720 +-1712113.0179281300 -349656.0205056490 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/Pig/Pig.par =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/Pig/Pig.par (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/Pig/Pig.par (revision 18231) @@ -0,0 +1,135 @@ +% Parameters to change/Try +friction_coefficient = 10; % default [10] +Temp_change = 0; % default [0 K] + +%Name and hemisphere +md.miscellaneous.name='PIG'; +md.mesh.hemisphere='s'; + +% {{{ NetCdf Loading +disp(' Loading SeaRISE data from NetCDF'); +ncdata='../Data/Antarctica_5km_withshelves_v0.75.nc'; +x1 = ncread(ncdata,'x1'); +y1 = ncread(ncdata,'y1'); +usrf = ncread(ncdata,'usrf')'; +topg = ncread(ncdata,'topg')'; +temp = ncread(ncdata,'presartm')'; +smb = ncread(ncdata,'presprcp')'; +gflux = ncread(ncdata,'bheatflx_fox')'; + +disp(' Loading velocities data from NetCDF'); +nsidc_vel='../Data/Antarctica_ice_velocity.nc'; + +xmin = ncreadatt(nsidc_vel,'/','xmin'); +xmin = strtrim(xmin); %this is a string, and we need to recover the double value +xmin = xmin(1:end-2); %get rid of the unit +xmin = str2num(xmin); %convert to double + +ymax = ncreadatt(nsidc_vel,'/','ymax'); +ymax = strtrim(ymax); +ymax = ymax(1:end-2); +ymax = str2num(ymax); + +nx = ncreadatt(nsidc_vel,'/','nx'); +ny = ncreadatt(nsidc_vel,'/','ny'); + +spacing = ncreadatt(nsidc_vel,'/','spacing'); +spacing = strtrim(spacing); +spacing = spacing(1:end-2); +spacing = str2num(spacing); + +velx = double(ncread(nsidc_vel,'vx')); +vely = double(ncread(nsidc_vel,'vy')); + +x2=xmin+(0:1:nx)'*spacing; +x2=double(x2); + +y2=(ymax-ny*spacing)+(0:1:ny)'*spacing; +y2=double(y2); +% }}} +% {{{ Geometry +disp(' Interpolating surface and ice base'); +md.geometry.base = InterpFromGridToMesh(x1,y1,topg,md.mesh.x,md.mesh.y,0); +md.geometry.surface = InterpFromGridToMesh(x1,y1,usrf,md.mesh.x,md.mesh.y,0); +clear usrf, topg; + +disp(' Constructing thickness'); +md.geometry.thickness=md.geometry.surface-md.geometry.base; + +%ensure hydrostatic equilibrium on ice shelf: +di=md.materials.rho_ice/md.materials.rho_water; + +%Get the node numbers of floating nodes +pos=find(md.mask.groundedice_levelset<0); + +%apply a flotation criterion on the precedingly defined nodes and +%redefine base and thickness accordingly +md.geometry.thickness(pos)=1/(1-di)*md.geometry.surface(pos); +md.geometry.base(pos)=md.geometry.surface(pos)-md.geometry.thickness(pos); +md.geometry.hydrostatic_ratio=ones(md.mesh.numberofvertices,1); + +%Set min thickness to 1 meter +pos0=find(md.geometry.thickness<=0); +md.geometry.thickness(pos0)=1; +md.geometry.surface=md.geometry.thickness+md.geometry.base; +% }}} +% {{{ Initialization parameters +disp(' Interpolating temperatures'); +md.initialization.temperature=InterpFromGridToMesh(x1,y1,temp,md.mesh.x,md.mesh.y,0)+273.15+Temp_change; +clear temp; + +disp(' Set observed velocities') +vx_obs=InterpFromGridToMesh(x2,y2,flipud(velx'),md.mesh.x,md.mesh.y,0); +vy_obs=InterpFromGridToMesh(x2,y2,flipud(vely'),md.mesh.x,md.mesh.y,0); +clear velx vely; + +vel_obs=sqrt(vx_obs.^2+vy_obs.^2); +md.initialization.vx=vx_obs; +md.initialization.vy=vy_obs; +md.initialization.vz=zeros(md.mesh.numberofvertices,1); +md.initialization.vel=vel_obs; + +disp(' Set Pressure'); +md.initialization.pressure=md.materials.rho_ice*md.constants.g*md.geometry.thickness; + +% }}} + +disp(' Construct ice rheological properties'); +md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); +md.materials.rheology_B=paterson(md.initialization.temperature); + +% {{{ Forcings +disp(' Interpolating surface mass balance'); +md.surfaceforcings.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); +md.surfaceforcings.mass_balance=md.surfaceforcings.mass_balance*md.materials.rho_water/md.materials.rho_ice; +clear smb; + +disp(' Set geothermal heat flux'); +md.basalforcings.geothermalflux=InterpFromGridToMesh(x1,y1,gflux,md.mesh.x,md.mesh.y,0); +clear gflux; +% }}} + +% {{{ Friction and inversion set up +disp(' Construct basal friction parameters'); +md.friction.coefficient=friction_coefficient*ones(md.mesh.numberofvertices,1); +md.friction.p=ones(md.mesh.numberofelements,1); +md.friction.q=ones(md.mesh.numberofelements,1); + +%no friction applied on floating ice +pos=find(md.mask.groundedice_levelset<0); +md.friction.coefficient(pos)=0; + +md.inversion=m1qn3inversion(); +md.inversion.vx_obs=vx_obs; +md.inversion.vy_obs=vy_obs; +md.inversion.vel_obs=vel_obs; +% }}} + + +disp(' Set boundary conditions'); +md=SetMarineIceSheetBC(md); +md.basalforcings.floatingice_melting_rate = zeros(md.mesh.numberofvertices,1); +md.basalforcings.groundedice_melting_rate = zeros(md.mesh.numberofvertices,1); +md.thermal.spctemperature = [md.initialization.temperature;1]; %impose observed temperature on surface +md.masstransport.spcthickness = NaN*ones(md.mesh.numberofvertices,1); + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/Pig/PigRegion.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/Pig/PigRegion.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/Pig/PigRegion.m (revision 18231) @@ -0,0 +1,54 @@ +% {{{ Getting the velocity in PIG vicinity for the ExpDraw + +% Load Velocities +% http://nsidc.org/data/nsidc-0484.html +nsidc_vel='../Data/Antarctica_ice_velocity.nc'; + +% Get necessary data to build up the velocity grid +xmin = ncreadatt(nsidc_vel,'/','xmin'); +xmin = strtrim(xmin); % this is a string, and we need to recover the double value +xmin = xmin(1:end-2); % get rid of the unit +xmin = str2num(xmin); % convert to double + +ymax = ncreadatt(nsidc_vel,'/','ymax'); +ymax = strtrim(ymax); +ymax = ymax(1:end-2); +ymax = str2num(ymax); + +nx = ncreadatt(nsidc_vel,'/','nx'); +ny = ncreadatt(nsidc_vel,'/','ny'); + +spacing = ncreadatt(nsidc_vel,'/','spacing'); +spacing = strtrim(spacing); +spacing = spacing(1:end-2); +spacing = str2num(spacing); + + +x=xmin+(0:1:nx-1)'*spacing; +x=double(x); +y=(ymax)-(0:1:ny-1)'*spacing; +y=double(y); + +posx=find(x<=-12.0e5); +id1x=find(x>=-18.0e5,1); +id2x=posx(end); + +posy=find(y>=-4.0e5); +id1y=find(y<=1.0e5,1); +id2y=posy(end); + +%Get velocity subset +vx = double(ncread(nsidc_vel,'vx')); +vx_obs = vx(id1x:id2x,id1y:id2y); +vx_obs = flipud(vx_obs'); + +vy = double(ncread(nsidc_vel,'vy')); +vy_obs = vy (id1x:id2x,id1y:id2y); +vy_obs = flipud(vy_obs'); + +xred=x(id1x:id2x); +yred=y(id1y:id2y); +vel_obs=sqrt(vx_obs.^2.+vy_obs.^2.); +imagesc(xred,yred,vel_obs) + +%}}} Index: /issm/branches/trunk-jpl-ad2-integrated/examples/Pig/runme.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/Pig/runme.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/Pig/runme.m (revision 18231) @@ -0,0 +1,228 @@ +%Which steps to be performed +steps=[1:5] ; + +%Run Steps + +% {{{ Mesh Generation #1 +if any(steps==1) + + md.miscellaneous.name='PIG.Mesh_generation'; + + %Mesh parameters + domain =['./DomainOutline.exp']; + hmax=40000; % maximum element size of the final mesh + hmin=5000; % minimum element size of the final mesh + hinit=10000; % element size for the initial mesh + gradation=1.7; % maximum size ratio between two neighboring elements + err=8; % maximum error between interpolated and control field + + % Generate an initial uniform mesh (resolution = hinit m) + md=bamg(model,'domain',domain,'hmax',hinit,'MaxCornerAngle',1); + + %ploting + plotmodel(md,'data','mesh') + + % Load Velocities + % http://nsidc.org/data/nsidc-0484.html + nsidc_vel='../Data/Antarctica_ice_velocity.nc'; + + % Get necessary data to build up the velocity grid + xmin = ncreadatt(nsidc_vel,'/','xmin'); + xmin = strtrim(xmin); % this is a string, and we need to recover the double value + xmin = xmin(1:end-2); % get rid of the unit + xmin = str2num(xmin); % convert to double + + ymax = ncreadatt(nsidc_vel,'/','ymax'); + ymax = strtrim(ymax); + ymax = ymax(1:end-2); + ymax = str2num(ymax); + + nx = ncreadatt(nsidc_vel,'/','nx'); + ny = ncreadatt(nsidc_vel,'/','ny'); + + spacing = ncreadatt(nsidc_vel,'/','spacing'); + spacing = strtrim(spacing); + spacing = spacing(1:end-2); + spacing = str2num(spacing); + + % Get velocities (Note: You can use ncdisp('file') to see an ncdump) + vx = double(ncread(nsidc_vel,'vx')); + vy = double(ncread(nsidc_vel,'vy')); + + x=xmin+(0:1:nx)'*spacing; + x=double(x); + y=(ymax-ny*spacing)+(0:1:ny)'*spacing; + y=double(y); + + % Interpolate velocities onto coarse mesh + vx_obs=InterpFromGridToMesh(x,y,flipud(vx'),md.mesh.x,md.mesh.y,0); + vy_obs=InterpFromGridToMesh(x,y,flipud(vy'),md.mesh.x,md.mesh.y,0); + vel_obs=sqrt(vx_obs.^2+vy_obs.^2); + clear vx vy x y; + + % Adapt the mesh to minimize error in velocity interpolation + md=bamg(md,'hmax',hmax,'hmin',hmin,'gradation',gradation,'field',vel_obs,'err',err); + + %ploting + plotmodel(md,'data','mesh') + + % Convert x,y coordinates (Polar stereo) to lat/lon + [md.mesh.lat,md.mesh.long]=xy2ll(md.mesh.x,md.mesh.y,-1); + + % Save model + save ./Models/PIG.Mesh_generation md; +end +% }}} + +% {{{ Masks #2 +if any(steps==2) + + md = loadmodel('./Models/PIG.Mesh_generation'); + + % Load SeaRISe dataset for Antarctica + % http://websrv.cs.umt.edu/isis/index.php/Present_Day_Antarctica + searise='../Data/Antarctica_5km_withshelves_v0.75.nc'; + + %read thickness mask from SeaRISE + x1=double(ncread(searise,'x1')); + y1=double(ncread(searise,'y1')); + thkmask=double(ncread(searise,'thkmask')); + + %interpolate onto our mesh vertices + groundedice=double(InterpFromGridToMesh(x1,y1,thkmask',md.mesh.x,md.mesh.y,0)); + groundedice(groundedice<=0)=-1; + clear thkmask; + + %fill in the md.mask structure + md.mask.groundedice_levelset=groundedice; %ice is grounded for mask equal one + md.mask.ice_levelset=-1*ones(md.mesh.numberofvertices,1);%ice is present when negatvie + + %ploting + plotmodel(md,'data',md.mask.groundedice_levelset,'title','grounded/floating','data',md.mask.ice_levelset,'title','ice/no-ice') + + % Save model + save ./Models/PIG.SetMask md; +end +% }}} + +% {{{ Parameterization #3 +if any(steps==3) + + md = loadmodel('./Models/PIG.SetMask'); + md = parameterize(md,'./Pig.par'); + + % Use a MacAyeal flow model + md = setflowequation(md,'SSA','all'); + + % Save model + save ./Models/PIG.Parameterization md; +end +% }}} + +% {{{ Control Method #4 +if any(steps==4) + + md = loadmodel('./Models/PIG.Parameterization'); + + % Control general + md.inversion.iscontrol=1; + md.inversion.maxsteps=20; + md.inversion.maxiter=40; + md.inversion.dxmin=0.1; + md.inversion.gttol=1.0e-4; + md.verbose=verbose('solution',true,'control',true); + + % Cost functions + md.inversion.cost_functions=[101 103 501]; + md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,3); + md.inversion.cost_functions_coefficients(:,1)=1; + md.inversion.cost_functions_coefficients(:,2)=1; + md.inversion.cost_functions_coefficients(:,3)=8e-15; + + % Controls + md.inversion.control_parameters={'FrictionCoefficient'}; + md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); + md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); + + % Additional parameters + md.stressbalance.restol=0.01; + md.stressbalance.reltol=0.1; + md.stressbalance.abstol=NaN; + + % Solve + md.toolkits=toolkits; + md.cluster=generic('name',oshostname,'np',2); + md=solve(md,StressbalanceSolutionEnum); + + % Update model friction fields accordingly + md.friction.coefficient=md.results.StressbalanceSolution.FrictionCoefficient; + + plotmodel(md,'data',md.friction.coefficient) + + % Save model + save ./Models/PIG.Control_drag md; +end +% }}} + +% {{{ Plot #5 +if any(steps==5) + + md = loadmodel('./Models/PIG.Control_drag'); + + plotmodel(md,'nlines',2,'ncols',2,'unit#all','km','axis#all','equal',... + 'xlim#all',[min(md.mesh.x) max(md.mesh.x)]/10^3,... + 'ylim#all',[min(md.mesh.y) max(md.mesh.y)]/10^3,... + 'FontSize#all',12,... + 'data',md.initialization.vel,'title','Observed velocity',... + 'data',md.results.StressbalanceSolution.Vel,'title','Modeled Velocity',... + 'data',md.geometry.base,'title','Bed elevation',... + 'data',md.results.StressbalanceSolution.FrictionCoefficient,'title','Friction Coefficient',... + 'colorbar#all','on','colorbartitle#1-2','[m/yr]',... + 'caxis#1-2',([1.5,4000]),... + 'colorbartitle#3','[m]', 'log#1-2',10); +end +% }}} + +% {{{ HO #6 +if any(steps==6) + + % Load Model + + % Disable inversion + + %Extrude Mesh + + % Set Flowequation + + % Solve + + % Save Model + +end +% }}} + +% {{{ Plot #7 +if any(steps==7) + + mdHO = loadmodel('./Models/PIG.ModelHO'); + mdSSA = loadmodel('./Models/PIG.Control_drag'); + + basal=find(mdHO.mesh.vertexonbase); + surf=find(mdHO.mesh.vertexonsurface); + + plotmodel(md,'nlines',3,'ncols',2,'unit#all','km','axis#all','equal',... + 'xlim#all',[min(md.mesh.x) max(md.mesh.x)]/10^3,... + 'ylim#all',[min(md.mesh.y) max(md.mesh.y)]/10^3,... + 'FontSize#all',12,... + 'data',mdHO.initialization.vel,'title','Observed velocity',... + 'data',(mdHO.results.StressbalanceSolution.Vel(surf)-mdHO.initialization.vel(surf)),'title','(HO-observed) velocities',... + 'data',mdSSA.results.StressbalanceSolution.Vel,'title','Modeled SSA Velocity',... + 'data',(mdHO.results.StressbalanceSolution.Vel(surf)-mdSSA.results.StressbalanceSolution.Vel),'title','(HO-SSA) velocities',... + 'data',mdHO.results.StressbalanceSolution.Vel,'title','Modeled HO surface Velocities',... + 'data',(mdHO.results.StressbalanceSolution.Vel(surf)-mdHO.results.StressbalanceSolution.Vel(basal)),'title','(HOsurf-HO base) velocities',... + 'caxis#1',([1.5,4000]),'caxis#3',([1.5,4000]),'caxis#5',([1.5,4000]),... + 'colorbar#all','on','view#all',2,... + 'colorbartitle#all','[m/yr]',... + 'layer#5',1, 'log#1', 10,'log#3', 10,'log#5', 10); +end +% }}} Index: /issm/branches/trunk-jpl-ad2-integrated/examples/SquareIceShelf/DomainOutline.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/SquareIceShelf/DomainOutline.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/SquareIceShelf/DomainOutline.exp (revision 18231) @@ -0,0 +1,10 @@ +## Name:DomainOutline +## Icon:0 +# Points Count Value +5 1.000000 +# X pos Y pos +0 0 +1000000 0 +1000000 1000000 +0 1000000 +0 0 Index: /issm/branches/trunk-jpl-ad2-integrated/examples/SquareIceShelf/Front.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/SquareIceShelf/Front.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/SquareIceShelf/Front.exp (revision 18231) @@ -0,0 +1,10 @@ +## Name:icefront +## Icon:0 +# Points Count Value +5 1. +# X pos Y pos +-1000 999999 +-1000 1100000 +1100000 1100000 +1100000 999999 +-1000 999999 Index: /issm/branches/trunk-jpl-ad2-integrated/examples/SquareIceShelf/README =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/SquareIceShelf/README (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/SquareIceShelf/README (revision 18231) @@ -0,0 +1,6 @@ +md=model; +md=mesh(md,'DomainOutline.exp',50000); +md=geography(md,'all',''); +md=parameterize(md,'Square.par'); +md=setelementstype(md,'macayeal','all'); +md=solve(md,DiagnosticSolutionEnum); Index: /issm/branches/trunk-jpl-ad2-integrated/examples/SquareIceShelf/Square.par =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/SquareIceShelf/Square.par (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/SquareIceShelf/Square.par (revision 18231) @@ -0,0 +1,30 @@ +%Start defining model parameters here + +disp(' creating thickness'); +hmin=300; +hmax=1000; +ymin=min(md.mesh.y); +ymax=max(md.mesh.y); +md.geometry.thickness = hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin); +md.geometry.base = -md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; +md.geometry.surface = md.geometry.base+md.geometry.thickness; + +disp(' creating drag'); +md.friction.coefficient=200*ones(md.mesh.numberofvertices,1); +md.friction.coefficient(find(md.mask.groundedice_levelset<0.))=0.; +md.friction.p=ones(md.mesh.numberofelements,1); +md.friction.q=ones(md.mesh.numberofelements,1); + +disp(' initial velocity'); +md.initialization.vx=zeros(md.mesh.numberofvertices,1); +md.initialization.vy=zeros(md.mesh.numberofvertices,1); +md.initialization.vz=zeros(md.mesh.numberofvertices,1); +md.initialization.vel=zeros(md.mesh.numberofvertices,1); + +disp(' creating flow law parameter'); +md.materials.rheology_B=paterson((273-20)*ones(md.mesh.numberofvertices,1)); +md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); +md.damage.D=zeros(md.mesh.numberofvertices,1); + +disp(' creating boundary conditions'); +md=SetIceShelfBC(md,'Front.exp'); Index: /issm/branches/trunk-jpl-ad2-integrated/examples/SquareIceShelf/runme.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/SquareIceShelf/runme.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/SquareIceShelf/runme.m (revision 18231) @@ -0,0 +1,7 @@ +md=model; +md=triangle(md,'DomainOutline.exp',100000); +md=setmask(md,'all',''); +md=parameterize(md,'Square.par'); +md=setflowequation(md,'SSA','all'); +md.cluster=generic('name',oshostname,'np',2); +md=solve(md,StressbalanceSolutionEnum); Index: /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/ErrorContour.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/ErrorContour.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/ErrorContour.exp (revision 18231) @@ -0,0 +1,24 @@ +## Name:ErrorContour +## Icon:0 +# Points Count Value +18 1.000000 +# X pos Y pos +-1642090.6657102096 -328038.7002928721 +-1665417.0018035804 -319119.8070807009 +-1681882.6508106657 -304712.3641995014 +-1666103.0705122089 -245710.4552574461 +-1632485.7037894099 -232675.1497935036 +-1616020.0547823247 -224442.3252899610 +-1598182.2683579824 -200429.9204879618 +-1596810.1309407253 -181219.9966463624 +-1615333.9860736963 -160637.9353875059 +-1559762.4206747836 -147602.6299235635 +-1527517.1913692418 -188080.6837326479 +-1566623.1077610692 -218953.7756209326 +-1533691.8097468987 -229244.8062503609 +-1523400.7791174706 -309514.8451599012 +-1533691.8097468987 -350678.9676776142 +-1594751.9248148398 -371261.0289364707 +-1636602.1160411814 -349306.8302603571 +-1642090.6657102096 -328038.7002928721 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux1.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux1.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux1.exp (revision 18231) @@ -0,0 +1,22 @@ +## Name:MassFlux1 +## Icon:0 +# Points Count Value +16 1.000000 +# X pos Y pos +-1638344.3538415846 -328022.1178486745 +-1636175.0592654669 -328022.1178486745 +-1634647.1933393457 -327710.7373731936 +-1631836.4701132313 -326087.2311287920 +-1629847.9500851235 -324428.7567974643 +-1626413.2336729371 -321756.7703747695 +-1622074.6445207016 -320098.2960434417 +-1618278.3790124957 -319637.6087291840 +-1614210.9516822749 -319729.7461920356 +-1609601.2007080249 -320466.8458948479 +-1604539.5133637502 -322954.5573918396 +-1602370.2187876324 -324613.0317231673 +-1599206.6641974607 -326824.3308316044 +-1595681.5605112694 -327008.6057573075 +-1593150.7168391321 -327653.5679972683 +-1590710.2604409996 -330786.2417342208 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux10.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux10.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux10.exp (revision 18231) @@ -0,0 +1,8 @@ +## Name:MassFlux11 +## Icon:0 +# Points Count Value +2 1.000000 +# X pos Y pos +-1539536.1089629673 -171232.8272031187 +-1540384.1546699132 -200614.0179257037 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux11.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux11.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux11.exp (revision 18231) @@ -0,0 +1,8 @@ +## Name:MassFlux12 +## Icon:0 +# Points Count Value +2 1.000000 +# X pos Y pos +-1559431.5986180613 -236969.7272119786 +-1549112.1094185982 -261719.2194756830 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux12.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux12.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux12.exp (revision 18231) @@ -0,0 +1,8 @@ +## Name:MassFlux13 +## Icon:0 +# Points Count Value +2 1.000000 +# X pos Y pos +-1572656.1032135738 -292391.9615161452 +-1573651.1418990945 -315407.7936937447 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux13.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux13.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux13.exp (revision 18231) @@ -0,0 +1,8 @@ +## Name:MassFlux14 +## Icon:0 +# Points Count Value +2 1.000000 +# X pos Y pos +-1579674.9916810417 -321516.2892665596 +-1587436.3185859676 -337140.9687259690 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux14.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux14.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux14.exp (revision 18231) @@ -0,0 +1,8 @@ +## Name:MassFlux14 +## Icon:0 +# Points Count Value +2 1.000000 +# X pos Y pos +-1579674.9916810417 -321516.2892665596 +-1587436.3185859676 -337140.9687259690 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux15.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux15.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux15.exp (revision 18231) @@ -0,0 +1,127 @@ +## Name: +## Icon:0 +# Points Count Value +121 25000.000000 +# X pos Y pos +-1712012.0818103175 -348661.1275967784 +-1711738.9446965172 -348380.8584401013 +-1709339.1962288069 -348358.9741029009 +-1707566.1624406802 -348048.0535193763 +-1706142.6423542583 -346463.0619396989 +-1703644.8906504354 -344421.7875470470 +-1701428.0245438961 -343211.6412474416 +-1699098.6802015656 -343202.0651453367 +-1698767.2671226400 -341251.8958583454 +-1694089.8466347910 -339325.0408948531 +-1691249.4280928215 -338644.2293668062 +-1688271.0930389061 -338423.0784381799 +-1686131.0738047434 -339115.2406933784 +-1682853.5065837551 -340300.2702040364 +-1681648.3224467863 -342890.2203795200 +-1681160.5378740367 -343956.3892846339 +-1681343.2453770319 -345059.2736684235 +-1680476.2008784728 -345129.3389066600 +-1679673.6094558411 -346405.5378093903 +-1679898.5797234357 -347818.5803631411 +-1677215.4777375804 -347397.3820658240 +-1674583.5118423651 -349115.8291018623 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/issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux2.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux2.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux2.exp (revision 18231) @@ -0,0 +1,171 @@ +## Name:MassFlux2 +## Icon:0 +# Points Count Value +165 1.000000 +# X pos Y pos +-1609993.8450579999 -266189.3103270000 +-1609790.4465310001 -265898.8271340000 +-1609587.0480040000 -265608.3439410000 +-1609383.6494770001 -265317.8607480000 +-1609136.7086169999 -265274.3184150000 +-1608933.3100900000 -264983.8352220000 +-1608686.3692300001 -264940.2928890000 +-1608236.0298430000 -264606.2673630000 +-1607989.0889830000 -264562.7250310000 +-1607785.6904559999 -264272.2418380000 +-1607538.7495960000 -264228.6995050000 +-1607291.8087370000 -264185.1571720000 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+-1579084.5040050000 -273979.3244510000 +-1578750.4784800000 -274429.6638380000 +-1578706.9361469999 -274676.6046980000 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux3.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux3.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux3.exp (revision 18231) @@ -0,0 +1,10 @@ +## Name:MassFlux4 +## Icon:0 +# Points Count Value +4 1.000000 +# X pos Y pos +-1605390.0162510793 -209047.7381093690 +-1592454.5133393104 -208141.0538114636 +-1574086.0992045982 -208918.2117810968 +-1560891.8862345938 -210472.5277203633 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux4.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux4.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux4.exp (revision 18231) @@ -0,0 +1,8 @@ +## Name:MassFlux5 +## Icon:0 +# Points Count Value +2 1.000000 +# X pos Y pos +-1660144.8928561222 -319887.0521198768 +-1630434.8468677206 -298387.4931837295 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux5.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux5.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux5.exp (revision 18231) @@ -0,0 +1,8 @@ +## Name:MassFlux6 +## Icon:0 +# Points Count Value +2 1.000000 +# X pos Y pos +-1635925.9455644884 -157610.4872330402 +-1625288.0602165582 -120861.2411445094 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux6.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux6.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux6.exp (revision 18231) @@ -0,0 +1,8 @@ +## Name:MassFlux7 +## Icon:0 +# Points Count Value +2 1.000000 +# X pos Y pos +-1642052.5574172530 -95522.7999921589 +-1610982.9267521810 -78949.7704229522 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux7.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux7.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux7.exp (revision 18231) @@ -0,0 +1,8 @@ +## Name:MassFlux8 +## Icon:0 +# Points Count Value +2 1.000000 +# X pos Y pos +-1605014.5365509845 -81707.1563440522 +-1566756.1417461073 -82763.2940976564 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux8.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux8.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux8.exp (revision 18231) @@ -0,0 +1,8 @@ +## Name:MassFlux9 +## Icon:0 +# Points Count Value +2 1.000000 +# X pos Y pos +-1555378.1885604258 -45179.9925785796 +-1550583.9034971579 -68415.0231578706 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux9.exp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux9.exp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/MassFluxes/MassFlux9.exp (revision 18231) @@ -0,0 +1,8 @@ +## Name:MassFlux10 +## Icon:0 +# Points Count Value +2 1.000000 +# X pos Y pos +-1565010.6613481115 -111795.8673475993 +-1537474.3225972611 -138442.9656094175 + Index: /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/runme.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/runme.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/examples/UncertaintyQuantification/runme.m (revision 18231) @@ -0,0 +1,290 @@ +%PIG Uncertainty Quantification Application +steps=[1]; + +if any(steps==1) + disp(' Step 1: plot flux gates'); + + md = loadmodel('../Pig/Models/PIG.Control_drag'); + + texts=cell(1,13); + textpositions=cell(1,13); + + for i=1:13, + contour=expread(['./MassFluxes/MassFlux' num2str(i) '.exp']); + textpositions{i}=[contour.x(end) contour.y(end)]; + end + + plotmodel(md,'data',md.results.StressbalanceSolution.Vel,'log',10,'expdisp',... + {'MassFluxes/MassFlux1.exp','MassFluxes/MassFlux2.exp',... + 'MassFluxes/MassFlux3.exp','MassFluxes/MassFlux4.exp',... + 'MassFluxes/MassFlux5.exp','MassFluxes/MassFlux6.exp',... + 'MassFluxes/MassFlux7.exp','MassFluxes/MassFlux8.exp',... + 'MassFluxes/MassFlux9.exp','MassFluxes/MassFlux10.exp',... + 'MassFluxes/MassFlux11.exp','MassFluxes/MassFlux12.exp',... + 'MassFluxes/MassFlux13.exp'},... + 'expstyle',{'k-','k-','k-','k-','k-','k-','k-',... + 'k-','k-','k-','k-','k-','k-'},'linewidth',2,... + 'text',{'1','2','3','4','5','6','7',... + '8','9','10','11','12','13'},... + 'textposition',textpositions); + +end +if any(steps==2) + disp(' Step 2: compute cross overs from CRESIS'); + + md = loadmodel('../Pig/Models/PIG.Control_drag'); + + %load cross overs: CRESIS McCord Antarctica, 2009 (courtesy of John Paden) + load('../Data/CrossOvers2009.mat'); + + %interpolate cross over errors over our mesh vertices + DeltaHH=InterpFromMeshToMesh2d(index,x,y,dhh,md.mesh.x,md.mesh.y); + + %avoid NaN values + pos=find(isnan(DeltaHH)); DeltaHH(pos)=0; + + %filter out unrealistic error ranges + flags=ContourToNodes(md.mesh.x,md.mesh.y,'ErrorContour.exp',1); + pos=find(~flags); DeltaHH(pos)=0; + + %avoid large unrealistic values + pos=find(DeltaHH>1); DeltaHH(pos)=1; + pos=find(DeltaHH<-1); DeltaHH(pos)=-1; + + %transform into absolute errors and setup a minimum error everywhere. + DeltaHH=abs(DeltaHH); + pos=find(DeltaHH==0); pos2=find(DeltaHH~=0); + DeltaHH(pos)=min(DeltaHH(pos2)); + + save Models/PIG.CrossOvers DeltaHH + +end +if any(steps==3) + disp(' Step 3: sampling analysis'); + + %load model and cross over errors + md = loadmodel('../Pig/Models/PIG.Control_drag'); + load -mat Models/PIG.CrossOvers + + %partition the mesh + md.qmu.numberofpartitions=50; + md=partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,... + 'weighting','on'); + md.qmu.partition=md.qmu.partition-1; %switch partition to c-indexing + + %make DeltaHH into our 3 sigma deviation + DeltaHH=DeltaHH/6; %2 (to transform DeltaHH into a radius) x 3 (for 3 sigma) + DeltaHH_on_partition=AreaAverageOntoPartition(md,DeltaHH); + DeltaHH_on_grids=DeltaHH_on_partition(md.qmu.partition+1); %just to check in case + + md.qmu.variables.thickness=normal_uncertain('scaled_Thickness',1,1); + md.qmu.variables.thickness.stddev=DeltaHH_on_partition; + + %responses + md.qmu.responses.MassFlux1=response_function('indexed_MassFlux_1',[],... + [0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.MassFlux2=response_function('indexed_MassFlux_2',[],... + [0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); %grounding line + md.qmu.responses.MassFlux3=response_function('indexed_MassFlux_3',[],... + [0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.MassFlux4=response_function('indexed_MassFlux_4',[],... + [0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.MassFlux5=response_function('indexed_MassFlux_5',[],... + [0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.MassFlux6=response_function('indexed_MassFlux_6',[],... + [0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.MassFlux7=response_function('indexed_MassFlux_7',[],... + [0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.MassFlux8=response_function('indexed_MassFlux_8',[],... + [0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.MassFlux9=response_function('indexed_MassFlux_9',[],... + [0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.MassFlux10=response_function('indexed_MassFlux_10',[],... + [0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.MassFlux11=response_function('indexed_MassFlux_11',[],... + [0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.MassFlux12=response_function('indexed_MassFlux_12',[],... + [0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.MassFlux13=response_function('indexed_MassFlux_13',[],... + [0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + + %mass flux profiles + md.qmu.mass_flux_profiles={'MassFlux1.exp',... + 'MassFlux2.exp',... + 'MassFlux3.exp',... + 'MassFlux4.exp',... + 'MassFlux5.exp',... + 'MassFlux6.exp',... + 'MassFlux7.exp',... + 'MassFlux8.exp',... + 'MassFlux9.exp',... + 'MassFlux10.exp',... + 'MassFlux11.exp',... + 'MassFlux12.exp',... + 'MassFlux13.exp'}; + md.qmu.mass_flux_profile_directory='../MassFluxes/'; + + %% sampling analysis + md.qmu.method =dakota_method('nond_samp'); + md.qmu.method(end)=dmeth_params_set(md.qmu.method(end),... + 'seed',1234,... + 'samples',30,... + 'sample_type','lhs'); %random or lhs + + %% a variety of parameters + md.qmu.params.evaluation_concurrency=1; + md.qmu.params.analysis_driver=''; + md.qmu.params.analysis_components=''; + md.qmu.params.tabular_graphics_data=true; + md.verbose=verbose('qmu',true); + + md.stressbalance.restol=10^-5; %tighten tolerances for UQ analyses + + %solve + md.qmu.isdakota=1; md.inversion.iscontrol=0; + md.cluster=generic('name',oshostname,'np',4); + md=solve(md,StressbalanceSolutionEnum,'overwrite','y'); + + save ./Models/PIG.Sampling md; +end +if any(steps==4) + disp(' Step 4: sensitivity analysis'); + + %load model + md = loadmodel('../Pig/Models/PIG.Control_drag'); + + %partition the mesh + md.qmu.numberofpartitions=10; + md=partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on'); + md.qmu.partition=md.qmu.partition-1; %switch partition to c-indexing + + %all types of variables and responses: scaled_Thickness, indexed_MassFlux_i,MaxVel,nodal_DragCoefficient_i. scaled variables are expanded. + + %variables + md.qmu.variables.DragCoefficient=normal_uncertain(... + 'scaled_FrictionCoefficient',1,0.05); + md.qmu.variables.rheology_B=normal_uncertain(... + 'scaled_MaterialsRheologyB',1,0.05); + md.qmu.variables.Thickness=normal_uncertain('scaled_Thickness',1,0.05); + + %responses + md.qmu.responses.MassFlux1=response_function('indexed_MassFlux_1',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.MassFlux2=response_function('indexed_MassFlux_2',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.MassFlux3=response_function('indexed_MassFlux_3',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.MassFlux4=response_function('indexed_MassFlux_4',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.MassFlux5=response_function('indexed_MassFlux_5',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.MassFlux6=response_function('indexed_MassFlux_6',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.MassFlux7=response_function('indexed_MassFlux_7',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.MassFlux8=response_function('indexed_MassFlux_8',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.MassFlux9=response_function('indexed_MassFlux_9',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.MassFlux10=response_function('indexed_MassFlux_10',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.MassFlux11=response_function('indexed_MassFlux_11',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.MassFlux12=response_function('indexed_MassFlux_12',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + md.qmu.responses.MassFlux13=response_function('indexed_MassFlux_13',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]); + + %mass flux profiles + md.qmu.mass_flux_profiles={'MassFlux1.exp',... + 'MassFlux2.exp',... + 'MassFlux3.exp',... + 'MassFlux4.exp',... + 'MassFlux5.exp',... + 'MassFlux6.exp',... + 'MassFlux7.exp',... + 'MassFlux8.exp',... + 'MassFlux9.exp',... + 'MassFlux10.exp',... + 'MassFlux11.exp',... + 'MassFlux12.exp',... + 'MassFlux13.exp'}; + md.qmu.mass_flux_profile_directory='../MassFluxes/'; + + %method: local reliability + md.qmu.method =dakota_method('nond_l'); + md.qmu.method(end)=dmeth_params_set(md.qmu.method(end),... + 'output','quiet'); + + %parameters + md.qmu.params.evaluation_concurrency=1; + md.qmu.params.analysis_driver=''; + md.qmu.params.analysis_components=''; + md.qmu.params.tabular_graphics_data=false; + + md.stressbalance.restol=10^-5; %tighten for qmu analyses + + %solve + md.qmu.isdakota=1; + md.inversion.iscontrol=0; + md.cluster=generic('name',oshostname,'np',2); + md.verbose=verbose('qmu',true); + md=solve(md,StressbalanceSolutionEnum,'overwrite','y'); + + save ./Models/PIG.Sensitivity md; +end +if any(steps==5) + disp(' Step 5: plot partition'); + + %load model + md = loadmodel('./Models/PIG.Sampling'); + + plotmodel(md,'data','mesh','partitionedges','on','meshlinewidth',1.5,... + 'linewidth',2, 'axis#all','image','unit','km','colorbar','off',... + 'title','','meshcolor','b','grid','on'); + +end +if any(steps==6) + disp(' Step 6: plot histogram'); + + %load model + md = loadmodel('./Models/PIG.Sampling'); + + %which profile are we looking at? + index=1; + + %retrieve results for the specific profile, mass flux in m^3 water equiv/s + result=md.results.dakota.dresp_dat(md.qmu.numberofpartitions+index); + result.sample=result.sample/1e12*60*60*24*365; + + %plot histogram + plot_hist_norm(result,'cdfleg','off','cdfplt','off','nrmplt','off',... + 'xlabelplt','M (Gt/yr)','ylabelplt','F','FontSize',8,'FaceColor',... + 'none','EdgeColor','red'); + +end +if any(steps==7) + disp(' Step 7: plot sensitivity'); + + %load model + md = loadmodel('./Models/PIG.Sensitivity'); + %copy dakota results into model qmu + md.qmu.results=md.results.dakota; + + %which profile are we looking at? + index=1; + + %To plot sensitivities + sa=md.results.dakota.dresp_out(index).sens(1:10); sa=sa(md.qmu.partition+1)/1e12*60*60*24*365; + sb=md.results.dakota.dresp_out(index).sens(11:20); sb=sb(md.qmu.partition+1)/1e12*60*60*24*365; + sh=md.results.dakota.dresp_out(index).sens(21:30); sh=sh(md.qmu.partition+1)/1e12*60*60*24*365; + + plotmodel(md,'data',sh,'data',sa,'data',sb,'expdisp#all',... + ['MassFluxes/MassFlux' num2str(index) '.exp'],... + 'expstyle#all','b-','linewidth#all',2,... + 'nlines',3,'ncols',1, 'axis#all','image',... + 'colorbar#all','on','colorbarfontsize#all',10,... + 'colorbartitle#1','S_{H}', 'colorbartitle#2','S_{\alpha}',... + 'colorbartitle#3','S_{B}','unit#all','km','figure',1); + + %To plot importance factors + ifa=importancefactors(md,'scaled_FrictionCoefficient',['indexed_MassFlux_' num2str(index)]); + ifb=importancefactors(md,'scaled_MaterialsRheologyB',['indexed_MassFlux_' num2str(index)]); + ifh=importancefactors(md,'scaled_Thickness',['indexed_MassFlux_' num2str(index)]); + + plotmodel(md,'data',ifh,'data',ifa,'data',ifb,'expdisp#all',... + ['MassFluxes/MassFlux' num2str(index) '.exp'],... + 'expstyle#all','b-','linewidth#all',2,'log#all',10,... + 'nlines',3,'ncols',1, 'axis#all','image','caxis#all',[1e-10 1],... + 'colorbar#all','on','colorbarfontsize#all',10,... + 'colorbartitle#1','If_{H}', 'colorbartitle#2','If_{\alpha}',... + 'colorbartitle#3','If_{B}','unit#all','km','figure',2); + +end Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/README =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/README (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/README (revision 18231) @@ -0,0 +1,22 @@ +To install all the ISSM libraries: + +1/ go into each library folder and type install.sh . + +2/ There is no guarantee the compilation will work on all systems. A lot of tweaking of the +install.sh files will probably be involved. Especially, the configuration part of the install. + +Update: +now install.sh can call configure.sh for the most complex libraries, ie Petsc and Dakota. For those +libraries, go in the configs/ directory, pick up the correct configuration file and copy it to the top +folder of the library compilation. Tweak if necessary. + +machine characteristics: + +-astrid: linux 64 bits +-castor: altix 64 bits +-cosmos: JPL cluster 32 bits +-macmathieu: iMac 24" 2009 32 bits +-macbookmathieu: MacBook Pro 13" 2010; OS X 10.6.7; 2.4GHz Intel Core 2 Duo 64 bits +-maceric: MacBook Pro 15" 2010 32 bits +-ogive: Mac Pro 2008 32 bits +-pleiades: AMES cluster Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adic/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adic/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adic/install.sh (revision 18231) @@ -0,0 +1,34 @@ +#!/bin/bash +set -eu + +#Erase install +rm -rf source build install + +#Download code +hg clone http://mercurial.mcs.anl.gov/ad/ADIC -r 631 source + +#Then update to -r 631 +cd source +hg update -r 631 + +#Configure and Compile +cd source +./autogen.sh +./aclocal +cd .. +mkdir build +cd build +../source/configure \ + --with-rose=$ISSM_DIR/externalpackages/rose/install \ + --with-openanalysis=$ISSM_DIR/externalpackages/openanalysis/openanalysis/x86_64-Linux \ + --with-boost=$ISSM_DIR/externalpackages/boost/install \ + --with-xerces=$ISSM_DIR/externalpackages/xerces/src \ + --with-xaifbooster=$ISSM_DIR/externalpackages/xaifbooster/xaifBooster \ + --with-colpack=$ISSM_DIR/externalpackages/colpack/install\ + --prefix=$ISSM_DIR/externalpackages/adic/install +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adic/tests/notes =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adic/tests/notes (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adic/tests/notes (revision 18231) @@ -0,0 +1,143 @@ +mini1.c is: +7:37 PM +#include + +void mini1(double *y, double *x) +{ + int i; + for (i = 0; i < 2; i=i+1) { + y[i] = x[i] + sin(x[i]*x[i]); + } + } + Eric Larour 7:37 PM + ok + Sri Hari Krishna Narayanan 7:37 PM + If you cat any of mini1_grad_length.ad.c mini1_dense_forward.ad.c mini1_sparse_forward.ad.c + 7:37 PM + You should be able to see the forward mode output + Eric Larour 7:38 PM + ok + Sri Hari Krishna Narayanan 7:38 PM + First the makefile compiles mini1_grad_length.ad.c with a runtime library to estimate the number of columns in the Jacobian. + Eric Larour 7:39 PM + ok, makes sense + Sri Hari Krishna Narayanan 7:39 PM + That generates the output : ADIC_GRADVEC_LENGTH 2 + Eric Larour 7:39 PM + where? + 7:39 PM + ok, sorry, got it + Sri Hari Krishna Narayanan 7:40 PM + The value is also written to : runtime_dense/adic_gradvec_length.h + Eric Larour 7:40 PM + where is the main for this? + 7:40 PM + oh, it creates a .h directly + Sri Hari Krishna Narayanan 7:40 PM + mini1_driver.c + 7:40 PM + yes. + 7:40 PM + The runtime library takes care of that + 7:40 PM + There is alot or #defined compilation going on + Eric Larour 7:41 PM + wraps around mini1_forward_array.exe ? + Sri Hari Krishna Narayanan 7:41 PM + /*intermediary: */ creates mini1_grad_length.exe + Eric Larour 7:41 PM + Isn't that the Makefile? what is the runtime library ? + 7:42 PM + ok, the Makefile launches the runtime library + Sri Hari Krishna Narayanan 7:42 PM + Makefile copies versions of the runtime library (bunch of macros in most cases) + Eric Larour 7:42 PM + what is the name of the runtime library? + Sri Hari Krishna Narayanan 7:43 PM + form $adicsrc/runtime/ + 7:43 PM + There are multiple versions + Eric Larour 7:44 PM + ah, I see the grad_length dir + 7:44 PM + is all that stuff compiled into adic2? + Sri Hari Krishna Narayanan 7:44 PM + The one used to estimate the grad_lengh is : $adicinstall/grad_length + 7:44 PM + yes + Eric Larour 7:44 PM + ok, makes sense + Sri Hari Krishna Narayanan 7:45 PM + For the next step though + 7:45 PM + the 'dense' case + 7:45 PM + the runtime library cannot be precompiled + 7:45 PM + the .h file has been created in the previous step + 7:46 PM + So we copy the runtime/dense to the local directory + Eric Larour 7:46 PM + because we can't guess the size of the gradient right? + Sri Hari Krishna Narayanan 7:46 PM + and copy the .h into it + 7:46 PM + correct + Eric Larour 7:46 PM + nice + Sri Hari Krishna Narayanan 7:46 PM + Then we compile it and create a .la file + 7:46 PM + which is then linked to create mini1_dense_forward.exe + 7:47 PM + When we run this, it also happens to run the analyticla derivates (the driver is built this way) + 7:47 PM + Also diveded differences + 7:47 PM + So you get the output: + 7:47 PM + Analytic result is: [1.968912] + Analytic result is: [1.968912] + DD result is: [1.968997] error {-8.45e-05} + DD result is: [1.968997] error {-8.45e-05} + AD result is: [1.968912] error {0.000000} + AD result is: [1.968912] error {0.000000} + 7:48 PM + The next step is to detect sparsity in the Jacobian and possibly compress it using Colpack (create a seed matrix). + 7:49 PM + The gradient computation takes place on the compressed matrix. + 7:49 PM + The output : ADIC_GRADVEC_LENGTH 1 + 7:49 PM + means that the seed matrix has one column. + 7:50 PM + After the calculation of the elements of the compressed matrix, it is then extracted to form the 'full Jacobian' (sorry if these tems are inexact). + 7:51 PM + The extracted output is then printed out: + 7:51 PM + AD result is: [1.968912] + AD result is: [1.968912] + 7:51 PM + And we are done! + Eric Larour 7:51 PM + This is a lot for me to take in at once I'm going to have to look through the makefile, + 7:51 PM + and your explanations, and figure it out + Sri Hari Krishna Narayanan 7:51 PM + Sure. + Eric Larour 7:52 PM + I'll get back to you as soon as I have injested all of this + Sri Hari Krishna Narayanan 7:52 PM + No problem. + Eric Larour 7:52 PM + I'll probably have a million questions + Sri Hari Krishna Narayanan 7:52 PM + This is an exhaustive test + 7:52 PM + FOr m ost purposes, we wil not need all of this + Eric Larour 7:52 PM + this is really nice, I'm pretty exited ! + Sri Hari Krishna Narayanan 7:52 PM + Jean belives for example the the grad_length version is pointless. I find it interesting though. + 7:53 PM + Okay. There are more interesting examples we can try Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adjoinablempi/install-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adjoinablempi/install-macosx64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adjoinablempi/install-macosx64.sh (revision 18231) @@ -0,0 +1,29 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install + +#Mercurial cloning: +hg clone http://mercurial.mcs.anl.gov//ad/AdjoinableMPI src + +export C_INCLUDE_PATH=:/usr/include/sys/:$C_INCLUDE_PATH + +#Configure adjoinablempi +cd src +autoreconf -fi + +./configure \ + --prefix="$ISSM_DIR/externalpackages/adjoinablempi/install" \ + --libdir="$ISSM_DIR/externalpackages/adjoinablempi/install/lib" \ + --with-mpi-root="$ISSM_DIR/externalpackages/mpich/install" \ + --enable-requestOnTrace + +#Compile adjoinablempi +make clean +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adjoinablempi/install-pleaides-gcc.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adjoinablempi/install-pleaides-gcc.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adjoinablempi/install-pleaides-gcc.sh (revision 18231) @@ -0,0 +1,27 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install + +#Mercurial cloning: +hg clone http://mercurial.mcs.anl.gov//ad/AdjoinableMPI src + +#Configure adjoinablempi +cd src +autoreconf -fi + +./configure \ + --prefix="$ISSM_DIR/externalpackages/adjoinablempi/install" \ + --libdir="$ISSM_DIR/externalpackages/adjoinablempi/install/lib" \ + --with-mpi-root="$ISSM_DIR/externalpackages/mpich/install" \ + --enable-requestOnTrace CFLAGS="-g -O0" + +#Compile adjoinablempi +make clean +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adjoinablempi/install-pleaides.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adjoinablempi/install-pleaides.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adjoinablempi/install-pleaides.sh (revision 18231) @@ -0,0 +1,27 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install + +#Mercurial cloning: +hg clone http://mercurial.mcs.anl.gov//ad/AdjoinableMPI src + +#Configure adjoinablempi +cd src +autoreconf -fi + +./configure \ + --prefix="$ISSM_DIR/externalpackages/adjoinablempi/install" \ + --libdir="$ISSM_DIR/externalpackages/adjoinablempi/install/lib" \ + --with-mpi-root="/nasa/sgi/mpt/2.06rp16/" \ + --enable-requestOnTrace + +#Compile adjoinablempi +make clean +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adjoinablempi/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adjoinablempi/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adjoinablempi/install.sh (revision 18231) @@ -0,0 +1,27 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install + +#Mercurial cloning: +hg clone http://mercurial.mcs.anl.gov//ad/AdjoinableMPI src + +#Configure adjoinablempi +cd src +autoreconf -fi + +./configure \ + --prefix="$ISSM_DIR/externalpackages/adjoinablempi/install" \ + --libdir="$ISSM_DIR/externalpackages/adjoinablempi/install/lib" \ + --with-mpi-root="$ISSM_DIR/externalpackages/mpich/install" \ + --enable-requestOnTrace + +#Compile adjoinablempi +make clean +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adolc/install-withampi-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adolc/install-withampi-macosx64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adolc/install-withampi-macosx64.sh (revision 18231) @@ -0,0 +1,31 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src + +git clone -b ampi git://git.mcs.anl.gov/adol-c.git src +#git reset --hard b254b2a001a1b7a024a9184cd087ae06eb975cad + +#Compile ADOL-C +cd src +autoreconf -f -i + +export CFLAGS="-O2 -L$ISSM_DIR/externalpackages/mpich/install/lib -lpmpich" +export CXXFLAGS="-O2 -L$ISSM_DIR/externalpackages/mpich/install/lib -lpmpich" + +./configure --prefix=$ISSM_DIR/externalpackages/adolc/install \ + --libdir=$ISSM_DIR/externalpackages/adolc/install/lib \ + --with-mpi-root=$ISSM_DIR/externalpackages/mpich/install \ + --enable-ampi \ + --with-ampi=$ISSM_DIR/externalpackages/adjoinablempi/install \ + --with-soname=adolc \ + --disable-tapedoc-values + +make clean +if [ $# -eq 0 ]; then + make V=1 +else + make -j $1 V=1 +fi +make V=1 install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adolc/install-withampi-pleiades-gcc.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adolc/install-withampi-pleiades-gcc.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adolc/install-withampi-pleiades-gcc.sh (revision 18231) @@ -0,0 +1,28 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src + +git clone -b ampi git://git.mcs.anl.gov/adol-c.git src +#git reset --hard b254b2a001a1b7a024a9184cd087ae06eb975cad + +#Compile ADOL-C +cd src +autoreconf -f -i + +./configure --prefix=$ISSM_DIR/externalpackages/adolc/install \ + --libdir=$ISSM_DIR/externalpackages/adolc/install/lib \ + --with-mpi-root=$ISSM_DIR/externalpackages/mpich/install \ + --enable-ampi \ + --with-ampi=$ISSM_DIR/externalpackages/adjoinablempi/install \ + --with-soname=adolc \ + --disable-tapedoc-values + +make clean +if [ $# -eq 0 ]; then + make V=1 +else + make -j $1 V=1 +fi +make V=1 install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adolc/install-withampi-pleiades.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adolc/install-withampi-pleiades.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adolc/install-withampi-pleiades.sh (revision 18231) @@ -0,0 +1,28 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src + +git clone -b ampi git://git.mcs.anl.gov/adol-c.git src +#git reset --hard b254b2a001a1b7a024a9184cd087ae06eb975cad + +#Compile ADOL-C +cd src +autoreconf -f -i + +./configure --prefix=$ISSM_DIR/externalpackages/adolc/install \ + --libdir=$ISSM_DIR/externalpackages/adolc/install/lib \ + --with-mpi-root="/nasa/sgi/mpt/2.06rp16/" \ + --enable-ampi \ + --with-ampi=$ISSM_DIR/externalpackages/adjoinablempi/install \ + --with-soname=adolc \ + --disable-tapedoc-values + +make clean +if [ $# -eq 0 ]; then + make V=1 +else + make -j $1 V=1 +fi +make V=1 install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adolc/install-withampi.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adolc/install-withampi.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adolc/install-withampi.sh (revision 18231) @@ -0,0 +1,28 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src + +git clone -b ampi git://git.mcs.anl.gov/adol-c.git src +#git reset --hard b254b2a001a1b7a024a9184cd087ae06eb975cad + +#Compile ADOL-C +cd src +autoreconf -f -i + +./configure --prefix=$ISSM_DIR/externalpackages/adolc/install \ + --libdir=$ISSM_DIR/externalpackages/adolc/install/lib \ + --with-mpi-root=$ISSM_DIR/externalpackages/mpich/install \ + --enable-ampi \ + --with-ampi=$ISSM_DIR/externalpackages/adjoinablempi/install \ + --with-soname=adolc \ + --disable-tapedoc-values + +make clean +if [ $# -eq 0 ]; then + make V=1 +else + make -j $1 V=1 +fi +make V=1 install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adolc/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adolc/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adolc/install.sh (revision 18231) @@ -0,0 +1,22 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src + +git clone -b ampi git://git.mcs.anl.gov/adol-c.git src +#git reset --hard b254b2a001a1b7a024a9184cd087ae06eb975cad + +#Compile ADOL-C +cd src + +autoreconf -f -i +./configure --prefix=$ISSM_DIR/externalpackages/adolc/install \ + --libdir=$ISSM_DIR/externalpackages/adolc/install/lib + +if [ $# -eq 0 ]; then + make V=1 +else + make -j $1 V=1 +fi +make V=1 install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adolc/old/install-2.2.0.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adolc/old/install-2.2.0.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adolc/old/install-2.2.0.sh (revision 18231) @@ -0,0 +1,60 @@ +#!/bin/bash +set -eu + +#some issues on macosx64 with ISSM's autoconf. you might want to run native to mac on this. + +#Some cleanup +rm -rf install ADOL-C-2.2.0 src trunk + +#Create install directories +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ADOL-C-2.2.0.tar.gz' 'ADOL-C-2.2.0.tar.gz' + +#Untar +tar -zxvf ADOL-C-2.2.0.tar.gz + +#Move ADOL-C into install directory +mv ADOL-C-2.2.0/* src +rm -rf ADOL-C-2.2.0 + +#Compile ADOL-C +cd src + +#export CC=gcc +#export CXX=g++ +#export CFLAGS="-arch x86_64" +#export CXXFLAGS="-arch x86_64" + +./configure \ + --prefix=$ISSM_DIR/externalpackages/adolc/install \ + --enable-sparse \ + --enable-docexa \ + --enable-addexa \ + --disable-shave + +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install + + +#Ok, bug with libtool: replace all LIBTOOL= by LIBTOOL=libtool +#in all Makefiles +for i in `find ./ -name Makefile ` +do + echo $i + cat $i | sed 's/LIBTOOL =/LIBTOOL = libtool/g' > $i.bak + mv $i.bak $i +done + +#remake: +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adolc/old/update.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adolc/old/update.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adolc/old/update.sh (revision 18231) @@ -0,0 +1,14 @@ +#!/bin/bash + +cd adolc_issm +git pull + +autoreconf -f -i +./configure --prefix=$ISSM_DIR/externalpackages/adolc/install + +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adolc/update-existing.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adolc/update-existing.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/adolc/update-existing.sh (revision 18231) @@ -0,0 +1,29 @@ +#!/bin/bash +set -eu + +#This script is very specific to the larour larsen nightly using adolc. +#It relies on just an update of adolc, and symlink to an existing adolc +#repo. + +#Some cleanup +rm -rf install src + +#symlink: +ln -s /proj/ice/larour2/issm-uci/trunk-jpl/externalpackages/adolc/adolc_issm ./src + +#update and compile +cd src +git pull origin +git checkout ampi +#git reset --hard b254b2a001a1b7a024a9184cd087ae06eb975cad + +autoreconf -f -i +./configure --prefix=$ISSM_DIR/externalpackages/adolc/install \ + --libdir=$ISSM_DIR/externalpackages/adolc/install/lib + +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/android/android-ndk/android_aux.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/android/android-ndk/android_aux.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/android/android-ndk/android_aux.sh (revision 18231) @@ -0,0 +1,43 @@ +#!/bin/bash +# +# android_aux.sh serves as an auxiliary script for all installation +# scripts with the Android suffix. +# +# TODO: include M4 macros for generic options. +# + +sdk_rev=22.6.2 +ndk_rev=9 +api_levels="android-14,android-15,android-16" +host_triplet="arm-linux-androideabi" +default_droid="android-4.1" + +step=0; +j=1; + +echo "" +echo "This install script utilizes 'android_aux.sh' to allow for options." +echo "For usage information enter: '--help'" +echo Number of arguments is: $# + +for arg in $* +do + if [[ "$arg" =~ --step=([0-9])* ]]; then + step=${BASH_REMATCH[1]}; + echo "Setting step to: " $step + elif [[ "$arg" == "--help" ]]; then + echo "" + echo "USAGE: $ install.sh [--step=#] [-j#]" + echo "" + echo "Where '#' is some integer." + echo "To check the number of steps check the install script." + echo "" + exit 1; + elif [[ "$arg" =~ -j=([1-9]+[0-9]*) ]]; then + j=${BASH_REMATCH[1]}; + echo "Number of jobs set to: " $j + else + echo "Option not recognized" + exit 1; + fi +done Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/android/android-ndk/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/android/android-ndk/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/android/android-ndk/install.sh (revision 18231) @@ -0,0 +1,31 @@ +#!/bin/bash + +# This installs the Android NDK (Native Development Kit) +# which is needed for the compilation of C/C++ code into the +# native architecture of the Android device. + +# The android-ndk-r8-darwin-x86.tar.bz2 ndk.tar.bz2 file was downloaded +# from the android developer website: +source $ANDROID_DIR/android_aux.sh + +if [[ $step == "1" || $step == "0" ]]; then + # Cleanup the install + rm -rf install + rm -rf $ANDROID_DIR/arm-linux-android-${default_droid} + + # Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/android-ndk-r'${ndk_rev}'-darwin-x86.tar.bz2' 'ndk.tar.bz2' + + # Untar + tar -zxvf ndk.tar.bz2 + rm -rf ndk.tar ndk.tar.bz2 + + # Move to install + mv android-ndk-r${ndk_rev} install +fi + +# Create Standalone Development Directory +# Note: API-14 corresponds to Android 4.0. +if [[ $step == "2" || $step == "0" ]]; then + $ANDROID_DIR/android-ndk/install/build/tools/make-standalone-toolchain.sh --platform=android-14 --install-dir=$ANDROID_DIR/android-ndk/install/arm-linux-android-install +fi Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/android/android-ndk/installNDK-linux-x86.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/android/android-ndk/installNDK-linux-x86.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/android/android-ndk/installNDK-linux-x86.sh (revision 18231) @@ -0,0 +1,39 @@ +#!/bin/bash + +# This installs the Android NDK (Native Development Kit) +# which is needed for the compilation of C/C++ code into the +# native architecture of the Android device. + +# The android-ndk-r8-darwin-x86.tar.bz2 ndk.tar.bz2 file was downloaded +# from the android developer website: +source $ANDROID_DIR/android_aux.sh + +if [[ $step == "1" || $step == "0" ]]; then + # Cleanup the install + rm -rf install + rm -rf $ANDROID_DIR/arm-linux-android-${default_droid} + + # Download from ISSM server +# $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/android-ndk-r'${ndk_rev}'-darwin-x86.tar.bz2' 'ndk.tar.bz2' + # Download from google +# if ["$(uname -m)" = "x86_64"]; then +# wget 'https://dl.google.com/android/ndk/android-ndk-r'${ndk_rev}'d-linux-x86_64.tar.bz2' 'ndk.tar.bz2' +# fi + +# if ["$(uname -m)" = "x86"]; then + wget 'https://dl.google.com/android/ndk/android-ndk-r'${ndk_rev}'d-linux-x86.tar.bz2' + # fi + # Install Android NDK + mv 'android-ndk-r'${ndk_rev}'d-linux-x86.tar.bz2' ndk.tar.bz2 + tar -xvf ndk.tar.bz2 + rm -rf ndk.tar ndk.tar.bz2 + + # Move to install + mv android-ndk-r${ndk_rev}d install +fi + +# Create Standalone Development Directory +# Note: API-14 corresponds to Android 4.0. +if [[ $step == "2" || $step == "0" ]]; then + $ANDROID_DIR/android-ndk/install/build/tools/make-standalone-toolchain.sh --platform=android-14 --install-dir=$ANDROID_DIR/android-ndk/install/arm-linux-android-install +fi Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/android/android-sdk/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/android/android-sdk/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/android/android-sdk/install.sh (revision 18231) @@ -0,0 +1,82 @@ +#!/bin/bash + +# This installs the Android SDK (Software Development Kit) +# which is needed for the compilation of the Java project. + +source $ANDROID_DIR/android_aux.sh + +# Different steps here. +# 0: do all +# 1: install sdk, ant and sdk tools +# 2: install an emulator. +# 3: test the emulator +# 4: cleanup + +present_dir=`pwd`; +sd_card="issm-sdcard" + +if [[ $step == "1" || $step == "0" ]]; then + + # Cleanup the install + rm -rf install + + # Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/android-sdk_r'$sdk_rev'-macosx.zip' 'android-sdk_r'${sdk_rev}'-macosx.zip' + + # Install Android SDK and NDK. + unzip -o android-sdk_r${sdk_rev}-macosx.zip + + # Move to install + mv -f android-sdk-macosx install + + # Post_install configuration: + # We need specific settings for specific platforms, for the SDK to + # function properly + + # For now, we need to install: + # android sdk platform tools + # and a specific android api: API 16, API 15 and API 14 + # Note: API 16, API 15 and 14 correspond to Android 4.1, 4.0.3 and 4.0 respectively. + + cd install/tools/ && source ./android update sdk -t platform-tool,${api_levels},system-image --no-ui + +fi + +if [[ $step == "2" || $step == "0" ]]; then + + # Once this is done, we need to install an emulator. Location will default to ~/.android/avd, + # which we will move to $ISSM_DIR/externalpackages/android-emulators. + # For now, it's called: Android-4.0.3 + + # Here we delete the Android-4.0.3 device if it already exists. + cd $present_dir/install/tools + + if [ -e $ANDROID_DIR/android-emulators/$default_droid ] + then + echo "Deleting previously created device: $default_droid" + ./android delete avd -n $default_droid + fi + + # Android will prompt the user to specify hardware emulation options. For now, default + # default settings will suffice. Press 'enter' to take default settings or enter 'no'. + + ./android create avd -f -n $default_droid -t 1 -p $ANDROID_DIR/android-emulators/$default_droid --abi armeabi-v7a + echo "Creating an SD Card" + ./mksdcard -l $sd_card 2G $ANDROID_DIR/android-emulators/$sd_card.img +fi + +if [[ $step == "3" || $step == "0" ]]; then + # Here we will start up our default emulator to test that it is working properly. + # Once the device has booted we will use the Android Debug Bridge tool to gain + # a terminal in our device. + + cd $present_dir/install/tools + ./emulator -avd $default_droid -sdcard $ANDROID_DIR/android-emulators/$sd_card.img & + + cd ../platform-tools + ./adb wait-for-device shell +fi + +if [[ $step == "4" || $step == "0" ]]; then + rm -rf install +fi Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/android/android-sdk/installSDK-linux-x86.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/android/android-sdk/installSDK-linux-x86.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/android/android-sdk/installSDK-linux-x86.sh (revision 18231) @@ -0,0 +1,85 @@ +#!/bin/bash + +# This installs the Android SDK (Software Development Kit) +# which is needed for the compilation of the Java project. + +source $ANDROID_DIR/android_aux.sh + +# Different steps here. +# 0: do all +# 1: install sdk, ant and sdk tools +# 2: install an emulator. +# 3: test the emulator +# 4: cleanup + +present_dir=`pwd`; +sd_card="issm-sdcard" + +if [[ $step == "1" || $step == "0" ]]; then + + # Cleanup the install + rm -rf install + + # Download from ISSM server +# $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://developer.android.com/sdk/index.html#download' 'android-sdk-linux.zip' + + #Download from Google server + wget https://dl.google.com/android/android-sdk_r$sdk_rev-linux.tgz + + # Install Android SDK. + tar -zxvf android-sdk_r$sdk_rev-linux.tgz + rm -rf android-sdk_r$sdk_rev-linux.tgz + # Move to install + mv -f android-sdk-linux install + + # Post_install configuration: + # We need specific settings for specific platforms, for the SDK to + # function properly + + # For now, we need to install: + # android sdk platform tools + # and a specific android api: API 16, API 15 and API 14 + # Note: API 16, API 15 and 14 correspond to Android 4.1, 4.0.3 and 4.0 respectively. + + cd install/tools/ && source ./android update sdk -t platform-tool,${api_levels},system-image --no-ui + +fi + +if [[ $step == "2" || $step == "0" ]]; then + + # Once this is done, we need to install an emulator. Location will default to ~/.android/avd, + # which we will move to $ISSM_DIR/externalpackages/android-emulators. + # For now, it's called: Android-4.0.3 + + # Here we delete the Android-4.0.3 device if it already exists. + cd $present_dir/install/tools + + if [ -e $ANDROID_DIR/android-emulators/$default_droid ] + then + echo "Deleting previously created device: $default_droid" + ./android delete avd -n $default_droid + fi + + # Android will prompt the user to specify hardware emulation options. For now, default + # default settings will suffice. Press 'enter' to take default settings or enter 'no'. + + ./android create avd -f -n $default_droid -t 1 -p $ANDROID_DIR/android-emulators/$default_droid --abi armeabi-v7a + echo "Creating an SD Card" + ./mksdcard -l $sd_card 2G $ANDROID_DIR/android-emulators/$sd_card.img +fi + +if [[ $step == "3" || $step == "0" ]]; then + # Here we will start up our default emulator to test that it is working properly. + # Once the device has booted we will use the Android Debug Bridge tool to gain + # a terminal in our device. + + cd $present_dir/install/tools + ./emulator -avd $default_droid -sdcard $ANDROID_DIR/android-emulators/$sd_card.img & + + cd ../platform-tools + ./adb wait-for-device shell +fi + +#if [[ $step == "4" || $step == "0" ]]; then +# rm -rf install +#fi Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/android/android_aux.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/android/android_aux.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/android/android_aux.sh (revision 18231) @@ -0,0 +1,43 @@ +#!/bin/bash +# +# android_aux.sh serves as an auxiliary script for all installation +# scripts with the Android suffix. +# +# TODO: include M4 macros for generic options. +# + +sdk_rev=20 +ndk_rev=8 +api_levels="android-14,android-15,android-16" +host_triplet="arm-linux-androideabi" +default_droid="android-4.1" + +step=0; +j=1; + +echo "" +echo "This install script utilizes 'android_aux.sh' to allow for options." +echo "For usage information enter: '--help'" +echo Number of arguments is: $# + +for arg in $* +do + if [[ "$arg" =~ --step=([0-9])* ]]; then + step=${BASH_REMATCH[1]}; + echo "Setting step to: " $step + elif [[ "$arg" == "--help" ]]; then + echo "" + echo "USAGE: $ install.sh [--step=#] [-j#]" + echo "" + echo "Where '#' is some integer." + echo "To check the number of steps check the install script." + echo "" + exit 1; + elif [[ "$arg" =~ -j=([1-9]+[0-9]*) ]]; then + j=${BASH_REMATCH[1]}; + echo "Number of jobs set to: " $j + else + echo "Option not recognized" + exit 1; + fi +done Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/angel/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/angel/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/angel/install.sh (revision 18231) @@ -0,0 +1,12 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf angel + +#download +svn co -r 82 https://angellib.svn.sourceforge.net/svnroot/angellib/trunk angel + +#Compile +cd angel +make Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/appscan/bin/genouncemakePFile.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/appscan/bin/genouncemakePFile.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/appscan/bin/genouncemakePFile.sh (revision 18231) @@ -0,0 +1,593 @@ +#!/bin/bash + +#---------------------------------------------------------------------- +#VARIABLES containing information to generate OunceMake Properties file +#---------------------------------------------------------------------- +XMLHEADER="" +OUNCEHEADER="" +MAKEOPT="-f Makefile" + +COMPILER_TAG="Compiler" +COMPILER_MACRO="macro" + +C_COMPILER_MVALUE="\"CC\"" +CPP_COMPILER_MVALUE="\"CXX\"" + +MAKE_TAG="Make" +MAKE_MACRO="macro" +MAKE_MVALUE="\"MAKE\"" + + +LINKER_TAG="Linker" +LINKER_MACRO="macro" +LINKER_MVALUE="\"LD\"" + + +ARCHIVE_TAG="Executable" +ARCHIVE_MACRO="macro" +ARCHIVE_MVALUE="\"ARCHIVE\"" + +OUNCEOPT="" + +OUNCE_MAIN_TAG="OunceMakeProperties" +OUNCE_COMPILER_GPO_TAG="GlobalProjectOptions" +OUNCE_COMPILER_OPT="compiler_options" +OUNCE_COMPILER_OPT_gpp="\"-g++_linux_i386\"" +OUNCE_COMPILER_OPT_gcc="\"-gcc_linux_i386\"" + +OUNCE_INCLUDE_PATH="include_paths" +OUNCE_MACRO_PATH="macros" + +OUNCE_COMPILER_FO_TAG="FileOptions" +OUNCE_COMPILER_EXT="extensions" + +OUNCE_COMPILER_EXT_CPP="cpp;cxx" +OUNCE_COMPILER_EXT_C="c" + +#Did the search for a particular tool pass/fail +FAIL_FILE="failed.status" + +#--------------------------------- +#COMPILER data extraction function +#--------------------------------- + +function initialize { +#Create Directory for info + echo;echo + echo -e "Initialization....\t\t\t[\c " + echo -e "\E[33mSTARTED\c "; tput sgr0 + echo "]" + search_tool which + FILEPRE=${1} + + case "$1" in + "gcc"|"cc") + TESTFILE="testfoo.c" + ;; + "g++"|"CC") + TESTFILE="testfoo.cpp" + ;; + *) + echo "Error setting prefix" + ;; + esac + + DATAFOLDER="${FILEPRE}results" +#Declare files to generate and store results + RESULTFILE="${DATAFOLDER}/${FILEPRE}libinc.result" + SLIMFILE="${DATAFOLDER}/${FILEPRE}slim.inc" + SLIM2FILE="${DATAFOLDER}/${FILEPRE}slim2.inc" + +#Declare the Tags that enclose the information needed + START_TAG="#include <...> search starts here:" + END_TAG="End of search list." + +#Declare Variable to track Tags + MARK_FOUND=0 + +#For Macros + MACROSDUMPFILE="${DATAFOLDER}/${FILEPRE}macrosd.result" + INTFILE1="${DATAFOLDER}/${FILEPRE}interf1.result" + INTFILE2="${DATAFOLDER}/${FILEPRE}interf2.result" + + +#The file extensions for (both) options +CONFIG_FOLDER="config" +C_EXT="${CONFIG_FOLDER}/cext.data" +CPP_EXT="${CONFIG_FOLDER}/cppext.data" + +if [ -d ${CONFIG_FOLDER} ]; then + echo +else + mkdir ${CONFIG_FOLDER} + echo ${OUNCE_COMPILER_EXT_CPP} > ${C_EXT} + echo ${OUNCE_COMPILER_EXT_C} > ${CPP_EXT} +fi + + echo -e "Initialization....\t\t\t[\c " + echo -e "\E[33mDONE\c "; tput sgr0 + echo "]" +} + +function purgefiles { + echo -e "Purging files....\t\t\t[\c " + echo -e "\E[33mSTARTED\c "; tput sgr0 + echo "]" + if [ -e ${DATAFOLDER} ]; then + rm -R ${DATAFOLDER} + mkdir ${DATAFOLDER} + else + mkdir ${DATAFOLDER} + fi + echo -e "Purging files....\t\t\t[\c " + echo -e "\E[33mDONE\c "; tput sgr0 + echo "]" +} + + +function processGNUInclude { +echo +#Create the dummy file is does not exist +if [ -e ${TESTFILE} ]; then + echo "Will use an existing ${TESTFILE} file" +else + echo -e "int main(){\n return 0;\n}" &> ${TESTFILE} + if [ -e ${TESTFILE} ]; then + echo -e "Generating new test file\t\t[\c " + echo -e "\E[31m${TESTFILE}\c " ; tput sgr0 + echo "]" + else + echo -e "Error generating new test file\t\t[\c " + echo -e "\E[31m${TESTFILE}\c " ; tput sgr0 + echo "]" + #TO DO + #Will the user like to continue or exit? + fi +fi + + + echo + echo -e "Generating information for Compiler\t\t[\c " + echo -e "\E[31m${COMPILER}\c " ; tput sgr0 + echo "]" + +${COMPILER} -v ${TESTFILE} &> ${RESULTFILE} + + +cat ${RESULTFILE} | while read line +do + + if [ "${line}" = "${START_TAG}" ] + then + MARK_FOUND=1 + fi + + + if [ "${line}" = "${END_TAG}" ] + then + MARK_FOUND=0 + fi + + + if [ "${MARK_FOUND}" = 1 ] && [ "${line}" != "${START_TAG}" ] + then + let "inclib += 1" + echo ${line} 1>> ${SLIMFILE} + fi +done + +if [ -e ${SLIMFILE} ]; then + sed -e :a -e N -e 's/\n/; /' -e ta ${SLIMFILE} > ${RESULTFILE} + echo -e "Inc & Lib results are in file...\t\t[\c " + echo -e "\033[1m\E[31m${RESULTFILE}\033[0m\c " ; tput sgr0 + echo "]" +fi + +#String to contatenate the include path +concatpath="include_paths=\"" +#Merge file content +sed -e 's/\n/;/' ${SLIMFILE} > ${SLIM2FILE} + +} + + +function processGNUMacro { +#***************************** +#Generate macros for system +#***************************** + echo + echo -e "Generating Macro data for Compiler\t\t[\c " + echo -e "\E[31m${COMPILER} \c " ; tput sgr0 + echo "]" + + ${COMPILER} -dM -E ${TESTFILE} >> ${MACROSDUMPFILE} + sed 's/#define //' ${MACROSDUMPFILE} > ${INTFILE1} + if [ -e ${INTFILE1} ]; then + sed 's/ /=/' ${INTFILE1} > ${INTFILE2} + else + echo -e "\033[1m Sorry <${INTFILE1}> was not created.. \033[0m" + fi + + if [ -e ${INTFILE2} ]; then + #Remove the Macro's that have no values + sed '/^_.*=$/d' ${INTFILE2} > ${INTFILE1} + #Join the individual line and delimit with a (; ) + sed -e :a -e N -e 's/\n/; /' -e ta ${INTFILE1} > ${MACROSDUMPFILE} + #All done display the results file + echo -e "Macro results are in file...\t\t\t[\c " + echo -e "\033[1m\E[31m${MACROSDUMPFILE}\033[0m\c " ; tput sgr0 + echo "]" + else + echo -e "\033[1m Sorry <${MACROSDUMPFILE}> was not created.. \033[0m" + fi +} + +function processSUNMacro { +#******************************************* +#This function is for the SUN Compilers ONLY +#******************************************* + echo + echo -e "Generating Macro data for Compiler\t\t[\c " + echo -e "\E[31m${COMPILER} \c " ; tput sgr0 + echo "]" + + ${COMPILER} -xdumpmacros ${TESTFILE} &> ${MACROSDUMPFILE} + sed 's/#define //' ${MACROSDUMPFILE} > ${INTFILE1} + if [ -e ${INTFILE1} ]; then + sed 's/ /=/' ${INTFILE1} > ${INTFILE2} + else + echo -e "\033[1m Sorry <${INTFILE1}> was not created.. \033[0m" + fi + + if [ -e ${INTFILE2} ]; then + #Remove the Macro's that have no values + sed '/^_.*=$/d' ${INTFILE2} > ${INTFILE1} + #Join the individual line and delimit with a (; ) + sed -e :a -e N -e 's/\n/; /' -e ta ${INTFILE1} > ${MACROSDUMPFILE} + #All done display the results file + echo -e "Macro results are in file...\t\t\t[\c " + echo -e "\033[1m\E[31m${MACROSDUMPFILE}\033[0m\c " ; tput sgr0 + echo "]" + else + echo -e "\033[1m Sorry <${MACROSDUMPFILE}> was not created.. \033[0m" + fi +} + +#-------------------------- +#DATA Processing variables +#-------------------------- +PROPFILE="ouncemake_properties.xml" +PROBEFILE="probe.results" +ERRORLOG="error.log" + +#--------------------------------------- +#FUNCTION TO CREATE FILE +#-------------------------------------- + +function create_file { +#If a previous copy of file exist, delete it +if [ -e ${PROPFILE} ]; then + rm ${PROPFILE} +fi + +echo;echo +echo "CREATING THE PROPERTIES XML FILE" +#insert file headers +echo ${XMLHEADER} >> ${PROPFILE} +echo ${OUNCEHEADER} >> ${PROPFILE} +echo ${MAKEOPT} >> ${PROPFILE} +case "${1}" in + 'gcc') + search_tool gcc + ;; + 'g++') + search_tool g++ + ;; + 'bothGNU') + search_tool gcc + search_tool g++ + ;; + 'cc') + search_tool cc + ;; + 'CC') + search_tool CC + ;; + 'bothSUN') + search_tool gcc + search_tool g++ + ;; + '*') + ;; +esac +search_tool make +search_tool ld +search_tool ar +echo " ${OUNCEOPT}" >> ${PROPFILE} + +case "${1}" in + 'gcc') + singleGNUC gcc + ;; + 'g++') + singleGNUC g++ + ;; + 'bothGNU') + bothGNUC gcc + bothGNUC g++ + ;; + 'cc') + singleSUNC cc + ;; + 'CC') + singleSUNC CC + ;; + 'bothSUN') + bothSUNC cc + bothSUNC CC + ;; + '*') + ;; +esac + +echo "" >> ${PROPFILE} + +echo +echo -e "Successully created Properties file\t\t[\c " +echo -e "\033[1m\E[31m${PROPFILE}\033[0m\c " ; tput sgr0 +echo "]" +echo +} + +#when the system is unable to locate the tool +#the user is prompted to provide that information +function usersupplypath { + echo "Please provide the path to ${1}." + read TOOLPATH +} + + +function search_tool { +which $1 &> ${PROBEFILE} +#Why this approach? I had to be able to non-interactively +#know if the pattern was successfully found. + +sed -n -e "/.*no[ ]${1}[ ]in[ ].*/w $FAIL_FILE" ${PROBEFILE} + +#If the file is empty, the process PASSED +#else the Fail criteria was found. Process FAILED +if [ -e ${FAIL_FILE} ]; then + exec < ${FAIL_FILE} + read FAILPASS + if [${FAILPASS} = ""]; then + SEARCHTOOL="PASSED" + rm ${FAIL_FILE} + else + SEARCHTOOL="FAILED" + fi +fi + + +if [ ${SEARCHTOOL} == "FAILED" ] ; then + echo "Failed to find ${1} in PATH" >> ${ERRORLOG} + echo -e "check for $1 in ${TLOC}\t\t\t[$SEARCHTOOL]" +elif [ ${SEARCHTOOL} == "PASSED" ]; then + #Redirects stdin to a file so that + exec < ${PROBEFILE} + #I can read line by line + read TLOC + echo -e "check for $1 in ${TLOC}\t\t\t[\c " + echo -e "\E[33m${SEARCHTOOL}\c "; tput sgr0 + echo "]" +else + echo "Unable to process the request" + #exit +fi + +case "$1" in + 'gcc') + #set up the sub strings + TAG_L="<${COMPILER_TAG} ${COMPILER_MACRO}=${C_COMPILER_MVALUE}>" + MVALUE="$TLOC" + TAG_R="" + ;; + 'g++') + TAG_L="<${COMPILER_TAG} ${COMPILER_MACRO}=${CPP_COMPILER_MVALUE}>" + MVALUE="$TLOC" + TAG_R="" + ;; + 'make') + TAG_L="<${MAKE_TAG} ${MAKE_MACRO}=${MAKE_MVALUE}>" + MVALUE="$TLOC" + TAG_R="" + ;; + 'ld') + TAG_L="<${LINKER_TAG} ${LINKER_MACRO}=${LINKER_MVALUE}>" + MVALUE="$TLOC" + TAG_R="" + ;; + 'ar') + TAG_L="<${ARCHIVE_TAG} ${ARCHIVE_MACRO}=${ARCHIVE_MVALUE}>" + MVALUE="$TLOC" + TAG_R="" + ;; + '*') + ;; +esac + +#then concatenate +FULL_STRING="${TAG_L}${MVALUE}${TAG_R}" +#and store in file +echo " $FULL_STRING" >> ${PROPFILE} +} +function singleGNUC { + +echo " <${OUNCE_COMPILER_GPO_TAG}" >> ${PROPFILE} + +case "$1" in + 'gcc') + echo -e "\t ${OUNCE_COMPILER_OPT}=${OUNCE_COMPILER_OPT_gcc}" >> ${PROPFILE} + ;; + 'g++') + echo -e "\t ${OUNCE_COMPILER_OPT}=${OUNCE_COMPILER_OPT_gpp}" >> ${PROPFILE} + ;; + '*') + ;; +esac + +exec < ${RESULTFILE} +read INCLUDE_DATA +echo -e "\t ${OUNCE_INCLUDE_PATH}=\"${INCLUDE_DATA}\"" >> ${PROPFILE} +exec < ${MACROSDUMPFILE} +read MACRO_DATA +#Using single quotes to wrap double quotes in data +echo -e "\t ${OUNCE_MACRO_PATH}='${MACRO_DATA}' />" >> ${PROPFILE} + +} + + +function bothGNUC { + +echo -e "\t<${OUNCE_COMPILER_FO_TAG}" >> ${PROPFILE} + +case "$1" in + 'gcc') + FILEPRE="$1" + exec < ${C_EXT} + read CEXTENSIONS + if [ ${CEXTENSIONS} = "" ]; then + CEXTENSIONS=${OUNCE_COMPILER_EXT_C} + else + OUNCE_COMPILER_EXT_C=${CEXTENSIONS} + fi + echo -e "\t ${OUNCE_COMPILER_EXT}=\"${OUNCE_COMPILER_EXT_C}\"" >> ${PROPFILE} + ;; + 'g++') + FILEPRE="$1" + exec < ${CPP_EXT} + read CPPEXTENSIONS + if [ ${CPPEXTENSIONS} = "" ]; then + CPPEXTENSIONS=${OUNCE_COMPILER_EXT_CPP} + else + OUNCE_COMPILER_EXT_CPP=${CPPEXTENSIONS} + fi + echo -e "\t ${OUNCE_COMPILER_EXT}=\"${OUNCE_COMPILER_EXT_CPP}\"" >> ${PROPFILE} + ;; + '*') + ;; +esac + +#To make sure that the correct folder and file is read +DATAFOLDER="${FILEPRE}results" +#Declare files to generate and store results +RESULTFILE="${DATAFOLDER}/${FILEPRE}libinc.result" + +exec < ${RESULTFILE} +read INCLUDE_DATA +echo -e "\t ${OUNCE_INCLUDE_PATH}=\"${INCLUDE_DATA}\"" >> ${PROPFILE} +exec < ${MACROSDUMPFILE} +read MACRO_DATA +echo -e "\t ${OUNCE_MACRO_PATH}='${MACRO_DATA}'/>" >> ${PROPFILE} + +} + + +clear +echo +echo -e "\t \E[34m\033[1mOUNCEMAKE PROPERTIES FILE GENERATOR (1.0)b\033[0m";tput sgr0 + +#Start of the program +case "$1" in + '-t') + case "$2" in + "gcc") + COMPILER=${2} + initialize ${2} + purgefiles + processGNUInclude + processGNUMacro + create_file ${2} + ;; + "g++") + COMPILER=${2} + initialize ${2} + purgefiles + processGNUInclude + processGNUMacro + create_file ${2} + ;; + "bothGNU") + COMPILER="gcc" + initialize ${2} + purgefiles + processGNUInclude + processGNUMacro + COMPILER="g++" + initialize ${2} + purgefiles + processGNUInclude + processGNUMacro + create_file ${2} + ;; + "cc") + COMPILER=${2} + initialize ${2} + purgefiles + processSUNInclude + processSUNMacro + create_file ${2} + ;; + "CC") + COMPILER=${2} + initialize ${2} + purgefiles + # processSUNInclude + processSUNMacro + # create_file ${2} + ;; + "bothSUN") + COMPILER="cc" + initialize cc + purgefiles + processSUNInclude + processSUNMacro + COMPILER="CC" + initialize CC + purgefiles + processSUNInclude + processSUNMacro + create_file both + ;; + '*') + echo "Usage: -t [gcc|g++|bothGNU]" + exit $? + ;; + esac + ;; + '-h') + echo -e "Usage: -t [Options] -v " + echo -e "Options:" + echo -e "\t[gcc]\tC project only"; + echo -e "\t[g++]\tCPP project only" + echo -e "\t[bothGNU]\tMixed C and CPP project" + echo + echo -e "\t-v \tDisplay version information" + exit $? + ;; + '-v') + echo "Version 1.0 beta" + exit $? + ;; + *) + echo -e "Usage: -t [Options] -v " + echo -e "Options:" + echo -e "\t[gcc]\tC project only"; + echo -e "\t[g++]\tCPP project only" + echo -e "\t[both]\tMixed C and CPP project" + echo + echo -e "\t-v \tDisplay version information" + exit $? + ;; +esac +echo "[ P R O C E S S C O M P L E T E !!! ]" +echo Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/appscan/hostname =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/appscan/hostname (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/appscan/hostname (revision 18231) @@ -0,0 +1,1 @@ +jplsec-codescan.jpl.nasa.gov Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/appscan/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/appscan/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/appscan/install.sh (revision 18231) @@ -0,0 +1,10 @@ +#!/bin/bash +set -eu + +#AppScan install directory. Just symlink to your existing AppScan software + +#Erase symlink +rm -rf install + +#Select or create a new simlink +ln -s /opt/IBM/AppScan_Source ./install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/apr-util/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/apr-util/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/apr-util/install.sh (revision 18231) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf apr-util-1.4.1 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/apr-util-1.4.1.tar.gz' 'apr-util-1.4.1.tar.gz' + +#Untar +tar -zxvf apr-util-1.4.1.tar.gz + +#Move apr-util into src directory +mv apr-util-1.4.1/* src +rm -rf apr-util-1.4.1 + +#Configure apr-util +cd src +./configure --prefix="$ISSM_DIR/externalpackages/apr-util/install" --with-apr="$ISSM_DIR/externalpackages/apr/install" + +#Compile and install apr-util +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/apr/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/apr/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/apr/install.sh (revision 18231) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf apr-1.4.6 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/apr-1.4.6.tar.gz' 'apr-1.4.6.tar.gz' + +#Untar +tar -zxvf apr-1.4.6.tar.gz + +#Move apr into src directory +mv apr-1.4.6/* src +rm -rf apr-1.4.6 + +#Configure apr +cd src +./configure --prefix="$ISSM_DIR/externalpackages/apr/install" + +#Compile and install apr +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/aspell/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/aspell/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/aspell/install.sh (revision 18231) @@ -0,0 +1,62 @@ +#!/bin/bash +set -eu + +#0: cleanup +#1: install aspell +#2: install en dictionary +step=2 + + +#Some cleanup +if [[ $step == "0" ]]; then + rm -rf src install dicts + rm -rf aspell-0.50.5 + rm -rf aspell5-en-6.0.0 +fi + +#install aspell +if [[ $step == "1" ]]; then + + mkdir src install dicts + + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/aspell-0.50.5.tar.gz' 'aspell-0.50.5.tar.gz' + + #Untar + tar -zxvf aspell-0.50.5.tar.gz + + #Move aspell into src directory + mv aspell-0.50.5/* src + rm -rf aspell-0.50.5 + + #Configure aspell + cd src + ./configure \ + --prefix="$ISSM_DIR/externalpackages/aspell/install" \ + + #Compile and install aspell + if [ -z $1 ]; then + make + else + make -j $1 + fi + make install +fi + +#languages +if [[ $step == "2" ]]; then + + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/aspell5-en-6.0.0.tar.gz' 'aspell5-en-6.0.0.tar.gz' + + #Untar + tar -zxvf aspell5-en-6.0.0.tar.gz + + #Move aspell into src directory + mv aspell5-en-6.0.0 dicts + + #install + cd dicts/aspell5-en-6.0.0 + ./configure + make install +fi Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/atlas/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/atlas/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/atlas/install.sh (revision 18231) @@ -0,0 +1,32 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install ATLAS build +mkdir src install build + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/atlas3.10.0.tar.bz2' 'atlas3.10.0.tar.bz2' + +#Untar +tar -zxvf atlas3.10.0.tar.bz2 + +#Move atlas into src directory +mv ATLAS/* src +rm -rf ATLAS + +#Configure atlas +cd build + +export CFLAGS=" -arch x86_64" + +../src/configure \ + --prefix="$ISSM_DIR/externalpackages/atlas/install" + +#Compile atlas +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/autotools/install-win.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/autotools/install-win.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/autotools/install-win.sh (revision 18231) @@ -0,0 +1,46 @@ +#!/bin/bash +set -eu + +rm -rf install +mkdir install + +export PATH="$ISSM_DIR/externalpackages/autotools/install/bin:$PATH" + +#install autoconf +echo " === INSTALLING AUTOCONF ==" +rm -rf src +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/autoconf-2.68.tar.gz' 'autoconf-2.68.tar.gz' +tar -zxvf autoconf-2.68.tar.gz +mv autoconf-2.68 src +cd src +./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" +make +make install +cd .. + +#install automake +echo " === INSTALLING AUTOMAKE ==" +rm -rf src +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/automake-1.11.3.tar.gz' 'automake-1.11.3.tar.gz' +tar -zxvf automake-1.11.3.tar.gz +mv automake-1.11.3 src +cd src +./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" +make +make install +cd .. + +#install libtool +echo " === INSTALLING LIBTOOL ==" +rm -rf src +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libtool-2.4.2.tar.gz' 'libtool-2.4.2.tar.gz' +tar -zxvf libtool-2.4.2.tar.gz +rm libtool-2.4.2.tar.gz +mv libtool-2.4.2 src +cd src +./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" +make +make install +cd .. + +patch ./install/share/aclocal/libtool.m4 < ./patches/libtool.m4.patch Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/autotools/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/autotools/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/autotools/install.sh (revision 18231) @@ -0,0 +1,44 @@ +#!/bin/bash +set -eu + +rm -rf install +mkdir install + +export PATH="$ISSM_DIR/externalpackages/autotools/install/bin:$PATH" + +#install autoconf +echo " === INSTALLING AUTOCONF ==" +rm -rf src +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/autoconf-2.69.tar.gz' 'autoconf-2.69.tar.gz' +tar -zxvf autoconf-2.69.tar.gz +mv autoconf-2.69 src +cd src +./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" +make +make install +cd .. + +#install automake +echo " === INSTALLING AUTOMAKE ==" +rm -rf src +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/automake-1.14.tar.gz' 'automake-1.14.tar.gz' +tar -zxvf automake-1.14.tar.gz +mv automake-1.14 src +cd src +./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" +make +make install +cd .. + +#install libtool +echo " === INSTALLING LIBTOOL ==" +rm -rf src +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libtool-2.4.2.tar.gz' 'libtool-2.4.2.tar.gz' +tar -zxvf libtool-2.4.2.tar.gz +rm libtool-2.4.2.tar.gz +mv libtool-2.4.2 src +cd src +./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" +make +make install +cd .. Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/autotools/patches/libtool.m4.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/autotools/patches/libtool.m4.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/autotools/patches/libtool.m4.patch (revision 18231) @@ -0,0 +1,38 @@ +--- m4/libtool.m4 2013-06-19 22:19:27.313488900 -0700 ++++ m4/libtool.m4.bak 2013-06-18 18:45:55.766285300 -0700 +@@ -4752,7 +4752,7 @@ + _LT_TAGVAR(exclude_expsyms, $1)=['[_]+GLOBAL_OFFSET_TABLE_|[_]+GLOBAL__[FID]_.*|[_]+head_[A-Za-z0-9_]+_dll|[A-Za-z0-9_]+_dll_iname'] + + if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then +- _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib' ++ _LT_TAGVAR(archive_cmds, $1)='$CC /LD $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib ' + # If the export-symbols file already is a .def file (1st line + # is EXPORTS), use it as is; otherwise, prepend... + _LT_TAGVAR(archive_expsym_cmds, $1)='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then +@@ -4761,7 +4761,7 @@ + echo EXPORTS > $output_objdir/$soname.def; + cat $export_symbols >> $output_objdir/$soname.def; + fi~ +- $CC -shared $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib' ++ $CC /LD $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib ' + else + _LT_TAGVAR(ld_shlibs, $1)=no + fi +@@ -6168,7 +6168,7 @@ + _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=yes + + if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then +- _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib' ++ _LT_TAGVAR(archive_cmds, $1)='$CC /LD -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib ' + # If the export-symbols file already is a .def file (1st line + # is EXPORTS), use it as is; otherwise, prepend... + _LT_TAGVAR(archive_expsym_cmds, $1)='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then +@@ -6177,7 +6177,7 @@ + echo EXPORTS > $output_objdir/$soname.def; + cat $export_symbols >> $output_objdir/$soname.def; + fi~ +- $CC -shared -nostdlib $output_objdir/$soname.def $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib' ++ $CC /LD -nostdlib $output_objdir/$soname.def $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib ' + else + _LT_TAGVAR(ld_shlibs, $1)=no + fi Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/bbftp/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/bbftp/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/bbftp/install.sh (revision 18231) @@ -0,0 +1,27 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install bbftp-client-3.2.0 + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/bbftp-client-3.2.0.tar.gz' 'bbftp-client-3.2.0.tar.gz' + +#Create install directories +mkdir install src + +#Untar +tar -zxvf bbftp-client-3.2.0.tar.gz + +#Move bbftp-client into install directory +mv bbftp-client-3.2.0/* src +rm -rf bbftp-client-3.2.0 + +#Apply patches +cd src + +#Configure and compile +cd bbftpc +./configure --prefix=$ISSM_DIR/externalpackages/bbftp/install +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/blas/configs/linux64/make.inc =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/blas/configs/linux64/make.inc (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/blas/configs/linux64/make.inc (revision 18231) @@ -0,0 +1,34 @@ +#################################################################### +# BLAS make include file. # +# March 2007 # +#################################################################### +# +SHELL = /bin/sh +# +# The machine (platform) identifier to append to the library names +# +PLAT = _LINUX +# +# Modify the FORTRAN and OPTS definitions to refer to the +# compiler and desired compiler options for your machine. NOOPT +# refers to the compiler options desired when NO OPTIMIZATION is +# selected. Define LOADER and LOADOPTS to refer to the loader and +# desired load options for your machine. +# +FORTRAN = gfortran +OPTS = -fPIC -O3 +DRVOPTS = $(OPTS) +NOOPT = +LOADER = gfortran +LOADOPTS = +# +# The archiver and the flag(s) to use when building archive (library) +# If you system has no ranlib, set RANLIB = echo. +# +ARCH = ar +ARCHFLAGS= cr +RANLIB = ranlib +# +# The location and name of the Reference BLAS library. +# +BLASLIB = blas$(PLAT).a Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/blas/configs/macosx64/make.inc =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/blas/configs/macosx64/make.inc (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/blas/configs/macosx64/make.inc (revision 18231) @@ -0,0 +1,34 @@ +#################################################################### +# BLAS make include file. # +# March 2007 # +#################################################################### +# +SHELL = /bin/sh +# +# The machine (platform) identifier to append to the library names +# +PLAT = _LINUX +# +# Modify the FORTRAN and OPTS definitions to refer to the +# compiler and desired compiler options for your machine. NOOPT +# refers to the compiler options desired when NO OPTIMIZATION is +# selected. Define LOADER and LOADOPTS to refer to the loader and +# desired load options for your machine. +# +FORTRAN = gfortran +OPTS = -fPIC -O3 +DRVOPTS = $(OPTS) +NOOPT = +LOADER = gfortran +LOADOPTS = +# +# The archiver and the flag(s) to use when building archive (library) +# If you system has no ranlib, set RANLIB = echo. +# +ARCH = ar +ARCHFLAGS= cr +RANLIB = ranlib +# +# The location and name of the Reference BLAS library. +# +BLASLIB = blas$(PLAT).a Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/blas/install-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/blas/install-linux64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/blas/install-linux64.sh (revision 18231) @@ -0,0 +1,29 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install BLAS blas.tgz +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/blas.tgz' 'blas.tgz' + +#Untar +tar -zxvf blas.tgz + +#Move blas into install directory +mv BLAS/* src +rm -rf BLAS + +#install +cd src +cp ../configs/linux64/make.inc ./ +make + +#Compile +cd ../install +mkdir lib +cd lib +cp ../../src/*.a . +ln -s blas_LINUX.a blas.a +ln -s blas_LINUX.a libblas.a Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/blas/install-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/blas/install-macosx64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/blas/install-macosx64.sh (revision 18231) @@ -0,0 +1,29 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install BLAS blas.tgz +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/blas.tgz' 'blas.tgz' + +#Untar +tar -zxvf blas.tgz + +#Move blas into install directory +mv BLAS/* src +rm -rf BLAS + +#install +cd src +cp ../configs/macosx64/make.inc ./ +make + +#Compile +cd ../install +mkdir lib +cd lib +cp ../../src/*.a . +ln -s blas_LINUX.a blas.a +ln -s blas_LINUX.a libblas.a Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/boost/configs/1.55/cas128strong.hpp.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/boost/configs/1.55/cas128strong.hpp.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/boost/configs/1.55/cas128strong.hpp.patch (revision 18231) @@ -0,0 +1,17 @@ +199c199 +< explicit base_atomic(value_type const& v) BOOST_NOEXCEPT : v_(0) +--- +> explicit base_atomic(value_type const& v) BOOST_NOEXCEPT +200a201 +> memset(&v_, 0, sizeof(v_)); +207c208,209 +< storage_type value_s = 0; +--- +> storage_type value_s; +> memset(&value_s, 0, sizeof(value_s)); +250c252,254 +< storage_type expected_s = 0, desired_s = 0; +--- +> storage_type expected_s, desired_s; +> memset(&expected_s, 0, sizeof(expected_s)); +> memset(&desired_s, 0, sizeof(desired_s)); Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/boost/configs/1.55/gcc-atomic.hpp.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/boost/configs/1.55/gcc-atomic.hpp.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/boost/configs/1.55/gcc-atomic.hpp.patch (revision 18231) @@ -0,0 +1,28 @@ +961c961 +< explicit base_atomic(value_type const& v) BOOST_NOEXCEPT : v_(0) +--- +> explicit base_atomic(value_type const& v) BOOST_NOEXCEPT +962a963 +> memset(&v_, 0, sizeof(v_)); +968c969,970 +< storage_type tmp = 0; +--- +> storage_type tmp; +> memset(&tmp, 0, sizeof(tmp)); +983c985,986 +< storage_type tmp = 0; +--- +> storage_type tmp; +> memset(&tmp, 0, sizeof(tmp)); +997c1000,1002 +< storage_type expected_s = 0, desired_s = 0; +--- +> storage_type expected_s, desired_s; +> memset(&expected_s, 0, sizeof(expected_s)); +> memset(&desired_s, 0, sizeof(desired_s)); +1013c1018,1020 +< storage_type expected_s = 0, desired_s = 0; +--- +> storage_type expected_s, desired_s; +> memset(&expected_s, 0, sizeof(expected_s)); +> memset(&desired_s, 0, sizeof(desired_s)); Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/boost/install-1.49-linux.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/boost/install-1.49-linux.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/boost/install-1.49-linux.sh (revision 18231) @@ -0,0 +1,35 @@ +#!/bin/bash +set -eu + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_49_0 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_49_0.tar.gz' 'boost_1_49_0.tar.gz' + +#Untar +tar -zxvf boost_1_49_0.tar.gz + +#Move boost into install directory +mv boost_1_49_0/* src +rm -rf boost_1_49_0 +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python3.2 \ + --with-python-root="$ISSM_DIR/externalpackages/python/install" + +#Compile boost +./bjam install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/boost/install-1.55-macosx-mavericks.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/boost/install-1.55-macosx-mavericks.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/boost/install-1.55-macosx-mavericks.sh (revision 18231) @@ -0,0 +1,40 @@ +#!/bin/bash +set -eu + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_55_0 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' + +#Untar +tar -zxvf boost_1_55_0.tar.gz + +#Move boost into install directory +mv boost_1_55_0/* src +rm -rf boost_1_55_0 + +patch src/boost/atomic/detail/cas128strong.hpp ./configs/1.55/cas128strong.hpp.patch +patch src/boost/atomic/detail/gcc-atomic.hpp ./configs/1.55/gcc-atomic.hpp.patch + +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python3.2 \ + --with-python-root="$ISSM_DIR/externalpackages/python/install" + +#Compile boost +./b2 toolset=clang cxxflags=-stdlib=libstdc++ linkflags=-stdlib=libstdc++ -j2 variant=release link=static threading=multi install +#./bjam install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/boost/install-macosx-snowleopard.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/boost/install-macosx-snowleopard.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/boost/install-macosx-snowleopard.sh (revision 18231) @@ -0,0 +1,35 @@ +#!/bin/bash + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_49_0 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_49_0.tar.gz' 'boost_1_49_0.tar.gz' + +#Untar +tar -zxvf boost_1_49_0.tar.gz + +#Move boost into install directory +mv boost_1_49_0/* src +rm -rf boost_1_49_0 +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python2.7 \ + --with-python-root="$ISSM_DIR/externalpackages/python/install" + +#Compile boost +#./b2 address-model=32 architecture=x86 cxxflags="-arch i386" variant=release threading=multi install +./b2 toolset=darwin address-model=32 architecture=x86 variant=release threading=multi install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/boost/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/boost/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/boost/install.sh (revision 18231) @@ -0,0 +1,35 @@ +#!/bin/bash +set -eu + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_49_0 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_49_0.tar.gz' 'boost_1_49_0.tar.gz' + +#Untar +tar -zxvf boost_1_49_0.tar.gz + +#Move boost into install directory +mv boost_1_49_0/* src +rm -rf boost_1_49_0 +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python3.2 \ + --with-python-root="$ISSM_DIR/externalpackages/python/install" + +#Compile boost +./bjam install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/bsdtar/install-win7.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/bsdtar/install-win7.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/bsdtar/install-win7.sh (revision 18231) @@ -0,0 +1,21 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src libarchive-3.0.3 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libarchive-3.0.3.tar.gz' 'libarchive-3.0.3.tar.gz' + +#Untar +tar -zxvf libarchive-3.0.3.tar.gz + +#Move libarchive into src directory +mv libarchive-3.0.3/* src +rm -rf libarchive-3.0.3 + +cd src +./configure --prefix="$ISSM_DIR/externalpackages/bsdtar/install" +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/canos/InterX.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/canos/InterX.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/canos/InterX.m (revision 18231) @@ -0,0 +1,82 @@ +function P = InterX(L1,varargin) +%INTERX Intersection of curves +% P = INTERX(L1,L2) returns the intersection points of two curves L1 +% and L2. The curves L1,L2 can be either closed or open and are described +% by two-row-matrices, where each row contains its x- and y- coordinates. +% The intersection of groups of curves (e.g. contour lines, multiply +% connected regions etc) can also be computed by separating them with a +% column of NaNs as for example +% +% L = [x11 x12 x13 ... NaN x21 x22 x23 ...; +% y11 y12 y13 ... NaN y21 y22 y23 ...] +% +% P has the same structure as L1 and L2, and its rows correspond to the +% x- and y- coordinates of the intersection points of L1 and L2. If no +% intersections are found, the returned P is empty. +% +% P = INTERX(L1) returns the self-intersection points of L1. To keep +% the code simple, the points at which the curve is tangent to itself are +% not included. P = INTERX(L1,L1) returns all the points of the curve +% together with any self-intersection points. +% +% Example: +% t = linspace(0,2*pi); +% r1 = sin(4*t)+2; x1 = r1.*cos(t); y1 = r1.*sin(t); +% r2 = sin(8*t)+2; x2 = r2.*cos(t); y2 = r2.*sin(t); +% P = InterX([x1;y1],[x2;y2]); +% plot(x1,y1,x2,y2,P(1,:),P(2,:),'ro') + +% Author : NS +% Version: 3.0, 21 Sept. 2010 + +% Two words about the algorithm: Most of the code is self-explanatory. +% The only trick lies in the calculation of C1 and C2. To be brief, this +% is essentially the two-dimensional analog of the condition that needs +% to be satisfied by a function F(x) that has a zero in the interval +% [a,b], namely +% F(a)*F(b) <= 0 +% C1 and C2 exactly do this for each segment of curves 1 and 2 +% respectively. If this condition is satisfied simultaneously for two +% segments then we know that they will cross at some point. +% Each factor of the 'C' arrays is essentially a matrix containing +% the numerators of the signed distances between points of one curve +% and line segments of the other. + + %...Argument checks and assignment of L2 + error(nargchk(1,2,nargin)); + if nargin == 1, + L2 = L1; hF = @lt; %...Avoid the inclusion of common points + else + L2 = varargin{1}; hF = @le; + end + + %...Preliminary stuff + x1 = L1(1,:)'; x2 = L2(1,:); + y1 = L1(2,:)'; y2 = L2(2,:); + dx1 = diff(x1); dy1 = diff(y1); + dx2 = diff(x2); dy2 = diff(y2); + + %...Determine 'signed distances' + S1 = dx1.*y1(1:end-1) - dy1.*x1(1:end-1); + S2 = dx2.*y2(1:end-1) - dy2.*x2(1:end-1); + + C1 = feval(hF,D(bsxfun(@times,dx1,y2)-bsxfun(@times,dy1,x2),S1),0); + C2 = feval(hF,D((bsxfun(@times,y1,dx2)-bsxfun(@times,x1,dy2))',S2'),0)'; + + %...Obtain the segments where an intersection is expected + [i,j] = find(C1 & C2); + if isempty(i),P = zeros(2,0);return; end; + + %...Transpose and prepare for output + i=i'; dx2=dx2'; dy2=dy2'; S2 = S2'; + L = dy2(j).*dx1(i) - dy1(i).*dx2(j); + i = i(L~=0); j=j(L~=0); L=L(L~=0); %...Avoid divisions by 0 + + %...Solve system of eqs to get the common points + P = unique([dx2(j).*S1(i) - dx1(i).*S2(j), ... + dy2(j).*S1(i) - dy1(i).*S2(j)]./[L L],'rows')'; + + function u = D(x,y) + u = bsxfun(@minus,x(:,1:end-1),y).*bsxfun(@minus,x(:,2:end),y); + end +end Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/canos/license.txt =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/canos/license.txt (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/canos/license.txt (revision 18231) @@ -0,0 +1,25 @@ +Copyright (c) 2006, Antoni J. Canós +Copyright (c) 2008, Douglas M. Schwarz +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are +met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in + the documentation and/or other materials provided with the distribution + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE +LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/canos/licenseNS.txt =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/canos/licenseNS.txt (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/canos/licenseNS.txt (revision 18231) @@ -0,0 +1,24 @@ +Copyright (c) 2009, NS +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are +met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in + the documentation and/or other materials provided with the distribution + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE +LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/canos/selfintersect.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/canos/selfintersect.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/canos/selfintersect.m (revision 18231) @@ -0,0 +1,174 @@ +function [x0,y0,segments]=selfintersect(x,y) + +%SELFINTERSECT Self-intersections of a curve. +% +% [X0,Y0,SEGMENTS] = SELFINTERSECT(X,Y) computes the locations where +% a curve self-intersects in a fast and robust way. +% The curve can be broken with NaNs or have vertical segments. +% Segments of the curve involved in each of the self-interesections are +% also provided. +% +% Vectors X and Y are equal-length vectors of at least four points defining +% the curve. +% X0 and Y0 are column vectors with the x- and y- coordinates, respectively +% of the N self-intersections. +% SEGMENTS is an N x 2 matrix containing the pairs of segments involved in +% each self-intersection. +% +% This program uses the theory of operation of the file "Fast and Robust Curve +% Intersections" submitted by Douglas M. Schwartz (intersections.m, F.Id: 11837). +% +% Example of use +% N=201; +% th=linspace(-3*pi,4*pi,N); +% R=1; +% x=R*cos(th)+linspace(0,6,N); +% y=R*sin(th)+linspace(0,1,N); +% t0=clock; +% [x0,y0,segments]=selfintersect(x,y) +% etime(clock,t0) +% plot(x,y,'b',x0,y0,'.r'); +% axis ('equal'); grid + +% +% See also INTERSECTIONS. +% +%Version: 1.0, December 11, 2006 +%Tested under MATLAB 6.5.0. R13. +% +% (c) Antoni J. Canos. +% ITACA. Techincal University of Valencia (Spain) +% Email: ancama2@dcom.upv.es + + +% Input checks. +error(nargchk(2,2,nargin)) +% x and y must be vectors with same number of points (at least 4 for self-intersection). +if sum(size(x) > 3) ~= 1 || sum(size(y) > 3) ~= 1 || ... + length(x) ~= length(y) + error('X and Y must be equal-length vectors of at least 4 points.') +end + +x0=[]; +y0=[]; +segments=[]; + +% Two similar curves are firstly created. +x1=x; x2=x; +y1=y; y2=y; + +x1 = x1(:); +y1 = y1(:); +x2 = x2(:); +y2 = y2(:); + +% Compute number of line segments in each curve and some differences we'll +% need later. +n1 = length(x1) - 1; +n2 = length(x2) - 1; + +dxy1 = diff([x1 y1]); +dxy2 = diff([x2 y2]); + +% Determine the combinations of i and j where the rectangle enclosing the +% i'th line segment of curve 1 overlaps with the rectangle enclosing the +% j'th line segment of curve 2. +[i,j] = find(repmat(min(x1(1:end-1),x1(2:end)),1,n2) <= ... + repmat(max(x2(1:end-1),x2(2:end)).',n1,1) & ... + repmat(max(x1(1:end-1),x1(2:end)),1,n2) >= ... + repmat(min(x2(1:end-1),x2(2:end)).',n1,1) & ... + repmat(min(y1(1:end-1),y1(2:end)),1,n2) <= ... + repmat(max(y2(1:end-1),y2(2:end)).',n1,1) & ... + repmat(max(y1(1:end-1),y1(2:end)),1,n2) >= ... + repmat(min(y2(1:end-1),y2(2:end)).',n1,1)); + +% Removing coincident and adjacent segments. +remove=find(abs(i-j)<2); +i(remove)=[]; +j(remove)=[]; + +% Removing duplicate combinations of segments. +remove=[]; +for ii=1:size(i,1) + ind=find((i(ii)==j(ii:end))&(j(ii)==i(ii:end))); + remove=[remove;ii-1+ind]; +end +i(remove)=[]; +j(remove)=[]; + +% Find segments pairs which have at least one vertex = NaN and remove them. +% This line is a fast way of finding such segment pairs. We take +% advantage of the fact that NaNs propagate through calculations, in +% particular subtraction (in the calculation of dxy1 and dxy2, which we +% need anyway) and addition. +remove = isnan(sum(dxy1(i,:) + dxy2(j,:),2)); +i(remove) = []; +j(remove) = []; + +% Find segments pairs which have at least one vertex = NaN and remove them. +% This line is a fast way of finding such segment pairs. We take +% advantage of the fact that NaNs propagate through calculations, in +% particular subtraction (in the calculation of dxy1 and dxy2, which we +% need anyway) and addition. +remove = isnan(sum(dxy1(i,:) + dxy2(j,:),2)); +i(remove) = []; +j(remove) = []; + +% Initialize matrices. We'll put the T's and B's in matrices and use them +% one column at a time. For some reason, the \ operation below is faster +% on my machine when A is sparse so we'll initialize a sparse matrix with +% the fixed values and then assign the changing values in the loop. +n = length(i); +T = zeros(4,n); +A = sparse([1 2 3 4],[3 3 4 4],-1,4,4,8); +B = -[x1(i) x2(j) y1(i) y2(j)].'; +index_dxy1 = [1 3]; % A(1) = A(1,1), A(3) = A(3,1) +index_dxy2 = [6 8]; % A(6) = A(2,2), A(8) = A(4,2) + +% Loop through possibilities. Set warning not to trigger for anomalous +% results (i.e., when A is singular). +warning_state = warning('off','MATLAB:singularMatrix'); +try + for k = 1:n + A(index_dxy1) = dxy1(i(k),:); + A(index_dxy2) = dxy2(j(k),:); + T(:,k) = A\B(:,k); + end + warning(warning_state) +catch + warning(warning_state) + rethrow(lasterror) +end + +% Find where t1 and t2 are between 0 and 1 and return the corresponding x0 +% and y0 values. Anomalous segment pairs can be segment pairs that are +% colinear (overlap) or the result of segments that are degenerate (end +% points the same). The algorithm will return an intersection point that +% is at the center of the overlapping region. Because of the finite +% precision of floating point arithmetic it is difficult to predict when +% two line segments will be considered to overlap exactly or even intersect +% at an end point. For this algorithm, an anomaly is detected when any +% element of the solution (a single column of T) is a NaN. + +in_range = T(1,:) >= 0 & T(2,:) >= 0 & T(1,:) < 1 & T(2,:) < 1; +anomalous = any(isnan(T)); +if any(anomalous) + ia = i(anomalous); + ja = j(anomalous); + % set x0 and y0 to middle of overlapping region. + T(3,anomalous) = (max(min(x1(ia),x1(ia+1)),min(x2(ja),x2(ja+1))) + ... + min(max(x1(ia),x1(ia+1)),max(x2(ja),x2(ja+1))))/2; + T(4,anomalous) = (max(min(y1(ia),y1(ia+1)),min(y2(ja),y2(ja+1))) + ... + min(max(y1(ia),y1(ia+1)),max(y2(ja),y2(ja+1))))/2; + x0 = T(3,in_range | anomalous).'; + y0 = T(4,in_range | anomalous).'; + i=i(in_range | anomalous); + j=j(in_range | anomalous); +else + x0 = T(3,in_range).'; + y0 = T(4,in_range).'; + i=i(in_range); + j=j(in_range); +end + +segments=sort([i,j],2); Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cccl/install-win7.orig.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cccl/install-win7.orig.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cccl/install-win7.orig.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install cccl-0.03 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/cccl-0.03.tar.gz' 'cccl-0.03.tar.gz' + +#Untar +tar -zxvf cccl-0.03.tar.gz + +#Move cccl into install directory +mv cccl-0.03/* src +rm -rf cccl-0.03 + +cd src + +#Compile +./configure --prefix="$ISSM_DIR/externalpackages/cccl/install" + +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cccl/install-win7.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cccl/install-win7.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cccl/install-win7.sh (revision 18231) @@ -0,0 +1,11 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src cccl-0.03 +mkdir install +mkdir install/bin + +#Move cccl into install directory +cp issm/cccl install/bin +chmod 755 install/bin/cccl Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cccl/issm/cccl =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cccl/issm/cccl (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cccl/issm/cccl (revision 18231) @@ -0,0 +1,113 @@ +#!/bin/sh + +# cccl +# Wrapper around MS's cl.exe and link.exe to make them act more like +# Unix cc and ld +# +# Copyright (C) 2000-2003 Geoffrey Wossum (gwossum@acm.org) +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your optsion) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. +# + +usage() +{ + cat < hypercube, d => d-dimensional mesh */ + int ndims_tot, /* total number of cube dimensions to divide */ + int mesh_dims[3], /* dimensions of mesh of processors */ + double *goal, /* desired set sizes for each set */ + int global_method, /* global partitioning algorithm */ + int local_method, /* local partitioning algorithm */ + int rqi_flag, /* should I use RQI/Symmlq eigensolver? */ + int vmax, /* how many vertices to coarsen down to? */ + int ndims, /* number of eigenvectors (2^d sets) */ + double eigtol, /* tolerance on eigenvectors */ + long seed); /* for random graph mutations */ + +extern "C" void read_params(FILE* pfile); /* file with new user parameters */ +extern "C" void smalloc_stats(void); +extern "C" double* smalloc(unsigned int n); /* number of bytes to be allocated */ + +#endif //ifndef _CHACO_INCLUDES_H_ + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/chaco.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/chaco.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/chaco.patch (revision 18231) @@ -0,0 +1,572 @@ +Only in src/code/assign: assign.o +diff -rc src/code/assign/assign_out.c old/code/assign/assign_out.c +*** src/code/assign/assign_out.c 2010-07-16 16:28:47.352242454 -0700 +--- old/code/assign/assign_out.c 1995-08-08 14:32:10.000000000 -0700 +*************** +*** 3,9 **** + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + + #include +- #include "defs.h" + + static void assign_out_normal(), assign_out_inv(); + +--- 3,8 ---- +Only in src/code/assign: assign_out.o +Only in src/code/assign: mapper.o +Only in src/code/assign: median.o +Only in src/code/assign: merge_assign.o +Only in src/code/assign: rec_median.o +Only in src/code/assign: rotate.o +Only in src/code/assign: y2x.o +Only in src/code/bpmatch: checkbp.o +Only in src/code/bpmatch: genvals2d.o +Only in src/code/bpmatch: genvals3d.o +Only in src/code/bpmatch: inits2d.o +Only in src/code/bpmatch: inits3d.o +Only in src/code/bpmatch: map2d.o +Only in src/code/bpmatch: map3d.o +Only in src/code/bpmatch: movevtxs.o +Only in src/code/bpmatch: sorts2d.o +Only in src/code/bpmatch: sorts3d.o +Only in src/code: chacominusblas.a +Only in src/code/coarsen: coarsen1.o +Only in src/code/coarsen: coarsen.o +Only in src/code/coarsen: interpolate.o +Only in src/code/coarsen: makeccoords.o +Only in src/code/coarsen: makefgraph.o +Only in src/code/coarsen: makev2cv.o +Only in src/code/coarsen: maxmatch1.o +Only in src/code/coarsen: maxmatch2.o +Only in src/code/coarsen: maxmatch3.o +Only in src/code/coarsen: maxmatch4.o +Only in src/code/coarsen: maxmatch5.o +Only in src/code/coarsen: maxmatch.o +Only in src/code/connect: add_edges.o +Only in src/code/connect: connected.o +Only in src/code/connect: find_edges.o +Only in src/code/eigen: bidir.o +Only in src/code/eigen: bisect.o +Only in src/code/eigen: checkeig_ext.o +Only in src/code/eigen: checkeig.o +Only in src/code/eigen: checkorth.o +Only in src/code/eigen: cksturmcnt.o +Only in src/code/eigen: eigensolve.o +diff -rc src/code/eigen/get_extval.c old/code/eigen/get_extval.c +*** src/code/eigen/get_extval.c 2010-07-16 16:28:47.353242463 -0700 +--- old/code/eigen/get_extval.c 1995-08-08 14:32:20.000000000 -0700 +*************** +*** 4,10 **** + + #include + #include +- #include "defs.h" + + /* Finds first extended eigenpair of system corresponding to + tridiagonal T using using Rafael's bisection technique. */ +--- 4,9 ---- +Only in src/code/eigen: get_extval.o +Only in src/code/eigen: get_ritzvals.o +Only in src/code/eigen: lanc_seconds.o +Only in src/code/eigen: lanczos_ext_float.o +Only in src/code/eigen: lanczos_ext.o +Only in src/code/eigen: lanczos_FO.o +Only in src/code/eigen: lanczos_SO_float.o +Only in src/code/eigen: lanczos_SO.o +Only in src/code/eigen: lanpause.o +Only in src/code/eigen: makeorthlnk.o +Only in src/code/eigen: mkeigvecs.o +Only in src/code/eigen: mkscanlist.o +Only in src/code/eigen: orthog1.o +Only in src/code/eigen: orthogonalize.o +Only in src/code/eigen: orthogvec.o +Only in src/code/eigen: ql.o +Only in src/code/eigen: rqi_ext.o +Only in src/code/eigen: rqi.o +Only in src/code/eigen: scale_diag.o +Only in src/code/eigen: scanmax.o +Only in src/code/eigen: scanmin.o +Only in src/code/eigen: solistout.o +Only in src/code/eigen: sorthog.o +Only in src/code/eigen: splarax.o +Only in src/code/eigen: sturmcnt.o +Only in src/code/eigen: Tevec.o +Only in src/code/eigen: tri_solve.o +Only in src/code/eigen: warnings.o +Only in src/code/graph: check_graph.o +Only in src/code/graph: free_graph.o +Only in src/code/graph: graph_out.o +Only in src/code/graph: reformat.o +Only in src/code/graph: subgraph.o +Only in src/code/inertial: eigenvec2.o +Only in src/code/inertial: eigenvec3.o +Only in src/code/inertial: inertial1d.o +Only in src/code/inertial: inertial2d.o +Only in src/code/inertial: inertial3d.o +Only in src/code/inertial: inertial.o +Only in src/code/inertial: make_subgeom.o +Only in src/code/input: check_input.o +Only in src/code/input: input_assign.o +Only in src/code/input: input_geom.o +Only in src/code/input: input_graph.o +Only in src/code/input: input.o +Only in src/code/input: read_params.o +Only in src/code/input: read_val.o +Only in src/code/input: reflect_input.o +Only in src/code/internal: check_internal.o +Only in src/code/internal: force_internal.o +Only in src/code/internal: improve_internal.o +Only in src/code/klspiff: bilistops.o +Only in src/code/klspiff: buckets1.o +Only in src/code/klspiff: buckets_bi.o +Only in src/code/klspiff: buckets.o +Only in src/code/klspiff: coarsen_kl.o +Only in src/code/klspiff: compress_ewgts.o +Only in src/code/klspiff: count_weights.o +Only in src/code/klspiff: kl_init.o +Only in src/code/klspiff: kl_output.o +Only in src/code/klspiff: klspiff.o +Only in src/code/klspiff: make_bndy_list.o +Only in src/code/klspiff: make_kl_list.o +Only in src/code/klspiff: nway_kl.o +Only in src/code/klvspiff: bpm_improve.o +Only in src/code/klvspiff: bucketsv.o +Only in src/code/klvspiff: clear_dvals.o +Only in src/code/klvspiff: coarsen_klv.o +Only in src/code/klvspiff: countup_vtx_sep.o +Only in src/code/klvspiff: find_bndy.o +Only in src/code/klvspiff: flatten.o +Only in src/code/klvspiff: flow.o +Only in src/code/klvspiff: klv_init.o +Only in src/code/klvspiff: klvspiff.o +Only in src/code/klvspiff: make_bpgraph.o +Only in src/code/klvspiff: make_sep_list.o +diff -rc src/code/klvspiff/matching.c old/code/klvspiff/matching.c +*** src/code/klvspiff/matching.c 2010-07-16 16:28:47.356242493 -0700 +--- old/code/klvspiff/matching.c 1996-03-11 10:24:25.000000000 -0800 +*************** +*** 6,12 **** + code provided by Ed Rothberg at SGI. */ + + #include +- #include "defs.h" + + #define TRUE 1 + #define FALSE 0 +--- 6,11 ---- +Only in src/code/klvspiff: matching.o +Only in src/code/klvspiff: nway_klv.o +diff -rc src/code/main/defs.h old/code/main/defs.h +*** src/code/main/defs.h 2010-07-16 16:28:47.359242522 -0700 +--- old/code/main/defs.h 1995-08-08 14:32:41.000000000 -0700 +*************** +*** 1,39 **** +! #ifndef _CHACO_DEFS_H_ +! #define _CHACO_DEFS_H_ +! + #define TRUE 1 + #define FALSE 0 + +! #ifndef _HAVE_CHACO_ //protect ISSM compilation. This symbol is defined when we compile ISSM +! +! #define max(A, B) ((A) > (B) ? (A) : (B)) +! #define min(A, B) ((A) < (B) ? (A) : (B)) +! #define sign(A) ((A) < 0 ? -1 : 1) +! #define absval(A) ((A) < 0 ? -(A): (A)) +! +! /* Define constants that are needed in various places */ +! #define PI 3.141592653589793 +! #define TWOPI 6.283185307179586 +! #define HALFPI 1.570796326794896 +! +! #define check_graph chaco_check_graph +! +! +! #ifdef MATLAB +! #include "mat.h" +! #include "mex.h" +! #include "matrix.h" +! +! #define printf mexPrintf +! #define fprintf(file,...) (file == stdout || file == stderr ? mexPrintf(__VA_ARGS__) : fprintf(file,__VA_ARGS__)) +! #define malloc mxMalloc +! #define calloc mxCalloc +! #define realloc mxRealloc +! #define free mxFree +! #define exit(status) mexErrMsgTxt("exit=" #status) +! +! #endif +! +! #endif //#ifndef _HAVE_CHACO_ +! +! #endif //ifndef _CHACO_DEFS_H_ +--- 1,11 ---- +! #define max(A, B) ((A) > (B) ? (A) : (B)) +! #define min(A, B) ((A) < (B) ? (A) : (B)) +! #define sign(A) ((A) < 0 ? -1 : 1) +! #define absval(A) ((A) < 0 ? -(A): (A)) + #define TRUE 1 + #define FALSE 0 + +! /* Define constants that are needed in various places */ +! #define PI 3.141592653589793 +! #define TWOPI 6.283185307179586 +! #define HALFPI 1.570796326794896 +Only in src/code/main: interface.o +Only in src/code/main: main.o +diff -rc src/code/main/params.h old/code/main/params.h +*** src/code/main/params.h 2010-07-16 16:28:47.361242541 -0700 +--- old/code/main/params.h 1995-08-08 14:32:43.000000000 -0700 +*************** +*** 1,12 **** +- #ifndef _CHACO_PARAMS_H_ +- #define _CHACO_PARAMS_H_ +- +- + #define NAME_LENGTH 80 /* Maximum length of file name */ + #define LINE_LENGTH 200 /* Length of input files read at once */ + + #define MAXDIMS 3 /* Most cuts allowed at one time */ + #define MAXSETS 8 /* 2^MAXDIMS */ +- +- +- #endif //ifndef _CHACO_PARAMS_H_ +--- 1,5 ---- +Only in src/code/main: user_params.o +diff -rc src/code/Makefile old/code/Makefile +*** src/code/Makefile 2010-07-21 18:22:19.909939194 -0700 +--- old/code/Makefile 1997-10-02 10:23:22.000000000 -0700 +*************** +*** 2,18 **** + DEST= ${DEST_DIR}/chaco + CC = gcc + IFLAG = -Imain +! #IFLAG = -Imain -I/usr/local/pkgs/matlab-7.6/extern/include +! #CFLAGS = -O2 +! #OFLAGS = -O2 +! #CFLAGS = -fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread -fexceptions +! CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g +! #CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB +! OFLAGS = -O2 +! #AR = /usr/ccs/bin/ar rcv # for solaris 2 +! AR = /usr/bin/ar rcv +! #RANLIB = /usr/ccs/bin/ranlib # for solaris 2 +! RANLIB = /usr/bin/ranlib + + FILES.c= main/user_params.c main/interface.c main/main.c \ + submain/balance.c submain/divide.c submain/submain.c \ +--- 2,9 ---- + DEST= ${DEST_DIR}/chaco + CC = gcc + IFLAG = -Imain +! CFLAGS = -O2 +! OFLAGS = -O2 + + FILES.c= main/user_params.c main/interface.c main/main.c \ + submain/balance.c submain/divide.c submain/submain.c \ +*************** +*** 96,196 **** + util/update.c util/vecout.c util/vecran.c \ + util/vecscale.c + +- +- FILESMINUSBLAS.c= main/user_params.c main/interface.c main/main.c \ +- submain/balance.c submain/divide.c submain/submain.c \ +- input/input_assign.c \ +- input/check_input.c input/input.c input/input_geom.c \ +- input/input_graph.c input/read_params.c input/reflect_input.c \ +- input/read_val.c \ +- graph/check_graph.c graph/free_graph.c \ +- graph/reformat.c graph/subgraph.c graph/graph_out.c \ +- inertial/eigenvec2.c inertial/eigenvec3.c inertial/inertial.c \ +- inertial/inertial1d.c inertial/inertial2d.c \ +- inertial/inertial3d.c inertial/make_subgeom.c \ +- klspiff/buckets.c klspiff/buckets_bi.c klspiff/buckets1.c \ +- klspiff/bilistops.c klspiff/coarsen_kl.c klspiff/count_weights.c \ +- klspiff/compress_ewgts.c klspiff/kl_init.c klspiff/kl_output.c \ +- klspiff/klspiff.c klspiff/make_bndy_list.c \ +- klspiff/make_kl_list.c klspiff/nway_kl.c \ +- klvspiff/bpm_improve.c klvspiff/bucketsv.c \ +- klvspiff/clear_dvals.c klvspiff/coarsen_klv.c \ +- klvspiff/countup_vtx_sep.c klvspiff/find_bndy.c klvspiff/flow.c \ +- klvspiff/klv_init.c klvspiff/klvspiff.c klvspiff/make_bpgraph.c \ +- klvspiff/make_sep_list.c klvspiff/matching.c klvspiff/nway_klv.c \ +- klvspiff/flatten.c \ +- coarsen/coarsen.c coarsen/interpolate.c coarsen/makefgraph.c \ +- coarsen/makeccoords.c \ +- coarsen/coarsen1.c coarsen/makev2cv.c \ +- coarsen/maxmatch.c coarsen/maxmatch1.c coarsen/maxmatch2.c \ +- coarsen/maxmatch3.c coarsen/maxmatch4.c coarsen/maxmatch5.c \ +- connect/add_edges.c connect/connected.c connect/find_edges.c \ +- eigen/bidir.c eigen/bisect.c eigen/checkeig.c \ +- eigen/checkeig_ext.c \ +- eigen/checkorth.c eigen/cksturmcnt.c eigen/mkeigvecs.c\ +- eigen/eigensolve.c eigen/get_extval.c eigen/get_ritzvals.c \ +- eigen/lanczos_FO.c eigen/lanczos_SO.c eigen/lanczos_SO_float.c \ +- eigen/lanczos_ext.c eigen/lanczos_ext_float.c eigen/lanc_seconds.c\ +- eigen/lanpause.c eigen/makeorthlnk.c eigen/mkscanlist.c \ +- eigen/orthog1.c eigen/orthogonalize.c eigen/orthogvec.c \ +- eigen/ql.c eigen/rqi.c eigen/rqi_ext.c eigen/scale_diag.c \ +- eigen/scanmax.c eigen/scanmin.c eigen/solistout.c \ +- eigen/sorthog.c eigen/splarax.c eigen/sturmcnt.c \ +- eigen/Tevec.c eigen/tri_solve.c eigen/warnings.c \ +- symmlq/aprod.c symmlq/msolve.c symmlq/pow_dd.c \ +- symmlq/symmlq.c \ +- tinvit/tinvit.c tinvit/pythag.c tinvit/epslon.c \ +- optimize/determinant.c optimize/func2d.c \ +- optimize/func3d.c optimize/opt2d.c optimize/opt3d.c \ +- assign/assign.c assign/assign_out.c assign/mapper.c \ +- assign/median.c assign/merge_assign.c \ +- assign/rec_median.c assign/rotate.c assign/y2x.c \ +- bpmatch/checkbp.c bpmatch/inits2d.c bpmatch/inits3d.c \ +- bpmatch/genvals2d.c bpmatch/genvals3d.c bpmatch/map2d.c \ +- bpmatch/map3d.c bpmatch/movevtxs.c \ +- bpmatch/sorts2d.c bpmatch/sorts3d.c \ +- refine_map/compute_cube_edata.c refine_map/compute_cube_vdata.c \ +- refine_map/refine_cube.c refine_map/update_cube_edata.c \ +- refine_map/update_cube_vdata.c refine_map/find_edge_cube.c \ +- refine_map/init_cube_edata.c refine_map/compute_mesh_edata.c \ +- refine_map/compute_mesh_vdata.c refine_map/find_edge_mesh.c \ +- refine_map/init_mesh_edata.c refine_map/refine_mesh.c \ +- refine_map/update_mesh_edata.c refine_map/update_mesh_vdata.c \ +- refine_map/refine_map.c refine_map/make_comm_graph.c \ +- refine_part/refine_part.c refine_part/kl_refine.c \ +- refine_part/make_maps_ref.c refine_part/make_terms_ref.c \ +- internal/force_internal.c internal/improve_internal.c \ +- internal/check_internal.c \ +- misc/define_subcubes.c misc/define_submeshes.c \ +- misc/divide_procs.c misc/merge_goals.c misc/make_term_props.c \ +- misc/count.c misc/countup.c misc/countup_cube.c \ +- misc/countup_mesh.c misc/make_subgoal.c \ +- misc/find_maxdeg.c misc/make_maps.c misc/make_setlists.c \ +- misc/sequence.c misc/perturb.c misc/simple_part.c \ +- misc/time_kernels.c misc/timing.c \ +- util/affirm.c util/array_alloc_2D.c util/bit_reverse.c \ +- util/checkpnt.c util/cpvec.c util/dot.c \ +- util/doubleout.c util/input_int.c util/gray.c \ +- util/machine_params.c util/makevwsqrt.c util/mkvec.c util/norm.c \ +- util/normalize.c util/mergesort.c \ +- util/randomize.c util/smalloc.c util/bail.c \ +- util/scadd.c util/seconds.c util/setvec.c util/shell_sort.c \ +- util/strout.c util/tri_prod.c util/true_or_false.c \ +- util/update.c util/vecout.c util/vecran.c \ +- util/vecscale.c +- + FILES.o= $(FILES.c:.c=.o) +- FILESMINUSBLAS.o= $(FILESMINUSBLAS.c:.c=.o) +- +- +- ${DEST}: ${FILES.c} chaco.a Makefile +- ${CC} ${OFLAGS} chaco.a -lm -o ${DEST} + +- chaco.a: ${FILES.o} +- ${AR} chaco.a ${FILES.o} ; ${RANLIB} chaco.a + +! chacominusblas.a: ${FILESMINUSBLAS.o} +! ${AR} chacominusblas.a ${FILESMINUSBLAS.o} ; ${RANLIB} chacominusblas.a + + lint: + lint ${IFLAG} ${FILES.c} -lm +--- 87,97 ---- + util/update.c util/vecout.c util/vecran.c \ + util/vecscale.c + + FILES.o= $(FILES.c:.c=.o) + + +! ${DEST}: ${FILES.o} Makefile +! ${CC} ${OFLAGS} ${FILES.o} -lm -o ${DEST} + + lint: + lint ${IFLAG} ${FILES.c} -lm +Only in src/code/misc: count.o +Only in src/code/misc: countup_cube.o +Only in src/code/misc: countup_mesh.o +Only in src/code/misc: countup.o +Only in src/code/misc: define_subcubes.o +Only in src/code/misc: define_submeshes.o +Only in src/code/misc: divide_procs.o +Only in src/code/misc: find_maxdeg.o +Only in src/code/misc: make_maps.o +Only in src/code/misc: make_setlists.o +Only in src/code/misc: make_subgoal.o +Only in src/code/misc: make_term_props.o +Only in src/code/misc: merge_goals.o +Only in src/code/misc: perturb.o +Only in src/code/misc: sequence.o +Only in src/code/misc: simple_part.o +Only in src/code/misc: time_kernels.o +diff -rc src/code/misc/timing.c old/code/misc/timing.c +*** src/code/misc/timing.c 2010-07-16 16:28:47.366242590 -0700 +--- old/code/misc/timing.c 1997-01-03 09:10:52.000000000 -0800 +*************** +*** 3,9 **** + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + + #include +- #include "defs.h" + + /* Timing parameters. */ + +--- 3,8 ---- +Only in src/code/misc: timing.o +Only in src/code/optimize: determinant.o +Only in src/code/optimize: func2d.o +Only in src/code/optimize: func3d.o +Only in src/code/optimize: opt2d.o +Only in src/code/optimize: opt3d.o +Only in src/code/refine_map: compute_cube_edata.o +Only in src/code/refine_map: compute_cube_vdata.o +Only in src/code/refine_map: compute_mesh_edata.o +Only in src/code/refine_map: compute_mesh_vdata.o +Only in src/code/refine_map: find_edge_cube.o +Only in src/code/refine_map: find_edge_mesh.o +Only in src/code/refine_map: init_cube_edata.o +Only in src/code/refine_map: init_mesh_edata.o +Only in src/code/refine_map: make_comm_graph.o +Only in src/code/refine_map: refine_cube.o +Only in src/code/refine_map: refine_map.o +Only in src/code/refine_map: refine_mesh.o +Only in src/code/refine_map: update_cube_edata.o +Only in src/code/refine_map: update_cube_vdata.o +Only in src/code/refine_map: update_mesh_edata.o +Only in src/code/refine_map: update_mesh_vdata.o +Only in src/code/refine_part: kl_refine.o +Only in src/code/refine_part: make_maps_ref.o +Only in src/code/refine_part: make_terms_ref.o +Only in src/code/refine_part: refine_part.o +Only in src/code/submain: balance.o +Only in src/code/submain: divide.o +Only in src/code/submain: submain.o +Only in src/code/symmlq: aprod.o +Only in src/code/symmlq: msolve.o +Only in src/code/symmlq: pow_dd.o +diff -rc src/code/symmlq/symmlqblas.f old/code/symmlq/symmlqblas.f +*** src/code/symmlq/symmlqblas.f 2010-07-21 18:09:10.370123273 -0700 +--- old/code/symmlq/symmlqblas.f 2010-07-21 14:02:09.633743650 -0700 +*************** +*** 16,22 **** + c uses unrolled loops for increments equal to one. + c jack dongarra, linpack, 3/11/78. + c +! double precision dx(1),dy(1),da + integer i,incx,incy,ix,iy,m,mp1,n + c + if(n.le.0)return +--- 16,22 ---- + c uses unrolled loops for increments equal to one. + c jack dongarra, linpack, 3/11/78. + c +! double precision dx(*),dy(*),da + integer i,incx,incy,ix,iy,m,mp1,n + c + if(n.le.0)return +Only in src/code/symmlq: symmlqblas.o +Only in src/code/symmlq: symmlq.o +Only in src/code/tinvit: epslon.o +Only in src/code/tinvit: pythag.o +Only in src/code/tinvit: tinvit.o +Only in src/code/util: affirm.o +Only in src/code/util: array_alloc_2D.o +diff -rc src/code/util/bail.c old/code/util/bail.c +*** src/code/util/bail.c 2010-07-16 16:28:47.368242609 -0700 +--- old/code/util/bail.c 1995-08-08 14:33:01.000000000 -0700 +*************** +*** 4,10 **** + + #include + #include +- #include "defs.h" + + /* Wrapper for exit() - print message and exit with status code. Exit code + of 0 indicates normal termination. Exit code of 1 indicates early +--- 4,9 ---- +*************** +*** 15,20 **** +--- 14,20 ---- + int status; + { + extern FILE *Output_File; /* Output file or NULL */ ++ void exit(); + + if (msg != NULL && (int) strlen(msg) > 0) { + printf("%s\n", msg); +Only in src/code/util: bail.o +Only in src/code/util: bit_reverse.o +diff -rc src/code/util/checkpnt.c old/code/util/checkpnt.c +*** src/code/util/checkpnt.c 2010-07-16 16:28:47.370242629 -0700 +--- old/code/util/checkpnt.c 1995-08-08 14:33:01.000000000 -0700 +*************** +*** 4,10 **** + + #include + #include +- #include "defs.h" + + /* Debug break point. */ + void checkpnt(tag) +--- 4,9 ---- +Only in src/code/util: checkpnt.o +Only in src/code/util: cpvec.o +Only in src/code/util: dot.o +diff -rc src/code/util/doubleout.c old/code/util/doubleout.c +*** src/code/util/doubleout.c 2010-07-16 16:28:47.372242648 -0700 +--- old/code/util/doubleout.c 1995-08-08 14:33:02.000000000 -0700 +*************** +*** 3,9 **** + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + + #include +- #include "defs.h" + + /* Print a double precision number with filtering format to screen. */ + void doubleout(number, mode) +--- 3,8 ---- +Only in src/code/util: doubleout.o +Only in src/code/util: gray.o +Only in src/code/util: input_int.o +Only in src/code/util: machine_params.o +Only in src/code/util: makevwsqrt.o +Only in src/code/util: mergesort.o +Only in src/code/util: mkvec.o +Only in src/code/util: normalize.o +Only in src/code/util: norm.o +Only in src/code/util: randomize.o +Only in src/code/util: scadd.o +Only in src/code/util: seconds.o +Only in src/code/util: setvec.o +Only in src/code/util: shell_sort.o +diff -rc src/code/util/smalloc.c old/code/util/smalloc.c +*** src/code/util/smalloc.c 2010-07-16 16:28:47.375242677 -0700 +--- old/code/util/smalloc.c 1996-03-11 10:44:07.000000000 -0800 +*************** +*** 4,10 **** + + #include + #include +- #include "defs.h" + + static int nmalloc = 0; /* number of calls to malloc */ + static int nfree = 0; /* number of calls to free */ +--- 4,9 ---- +Only in src/code/util: smalloc.o +diff -rc src/code/util/strout.c old/code/util/strout.c +*** src/code/util/strout.c 2010-07-16 16:28:47.377242697 -0700 +--- old/code/util/strout.c 1995-08-08 14:33:05.000000000 -0700 +*************** +*** 4,10 **** + + #include + #include +- #include "defs.h" + + /* Wrapper for a printf statement with a string as only arg. + Prints to screen and to output file if there is one. */ +--- 4,9 ---- +Only in src/code/util: strout.o +Only in src/code/util: tri_prod.o +Only in src/code/util: true_or_false.o +Only in src/code/util: update.o +Only in src/code/util: vecout.o +Only in src/code/util: vecran.o +Only in src/code/util: vecscale.o Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/chaco_README.txt =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/chaco_README.txt (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/chaco_README.txt (revision 18231) @@ -0,0 +1,55 @@ +Chaco-2.2.tar (5/03/00? -- 2.0 was 2/95) +http://www.sandia.gov/~bahendr/chaco.html + + +Note that meshpart pulls the object files from here, compiled with +the MATLAB flag for use in the mlchaco mex function, and assembles +them into a library in its own directory. This means that any +objects compiled for the mlchaco mex function and left here should +not be used for the stand-alone chaco executable, and vice versa. + + +[jschierm@astrid main]$ diff defs_old.h defs.h +11a12,27 [for running as a matlab mex function] +> +> #ifdef MATLAB +> #include "mat.h" +> #include "mex.h" +> #include "matrix.h" +> +> #define printf mexPrintf +> #define fprintf(file,...) (file == stdout || file == stderr ? mexPrintf(__VA_ARGS__) : fprintf(file,__VA_ARGS__)) +> #define malloc mxMalloc +> #define calloc mxCalloc +> #define realloc mxRealloc +> #define free mxFree +> +> #define check_graph chaco_check_graph +> #endif +> + + +added #include "defs.h" to the following: +assign/assign_out.c +eigen/get_extval.c +klvspiff/matching.c +misc/timing.c +util/bail.c +util/checkpnt.c +util/doubleout.c +util/smalloc.c +util/strout.c + + +[jschierm@astrid code]$ diff Makefile_old Makefile +4,5c4,9 [fPIC required, CFLAGS and OFLAGS copied from Cielo gccopts_v75.sh for glnxa64] +< IFLAG = -Imain +< CFLAGS = -O2 +--- +> IFLAG = -Imain -I/usr/local/pkgs/matlab-7.6/extern/include +> #CFLAGS = -O2 +> #OFLAGS = -O2 +> #CFLAGS = -fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread -fexceptions +> CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB +> #CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/chaco_jes_notes.txt =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/chaco_jes_notes.txt (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/chaco_jes_notes.txt (revision 18231) @@ -0,0 +1,86 @@ +7/13/09: + +[jschierm@astrid Chaco-2.2]$ diff ../chaco/code/Makefile code +5,6c5,8 [fPIC required, CFLAGS and OFLAGS copied from Cielo gccopts_v75.sh for glnxa64] +< CFLAGS = -O2 +< OFLAGS = -O2 +--- +> #CFLAGS = -O2 +> #OFLAGS = -O2 +> CFLAGS = -fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread -fexceptions +> OFLAGS = -O -DNDEBUG +34a37,38 [added for meshpart chaco.a library, specified by its makefile] +> coarsen/makecgraph.c \ +> coarsen/countcedges.c \ + +7/30/09: + +[jschierm@astrid main]$ diff defs_old.h defs.h +11a12,26 [for running as a matlab mex function] +> +> #ifdef MATLAB +> #include "mat.h" +> #include "mex.h" +> #include "matrix.h" +> +> #define printf mexPrintf +> #define malloc mxMalloc +> #define calloc mxCalloc +> #define realloc mxRealloc +> #define free mxFree +> +> #define check_graph chaco_check_graph +> #endif +> + +added #include "defs.h" to the following: +assign/assign_out.c +eigen/get_extval.c +klvspiff/matching.c +misc/timing.c +util/bail.c +util/checkpnt.c +util/doubleout.c +util/smalloc.c +util/strout.c + +[jschierm@astrid code]$ diff Makefile_old Makefile | more +4,5c4,9 +< IFLAG = -Imain +< CFLAGS = -O2 +--- +> IFLAG = -Imain -I/usr/local/pkgs/matlab-7.6/extern/include +> #CFLAGS = -O2 +> #OFLAGS = -O2 +> #CFLAGS = -fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread +> -fexceptions +> CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB +> #CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions + +8/25/09: + +added macro for fprintf to capture missing output: +[jschierm@astrid main]$ diff defs_old.h defs.h +11a12,27 +> +> #ifdef MATLAB +> #include "mat.h" +> #include "mex.h" +> #include "matrix.h" +> +> #define printf mexPrintf +> #define fprintf(file,...) (file == stdout || file == stderr ? mexPrintf(__VA_ARGS__) : fprintf(file,__VA_ARGS__)) +> #define malloc mxMalloc +> #define calloc mxCalloc +> #define realloc mxRealloc +> #define free mxFree +> +> #define check_graph chaco_check_graph +> #endif +> + +6/15/10: + +- moved check_graph rename outside of MATLAB compiler directive. +- created library chaco.a (without MATLAB compiler directive) for Chaco x-layer to link and implemented it in chaco stand-alone link. + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/chaco_njs_notes.txt =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/chaco_njs_notes.txt (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/chaco_njs_notes.txt (revision 18231) @@ -0,0 +1,3 @@ +chaco build must be able to see malloc.h +sudo ln -s /usr/include/malloc/malloc.h /usr/include/malloc.h +or else make sure you include the malloc directory in path Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/install.sh (revision 18231) @@ -0,0 +1,51 @@ +#!/bin/bash +set -eu + +# Some cleanup +rm -rf Chaco-2.2 +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Chaco-2.2.tar.gz' 'Chaco-2.2.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/docs/chaco_guide.pdf' 'chaco_guide.pdf' + +# Untar +tar -xvzf Chaco-2.2.tar.gz + +# Move chaco to src directory +mv Chaco-2.2/* src +rm -rf Chaco-2.2 + +# Apply patches (all at once) +# (written by diff -rc src ~/Libs/Chaco-2.2 > chaco.patch) +patch -R -p0 < chaco.patch + +# Build chaco +cd src/code +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make chacominusblas.a + +# Clean up objects (but not library or executable) +make clean +cd ../.. + +# Populate install directory +cp -p src/exec/README install +cp -p src/exec/User_Params install +cp -p src/exec/*.coords install +cp -p src/exec/*.graph install +mkdir install/include +cp -p src/code/main/defs.h install/include/defs.h +cp -p src/code/main/params.h install/include/params.h +cp -p chaco.h install/include/chaco.h +mkdir install/lib +mv src/code/chaco.a install/lib/libchaco.a +mv src/code/chacominusblas.a install/lib/libchacominusblas.a +mkdir install/exec +mv src/exec/chaco install/exec Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mex/Chaco.c =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mex/Chaco.c (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mex/Chaco.c (revision 18231) @@ -0,0 +1,244 @@ + +#include +#include /* strcasecmp */ +#include /* clock,time,difftime */ +#include "mex.h" + + +#define THISFUNCTION "Chaco" + +/* Input Arguments */ + +#define A_IN prhs[0] +#define VWGTS_IN prhs[1] +#define EWGTS_IN prhs[2] +#define XYZ_IN prhs[3] +#define OPTNS_IN prhs[4] +#define NPARTS_IN prhs[5] +#define GOAL_IN prhs[6] + +/* Output Arguments */ + +#define ASSGN_OUT plhs[0] + + +void ChacoUsage( void ); + +int Chacox( + int nvtxs, /* number of vertices in graph */ + int *start, /* start of edge list for each vertex */ + int *adjacency, /* edge list data */ + int *vwgts, /* weights for all vertices */ + float *ewgts, /* weights for all edges */ + float *x, + float *y, + float *z, /* coordinates for inertial method */ + short *assignment, /* set number of each vtx (length nvtxs+1) */ + double options[10], /* architecture and partitioning options */ + int *nparts, /* number of parts options */ + double *goal /* desired set sizes */ +); + + +void mexFunction( + int nlhs, /* number of outputs */ + mxArray *plhs[], /* array of pointers to output arguments */ + int nrhs, /* number of inputs */ + const mxArray *prhs[] /* array of pointers to input arguments */ +) +{ + int nvtxs; /* number of vertices in graph */ + int *start; /* start of edge list for each vertex */ + int *adjacency; /* edge list data */ + int *vwgts=NULL; /* weights for all vertices */ + float *ewgts=NULL; /* weights for all edges */ + float *x=NULL; + float *y=NULL; + float *z=NULL; /* coordinates for inertial method */ + short *assignment=NULL; /* set number of each vtx (length nvtxs+1) */ + double options[10]={1,1,0,0,1,1,50,0,.001,7654321}; + /* architecture and partitioning options */ + int *nparts=NULL; /* number of parts options */ + double *goal=NULL; /* desired set sizes */ + + int i, nedges, nterms, ncols, ierr=0; + double *p; + mwIndex *mwstart, *mwadjacency; + + clock_t clock0,clock1; + time_t time0, time1; + + /* Check for proper number of arguments */ + + if (nrhs == 0 && nlhs == 0) { + ChacoUsage(); + return; + } + else if (nrhs < 1 || nlhs > 1) { + ChacoUsage(); + mexErrMsgTxt(" "); + } + + clock0=clock(); + time0 =time(NULL); + mexPrintf("\nChaco Module -- %s",ctime(&time0)); + + /* Assign pointers to the various parameters */ + /* and convert to the appropriate format for Chaco */ + + if (!mxIsEmpty(A_IN) && mxIsNumeric(A_IN) && mxIsSparse(A_IN)) { + nvtxs = mxGetN(A_IN); + mwstart = mxGetJc(A_IN); + start = mxMalloc((mxGetN(A_IN)+1)*sizeof(int)); + for (i=0; i<(mxGetN(A_IN)+1); i++) + start[i]= (int)mwstart[i]; + nedges = start[nvtxs]; + mwadjacency = mxGetIr(A_IN); + adjacency = mxMalloc(mxGetNzmax(A_IN)*sizeof(int)); + for (i=0; i= 2 && !mxIsEmpty(VWGTS_IN)) { + if (mxIsNumeric(VWGTS_IN) && !mxIsSparse(VWGTS_IN) && + (nterms=mxGetM(VWGTS_IN)*mxGetN(VWGTS_IN)) == nvtxs) { + vwgts = (int *) mxCalloc(nvtxs, sizeof(int)); + p = mxGetPr(VWGTS_IN); + for (i = 0; i < nvtxs; vwgts[i++] = (int) *p++); + } + else { + mexPrintf("%s -- Vertex weight vector must be numeric, full, and length=%d.\n", + THISFUNCTION,nvtxs); + mexErrMsgTxt(" "); + } + } + + if (nrhs >= 3 && !mxIsEmpty(EWGTS_IN)) { + if (mxIsNumeric(EWGTS_IN) && mxIsSparse(EWGTS_IN) && + (nterms=mxGetNzmax(EWGTS_IN)) == nedges) { + ewgts = (float *) mxCalloc(nedges, sizeof(float)); + p = mxGetPr(A_IN); + for (i = 0; i < nedges; ewgts[i++] = (float) *p++); + } + else { + mexPrintf("%s -- Edge weight matrix must be numeric, sparse, and nonzeroes=%d.\n", + THISFUNCTION,nedges); + mexErrMsgTxt(" "); + } + } + + if (nrhs >= 4 && (ncols = mxGetN(XYZ_IN)) >= 1) { + if (mxIsNumeric(XYZ_IN) && !mxIsSparse(XYZ_IN) && + mxGetM(XYZ_IN) == nvtxs) { + x = (float *) mxCalloc(nvtxs, sizeof(float)); + p = mxGetPr(XYZ_IN); + for (i = 0; i < nvtxs; x[i++] = (float) *p++); + } + else { + mexPrintf("%s -- XYZ coordinate matrix must be numeric, full, and length=%d.\n", + THISFUNCTION,nvtxs); + mexErrMsgTxt(" "); + } + if ((ncols ) >= 2) { + y = (float *) mxCalloc(nvtxs, sizeof(float)); + for (i = 0; i < nvtxs; y[i++] = (float) *p++); + if ((ncols ) >= 3) { + z = (float *) mxCalloc(nvtxs, sizeof(float)); + for (i = 0; i < nvtxs; z[i++] = (float) *p++); + } + } + } + + if (nrhs >= 5 && !mxIsEmpty(OPTNS_IN)) { + if (mxIsNumeric(OPTNS_IN) && !mxIsSparse(OPTNS_IN) && + (nterms=mxGetM(OPTNS_IN)*mxGetN(OPTNS_IN))) { + p = mxGetPr(OPTNS_IN); + for (i = 0; i < (nterms<10 ? nterms : 10); options[i++] = *p++); + } + else { + mexPrintf("%s -- Options vector must be numeric and full.\n", + THISFUNCTION); + mexErrMsgTxt(" "); + } + } + + if (nrhs >= 6 && !mxIsEmpty(NPARTS_IN)) { + if (mxIsNumeric(NPARTS_IN) && !mxIsSparse(NPARTS_IN) && + (nterms=mxGetM(NPARTS_IN)*mxGetN(NPARTS_IN))) { + nparts = (int *) mxCalloc(nterms, sizeof(int)); + p = mxGetPr(NPARTS_IN); + for (i = 0; i < nterms; nparts[i++] = (int) *p++); + } + else { + mexPrintf("%s -- Parts vector must be numeric and full.\n", + THISFUNCTION); + mexErrMsgTxt(" "); + } + } + + if (nrhs >= 7 && !mxIsEmpty(GOAL_IN)) { + if (mxIsNumeric(GOAL_IN) && !mxIsSparse(GOAL_IN) && + (nterms=mxGetM(GOAL_IN)*mxGetN(GOAL_IN))) { + goal = (double *) mxCalloc(nterms, sizeof(double)); + p = mxGetPr(GOAL_IN); + for (i = 0; i < nterms; goal[i++] = *p++); + } + else { + mexPrintf("%s -- Goal vector must be numeric and full.\n", + THISFUNCTION); + mexErrMsgTxt(" "); + } + } + + assignment = (short *) mxCalloc(nvtxs, sizeof(short)); + + /* Do the actual computations in a subroutine */ + + ierr = Chacox(nvtxs, start, adjacency, vwgts, ewgts, x, y, z, + assignment, options, nparts, goal); + + /* Create matrices for the return arguments */ + + if (!ierr) { + ASSGN_OUT = mxCreateDoubleMatrix(1,nvtxs,mxREAL); + p = mxGetPr(ASSGN_OUT); + for (i = 0; i < nvtxs; *p++ = (double) assignment[i++]); + } + else + ASSGN_OUT = mxCreateDoubleMatrix(0,0,mxREAL); + + /* Free what we allocated */ + + if (!assignment) mxFree((void *) assignment); + if (!goal) mxFree((void *) goal); + if (!nparts) mxFree((void *) nparts); + if (!z) mxFree((void *) z); + if (!y) mxFree((void *) y); + if (!x) mxFree((void *) x); + if (!ewgts) mxFree((void *) ewgts); + if (!vwgts) mxFree((void *) vwgts); + if (!adjacency) mxFree((void *) adjacency); + if (!start) mxFree((void *) start); + + clock1=clock(); + time1 =time(NULL); + mexPrintf("Chaco Module -- %f CPU seconds; %f elapsed seconds.\n\n", + ((double)(clock1-clock0))/CLOCKS_PER_SEC,difftime(time1,time0)); + + return; +} + +void ChacoUsage( void ) +{ + mexPrintf("\n"); + mexPrintf("Usage: [assgn] = Chaco(A,vwgts,ewgts,xyz,options,nparts,goal);\n"); + mexPrintf("\n"); + + return; +} + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mex/Chaco_m.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mex/Chaco_m.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mex/Chaco_m.m (revision 18231) @@ -0,0 +1,217 @@ +function [part1,part2,chaco_time] = chaco(A,xy,method,nparts,goal) +% CHACO : Hendrickson/Leland's graph partitioner. +% +% [part1,part2,chaco_time] = chaco(A) returns a 50/50 vertex partition of the mesh +% whose symmetric adjacency matrix is A. +% +% Optional arguments: +% map = chaco(A, xy, method, nparts, goal); +% map = chaco(A, xy, method, inmap, goal); +% +% A: Depending on "method", A may contain vertex and edge weights. +% +% xy: Each row of xy is the coordinates of a vertex. +% If xy is non-null and there is no output, draw a picture. +% +% method: Scalar or vector describing the desired method. +% Default is multilevel Kernighan-Lin; other possibilities below. +% +% nparts Number of parts to divide into. Default is 2. If nparts is +% or present, the output is a "map vector", see below. (If method(5) +% inmap: is specified, nparts is interpreted differently; see below. In +% any case, the default is to divide into two parts.) +% If method(1) = 7 (see below), this argument is a map vector +% specifying an initial 2-way partition, and Chaco refines it. +% +% goal: Optionally, a vector of desired sizes (or total vertex weights) +% for each of the nparts parts. Default is all sizes equal. +% +% map: If nparts and inmap are not present, the output is a vector of +% the n/2 vertex numbers in one part of the 2-way partition, for +% compatibility with geopart and specpart. +% If nparts or imap is present, the output is a vector of the +% n part numbers, from 0 to nparts-1, assigned to the vertices. +% +% This is a Matlab interface to the graph partitioning software described +% in B. Hendrickson and R. Leland, "The Chaco User's Guide (Version 2.0)", +% Sandia National Laboratories report SAND94-2692, October 1994. +% This interface was written by John Gilbert, Xerox PARC, and is +% Copyright (c) 1994-1996 by Xerox Corporation. All rights reserved. +% HELP COPYRIGHT for complete copyright and licensing notice. +% +% Modified by Tim Davis, for Matlab 5.1. July 6, 1998. +% 05/28/10 jes Reorganization into Matlab-layer and x-layer. +% +% See also GEOPART, SPECPART. +% +% "method" is a vector of flags as follows. Not all combinations are supported. +% See Section 6.10 of the Chaco manual for more details on all the arguments. +% If "method" is shorter than 10, we use the defaults for unspecified entries. +% +% method(1): Global partitioning method ("global_method" in the Chaco manual). +% 1 Multilevel Kernighan-Lin (default) +% 2 Spectral +% 3 Inertial +% 4 Linear +% 5 Random +% 6 Scattered +% 7 Use "inmap" as the global (2-way) partition +% +% method(2): Local refinement method ("local_method" in the Chaco manual). +% 1 Kernighan-Lin (default) +% 2 None +% +% method(3): Vertex weighting. +% 0 No weights (default) +% 1 Use diag(A) as (positive integer) vertex weights +% +% method(4): Edge weighting. +% 0 No weights (default) +% 1 Use off-diagonals of A as (positive integer) edge weights +% +% method(5): Target architecture ("architecture" in the Chaco manual). +% If method(5) = 0, the target is a hypercube, "nparts" is the +% number of dimensions, and the partition is into 2^nparts parts. +% If method(5) = 1, 2, or 3, the target is a 1-, 2-, or 3-D grid, +% "nparts" is a vector of the sizes of the grid in each dimension, +% and the partition is into prod(nparts) parts. +% Default is method(5) = 1, so nparts is the number of parts. +% +% method(6): Partitioning dimension ("ndims" in the Chaco manual). +% 1 Bisection (default) +% 2 Quadrisection +% 3 Octasection +% +% method(7): Number of vertices to coarsen to ("vmax" in the Chaco manual). +% Default is 50. +% +% method(8): Eigensolver ("rqi_flag" in the Chaco manual). +% 0 RQI/Symmlq (default) +% 1 Lanczos +% +% method(9): Eigensolver convergence tolerance ("eigtol" in the Chaco manual). +% Default is .001 +% +% method(10): Seed for random number generator ("seed" in the Chaco manual). +% Default is 7654321. +% +% Many esoteric details of Chaco's behavior can be changed by placing a file +% called "User_Params" in the same directory as the executable mlchaco.mex. +% As always, see the manual for details. + +DefaultMethod = [1 1 0 0 1 1 50 0 .001 7654321]; + +% Fill in default arguments. +if nargin < 2, xy = []; end; +if nargin < 3, method = DefaultMethod; end; +if nargin < 4, nparts = []; end; +if nargin < 5, goal = []; end; +if length(method) < length(DefaultMethod) + method = [method DefaultMethod(length(method)+1 : length(DefaultMethod))]; +end; + +% Decide on output and graphics. +if (isempty (nparts)) + mapvector = 0; +else + mapvector = 1; +end; +picture = (nargout == 0) & (size(xy,2) >= 2); + +% Chaco numbers vertices from 1 and the Matlab sparse data structure +% numbers rows from 0, so we add an empty first row to make things line up. +% This code also makes sure the arg to Chaco will be sparse. +[n,n] = size(A); +Adiag = diag(diag(A)); +%Aout = [sparse(1,n) ; A-Adiag]; +Aout = sparse(A-Adiag); + +% Make sure all args except the adj matrix are full; +if issparse(xy) + xy = full(xy); +end; +if issparse(method) + method = full(method); +end; +if issparse(nparts) + nparts = full(nparts); +end; +if issparse(goal) + goal = full(goal); +end; + +% Decode "method" to get the actual args to Chaco. +% Note that "nparts" may correspond to any of several Chaco +% parameters, depending on the method. + +if method(3) + vwgts = full(diag(A)); + totalvwgt = sum(vwgts); +else + vwgts = []; + totalvwgt = size(A,2); +end; +if method(4) + ewgts = Aout; +else + ewgts = []; +end; +if method(1) == 7 + % Refine an input partition: "nparts" is the input partition. + % This seems to work only for hypercube architecture, + % so we force a 1-D hypercube with 2-way partitioning. + nsets = 2; +elseif method(5) == 0 + % Partition for hypercube: "nparts" is # of dimensions (default 1). + if (isempty (nparts)) + nsets = 2^1; + else + nsets = 2^nparts; + end; +else + % Partition for mesh: "nparts" is vector of mesh sizes in each + % dimension, default [2 1 ... 1] with "architecture" dimensions. + if (isempty (nparts)) + nsets = prod(2); + else + nsets = prod(nparts); + end; +end; +if length(goal) ~= nsets + goal = totalvwgt/nsets * ones(1,nsets); +end; + +[map,chaco_time]=Chaco(Aout, vwgts, ewgts, xy, method, nparts, goal); + +% Draw the picture. +if picture + if size(xy,2) >= 3 && unique(xy(:,3)) == 0 + xy=xy(:,1:2); + end + if length(unique(map)) == 2 + gplotpart(A,xy,find(map==0)); + else + gplotmap(A,xy,map); + end; + if method(1)==1, heading = 'Multilevel Kernighan-Lin'; + elseif method(1)==2, heading = 'Spectral'; + elseif method(1)==3, heading = 'Inertial'; + elseif method(1)==4, heading = 'Linear'; + elseif method(1)==5, heading = 'Random'; + elseif method(1)==6, heading = 'Scattered'; + elseif method(1)==7, heading = 'Input'; + end; + heading = [heading ' Partition']; + if method(2)==1 & method(1) ~= 1 + heading =[heading ' Refined by KL']; + end; + title(heading); +end; + +% Put output in the right form. +if mapvector + part1 = map; +else + part1 = find(map==0); + part2 = find(map==1); +end; Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mex/Chacox.c =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mex/Chacox.c (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mex/Chacox.c (revision 18231) @@ -0,0 +1,471 @@ +/* This software was developed by Bruce Hendrickson and Robert Leland * + * at Sandia National Laboratories under US Department of Energy * + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + +#include +#include +#include "defs.h" +#include "params.h" + +#define THISFUNCTION "Chacox" + +#define OPT_GLOBAL 0 +#define OPT_LOCAL 1 +#define OPT_VWGTS 2 +#define OPT_EWGTS 3 +#define OPT_ARCH 4 +#define OPT_NDIMS 5 +#define OPT_VMAX 6 +#define OPT_RQI 7 +#define OPT_EIGTOL 8 +#define OPT_SEED 9 + +int input_parse( + char *outassignname, /* name of assignment output file */ + char *outfilename, /* name of file for outputing run results */ + int *architecture, /* 0=> hypercube, d=> d-dimensional mesh */ + int *ndims_tot, /* target number of hypercube dimensions */ + int mesh_dims[3], /* mesh dimensions */ + int *global_method, /* what global partitioning strategy to use? */ + int *local_method, /* what local refinement strategy to use? */ + int *rqi_flag, /* should I use multilevel eigensolver? */ + int *vmax, /* if so, how far should I coarsen? */ + int *ndims, /* number of divisions at each stage */ + int *nprocs, /* number of processors being divided into */ + double options[10], /* architecture and partitioning options */ + int *nparts /* number of parts options */ +); + + +int Chacox( + int nvtxs, /* number of vertices in graph */ + int *start, /* start of edge list for each vertex */ + int *adjacency, /* edge list data */ + int *vwgts, /* weights for all vertices */ + float *ewgts, /* weights for all edges */ + float *x, + float *y, + float *z, /* coordinates for inertial method */ + short *assignment, /* set number of each vtx (length nvtxs+1) */ + double options[10], /* architecture and partitioning options */ + int *nparts, /* number of parts options */ + double *goal /* desired set sizes */ +) +{ + extern int Using_Main; /* is main routine being called? */ + extern char *PARAMS_FILENAME; /* name of file with parameter updates */ + extern double EIGEN_TOLERANCE; /* tolerance for eigen calculations */ + extern int OUTPUT_ASSIGN; /* whether to write assignment to file */ + extern int DEBUG_MEMORY; /* debug memory allocation and freeing? */ + extern int DEBUG_TRACE; /* trace main execution path */ + extern int DEBUG_PARAMS; /* debug flag for reading parameters */ + extern long RANDOM_SEED; /* seed for random number generators */ + extern int ECHO; /* controls amount of output */ + extern int PROMPT; /* prompt for input or not? */ + extern int PRINT_HEADERS; /* print lines for output sections? */ + extern int MATCH_TYPE; /* matching routine to call */ + extern double input_time; /* times data file input */ + extern double start_time; /* time partitioning starts */ + FILE *params_file; /* file with parameter value updates */ + int global_method; /* global partitioning method */ + int local_method; /* local partitioning method */ + double eigtol; /* tolerance in eigenvector calculation */ + int ndims; /* dimension of recursive partitioning */ + int architecture; /* 0 => hypercube, d => d-dimensional mesh */ + int ndims_tot; /* total number of cube dimensions to divide */ + int mesh_dims[3]; /* dimensions of mesh of processors */ + long seed; /* for random graph mutations */ + int rqi_flag; /* use RQI/Symmlq eigensolver? */ + int vmax; /* if so, how many vertices to coarsen down to? */ + char outassignname[NAME_LENGTH]; /* assignment output file name */ + char outfilename[NAME_LENGTH]; /* name of output file */ + char *outassignptr; /* name or null pointer for output assignment */ + char *outfileptr; /* name or null pointer for output file */ + int nprocs; /* number of processors being divided into */ + double time; /* timing marker */ + int flag; /* return code from input routines */ + double *smalloc(); /* safe version of malloc */ + double seconds(); /* returns elapsed time in seconds */ + int sfree(), interface(), affirm(); + void input_queries(), smalloc_stats(), read_params(), clear_timing(); + + int i,tvwgt; + double tgoal; + + if (DEBUG_TRACE > 0) { + printf("\n"); + } + + if (PRINT_HEADERS) { + printf("\n Chaco 2.0\n"); + printf(" Sandia National Laboratories\n\n"); + } + + Using_Main = TRUE; + params_file = fopen(PARAMS_FILENAME, "r"); + if (params_file == NULL && DEBUG_PARAMS > 1) { + printf("Parameter file `%s' not found; using default parameters.\n", + PARAMS_FILENAME); + } + + start_time = time = seconds(); + + read_params(params_file); + + flag = input_parse(outassignname, outfilename, + &architecture, &ndims_tot, mesh_dims, + &global_method, &local_method, &rqi_flag, &vmax, &ndims, &nprocs, + options, nparts); + if (flag) + return(flag); + + if (OUTPUT_ASSIGN > 0) + outassignptr = outassignname; + else + outassignptr = NULL; + + if (ECHO < 0) + outfileptr = outfilename; + else + outfileptr = NULL; + + if ((int)options[OPT_VWGTS] && vwgts) { + printf("%s -- Applying weights for %d vertices.\n", + THISFUNCTION,nvtxs); + tvwgt = 0.; + for (i=0; i 0) + eigtol = options[OPT_EIGTOL]; + else + eigtol = EIGEN_TOLERANCE; + if ((int)options[OPT_SEED] > 0) + seed = (int)options[OPT_SEED]; + else + seed = RANDOM_SEED; + +/* Chaco numbers vertices from 1 and the Matlab sparse data structure + numbers rows from 0, so increment the row indices for each column. */ + + for (i=0; i 0) { + printf("\n"); + smalloc_stats(); + } + + if (params_file != NULL) + fclose(params_file); + + if (DEBUG_TRACE > 1) { + printf("\n"); + } + + return(0); +} + + +int input_parse( + char *outassignname, /* name of assignment output file */ + char *outfilename, /* name of file for outputing run results */ + int *architecture, /* 0=> hypercube, d=> d-dimensional mesh */ + int *ndims_tot, /* target number of hypercube dimensions */ + int mesh_dims[3], /* mesh dimensions */ + int *global_method, /* what global partitioning strategy to use? */ + int *local_method, /* what local refinement strategy to use? */ + int *rqi_flag, /* should I use multilevel eigensolver? */ + int *vmax, /* if so, how far should I coarsen? */ + int *ndims, /* number of divisions at each stage */ + int *nprocs, /* number of processors being divided into */ + double options[10], /* architecture and partitioning options */ + int *nparts /* number of parts options */ +) +{ + extern int SEQUENCE; /* sequence instead of partition graph? */ + extern int ARCHITECTURE; /* 0=> hypercube, d=> d-dimensional mesh */ + extern int OUTPUT_ASSIGN; /* write assignments to file? */ + extern int ECHO; /* copy input to screen? results to file? */ + extern int DEBUG_TRACE; /* trace main execution path */ + extern int PROMPT; /* prompt for input? */ + extern int MATCH_TYPE; /* max-matching routine to call */ + int eigensolver; /* which kind of eigensolver to use */ + + if (DEBUG_TRACE > 0) { + printf("\n"); + } + + if (PROMPT) { + printf("Parallel machine architecture:\n"); + printf(" (0) Hypercube\n"); + printf(" (1) One-dimensional mesh\n"); + printf(" (2) Two-dimensional mesh\n"); + printf(" (3) Three-dimensional mesh\n"); + } + *architecture = (int)options[OPT_ARCH]; + if (*architecture < 0 || *architecture > 3) { + printf("%s -- Architecture %d must be between 0 and 3.\n", + THISFUNCTION,options[OPT_ARCH]); + return(-1); + } + + /* Name output assignment file. */ + if (PROMPT) + printf("Assignment output file: "); + outassignname = NULL; + + /* Name output results file. */ + if (PROMPT) + printf("File name for saving run results: "); + outfilename = NULL; + + /* Initialize the method flags */ + *rqi_flag = 0; + *global_method = 0; + + /* Get global method, if any. */ + if (SEQUENCE) { + *global_method = 2; + } + else { + if (PROMPT) { + printf("Global partitioning method:\n"); + printf(" (1) Multilevel-KL\n"); + printf(" (2) Spectral\n"); + printf(" (3) Inertial\n"); + printf(" (4) Linear\n"); + printf(" (5) Random\n"); + printf(" (6) Scattered\n"); + printf(" (7) Read-from-file\n"); + } + *global_method = (int)options[OPT_GLOBAL]; + if (*global_method < 1 || *global_method > 7) { + printf("%s -- Global method %d must be between 1 and 7.\n", + THISFUNCTION,options[OPT_GLOBAL]); + return(-1); + } + } + + if (*global_method == 7) { /* Name and open input assignment file. */ + if (PROMPT) + printf("Assignment input file: "); + } + + else if (*global_method == 3) { + if (PROMPT) + printf("Geometry input file name: "); + } + + else if (*global_method == 2) { + if (PROMPT) { + printf("Eigensolver:\n"); + printf(" (1) Multilevel RQI/Symmlq\n"); + printf(" (2) Lanczos\n"); + } + eigensolver = (int)options[OPT_RQI]; + if (eigensolver < 0 || eigensolver > 2) { + printf("%s -- RQI/Symmlq flag %d must be between 0 and 2.\n", + THISFUNCTION,options[OPT_RQI]); + return(-1); + } + if (eigensolver == 1) { + if (MATCH_TYPE == 5) { /* geometric matching */ + if (PROMPT) + printf("Geometry input file name: "); + } + *rqi_flag = 1; + if (PROMPT) + printf("Number of vertices to coarsen down to: "); + *vmax = (int)options[OPT_VMAX]; + if (*vmax <= 0) { + printf("%s -- Vmax %d must be greater then 0.\n", + THISFUNCTION,options[OPT_VMAX]); + return(-1); + } + } + else if (eigensolver == 0 || eigensolver == 2) { + *rqi_flag = 0; + } + } + + else if (*global_method == 1) { + if (MATCH_TYPE == 5) { /* geometric matching */ + if (PROMPT) + printf("Geometry input file name: "); + } + if (PROMPT) + printf("Number of vertices to coarsen down to: "); + *vmax = (int)options[OPT_VMAX]; + if (*vmax <= 0) { + printf("%s -- Vmax %d must be greater then 0.\n", + THISFUNCTION,options[OPT_VMAX]); + return(-1); + } + } + + if (SEQUENCE) { + *local_method = 2; + if (*architecture == 0) { + *ndims_tot = 1; + } + else if (*architecture > 0) { + mesh_dims[0] = 2; + mesh_dims[1] = mesh_dims[2] = 1; + } + *ndims = 1; + goto End_Label; + } + + /* Get local method, if any */ + *local_method = 0; + if (*global_method == 1) + *local_method = 1; + else { + if (PROMPT) { + printf("Local refinement method:\n"); + printf(" (1) Kernighan-Lin\n"); + printf(" (2) None\n"); + } + *local_method = (int)options[OPT_LOCAL]; + if (*local_method < 1 || *local_method > 2) { + printf("%s -- Local method %d must be 1 and 2.\n", + THISFUNCTION,options[OPT_LOCAL]); + return(-1); + } + } + + /* Now learn about the parallel architecture. */ + if (*architecture == 0) { + /* Get total number of hypercube dimensions in which to partition. */ + *ndims_tot = 0; + if (PROMPT) + printf("Total number of target hypercube dimensions: "); + *ndims_tot = nparts[0]; + if (*ndims_tot < 1) { + printf(" Number of divisions must be at least 1\n"); + printf("%s -- Number of divisions %d must be at least 1.\n", + THISFUNCTION,nparts[0]); + return(-1); + } + *nprocs = 1 << (*ndims_tot); + } + + else { /* Get dimensions of mesh. */ + mesh_dims[1] = mesh_dims[2] = 1; + if (*architecture == 2) { + if (PROMPT) + printf("X and Y extent of of 2-D mesh: "); + mesh_dims[0] = nparts[0]; + mesh_dims[1] = nparts[1]; + } + else if (*architecture == 3) { + if (PROMPT) + printf("X, Y and Z extent of 3-D mesh: "); + mesh_dims[0] = nparts[0]; + mesh_dims[1] = nparts[1]; + mesh_dims[2] = nparts[2]; + } + else { /* Anything else => 1-D mesh */ + if (PROMPT) + printf("Size of 1-D mesh: "); + mesh_dims[0] = nparts[0]; + *architecture = 1; + } + *nprocs = mesh_dims[0] * mesh_dims[1] * mesh_dims[2]; + } + + /* Get number of dimensions in which to partition at each level. */ + *ndims = 0; + if (*nprocs <= 3) { + *ndims = 1; + } + else if (*nprocs <= 7) { + if (PROMPT) { + printf("Partitioning dimension: \n"); + printf(" (1) Bisection\n"); + printf(" (2) Quadrisection\n"); + } + *ndims = (int)options[OPT_NDIMS]; + if (*ndims < 1 || *ndims > 2) { + printf("%s -- Ndims %d must be 1 or 2 for %d processors.\n", + THISFUNCTION,options[OPT_NDIMS],*nprocs); + return(-1); + } + } + else { + if (PROMPT) { + printf("Partitioning dimension: \n"); + printf(" (1) Bisection\n"); + printf(" (2) Quadrisection\n"); + printf(" (3) Octasection\n"); + } + *ndims = (int)options[OPT_NDIMS]; + if (*ndims < 1 || *ndims > 3) { + printf("%s -- Ndims %d must be between 1 and 3 for %d processors.\n", + THISFUNCTION,options[OPT_NDIMS],*nprocs); + return(-1); + } + } +End_Label: + + if (*global_method == 1 || *rqi_flag) { + if (*vmax < 2 * (1 << *ndims)) { + *vmax = 2 * (1 << *ndims); + } + } + + return(0); +} Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mex/Makefile =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mex/Makefile (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mex/Makefile (revision 18231) @@ -0,0 +1,293 @@ +# This is the Makefile for the mex-file version of Chaco, to be dynamically +# linked with Matlab using the interface in the "meshpart" toolbox. +# See file "README" for more information. +# +# You may need to change the following variables: +# +# MATLAB Matlab's top-level directory, often "/usr/matlab" or similar. +# CHACO Chaco's source directory, normally the "code" subdirectory +# of the Chaco distribution. +# MLCHACO Directory with Chaco files modified for Matlab, normally +# the directory containing this Makefile. +# DEST_DIR Directory for the executable mlchaco.mex, normally the +# "meshpart" directory, which is normally the parent of the +# directory containing this Makefile. +# CC Choice of C compiler. gcc seems to work best for Matlab for me. +# IFLAGS, CFLAGS, OFLAGS Flags to go with the compiler and linker. +# +# This Makefile works under Solaris 2. To use it with a different Unix, +# you may need to change the references to "ar" and/or "ranlib" and +# possibly other things. +# +# John Gilbert, 1996. +# Copyright (c) 1990-1996 by Xerox Corporation. All rights reserved. +# See file ../copyright.m for complete copyright and licensing notice. + +#MATLAB = /import/matlab +#MATLAB = /usr/local/libexec/matlab +#MATLAB = /usr/local/pkgs/matlab-7.6 +MATLAB = ${MATLAB_DIR} + +#CHACO = /project/sparse/chaco/version2/code +#CHACO = ../../Chaco-2.0/code +#CHACO = ../../Chaco-2.2/code +#CHACO = ../../../chaco/src/code +CHACO = ${CHACO_DIR}/../src/code + +MLCHACO = . +DEST_DIR = .. +CC = gcc +#CC = cc +IFLAGS = -I${MATLAB}/extern/include -I${CHACO}/main +#CFLAGS = -Xa -G -xO4 -xcg92 +#CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB +CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions +#OFLAGS = -xO4 -xcg92 +OFLAGS = -O2 +#AR = /usr/ccs/bin/ar rcv # for solaris 2 +AR = /usr/bin/ar rcv # for solaris 2 +#RANLIB = /usr/ccs/bin/ranlib # for solaris 2 +RANLIB = /usr/bin/ranlib # for solaris 2 + + +MLFILES.c= ${MLCHACO}/Chacox.c \ + ${MLCHACO}/user_params.c +# ${MLCHACO}/bail.c \ # redefined original with -DMATLAB +# ${MLCHACO}/chaco_check_graph.c \ # redefined original with -DMATLAB +# ${MLCHACO}/check_input.c \ # redefined original with -DMATLAB +# ${MLCHACO}/smalloc.c \ # redefined original with -DMATLAB + +CHFILES.c= ${CHACO}/main/interface.c \ + ${CHACO}/main/main.c \ + ${CHACO}/submain/balance.c \ + ${CHACO}/submain/divide.c \ + ${CHACO}/submain/submain.c \ + ${CHACO}/input/input_assign.c \ + ${CHACO}/input/check_input.c \ + ${CHACO}/input/input.c \ + ${CHACO}/input/input_geom.c \ + ${CHACO}/input/input_graph.c \ + ${CHACO}/input/read_params.c \ + ${CHACO}/input/reflect_input.c \ + ${CHACO}/input/read_val.c \ + ${CHACO}/graph/check_graph.c \ + ${CHACO}/graph/free_graph.c \ + ${CHACO}/graph/reformat.c \ + ${CHACO}/graph/subgraph.c \ + ${CHACO}/graph/graph_out.c \ + ${CHACO}/inertial/eigenvec2.c \ + ${CHACO}/inertial/eigenvec3.c \ + ${CHACO}/inertial/inertial.c \ + ${CHACO}/inertial/inertial1d.c \ + ${CHACO}/inertial/inertial2d.c \ + ${CHACO}/inertial/inertial3d.c \ + ${CHACO}/inertial/make_subgeom.c \ + ${CHACO}/klspiff/buckets.c \ + ${CHACO}/klspiff/buckets_bi.c \ + ${CHACO}/klspiff/buckets1.c \ + ${CHACO}/klspiff/bilistops.c \ + ${CHACO}/klspiff/coarsen_kl.c \ + ${CHACO}/klspiff/count_weights.c \ + ${CHACO}/klspiff/compress_ewgts.c \ + ${CHACO}/klspiff/kl_init.c \ + ${CHACO}/klspiff/kl_output.c \ + ${CHACO}/klspiff/klspiff.c \ + ${CHACO}/klspiff/make_bndy_list.c \ + ${CHACO}/klspiff/make_kl_list.c \ + ${CHACO}/klspiff/nway_kl.c \ + ${CHACO}/klvspiff/bpm_improve.c \ + ${CHACO}/klvspiff/bucketsv.c \ + ${CHACO}/klvspiff/clear_dvals.c \ + ${CHACO}/klvspiff/coarsen_klv.c \ + ${CHACO}/klvspiff/countup_vtx_sep.c \ + ${CHACO}/klvspiff/find_bndy.c \ + ${CHACO}/klvspiff/flow.c \ + ${CHACO}/klvspiff/klv_init.c \ + ${CHACO}/klvspiff/klvspiff.c \ + ${CHACO}/klvspiff/make_bpgraph.c \ + ${CHACO}/klvspiff/make_sep_list.c \ + ${CHACO}/klvspiff/matching.c \ + ${CHACO}/klvspiff/nway_klv.c \ + ${CHACO}/klvspiff/flatten.c \ + ${CHACO}/coarsen/coarsen.c \ + ${CHACO}/coarsen/interpolate.c \ + ${CHACO}/coarsen/makefgraph.c \ + ${CHACO}/coarsen/makeccoords.c \ + ${CHACO}/coarsen/coarsen1.c \ + ${CHACO}/coarsen/makev2cv.c \ + ${CHACO}/coarsen/maxmatch.c \ + ${CHACO}/coarsen/maxmatch1.c \ + ${CHACO}/coarsen/maxmatch2.c \ + ${CHACO}/coarsen/maxmatch3.c \ + ${CHACO}/coarsen/maxmatch4.c \ + ${CHACO}/coarsen/maxmatch5.c \ + ${CHACO}/connect/add_edges.c \ + ${CHACO}/connect/connected.c \ + ${CHACO}/connect/find_edges.c \ + ${CHACO}/eigen/bidir.c \ + ${CHACO}/eigen/bisect.c \ + ${CHACO}/eigen/checkeig.c \ + ${CHACO}/eigen/checkeig_ext.c \ + ${CHACO}/eigen/checkorth.c \ + ${CHACO}/eigen/cksturmcnt.c \ + ${CHACO}/eigen/mkeigvecs.c\ + ${CHACO}/eigen/eigensolve.c \ + ${CHACO}/eigen/get_extval.c \ + ${CHACO}/eigen/get_ritzvals.c \ + ${CHACO}/eigen/lanczos_FO.c \ + ${CHACO}/eigen/lanczos_SO.c \ + ${CHACO}/eigen/lanczos_SO_float.c \ + ${CHACO}/eigen/lanczos_ext.c \ + ${CHACO}/eigen/lanczos_ext_float.c \ + ${CHACO}/eigen/lanc_seconds.c\ + ${CHACO}/eigen/lanpause.c \ + ${CHACO}/eigen/makeorthlnk.c \ + ${CHACO}/eigen/mkscanlist.c \ + ${CHACO}/eigen/orthog1.c \ + ${CHACO}/eigen/orthogonalize.c \ + ${CHACO}/eigen/orthogvec.c \ + ${CHACO}/eigen/ql.c \ + ${CHACO}/eigen/rqi.c \ + ${CHACO}/eigen/rqi_ext.c \ + ${CHACO}/eigen/scale_diag.c \ + ${CHACO}/eigen/scanmax.c \ + ${CHACO}/eigen/scanmin.c \ + ${CHACO}/eigen/solistout.c \ + ${CHACO}/eigen/sorthog.c \ + ${CHACO}/eigen/splarax.c \ + ${CHACO}/eigen/sturmcnt.c \ + ${CHACO}/eigen/Tevec.c \ + ${CHACO}/eigen/tri_solve.c \ + ${CHACO}/eigen/warnings.c \ + ${CHACO}/symmlq/aprod.c \ + ${CHACO}/symmlq/msolve.c \ + ${CHACO}/symmlq/pow_dd.c \ + ${CHACO}/symmlq/symmlq.c \ + ${CHACO}/symmlq/symmlqblas.c \ + ${CHACO}/tinvit/tinvit.c \ + ${CHACO}/tinvit/pythag.c \ + ${CHACO}/tinvit/epslon.c \ + ${CHACO}/optimize/determinant.c \ + ${CHACO}/optimize/func2d.c \ + ${CHACO}/optimize/func3d.c \ + ${CHACO}/optimize/opt2d.c \ + ${CHACO}/optimize/opt3d.c \ + ${CHACO}/assign/assign.c \ + ${CHACO}/assign/assign_out.c \ + ${CHACO}/assign/mapper.c \ + ${CHACO}/assign/median.c \ + ${CHACO}/assign/merge_assign.c \ + ${CHACO}/assign/rec_median.c \ + ${CHACO}/assign/rotate.c \ + ${CHACO}/assign/y2x.c \ + ${CHACO}/bpmatch/checkbp.c \ + ${CHACO}/bpmatch/inits2d.c \ + ${CHACO}/bpmatch/inits3d.c \ + ${CHACO}/bpmatch/genvals2d.c \ + ${CHACO}/bpmatch/genvals3d.c \ + ${CHACO}/bpmatch/map2d.c \ + ${CHACO}/bpmatch/map3d.c \ + ${CHACO}/bpmatch/movevtxs.c \ + ${CHACO}/bpmatch/sorts2d.c \ + ${CHACO}/bpmatch/sorts3d.c \ + ${CHACO}/refine_map/compute_cube_edata.c \ + ${CHACO}/refine_map/compute_cube_vdata.c \ + ${CHACO}/refine_map/refine_cube.c \ + ${CHACO}/refine_map/update_cube_edata.c \ + ${CHACO}/refine_map/update_cube_vdata.c \ + ${CHACO}/refine_map/find_edge_cube.c \ + ${CHACO}/refine_map/init_cube_edata.c \ + ${CHACO}/refine_map/compute_mesh_edata.c \ + ${CHACO}/refine_map/compute_mesh_vdata.c \ + ${CHACO}/refine_map/find_edge_mesh.c \ + ${CHACO}/refine_map/init_mesh_edata.c \ + ${CHACO}/refine_map/refine_mesh.c \ + ${CHACO}/refine_map/update_mesh_edata.c \ + ${CHACO}/refine_map/update_mesh_vdata.c \ + ${CHACO}/refine_map/refine_map.c \ + ${CHACO}/refine_map/make_comm_graph.c \ + ${CHACO}/refine_part/refine_part.c \ + ${CHACO}/refine_part/kl_refine.c \ + ${CHACO}/refine_part/make_maps_ref.c \ + ${CHACO}/refine_part/make_terms_ref.c \ + ${CHACO}/internal/force_internal.c \ + ${CHACO}/internal/improve_internal.c \ + ${CHACO}/internal/check_internal.c \ + ${CHACO}/misc/define_subcubes.c \ + ${CHACO}/misc/define_submeshes.c \ + ${CHACO}/misc/divide_procs.c \ + ${CHACO}/misc/merge_goals.c \ + ${CHACO}/misc/make_term_props.c \ + ${CHACO}/misc/count.c \ + ${CHACO}/misc/countup.c \ + ${CHACO}/misc/countup_cube.c \ + ${CHACO}/misc/countup_mesh.c \ + ${CHACO}/misc/make_subgoal.c \ + ${CHACO}/misc/find_maxdeg.c \ + ${CHACO}/misc/make_maps.c \ + ${CHACO}/misc/make_setlists.c \ + ${CHACO}/misc/sequence.c \ + ${CHACO}/misc/perturb.c \ + ${CHACO}/misc/simple_part.c \ + ${CHACO}/misc/time_kernels.c \ + ${CHACO}/misc/timing.c \ + ${CHACO}/util/affirm.c \ + ${CHACO}/util/array_alloc_2D.c \ + ${CHACO}/util/bit_reverse.c \ + ${CHACO}/util/checkpnt.c \ + ${CHACO}/util/cpvec.c \ + ${CHACO}/util/dot.c \ + ${CHACO}/util/doubleout.c \ + ${CHACO}/util/input_int.c \ + ${CHACO}/util/gray.c \ + ${CHACO}/util/machine_params.c \ + ${CHACO}/util/makevwsqrt.c \ + ${CHACO}/util/mkvec.c \ + ${CHACO}/util/norm.c \ + ${CHACO}/util/normalize.c \ + ${CHACO}/util/mergesort.c \ + ${CHACO}/util/randomize.c \ + ${CHACO}/util/smalloc.c \ + ${CHACO}/util/bail.c \ + ${CHACO}/util/scadd.c \ + ${CHACO}/util/seconds.c \ + ${CHACO}/util/setvec.c \ + ${CHACO}/util/shell_sort.c \ + ${CHACO}/util/strout.c \ + ${CHACO}/util/tri_prod.c \ + ${CHACO}/util/true_or_false.c \ + ${CHACO}/util/update.c \ + ${CHACO}/util/vecout.c \ + ${CHACO}/util/vecran.c \ + ${CHACO}/util/vecscale.c +# ${CHACO}/main/user_params.c \ + +MLFILES.o= $(MLFILES.c:.c=.o) + +CHFILES.o= $(CHFILES.c:.c=.o) + +#mlchaco: ${MLFILES.o} chaco.a Makefile +# ${MATLAB}/bin/cmex CC='gcc -G' -lm ${OFLAGS} ${MLFILES.o} chaco.a; \ +# mv mlchaco.mex* ${DEST_DIR} + +#mlchaco: ${MLFILES.c} chaco.a Makefile +# mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main +# mv mlchaco.mex* ${DEST_DIR} + +#mlchaco: ${MLFILES.c} ${CHFILES.c} ${CHACO}/chaco.a Makefile +# ${MATLAB}/bin/mex mlchaco.c -largeArrayDims -DMATLAB ${MLFILES.c} ${CHACO}/chaco.a -I${CHACO}/main +# mv mlchaco.mex* ${DEST_DIR} + +Chaco: ${MLFILES.c} ${CHFILES.c} ${CHACO}/chaco.a Makefile + ${MATLAB}/bin/mex Chaco.c -largeArrayDims ${MLFILES.c} ${CHACO}/chaco.a -I${CHACO}/main +# mv Chaco.mex* ${DEST_DIR} + +chaco.a: ${CHFILES.o} + ${AR} ${CHACO}/chaco.a ${CHFILES.o} ; ${RANLIB} ${CHACO}/chaco.a + +clean: + rm -f ${CHACO}/*/*.o chaco.a ${MLCHACO}/*.o ${DEST_DIR}/core + +.c.o: + ${CC} -c ${IFLAGS} ${CFLAGS} -o $*.o $*.c + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mex/User_Params.debug =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mex/User_Params.debug (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mex/User_Params.debug (revision 18231) @@ -0,0 +1,27 @@ +% This file, User_Params, is read at runtime to modify Chaco's defaults. +% The purpose of this version is to turn on some debugging stuff that +% the Matlab version will normally have off. + +ECHO = 2 +OUTPUT_METRICS = 2 +OUTPUT_TIME = 2 +PRINT_HEADERS = 1 + +DEBUG_EVECS = 1 +DEBUG_KL = 1 +DEBUG_INERTIAL = 1 +DEBUG_CONNECTED = 1 +DEBUG_PERTURB = 1 +DEBUG_ASSIGN = 1 +DEBUG_OPTIMIZE = 1 +DEBUG_BPMATCH = 1 +DEBUG_COARSEN = 1 +DEBUG_MEMORY = 1 +DEBUG_INPUT = 0 +DEBUG_PARAMS = 1 +DEBUG_INTERNAL = 1 +DEBUG_REFINE_PART = 1 +DEBUG_REFINE_MAP = 1 +DEBUG_SIMULATOR = 1 +DEBUG_TRACE = 1 +DEBUG_MACH_PARAMS = 1 Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mex/User_Params.verbose =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mex/User_Params.verbose (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mex/User_Params.verbose (revision 18231) @@ -0,0 +1,8 @@ +% This file, User_Params, is read at runtime to modify Chaco's defaults. +% The purpose of this version is to turn on some verbose output that +% the Matlab version will normally have off. + +ECHO = 1 +OUTPUT_METRICS = 1 +OUTPUT_TIME = 1 +PRINT_HEADERS = 1 Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mex/user_params.c =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mex/user_params.c (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mex/user_params.c (revision 18231) @@ -0,0 +1,142 @@ +/* This software was developed by Bruce Hendrickson and Robert Leland * + * at Sandia National Laboratories under US Department of Energy * + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + +/* Modified by John Gilbert 25 Aug 1995 for Matlab mex-file interface */ +/* Modified by Tim Davis, July 6, 1998, for Matlab 5.1 interface, and */ +/* a more picky compiler (cc) that complains about duplicate global */ +/* declarations. */ + +#include "params.h" + +#define TRUE 1 +#define FALSE 0 + + +/* Input and ouput control parameters */ + +int CHECK_INPUT = TRUE; /* Check input for consistency? (TRUE/FALSE) */ +int ECHO = 0; /* Print input/param options? to file? (-2..2) */ +int OUTPUT_METRICS = 0; /* Controls displaying of results (-2..2) */ +int OUTPUT_TIME = 0; /* At what level to display timings (0..2) */ +int OUTPUT_ASSIGN = FALSE; /* Write assignments to file? (TRUE/FALSE) */ +int OUT_ASSIGN_INV = FALSE;/* If so, use inverse form? (TRUE/FALSE) */ +int IN_ASSIGN_INV = FALSE; /* Input file in inverse form? (TRUE/FALSE) */ +int PROMPT = FALSE; /* Prompt for input? (TRUE/FALSE) */ +int PRINT_HEADERS = FALSE; /* Print pretty output headers (TRUE/FALSE) */ + + +/* Eigenvector calculation parameters */ + +int LANCZOS_TYPE = 3; /* type of Lanczos to use */ + /* 1 => full orthog, 2 => full inverse operator */ + /* 3 => selective orthogonalization */ +double EIGEN_TOLERANCE = 1e-3; /* Numerical eigen-tolerance */ +double SRESTOL = -1.; /* Rel resid tol on T evec; autoset if <= 0 */ +int LANCZOS_SO_INTERVAL = 10; /* Itns. between SO orthog checks; set >= 2 */ +int LANCZOS_MAXITNS = -1; /* Max Lanczos its; autoset if <= 0 */ +double BISECTION_SAFETY = 10; /* Divides Lanczos bisection tol */ +int LANCZOS_CONVERGENCE_MODE = 0; /* Lanczos convergence test type: */ + /* 0=> residual, 1=> partition */ +int RQI_CONVERGENCE_MODE = 1; /* RQI convergence test type: */ + /* 0=> residual, 1=> partition */ +int LANCZOS_SO_PRECISION = 2; /* 2 => double Lanczos, 1 => float */ +int WARNING_EVECS = 2; /* Warnings in eigenvector generation (0..3) */ +double WARNING_ORTHTOL = 2; /* Warning if Ares and bjitol have this ratio */ +double WARNING_MISTOL = 100; /* Warning if Ares and bjitol have this ratio */ +int LANCZOS_TIME = FALSE; /* Detailed Lanczos times? (TRUE/FALSE) */ +int TIME_KERNELS = FALSE; /* Time numerical kernels? (TRUE/FALSE) */ + + +/* Other parameters for spectral methods */ + +int MAKE_CONNECTED = TRUE;/* Connect graph if using spectral method? */ +int PERTURB = TRUE; /* Randomly perturb matrix in spectral method? */ +int NPERTURB = 2; /* If so, how many edges to modify? */ +double PERTURB_MAX = 3.0e-3; /* Largest value for perturbation */ +int MAPPING_TYPE = 1; /* How to map from eigenvectors to partition */ + /* 0 => cut at origin, 1 => min-cost assign */ +int COARSE_NLEVEL_RQI = 2;/* # levels between RQI calls in uncoarsening */ +int OPT3D_NTRIES = 5; /* # local opts to look for global min in opt3d */ + + +/* Kernighan--Lin/Fiduccia--Mattheyses parameters */ + +int KL_METRIC = 2; /* KL interset cost: 1=>cuts, 2=>hops */ +int KL_RANDOM = TRUE; /* Use randomness in Kernighan-Lin? (TRUE/FALSE)*/ +int KL_BAD_MOVES = 20; /* Number of unhelpful moves in a row allowed */ +int KL_NTRIES_BAD = 1; /* # unhelpful passes before quitting KL */ +int KL_UNDO_LIST = TRUE; /* Only resort changed vtxs? (TRUE/FALSE) */ +double KL_IMBALANCE = 0.0; /* Fractional imbalance allowed by KL */ + + +/* Coarsening parameters */ + +double COARSEN_RATIO_MIN = .7; /* Min vtx reduction each coarsen stage */ +int COARSE_NLEVEL_KL = 2; /* # levels between KL calls in uncoarsening */ +int MATCH_TYPE = 1; /* Type of contraction matching (1..4) */ +int HEAVY_MATCH = FALSE; /* Encourage heavy match edges? (TRUE/FALSE) */ +int COARSE_KL_BOTTOM = TRUE; /* Force KL at lowest level (TRUE/FALSE) */ +int COARSEN_VWGTS = TRUE; /* Sum vtx weights in coarsening? (TRUE/FALSE) */ +int COARSEN_EWGTS = TRUE; /* Sum edge weights in coarsening? (TRUE/FALSE) */ +int KL_ONLY_BNDY = TRUE; /* Start moving vtxs on boundary? (TRUE/FALSE) */ + + +/* Parameters for post-processing options */ + +int REFINE_PARTITION = FALSE; /* Postprocess to improve cuts? */ +int INTERNAL_VERTICES = FALSE; /* ... to up internal vtxs? (TRUE/FALSE) */ +int REFINE_MAP = FALSE; /* ... to reduce hops? (TRUE/FALSE) */ + + +/* Architecture and simulator parameters */ + +int ARCHITECTURE = 0; /* 0=> hypercube, d=> d-dimensional mesh (0..3)*/ + +/* Modified by Tim Davis: remove duplicate definitions */ +#ifdef DUPLICATE_DEFINITIONS_REMOVED +int SIMULATOR = 0; /* Run simulator? In what mode? */ +int SIMULATION_ITNS = 1; /* # iterations simulator is to imitate. */ +int PERCENTAGE_OUTPUT = FALSE; /* Output in percent? (TRUE/FALSE) */ +double CUT_COST = 0.0; /* Communication cost of a cut-edge. */ +double HOP_COST = 0.0; /* Communication cost of a hop. */ +double BDY_COST = 0.0; /* Cost associated with boundary vertices. */ +double BDY_HOP_COST = 0.0; /* Cost associated with boundary hops. */ +double STARTUP_COST = 0.0; /* Communication cost of a message startup. */ + /* Note: nCUBE2 startup: 112e-6, per byte: 4.6e-6, buffering 5.6e-6 */ + /* Intel Paragon startup: 70e-6, per byte: 5.3e-8 */ +#endif + +/* Miscellaneous parameters */ + +int TERM_PROP = FALSE; /* Invoke terminal propagation? (TRUE/FALSE) */ +double CUT_TO_HOP_COST = 1; /* ..if so, relative importance of cuts/hops */ +int SEQUENCE = FALSE; /* Only do spectral ordering? (TRUE/FALSE) */ +char SEQ_FILENAME[NAME_LENGTH] = "Sequence.out"; /* If so, file name */ +long RANDOM_SEED = 7654321L; /* Seed for random number generator */ +int NSQRTS = 1000; /* # square roots to precompute if coarsening */ +int MAKE_VWGTS = FALSE; /* Make vtx weights degrees+1? (TRUE/FALSE) */ +int FREE_GRAPH = FALSE; /* Free input graph data? (TRUE/FALSE) */ +char *PARAMS_FILENAME = "User_Params"; /* File of parameter changes */ + + +/* Parameters that control debugging output */ + +int DEBUG_EVECS = 0; /* Debug flag for eigenvector generation (0..5) */ +int DEBUG_KL = 0; /* Debug flag for Kernighan-Lin (0..3) */ +int DEBUG_INERTIAL = 0; /* Debug flag for inertial method (0..1) */ +int DEBUG_CONNECTED = 0; /* Debug flag for connected components (0..1) */ +int DEBUG_PERTURB = 0; /* Debug flag for matrix perturbation (0..1) */ +int DEBUG_ASSIGN = 0; /* Debug flag for assignment to sets (0..1) */ +int DEBUG_OPTIMIZE = 0; /* Debug flag for optimization/rotation (0..2) */ +int DEBUG_BPMATCH = 0; /* Debug flag for bipartite matching code (0..2) */ +int DEBUG_COARSEN = 0; /* Debug flag for coarsening/uncoarsening (0..1) */ +int DEBUG_MEMORY = 0; /* Debug flag for smalloc/sfree (0..3) */ +int DEBUG_INPUT = 0; /* Debug flag for having read input files (0..1) */ +int DEBUG_PARAMS = 1; /* Debug flag for reading parameter file (0..2) */ +int DEBUG_INTERNAL = 0; /* Debug flag for internal vertices (0..2) */ +int DEBUG_REFINE_PART = 0;/* Debug flag for refine partition (0..1) */ +int DEBUG_REFINE_MAP = 0; /* Debug flag for refining mapping (0..1) */ +int DEBUG_SIMULATOR = 0; /* Debug flag for comm simulator (0..2) */ +int DEBUG_TRACE = 0; /* Trace main execution path (0..2) */ +int DEBUG_MACH_PARAMS = 0;/* Print computed machine params? (0..1) */ Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mlchaco_README.txt =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mlchaco_README.txt (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mlchaco_README.txt (revision 18231) @@ -0,0 +1,136 @@ +mlchaco (from meshpartdist.tar, 2/08/02) +http://www.cerfacs.fr/algor/Softs/MESHPART/ + + +[jschierm@astrid chaco]$ diff mlchaco_old.c mlchaco.c +34a35 [CLK_TCK undefined, so use CLOCKS_PER_SEC] +> #include /* CLOCKS_PER_SEC */ +56,61c57,62 [update for current Matlab] +< void mexFunction( +< int nlhs, /* number of expected outputs */ +< Matrix *plhs[], /* matrix pointer array returning outputs */ +< int nrhs, /* number of inputs */ +< Matrix *prhs[] /* matrix pointer array for inputs */ +< ) +--- +> void mexFunction( +> int nlhs, /* number of expected outputs */ +> mxArray *plhs[], /* array of pointers to output arguments +> */ +> int nrhs, /* number of inputs */ +> const mxArray *prhs[] /* array of pointers to input arguments */ +> ) +87a89 [update for current Matlab] +> mwIndex *mwstart,*mwadjacency; +104c106,110 [update for current Matlab] +< start = mxGetJc(A_in); +--- +> /* start = mxGetJc(A_in);*/ +> mwstart = mxGetJc(A_in); +> start = mxMalloc((mxGetN(A_in)+1)*sizeof(int)); +> for (i=0; i<(mxGetN(A_in)+1); i++) +> start[i]= (int)mwstart[i]; +106c112,116 [update for current Matlab] +< adjacency = mxGetIr(A_in); +--- +> /* adjacency = mxGetIr(A_in);*/ +> mwadjacency = mxGetIr(A_in); +> adjacency = mxMalloc(mxGetNzmax(A_in)*sizeof(int)); +> for (i=0; i adjacency[i]= (int)mwadjacency[i]; +131,132c141,144 [provide default filenames, since no way to input] +< outassignname = NULL; +< outfilename = NULL; +--- +> /* outassignname = NULL; +> outfilename = NULL;*/ +> outassignname = "chaco_assign.txt"; +> outfilename = "chaco_out.txt"; +169c181 [update for current Matlab] +< plhs [1] = mxCreateFull (1, 1, REAL) ; +--- +> plhs [1] = mxCreateDoubleMatrix (1, 1, mxREAL) ; +173c185 [CLK_TCK undefined, so use CLOCKS_PER_SEC] +< ((double) CLK_TCK) ; +--- +> ((double) CLOCKS_PER_SEC) ; +179c191 [update for current Matlab] +< map_out = mxCreateFull(1,nvtxs,REAL); +--- +> map_out = mxCreateDoubleMatrix(1,nvtxs,mxREAL); +185a198,199 [update for current Matlab] +> if (start != NULL) mxFree((char *) start); +> if (adjacency != NULL) mxFree((char *) adjacency); + + +[jschierm@astrid chaco]$ diff Makefile_old Makefile +27c27,28 [current Matlab location] +< MATLAB = /usr/local/libexec/matlab +--- +> #MATLAB = /usr/local/libexec/matlab +> MATLAB = /usr/local/pkgs/matlab-7.6 +30c31,32 [current Chaco 2.2 location] +< CHACO = ../../Chaco-2.0/code +--- +> #CHACO = ../../Chaco-2.0/code +> CHACO = ../../Chaco-2.2/code +34,35c36,37 [use gcc instead of cc] +< #CC = gcc +< CC = cc +--- +> CC = gcc +> #CC = cc +37c39,40 [add MATLAB flag to compile for mex-function] +< CFLAGS = -Xa -G -xO4 -xcg92 +--- +> #CFLAGS = -Xa -G -xO4 -xcg92 +> CFLAGS = -Xa -G -xO4 -xcg92 -DMATLAB +39,40c42,45 [current function locations] +< AR = /usr/ccs/bin/ar rcv # for solaris 2 +< RANLIB = /usr/ccs/bin/ranlib # for solaris 2 +--- +> #AR = /usr/ccs/bin/ar rcv # for solaris 2 +> AR = /usr/bin/ar rcv # for solaris 2 +> #RANLIB = /usr/ccs/bin/ranlib # for solaris 2 +> RANLIB = /usr/bin/ranlib # for solaris 2 +45,47d49 [use Chaco versions with MATLAB switch rather than local versions] +< ${MLCHACO}/chaco_check_graph.c \ +< ${MLCHACO}/check_input.c \ +< ${MLCHACO}/smalloc.c \ +48a51,53 +> # ${MLCHACO}/chaco_check_graph.c \ +> # ${MLCHACO}/check_input.c \ +> # ${MLCHACO}/smalloc.c \ +55a61 [update CHLIST to match Chaco 2.2] +> ${CHACO}/input/check_input.c \ +61a68 [update CHLIST to match Chaco 2.2] +> ${CHACO}/graph/check_graph.c \ +91a99 [update CHLIST to match Chaco 2.2] +> ${CHACO}/klvspiff/flow.c \ +97a106 [update CHLIST to match Chaco 2.2] +> ${CHACO}/klvspiff/flatten.c \ +100c109,110 [update CHLIST to match Chaco 2.2] +< ${CHACO}/coarsen/makecgraph.c \ +--- +> ${CHACO}/coarsen/makefgraph.c \ +> ${CHACO}/coarsen/makeccoords.c \ +102d111 [update CHLIST to match Chaco 2.2] +< ${CHACO}/coarsen/countcedges.c \ +108a118 [update CHLIST to match Chaco 2.2] +> ${CHACO}/coarsen/maxmatch5.c \ +234a245 [update CHLIST to match Chaco 2.2] +> ${CHACO}/util/smalloc.c \ +245a257,258 [use local versions rather than Chaco versions (added for clarity)] +> # ${CHACO}/main/user_params.c \ +> # ${CHACO}/util/bail.c \ +254a268,271 [update for current mex] +> #mlchaco: ${MLFILES.c} chaco.a Makefile +> # mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main +> # mv mlchaco.mex* ${DEST_DIR} +> +256c273 [update for current mex] +< mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main +--- +> mex -output mlchaco -largeArrayDims -DMATLAB ${MLFILES.c} +> chaco.a -I${CHACO}/main + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mlchaco_jes_notes.txt =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mlchaco_jes_notes.txt (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/chaco/mlchaco_jes_notes.txt (revision 18231) @@ -0,0 +1,182 @@ +7/15/09: + +[jschierm@astrid chaco]$ diff Makefile_old Makefile +27c27,28 +< MATLAB = /usr/local/libexec/matlab +--- +> #MATLAB = /usr/local/libexec/matlab +> MATLAB = /usr/local/matlab780 +30c31,32 +< CHACO = ../../Chaco-2.0/code +--- +> #CHACO = ../../Chaco-2.0/code +> CHACO = ../../Chaco-2.2/code +34,35c36,37 +< #CC = gcc +< CC = cc +--- +> CC = gcc +> #CC = cc +39,40c41,44 +< AR = /usr/ccs/bin/ar rcv # for solaris 2 +< RANLIB = /usr/ccs/bin/ranlib # for solaris 2 +--- +> #AR = /usr/ccs/bin/ar rcv # for solaris 2 +> AR = /usr/bin/ar rcv # for solaris 2 +> #RANLIB = /usr/ccs/bin/ranlib # for solaris 2 +> RANLIB = /usr/bin/ranlib # for solaris 2 +91a96,97 [missing symbols] +> ${CHACO}/klvspiff/flatten.c \ +> ${CHACO}/klvspiff/flow.c \ +99a106 [missing symbols] +> ${CHACO}/coarsen/makeccoords.c \ +102a110 [missing symbols] +> ${CHACO}/coarsen/makefgraph.c \ +108a117 [missing symbols] +> ${CHACO}/coarsen/maxmatch5.c \ +254a264,267 +> #mlchaco: ${MLFILES.c} chaco.a Makefile +> # mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main +> # mv mlchaco.mex* ${DEST_DIR} +> +256c269 +< mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main +--- +> mex -output mlchaco -largeArrayDims ${MLFILES.c} chaco.a -I${CHACO}/main + +[jschierm@astrid chaco]$ diff mlchaco_old.c mlchaco.c +34a35 +> #include /* CLOCKS_PER_SEC */ +56,61c57,62 +< void mexFunction( +< int nlhs, /* number of expected outputs */ +< Matrix *plhs[], /* matrix pointer array returning outputs */ +< int nrhs, /* number of inputs */ +< Matrix *prhs[] /* matrix pointer array for inputs */ +< ) +--- +> void mexFunction( +> int nlhs, /* number of expected outputs */ +> mxArray *plhs[], /* array of pointers to output arguments +> */ +> int nrhs, /* number of inputs */ +> const mxArray *prhs[] /* array of pointers to input arguments */ +> ) +87a89 +> mwIndex *mwstart,*mwadjacency; +104c106,110 +< start = mxGetJc(A_in); +--- +> /* start = mxGetJc(A_in);*/ +> mwstart = mxGetJc(A_in); +> start = mxMalloc((mxGetN(A_in)+1)*sizeof(int)); +> for (i=0; i<(mxGetN(A_in)+1); i++) +> start[i]= (int)mwstart[i]; +106c112,116 +< adjacency = mxGetIr(A_in); +--- +> /* adjacency = mxGetIr(A_in);*/ +> mwadjacency = mxGetIr(A_in); +> adjacency = mxMalloc(mxGetNzmax(A_in)*sizeof(int)); +> for (i=0; i adjacency[i]= (int)mwadjacency[i]; +169c181 +< plhs [1] = mxCreateFull (1, 1, REAL) ; +--- +> plhs [1] = mxCreateDoubleMatrix (1, 1, mxREAL) ; +173c185 +< ((double) CLK_TCK) ; +--- +> ((double) CLOCKS_PER_SEC) ; +179c191 +< map_out = mxCreateFull(1,nvtxs,REAL); +--- +> map_out = mxCreateDoubleMatrix(1,nvtxs,mxREAL); +185a198,199 +> if (start != NULL) mxFree((char *) start); +> if (adjacency != NULL) mxFree((char *) adjacency); + + +7/29/09: + +[jschierm@astrid chaco]$ diff mlchaco_old.c mlchaco.c +131,132c141,144 +< outassignname = NULL; +< outfilename = NULL; +--- +> /* outassignname = NULL; +> outfilename = NULL;*/ +> outassignname = "chaco_assign.txt"; +> outfilename = "chaco_out.txt"; + +7/30/09: + +[jschierm@astrid chaco]$ diff Makefile_old Makefile +27c27,28 +< MATLAB = /usr/local/libexec/matlab +--- +> #MATLAB = /usr/local/libexec/matlab +> MATLAB = /usr/local/pkgs/matlab-7.6 +37c39,40 +< CFLAGS = -Xa -G -xO4 -xcg92 +--- +> #CFLAGS = -Xa -G -xO4 -xcg92 +> CFLAGS = -Xa -G -xO4 -xcg92 -DMATLAB +45,47d49 [using Chaco versions with MATLAB switch] +< ${MLCHACO}/chaco_check_graph.c \ +< ${MLCHACO}/check_input.c \ +< ${MLCHACO}/smalloc.c \ +48a51,53 +> # ${MLCHACO}/chaco_check_graph.c \ +> # ${MLCHACO}/check_input.c \ +> # ${MLCHACO}/smalloc.c \ +55a61 +> ${CHACO}/input/check_input.c \ +61a68 +> ${CHACO}/graph/check_graph.c \ +91a99 [compared CHFILES with Chaco Makefile CHFILES] +> ${CHACO}/klvspiff/flow.c \ +97a106 [compared CHFILES with Chaco Makefile CHFILES] +> ${CHACO}/klvspiff/flatten.c \ +100c109,110 [compared CHFILES with Chaco Makefile CHFILES] +< ${CHACO}/coarsen/makecgraph.c \ +--- +> ${CHACO}/coarsen/makefgraph.c \ +> ${CHACO}/coarsen/makeccoords.c \ +102d111 [compared CHFILES with Chaco Makefile CHFILES] +< ${CHACO}/coarsen/countcedges.c \ +108a118 [compared CHFILES with Chaco Makefile CHFILES] +> ${CHACO}/coarsen/maxmatch5.c \ +234a245 +> ${CHACO}/util/smalloc.c \ +245a257,258 +> # ${CHACO}/main/user_params.c \ +> # ${CHACO}/util/bail.c \ +254a268,271 +> #mlchaco: ${MLFILES.c} chaco.a Makefile +> # mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main +> # mv mlchaco.mex* ${DEST_DIR} +> +256c273 +< mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main +--- +> mex -output mlchaco -largeArrayDims -DMATLAB ${MLFILES.c} +> chaco.a -I${CHACO}/main + +5/25/10: + +- reorganized chaco.m and mlchaco.c drivers into Chaco.c matlab-layer (independent of chaco) and Chacox.c x-layer (independent of matlab). + +5/26/10: + +- added mexchaco target to Makefile (and related changes). + +5/27/10 + +- added define for exit(status) to ${CHACO}/main/defs.h so that local bail.c is + unnecessary. + +6/15/10: + +- separated chaco x-layer from meshpart build. + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cmake/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cmake/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cmake/install.sh (revision 18231) @@ -0,0 +1,26 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install cmake-2.8.11.2 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/cmake-2.8.11.2.tar.gz' 'cmake-2.8.11.2.tar.gz' + +#Untar +tar -zxvf cmake-2.8.11.2.tar.gz + +#Move cmake into install directory +mv cmake-2.8.11.2/* install +rm -rf cmake-2.8.11.2 + +#Compile cmake +cd install +./bootstrap --prefix=$ISSM_DIR/externalpackages/cmake/install +if [ $# -eq 0 ]; then + make +else + make -j $1; +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/colpack/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/colpack/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/colpack/install.sh (revision 18231) @@ -0,0 +1,26 @@ +#!/bin/bash +set -eu + +#Erase install +rm -rf install src ColPack + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ColPack-1.0.3.tar.gz' 'ColPack-1.0.3.tar.gz' + +#install directory +mkdir src +tar -zxvf ColPack-1.0.3.tar.gz +mv ColPack/* src +rm -rf ColPack + +#compile +cd src +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +cd .. + +#install +ln -s src/build ./install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cppcheck/install-dev.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cppcheck/install-dev.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cppcheck/install-dev.sh (revision 18231) @@ -0,0 +1,18 @@ +#!/bin/bash +set -eu + +#Erase install +rm -rf install src + +#Download +git clone git://github.com/danmar/cppcheck.git src + +#compile +cd src +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install PREFIX=$ISSM_DIR/externalpackages/cppcheck/install +cd .. Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cppcheck/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cppcheck/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cppcheck/install.sh (revision 18231) @@ -0,0 +1,23 @@ +#!/bin/bash +set -eu + +#Erase install +rm -rf install src cppcheck-1.48 +mkdir src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/cppcheck-1.48.tar' 'cppcheck-1.48.tar' +tar -xvf cppcheck-1.48.tar + +mv cppcheck-1.48/* src +rm -rf cppcheck-1.48 + +#compile +cd src +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install PREFIX=$ISSM_DIR/externalpackages/cppcheck/install +cd .. Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cython/install-18.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cython/install-18.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cython/install-18.sh (revision 18231) @@ -0,0 +1,13 @@ +#!/bin/bash +set -eu + +#clean up +rm -rf Cython-0.18 + +#download numpy first +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Cython-0.18.tar.gz' 'cython.tar.gz' + +#install numpy +tar -zxvf cython.tar.gz +cd Cython-0.18 +python setup.py install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cython/install-19.2.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cython/install-19.2.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cython/install-19.2.sh (revision 18231) @@ -0,0 +1,13 @@ +#!/bin/bash +set -eu + +#clean up +rm -rf Cython-0.19.2 + +#download numpy first +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Cython-0.19.2.tar.gz' 'cython.tar.gz' + +#install numpy +tar -zxvf cython.tar.gz +cd Cython-0.19.2 +python setup.py install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cython/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cython/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/cython/install.sh (revision 18231) @@ -0,0 +1,12 @@ +#!/bin/bash +set -eu + +#clean up +rm -rf cython + +#download cython first +git clone https://github.com/cython/cython.git + +#install cython +cd cython +python setup.py install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dace/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dace/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dace/install.sh (revision 18231) @@ -0,0 +1,16 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install dace +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dace.zip' 'dace.zip' + +#uncompress +unzip dace.zip + +#move to install directory +mv dace/* install +rm -rf dace Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/4.2/LHSDriver.cpp.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/4.2/LHSDriver.cpp.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/4.2/LHSDriver.cpp.patch (revision 18231) @@ -0,0 +1,8 @@ +766c766 +< /*char output_string[32], message_string[32], title_string[32], +--- +> char output_string[32], message_string[32], title_string[32], +802c802 +< check_error(err_code, "lhs_files");*/ +--- +> check_error(err_code, "lhs_files"); Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/4.2/NIDRProblemDescDB.C.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/4.2/NIDRProblemDescDB.C.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/4.2/NIDRProblemDescDB.C.patch (revision 18231) @@ -0,0 +1,4 @@ +95a96,98 +> +> //close the input file +> fclose(nidrin); Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/4.2/NonDLocalReliability.C.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/4.2/NonDLocalReliability.C.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/4.2/NonDLocalReliability.C.patch (revision 18231) @@ -0,0 +1,7 @@ +2276a2277 +> // add sensitivity output to importance factors (jes, 8/06/10) +2280c2281,2282 +< << impFactor[i][j] << '\n'; +--- +> << impFactor[i][j] << " Sensitivity = " << setw(write_precision+7) +> << fnGradsMeanX(i, j) << '\n'; Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/4.2/NonDSampling.C.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/4.2/NonDSampling.C.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/4.2/NonDSampling.C.patch (revision 18231) @@ -0,0 +1,15 @@ +656a657,658 +> +> +659a662,663 +> +> return; //don't compute for now, too expensive. +705c709 +< //calculate simple rank correlation coeff +--- +> //calculate simple correlation coeff +710a715 +> +1071a1077,1078 +> +> return; //don't output for now. Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/4.2/NonDUnilevelRBDO.C.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/4.2/NonDUnilevelRBDO.C.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/4.2/NonDUnilevelRBDO.C.patch (revision 18231) @@ -0,0 +1,10 @@ +1052,1053c1052,1057 +< s << " Importance Factor for variable " << setw(11) +< << uv_labels[j].data() << " = " << impFactor[i][j] << '\n'; +--- +> // add sensitivity output to importance factors (jes, 8/06/10) +> s << " Importance Factor for variable " << setiosflags(ios::left) +> << setw(11) << uv_labels[j].data() << " = " +> << resetiosflags(ios::adjustfield) << setw(write_precision+7) +> << impFactor[i][j] << " Sensitivity = " << setw(write_precision+7) +> << fnGradsMeanX(i, j) << '\n'; Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/4.2/ParallelLibrary.C.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/4.2/ParallelLibrary.C.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/4.2/ParallelLibrary.C.patch (revision 18231) @@ -0,0 +1,34 @@ +134a135 +> initialized=0; //we run serially all the time! +165a167,197 +> /** This constructor is provided for the Issm software, to run serial +> * Dakota in a parallel MPI ring: */ +> ParallelLibrary::ParallelLibrary(char* serial_mode): worldRank(0), worldSize(1), +> mpirunFlag(false), ownMPIFlag(false), dryRunFlag(false), dummyFlag(false), +> stdOutputFlag(false), stdErrorFlag(false), startClock(0), +> stdOutputFilename(NULL), stdErrorFilename(NULL), readRestartFilename(NULL), +> writeRestartFilename(NULL), stopRestartEvals(0), +> currPLIter(parallelLevels.end()), currPCIter(parallelConfigurations.end()) +> { +> startClock = clock(); +> #ifdef DAKOTA_UTILIB +> utilib::exception_mngr::set_mode(utilib::exception_mngr::Abort); +> startCPUTime = CPUSeconds(); // see utilib/src/sys/seconds.cpp +> startWCTime = WallClockSeconds(); // see utilib/src/sys/seconds.cpp +> #endif // DAKOTA_UTILIB +> +> // do not initialize MPI. Get worldRank/worldSize if available +> ParallelLevel pl; +> #ifdef HAVE_MPI // mpi available, we still don't want to run in parallel for Dakota! +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota in serial mode on CPU 0, inside an MPI ring."; +> #else // mpi not available +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota in serial mode.\n"; +> #endif // HAVE_MPI +> +> parallelLevels.insert(pl); +> currPLIter = parallelLevels.begin(); +> increment_parallel_configuration(); +> } +> Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/4.2/ParallelLibrary.H.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/4.2/ParallelLibrary.H.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/4.2/ParallelLibrary.H.patch (revision 18231) @@ -0,0 +1,3 @@ +346a347,348 +> /// library mode constructor, serial mode +> ParallelLibrary(char* serial_mode); Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.2/NIDRProblemDescDB.C.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.2/NIDRProblemDescDB.C.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.2/NIDRProblemDescDB.C.patch (revision 18231) @@ -0,0 +1,5 @@ +109a110,113 +> +> //close the input file +> fclose(nidrin); +> Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.2/NonDLocalReliability.C.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.2/NonDLocalReliability.C.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.2/NonDLocalReliability.C.patch (revision 18231) @@ -0,0 +1,9 @@ +2218a2219 +> // add sensitivity output to importance factors (jes, 8/06/10) +2223c2224,2227 +< << std::setw(width) << impFactor(j,i) << '\n'; +--- +> << std::setw(width) << impFactor(j,i) +> << " Sensitivity = " +> << std::resetiosflags(std::ios::adjustfield) +> << std::setw(width) << fnGradsMeanX(j,i) << '\n'; Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.2/NonDSampling.C.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.2/NonDSampling.C.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.2/NonDSampling.C.patch (revision 18231) @@ -0,0 +1,14 @@ +438,439c438,440 +< if (!subIteratorFlag) +< nonDSampCorr.compute_correlations(vars_samples, resp_samples); +--- +> //don't compute for now, too expensive. +> // if (!subIteratorFlag) +> // nonDSampCorr.compute_correlations(vars_samples, resp_samples); +894,895c895,897 +< nonDSampCorr.print_correlations(s, cv_labels, div_labels, drv_labels, +< iteratedModel.response_labels()); +--- +> //don't output for now. +> // nonDSampCorr.print_correlations(s, cv_labels, div_labels, drv_labels, +> // iteratedModel.response_labels()); Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.2/NonDUnilevelRBDO.C.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.2/NonDUnilevelRBDO.C.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.2/NonDUnilevelRBDO.C.patch (revision 18231) @@ -0,0 +1,7 @@ +1046a1047 +> // add sensitivity output to importance factors (jes, 8/06/10) +1048c1049,1050 +< << uv_labels[j].data() << " = " << impFactor[i][j] << '\n'; +--- +> << uv_labels[j].data() << " = " << impFactor[i][j] +> << " Sensitivity = " << fnGradsMeanX(i,j) << '\n'; Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.2/ParallelLibrary.C.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.2/ParallelLibrary.C.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.2/ParallelLibrary.C.patch (revision 18231) @@ -0,0 +1,36 @@ +178a179 +> initialized=0; //we run serially all the time! +214a216,248 +> /** This constructor is provided for the Issm software, to run serial +> * Dakota in a parallel MPI ring: */ +> ParallelLibrary::ParallelLibrary(char* serial_mode): +> worldRank(0), worldSize(1), +> mpirunFlag(false), ownMPIFlag(false), dummyFlag(false), +> stdOutputToFile(false), stdErrorToFile(false), checkFlag(false), +> preRunFlag(true), runFlag(true), postRunFlag(true), userModesFlag(false), +> startClock(0), stopRestartEvals(0), +> currPLIter(parallelLevels.end()), currPCIter(parallelConfigurations.end()) +> { +> startClock = clock(); +> #ifdef DAKOTA_UTILIB +> utilib::exception_mngr::set_mode(utilib::exception_mngr::Abort); +> startCPUTime = CPUSeconds(); // see utilib/src/sys/seconds.cpp +> startWCTime = WallClockSeconds(); // see utilib/src/sys/seconds.cpp +> #endif // DAKOTA_UTILIB +> +> // do not initialize MPI. Get worldRank/worldSize if available +> ParallelLevel pl; +> #ifdef HAVE_MPI // mpi available, we still don't want to run in parallel for Dakota! +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota 5.2 MPI executable in serial mode on CPU 0 for ISSM."; +> #else // mpi not available +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota 5.2 serial executable in serial mode for ISSM.\n"; +> #endif // HAVE_MPI +> +> parallelLevels.push_back(pl); +> currPLIter = parallelLevels.begin(); +> increment_parallel_configuration(); +> } +> +> Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.2/ParallelLibrary.H.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.2/ParallelLibrary.H.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.2/ParallelLibrary.H.patch (revision 18231) @@ -0,0 +1,3 @@ +358a359,360 +> /// library mode constructor, serial mode (for the Issm software) +> ParallelLibrary(char* serial_mode); Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.2/Teuchos_ConfigDefs.hpp.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.2/Teuchos_ConfigDefs.hpp.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.2/Teuchos_ConfigDefs.hpp.patch (revision 18231) @@ -0,0 +1,2 @@ +87a88 +> #include Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.2/pecos_global_defs.hpp.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.2/pecos_global_defs.hpp.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.2/pecos_global_defs.hpp.patch (revision 18231) @@ -0,0 +1,4 @@ +24a25 +> #ifndef PI +25a27 +> #endif Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.patch (revision 18231) @@ -0,0 +1,26 @@ +64,65c64,65 +< #set( DAKOTA_HAVE MPI ON +< # CACHE BOOL "Build with MPI enabled" FORCE) +--- +> set( DAKOTA_HAVE MPI OFF +> CACHE BOOL "Build with MPI disabled" FORCE) +73,77c73,77 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "$ENV{ISSM_DIR}/externalpackages/boost/install" +> CACHE PATH "Use non-standard Boost install" FORCE) +> set( Boost_NO_SYSTEM_PATHS TRUE +> CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3.1/DakotaDev.cmake.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3.1/DakotaDev.cmake.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3.1/DakotaDev.cmake.patch (revision 18231) @@ -0,0 +1,16 @@ +4,8c4,8 +< set(DAKOTA_HAVE_MPI TRUE CACHE BOOL "Enable MPI in DAKOTA?") +< set(ENABLE_DAKOTA_DOCS TRUE CACHE BOOL "Enable DAKOTA documentation build") +< set(ENABLE_SPEC_MAINT TRUE CACHE BOOL +< "Enable DAKOTA specification maintenance mode?") +< set(PECOS_ENABLE_TESTS TRUE CACHE BOOL "Enable Pecos-specific tests?") +--- +> #set(DAKOTA_HAVE_MPI TRUE CACHE BOOL "Enable MPI in DAKOTA?") +> #set(ENABLE_DAKOTA_DOCS TRUE CACHE BOOL "Enable DAKOTA documentation build") +> #set(ENABLE_SPEC_MAINT TRUE CACHE BOOL +> # "Enable DAKOTA specification maintenance mode?") +> #set(PECOS_ENABLE_TESTS TRUE CACHE BOOL "Enable Pecos-specific tests?") +14c14 +< #set(HAVE_X_GRAPHICS OFF CACHE BOOL "Disable dependency on X libraries" FORCE) +--- +> set(HAVE_X_GRAPHICS OFF CACHE BOOL "Disable dependency on X libraries" FORCE) Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3.1/NonDLocalReliability.cpp.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3.1/NonDLocalReliability.cpp.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3.1/NonDLocalReliability.cpp.patch (revision 18231) @@ -0,0 +1,9 @@ +2587a2588 +> // add sensitivity output to importance factors (jes, 8/06/10) +2592c2593,2596 +< << std::setw(width) << impFactor(j,i) << '\n'; +--- +> << std::setw(width) << impFactor(j,i) +> << " Sensitivity = " +> << std::resetiosflags(std::ios::adjustfield) +> << std::setw(width) << fnGradsMeanX(j,i) << '\n'; Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3.1/NonDSampling.cpp.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3.1/NonDSampling.cpp.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3.1/NonDSampling.cpp.patch (revision 18231) @@ -0,0 +1,25 @@ +703,709c703,710 +< if (!subIteratorFlag) { +< nonDSampCorr.compute_correlations(vars_samples, resp_samples); +< // archive the correlations to the results DB +< nonDSampCorr.archive_correlations(run_identifier(), resultsDB, +< cv_labels, div_labels, drv_labels, +< iteratedModel.response_labels()); +< } +--- +> //don't compute for now, too expensive. +> // if (!subIteratorFlag) { +> // nonDSampCorr.compute_correlations(vars_samples, resp_samples); +> // // archive the correlations to the results DB +> // nonDSampCorr.archive_correlations(run_identifier(), resultsDB, +> // cv_labels, div_labels, drv_labels, +> // iteratedModel.response_labels()); +> // } +1196,1197c1197,1200 +< nonDSampCorr.print_correlations(s, cv_labels, div_labels, drv_labels, +< iteratedModel.response_labels()); +--- +> +> //don't output for now. +> // nonDSampCorr.print_correlations(s, cv_labels, div_labels, drv_labels, +> // iteratedModel.response_labels()); Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3.1/ParallelLibrary.cpp.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3.1/ParallelLibrary.cpp.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3.1/ParallelLibrary.cpp.patch (revision 18231) @@ -0,0 +1,35 @@ +107a108 +> initialized=0; //we run serially all the time! +133a135 +> initialized=0; //we run serially all the time! +141a144,171 +> /** This constructor is provided for the ISSM software, to run serial +> * Dakota in a parallel MPI ring: */ +> ParallelLibrary::ParallelLibrary(char* serial_mode): +> dakotaMPIComm(MPI_COMM_WORLD), worldRank(0), worldSize(1), +> mpirunFlag(false), ownMPIFlag(false), dummyFlag(false), +> stdOutputToFile(false), stdErrorToFile(false), checkFlag(false), +> preRunFlag(true), runFlag(true), postRunFlag(true), userModesFlag(false), +> outputTimings(true), startClock(0), stopRestartEvals(0), +> currPLIter(parallelLevels.end()), currPCIter(parallelConfigurations.end()) +> { +> initialize_timers(); +> +> // do not initialize MPI. Get worldRank/worldSize if available +> ParallelLevel pl; +> #ifdef HAVE_MPI // mpi available, we still don't want to run in parallel for Dakota! +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota 5.3.1 MPI executable in serial mode on CPU 0 for ISSM." << std::endl; +> #else // mpi not available +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota 5.3.1 serial executable in serial mode for ISSM." << std::endl; +> #endif // HAVE_MPI +> +> parallelLevels.push_back(pl); +> currPLIter = parallelLevels.begin(); +> increment_parallel_configuration(); +> } +> +> +1536a1567 +> initialized=0; //we run serially all the time! Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3.1/ParallelLibrary.hpp.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3.1/ParallelLibrary.hpp.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3.1/ParallelLibrary.hpp.patch (revision 18231) @@ -0,0 +1,3 @@ +358a359,360 +> /// library mode constructor, serial mode (for the ISSM software) +> ParallelLibrary(char* serial_mode); Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3.1/pecos_global_defs.hpp.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3.1/pecos_global_defs.hpp.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3.1/pecos_global_defs.hpp.patch (revision 18231) @@ -0,0 +1,4 @@ +25a26 +> #ifndef PI +26a28 +> #endif Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3/BuildDakotaCustom.cmake.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3/BuildDakotaCustom.cmake.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3/BuildDakotaCustom.cmake.patch (revision 18231) @@ -0,0 +1,40 @@ +41,46c41,46 +< #set( BLAS_LIBS +< # "/usr/lib64" +< # CACHE FILEPATH "Use non-standard BLAS library path" FORCE ) +< #set( LAPACK_LIBS +< # "/usr/lib64" +< # CACHE FILEPATH "Use non-standard BLAS library path" FORCE ) +--- +> set( BLAS_LIBS +> "/usr/lib64/libblas.so.3.0.3" +> CACHE FILEPATH "Use non-standard BLAS library path" FORCE ) +> set( LAPACK_LIBS +> "/usr/lib64/liblapack.so.3.0.3" +> CACHE FILEPATH "Use non-standard BLAS library path" FORCE ) +64,65c64,65 +< #set( DAKOTA_HAVE MPI ON +< # CACHE BOOL "Build with MPI enabled" FORCE) +--- +> set( DAKOTA_HAVE MPI OFF +> CACHE BOOL "Build with MPI disabled" FORCE) +73,77c73,77 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "$ENV{ISSM_DIR}/externalpackages/boost/install" +> CACHE PATH "Use non-standard Boost install" FORCE) +> set( Boost_NO_SYSTEM_PATHS TRUE +> CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3/DakotaDev.cmake.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3/DakotaDev.cmake.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3/DakotaDev.cmake.patch (revision 18231) @@ -0,0 +1,14 @@ +4,7c4,7 +< set(DAKOTA_HAVE_MPI TRUE CACHE BOOL "Enable MPI in DAKOTA?") +< set(ENABLE_DAKOTA_DOCS TRUE CACHE BOOL "Enable DAKOTA documentation build") +< set(ENABLE_SPEC_MAINT TRUE CACHE BOOL +< "Enable DAKOTA specification maintenance mode?") +--- +> #set(DAKOTA_HAVE_MPI TRUE CACHE BOOL "Enable MPI in DAKOTA?") +> #set(ENABLE_DAKOTA_DOCS TRUE CACHE BOOL "Enable DAKOTA documentation build") +> #set(ENABLE_SPEC_MAINT TRUE CACHE BOOL +> # "Enable DAKOTA specification maintenance mode?") +13c13 +< #set(HAVE_X_GRAPHICS OFF CACHE BOOL "Disable dependency on X libraries" FORCE) +--- +> set(HAVE_X_GRAPHICS OFF CACHE BOOL "Disable dependency on X libraries" FORCE) Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3/NonDLocalReliability.cpp.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3/NonDLocalReliability.cpp.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3/NonDLocalReliability.cpp.patch (revision 18231) @@ -0,0 +1,9 @@ +2579a2580 +> // add sensitivity output to importance factors (jes, 8/06/10) +2584c2585,2588 +< << std::setw(width) << impFactor(j,i) << '\n'; +--- +> << std::setw(width) << impFactor(j,i) +> << " Sensitivity = " +> << std::resetiosflags(std::ios::adjustfield) +> << std::setw(width) << fnGradsMeanX(j,i) << '\n'; Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3/NonDSampling.cpp.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3/NonDSampling.cpp.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3/NonDSampling.cpp.patch (revision 18231) @@ -0,0 +1,25 @@ +703,709c703,710 +< if (!subIteratorFlag) { +< nonDSampCorr.compute_correlations(vars_samples, resp_samples); +< // archive the correlations to the results DB +< nonDSampCorr.archive_correlations(run_identifier(), resultsDB, +< cv_labels, div_labels, drv_labels, +< iteratedModel.response_labels()); +< } +--- +> //don't compute for now, too expensive. +> // if (!subIteratorFlag) { +> // nonDSampCorr.compute_correlations(vars_samples, resp_samples); +> // // archive the correlations to the results DB +> // nonDSampCorr.archive_correlations(run_identifier(), resultsDB, +> // cv_labels, div_labels, drv_labels, +> // iteratedModel.response_labels()); +> // } +1196,1197c1197,1200 +< nonDSampCorr.print_correlations(s, cv_labels, div_labels, drv_labels, +< iteratedModel.response_labels()); +--- +> +> //don't output for now. +> // nonDSampCorr.print_correlations(s, cv_labels, div_labels, drv_labels, +> // iteratedModel.response_labels()); Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3/ParallelLibrary.cpp.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3/ParallelLibrary.cpp.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3/ParallelLibrary.cpp.patch (revision 18231) @@ -0,0 +1,40 @@ +103a104 +> initialized=0; //we run serially all the time! +129a131 +> initialized=0; //we run serially all the time! +137a140,172 +> /** This constructor is provided for the ISSM software, to run serial +> * Dakota in a parallel MPI ring: */ +> ParallelLibrary::ParallelLibrary(char* serial_mode): +> worldRank(0), worldSize(1), +> mpirunFlag(false), ownMPIFlag(false), dummyFlag(false), +> stdOutputToFile(false), stdErrorToFile(false), checkFlag(false), +> preRunFlag(true), runFlag(true), postRunFlag(true), userModesFlag(false), +> startClock(0), stopRestartEvals(0), +> currPLIter(parallelLevels.end()), currPCIter(parallelConfigurations.end()) +> { +> startClock = clock(); +> #ifdef DAKOTA_UTILIB +> utilib::exception_mngr::set_mode(utilib::exception_mngr::Abort); +> startCPUTime = CPUSeconds(); // see utilib/src/sys/seconds.cpp +> startWCTime = WallClockSeconds(); // see utilib/src/sys/seconds.cpp +> #endif // DAKOTA_UTILIB +> +> // do not initialize MPI. Get worldRank/worldSize if available +> ParallelLevel pl; +> #ifdef HAVE_MPI // mpi available, we still don't want to run in parallel for Dakota! +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota 5.3 MPI executable in serial mode on CPU 0 for ISSM."; +> #else // mpi not available +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota 5.3 serial executable in serial mode for ISSM.\n"; +> #endif // HAVE_MPI +> +> parallelLevels.push_back(pl); +> currPLIter = parallelLevels.begin(); +> increment_parallel_configuration(); +> } +> +> +1517a1553 +> initialized=0; //we run serially all the time! Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3/ParallelLibrary.hpp.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3/ParallelLibrary.hpp.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3/ParallelLibrary.hpp.patch (revision 18231) @@ -0,0 +1,3 @@ +358a359,360 +> /// library mode constructor, serial mode (for the ISSM software) +> ParallelLibrary(char* serial_mode); Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3/pecos_global_defs.hpp.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3/pecos_global_defs.hpp.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3/pecos_global_defs.hpp.patch (revision 18231) @@ -0,0 +1,4 @@ +25a26 +> #ifndef PI +26a28 +> #endif Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3/utilibExpat_patch.txt =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3/utilibExpat_patch.txt (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/configs/5.3/utilibExpat_patch.txt (revision 18231) @@ -0,0 +1,58 @@ +Index: CMakeLists.txt +=================================================================== +--- CMakeLists.txt (revision 1968) ++++ CMakeLists.txt (working copy) +@@ -30,6 +30,17 @@ + if(UTILIB_YES_MEMDEBUG) + add_definitions(-DUTILIB_YES_MEMDEBUG=1) + endif() ++option(UTILIB_HAVE_EXPAT "Enable expat in utilib" OFF) ++if (UTILIB_HAVE_EXPAT) ++ find_package(EXPAT) ++ if (EXPAT_FOUND) ++ # Use the same definition as autotools build ++ add_definitions("-DUTILIB_HAVE_EXPAT_H") ++ # TODO: add include path (EXPAT_INCLUDE_DIRS) in relevant subdirs? ++ else() ++ message(WARNING "expat requested, but not found") ++ endif() ++endif() + + #inspect the system so that we can generate utilib_config.h + include(CheckFunctionExists) +@@ -47,7 +58,6 @@ + CHECK_INCLUDE_FILES("windows.h;dbghelp.h" UTILIB_HAVE_DBGHELP_H) + CHECK_INCLUDE_FILE(err.h UTILIB_HAVE_ERR_H) + CHECK_INCLUDE_FILE(execinfo.h UTILIB_HAVE_EXECINFO_H) +-CHECK_INCLUDE_FILE(expat.h UTILIB_HAVE_EXPAT_H) + CHECK_INCLUDE_FILE(float.h UTILIB_HAVE_FLOAT_H) + CHECK_INCLUDE_FILE(limits.h UTILIB_HAVE_LIMITS_H) + CHECK_INCLUDE_FILE(strings.h UTILIB_HAVE_STRINGS_H) +@@ -57,9 +67,7 @@ + CHECK_INCLUDE_FILE(values.h UTILIB_HAVE_VALUES_H) + CHECK_INCLUDE_FILE(windows.h UTILIB_HAVE_WINDOWS_H) + +-find_library(EXPAT_LIB expat) + +- + # Use common HAVE_BOOST to indicate usage of Boost across packages + # Ultimately need to #define UTILIB_HAVE_BOOST if used + set(HAVE_BOOST OFF CACHE BOOL "Should Utilib use BOOST?") + + +Index: CMakeLists.txt +=================================================================== +--- src/libs/CMakeLists.txt 2013/03/25 19:19:06 1970 ++++ src/libs/CMakeLists.txt 2013/03/25 19:51:47 1971 +@@ -77,8 +77,9 @@ + list(APPEND libs ${MPI_LIBRARY}) + endif() + +-if(UTILIB_HAVE_EXPAT_H AND EXPAT_LIB) +- list(APPEND libs ${EXPAT_LIB}) ++if(UTILIB_HAVE_EXPAT AND EXPAT_FOUND) ++ include_directories(${EXPAT_INCLUDE_DIRS}) ++ list(APPEND libs ${EXPAT_LIBRARIES}) + endif() + if(MSVC) + list(APPEND libs dbghelp) Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-4.2-altix64-cosmos.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-4.2-altix64-cosmos.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-4.2-altix64-cosmos.sh (revision 18231) @@ -0,0 +1,97 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/4.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/4.2/ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C configs/4.2/NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C configs/4.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/4.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/4.2/NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp configs/4.2/LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-blas=/opt/intel/mkl/9.1.023/lib/64/libmkl.so \ + --with-lapack=/opt/intel/mkl/9.1.023/lib/64/libmkl_lapack.so +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-4.2-discover.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-4.2-discover.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-4.2-discover.sh (revision 18231) @@ -0,0 +1,97 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/4.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/4.2/ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C configs/4.2/NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C configs/4.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/4.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/4.2/NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp configs/4.2/LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ +--prefix="$ISSM_DIR/externalpackages/dakota/install/" \ +--without-graphics \ +--with-pic \ +--disable-mpi \ +--with-blas="-L/usr/local/intel/mkl/10.1.2.024/lib/64 -lmkl_lapack -lmkl -lguide -lpthread" \ +--with-lapack="-L/usr/local/intel/mkl/10.1.2.024/lib/64 -lmkl_lapack -lmkl -lguide -lpthread" +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-4.2-linux64-cloud.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-4.2-linux64-cloud.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-4.2-linux64-cloud.sh (revision 18231) @@ -0,0 +1,97 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/4.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/4.2/ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C configs/4.2/NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C configs/4.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/4.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/4.2/NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp configs/4.2/LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-blas=/usr/lib/libblas.so \ + --with-lapack=/usr/lib/liblapack.so +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-4.2-linux64-murdo.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-4.2-linux64-murdo.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-4.2-linux64-murdo.sh (revision 18231) @@ -0,0 +1,97 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/4.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/4.2/ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C configs/4.2/NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C configs/4.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/4.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/4.2/NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp configs/4.2/LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-blas=/usr/lib64/libblas.so.3.1.1 \ + --with-lapack=/usr/lib64/liblapack.so.3.1.1 +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-4.2-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-4.2-macosx64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-4.2-macosx64.sh (revision 18231) @@ -0,0 +1,97 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/4.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/4.2/ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C configs/4.2/NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C configs/4.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/4.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/4.2/NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp configs/4.2/LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-blas="-L$ISSM_DIR/externalpackages/petsc/install/lib -lfblas " \ + --with-lapack="-L$ISSM_DIR/externalpackages/petsc/install/lib -lflapack " +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2 -D_NONSTD_SOURCE/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-4.2-pleiades-petsc3.3.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-4.2-pleiades-petsc3.3.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-4.2-pleiades-petsc3.3.sh (revision 18231) @@ -0,0 +1,103 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/4.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/4.2/ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C configs/4.2/NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C configs/4.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/4.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/4.2/NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp configs/4.2/LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ +--prefix="$ISSM_DIR/externalpackages/dakota/install/" \ +--without-graphics \ +--with-pic \ +--disable-mpi \ +--with-blas="-L$ISSM_DIR/externalpackages/petsc/install/lib -lfblas " \ +--with-lapack="-L$ISSM_DIR/externalpackages/petsc/install/lib -lflapack " + +#--with-blas="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" \ +#--with-lapack="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" +#--with-blas="-L/nasa/intel/Compiler/11.1/046/mkl/lib/em64t/ -lmkl_intel_lp64 -lmkl_lapack" \ +#--with-lapack="-L/nasa/intel/Compiler/11.1/046/mkl/lib/em64t/ -lmkl_intel_lp64 -lmkl_lapack" + +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-4.2-pleiades.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-4.2-pleiades.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-4.2-pleiades.sh (revision 18231) @@ -0,0 +1,97 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz' + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/4.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/4.2/ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C configs/4.2/NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C configs/4.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/4.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/4.2/NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp configs/4.2/LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ +--prefix="$ISSM_DIR/externalpackages/dakota/install/" \ +--without-graphics \ +--with-pic \ +--disable-mpi \ +--with-blas="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" \ +--with-lapack="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-5.2-discover.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-5.2-discover.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-5.2-discover.sh (revision 18231) @@ -0,0 +1,52 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_5_2.src.tar.gz' 'Dakota_5_2.src.tar.gz' + +#Untar +tar -zxvf Dakota_5_2.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/5.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/5.2/ParallelLibrary.H.patch +#patch src/src/NIDRProblemDescDB.C configs/5.2/NIDRProblemDescDB.C.patch # causes segfault in 5.2 +patch src/src/NonDSampling.C configs/5.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/5.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/5.2/NonDUnilevelRBDO.C.patch # source not even used? +patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.2/pecos_global_defs.hpp.patch + +#Configure dakota +cd src +./configure \ +--prefix="$ISSM_DIR/externalpackages/dakota/install/" \ +--without-graphics \ +--with-pic \ +--disable-mpi \ +--with-plugin \ +--with-blas="-L/usr/local/intel/mkl/10.1.2.024/lib/64 -lmkl_lapack -lmkl -lguide -lpthread" \ +--with-lapack="-L/usr/local/intel/mkl/10.1.2.024/lib/64 -lmkl_lapack -lmkl -lguide -lpthread" + +cd .. + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-5.2-linux64-larsen.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-5.2-linux64-larsen.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-5.2-linux64-larsen.sh (revision 18231) @@ -0,0 +1,49 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_5_2.src.tar.gz' 'Dakota_5_2.src.tar.gz' + +#Untar +tar -zxvf Dakota_5_2.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/5.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/5.2/ParallelLibrary.H.patch +patch src/src/NonDSampling.C configs/5.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/5.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/5.2/NonDUnilevelRBDO.C.patch # source not even used? +patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.2/pecos_global_defs.hpp.patch +patch src/packages/teuchos/src/Teuchos_ConfigDefs.hpp configs/5.2/Teuchos_ConfigDefs.hpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-plugin \ + --with-blas="$ISSM_DIR/externalpackages/petsc/install/lib/libfblas.a" \ + --with-lapack="$ISSM_DIR/externalpackages/petsc/install/lib/libflapack.a" + +#Compile and install dakota +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-5.2-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-5.2-macosx64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-5.2-macosx64.sh (revision 18231) @@ -0,0 +1,51 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_5_2.src.tar.gz' 'Dakota_5_2.src.tar.gz' + +#Untar +tar -zxvf Dakota_5_2.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/5.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/5.2/ParallelLibrary.H.patch +#patch src/src/NIDRProblemDescDB.C configs/5.2/NIDRProblemDescDB.C.patch # causes segfault in 5.2 +patch src/src/NonDSampling.C configs/5.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/5.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/5.2/NonDUnilevelRBDO.C.patch # source not even used? +patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.2/pecos_global_defs.hpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-plugin \ + --with-blas="-L$ISSM_DIR/externalpackages/petsc/install/lib -lfblas " \ + --with-lapack="-L$ISSM_DIR/externalpackages/petsc/install/lib -lflapack " +cd .. + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-5.2-pleiades-petsc3.3.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-5.2-pleiades-petsc3.3.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-5.2-pleiades-petsc3.3.sh (revision 18231) @@ -0,0 +1,59 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_5_2.src.tar.gz' 'Dakota_5_2.src.tar.gz' + +#Untar +tar -zxvf Dakota_5_2.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C configs/5.2/ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H configs/5.2/ParallelLibrary.H.patch +#patch src/src/NIDRProblemDescDB.C configs/5.2/NIDRProblemDescDB.C.patch # causes segfault in 5.2 +patch src/src/NonDSampling.C configs/5.2/NonDSampling.C.patch +patch src/src/NonDLocalReliability.C configs/5.2/NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C configs/5.2/NonDUnilevelRBDO.C.patch # source not even used? +patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.2/pecos_global_defs.hpp.patch + +#Configure dakota +cd src +./configure \ +--prefix="$ISSM_DIR/externalpackages/dakota/install/" \ +--without-graphics \ +--with-pic \ +--disable-mpi \ +--with-plugin \ +--with-blas="-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread" \ +--with-lapack="-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread" + +#--with-blas=/nasa/intel/Compiler/2012.0.032/mkl/lib/intel64/libmkl_intel_lp64.a \ +#--with-lapack=/nasa/intel/Compiler/2012.0.032/mkl/lib/intel64/libmkl_intel_lp64.a +#--with-blas="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" \ +#--with-lapack="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" +#--with-blas="-L/nasa/intel/Compiler/11.1/046/mkl/lib/em64t/ -lmkl_intel_lp64 -lmkl_lapack" \ +#--with-lapack="-L/nasa/intel/Compiler/11.1/046/mkl/lib/em64t/ -lmkl_intel_lp64 -lmkl_lapack" + +cd .. + +#Compile and install dakota +cd src +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-5.3.1-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-5.3.1-linux64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-5.3.1-linux64.sh (revision 18231) @@ -0,0 +1,50 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-5.3.1-public-src.tar.gz' 'dakota-5.3.1-public-src.tar.gz' + +#Untar +tar -zxvf dakota-5.3.1-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-5.3.1.src/* src +rm -rf dakota-5.3.1.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/5.3.1/BuildDakotaCustom.cmake.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/5.3.1/DakotaDev.cmake.patch + +#Apply patches +patch src/src/ParallelLibrary.cpp configs/5.3.1/ParallelLibrary.cpp.patch +patch src/src/ParallelLibrary.hpp configs/5.3.1/ParallelLibrary.hpp.patch +patch src/src/NonDSampling.cpp configs/5.3.1/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/5.3.1/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.3.1/pecos_global_defs.hpp.patch + +#Configure dakota +cd $DAK_BUILD +cmake -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC +cd .. + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-5.3.1-macosx64_mavericks.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-5.3.1-macosx64_mavericks.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dakota/install-5.3.1-macosx64_mavericks.sh (revision 18231) @@ -0,0 +1,50 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-5.3.1-public-src.tar.gz' 'dakota-5.3.1-public-src.tar.gz' + +#Untar +tar -zxvf dakota-5.3.1-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-5.3.1.src/* src +rm -rf dakota-5.3.1.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/5.3.1/BuildDakotaCustom.cmake.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/5.3.1/DakotaDev.cmake.patch + +#Apply patches +patch src/src/ParallelLibrary.cpp configs/5.3.1/ParallelLibrary.cpp.patch +patch src/src/ParallelLibrary.hpp configs/5.3.1/ParallelLibrary.hpp.patch +patch src/src/NonDSampling.cpp configs/5.3.1/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/5.3.1/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.3.1/pecos_global_defs.hpp.patch + +#Configure dakota +cd $DAK_BUILD +cmake -D CMAKE_C_COMPILER=/usr/local/gfortran/bin/gcc -D CMAKE_CXX_COMPILER=/usr/local/gfortran/bin/g++ -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC +cd .. + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dem/dem.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dem/dem.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dem/dem.m (revision 18231) @@ -0,0 +1,530 @@ +function [h,I]=dem(x,y,z,varargin) +%DEM Shaded relief image plot +% DEM(X,Y,Z) plots the Digital Elevation Model defined by X and Y +% coordinate vectors and elevation matrix Z, as a lighted image using +% specific "landcolor" and "seacolor" colormaps. DEM uses IMAGESC +% function which is much faster than SURFL when dealing with large +% high-resolution DEM. +% +% DEM(X,Y,Z,OPT) specifies options with OPT = [A,C,SCUT,ZMIN,ZMAX,ZCUT], +% where sorted optional scalars are: +% A = azimuth light (in degrees relative to North). Default is A = -45 +% for a natural northwestern illumination. +% C = controls contrast, as the exponent of the gradient value. Default +% is C = 1 for linear contrast; use C = 0 to remove lighting, +% C = 0.5 for moderate lighting, C = 2 or more for strong contrast. +% SCUT = controls lighting scale saturation with a median-style filter +% in % of elements. Default is SCUT = 0.2 (0.2% maximum gradient +% values is ignored). Use SCUT = 0 for full scale gradient. +% ZMIN,ZMAX = fixes min and max elevation values for colormap. Use NaN +% to keep real min and/or max data values. +% ZCUT = median-style filter to cut extremes values (in % of elements). +% Default is ZCUT = 0.5 to ignore the 0.5% of most min/max +% elevation values. Use ZCUT = 0 for full scale. +% Use OPT=[] to keep default values and define following arguments. +% +% DEM(...,CMAP) uses CMAP colormap instead of default (landcolor, if +% exists or jet). Note that defining CMAP disables the default SEACOLOR +% colormap attribution for Z<=0 elevations. +% +% DEM(...,NOVALUE) defines the values that will be replaced by NaN. This +% might be mandatory for DEM that use a value like -99999 or -32768 if +% you don't want a flat image... +% +% DEM(...,SEACOLOR) sets the colormap used for zero and negative values. +% Default is seacolor (if exists) or single color [0.7,0.9,1] (a light +% cyan) to simulate sea color. Use [] to apply colormap CMAP on the full +% elevation scale. +% +% DEM(...,'interp') interpolates linearly NaN values (fills the gaps). +% +% DEM(...,'lake') detects automaticaly flat areas different from sea +% level (non-zero elevations) and draws them as lake surfaces. +% +% DEM(...,'dec') plots classic basemap-style axis, considering +% coordinates as cartesian (decimal). +% +% DEM(...,'dms') plots geographic basemap-style axis in deg/min/sec, +% considering coordinates X as longitude and Y as latitude. Axis aspect +% ratio will be adjusted to approximatively preserve distances (this is +% not a real projection!). +% +% DEM(...,'scale') adds a legend to the right of graph, with elevation +% scale (colormap) and a distance scale if 'dms' option is used. +% +% [H,I]=DEM(...) returns graphic handle H and illuminated image as I, an +% MxNx3 matrix (if Z is MxN). +% +% Informations: +% - For optimization purpose, DEM will automatically decimate data to +% limit to a total of 1500x1500 pixels images. To avoid it, use option +% DEM(...,'nodecim') or DEM(...,'decim',N) where N is an integer, but +% be aware that large grids may require computer ressources and induce +% disk swap or memory errors. +% - Colormaps are Mx3 RGB matrix so it is easy to modify saturation +% (CMAP.^N), set darker (CMAP/N), lighter ((N - 1 + CMAP)/N), inverse +% it (flipud(CMAP)), etc... +% - To get free worldwide topographic data (SRTM), see READHGT function. +% +% Author: François Beauducel +% Created: 2007-05-17 +% Updated: 2013-01-05 + +% Copyright (c) 2013, François Beauducel, covered by BSD License. +% All rights reserved. +% +% Redistribution and use in source and binary forms, with or without +% modification, are permitted provided that the following conditions are +% met: +% +% * Redistributions of source code must retain the above copyright +% notice, this list of conditions and the following disclaimer. +% * Redistributions in binary form must reproduce the above copyright +% notice, this list of conditions and the following disclaimer in +% the documentation and/or other materials provided with the distribution +% +% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +% ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE +% LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +% CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +% SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +% CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +% ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +% POSSIBILITY OF SUCH DAMAGE. + +if nargin < 3 + error('Not enough input arguments.'); +end + +% default OPT arguments +a = -45; +c = 1; +scut = 0.2; +zmin = NaN; +zmax = NaN; +zcut = 0.5; +grey = 0.2*[1,1,1]; +csea = []; +fs = 10; % tick label fontsize + +dec = 0; +dms = 0; +scale = 0; +inter = 0; +lake = 0; +decimflag = 0; +decim = 0; + +novalue_color = [0,0,0]; + +if ~isnumeric(x) | ~isnumeric(y) | ~isnumeric(z) + error('X,Y and Z must be numeric.') +end + +if all(size(x) ~= 1) | all(size(y) ~= 1) + error('X and Y must be vectors, not matrix.') +end + +if length(x) ~= size(z,2) | length(y) ~= size(z,1) + error('If Z has a size of [M,N], X must have a length of N, and Y a length of M.') +end + +if nargin > 3 + dec = any(strcmp(varargin,'dec')); + dms = any(strcmp(varargin,'dms')); + if dms & any(abs(y) > 91) + error('With DMS option Y must be in valid latitudes interval (decimal degrees).') + end + scale = any(strcmp(varargin,'scale')); + inter = any(strcmp(varargin,'interp')); + lake = any(strcmp(varargin,'lake')); + if any(strcmp(varargin,'nodecim')) + decim = 1; + decimflag = 1; + end + kdecim = find(strcmp(varargin,'decim')); + if ~isempty(kdecim) + decimflag = 1; + if (kdecim + 1) <= nargin & isnumeric(varargin{kdecim+1}) + decim = round(varargin{kdecim+1}); + decimflag = 2; + end + end +end +nargs = decimflag + dec + dms + scale + lake + inter; + +if (nargin - nargs) > 3 + opt = varargin{1}; + if ~isnumeric(opt) + error('OPT = [A,C,S,ZMIN,ZMAX] argument must be numeric.'); + end + if ~isempty(opt) + a = opt(1); + end + if length(opt) > 1 + c = opt(2); + if c < 0 + error('C argument must be positive.'); + end + end + if length(opt) > 2 + scut = opt(3); + if scut < 0 | scut >= 100 + error('SCUT argument must be a positive percentage.'); + end + end + if length(opt) > 4 + zmin = opt(4); + zmax = opt(5); + end + if length(opt) > 5 + zcut = opt(6); + if zcut < 0 | zcut >= 100 + error('ZCUT argument must be a positive percentage.'); + end + end +end + +if (nargin - nargs) < 5 + cmap = []; +else + cmap = varargin{2}; + if ~isnumeric(cmap) | (~isempty(cmap) & (size(cmap,2) ~= 3 | min(cmap(:)) < 0 | max(cmap(:)) > 1)) + error('CMAP must be a valid colormap (3-column [R,G,B] matrix with 0.0 to 1.0 values).') + end +end + +if (nargin - nargs) < 6 + novalue = NaN; +else + novalue = varargin{3}; + if ~isnumeric(novalue) | numel(novalue) > 1 + error('NOVALUE must be scalar.') + end +end + +if (nargin - nargs) < 7 + if isempty(cmap) + if exist('seacolor','file') + csea = seacolor(256); + else + csea = [.7,.9,1]; + end + end +else + csea = varargin{4}; + if ~isnumeric(csea) + error('Unknown option') + elseif (~isempty(csea) & (size(csea,2) ~= 3 | min(csea) < 0 | max(csea) > 1)) + error('SEACOLOR must be a valid [R,G,B] vector with 0.0 to 1.0 values).') + end +end + +if isempty(cmap) + if exist('landcolor','file') + cmap = landcolor.^1.3; + else + cmap = jet(256); + end +end + + + +% decimates data to avoid disk swap/out of memory... +nmax = 1500; +if decim + n = decim; +else + n = ceil(sqrt(numel(z))/nmax); +end +if n > 1 + x = x(1:n:end); + y = y(1:n:end); + z = z(1:n:end,1:n:end); + fprintf('DEM: on the plot data has been decimated by a factor of %d...\n',n); +end + +z = double(z); % necessary for most of the following calculations... +z(z==novalue) = NaN; + +if inter + z = fillgap(x,y,z); +end + +if isempty(csea) + k = (z~=0 & ~isnan(z)); +else + k = ~isnan(z); +end + +if isnan(zmin) + zmin = nmedian(z(k),zcut/100); +end +if isnan(zmax) + zmax = nmedian(z(k),1 - zcut/100); +end +dz = zmax - zmin; + +if dz > 0 + % builds the colormap: concatenates seacolor and landcolor around 0 + if ~isempty(csea) & zmin < 0 & zmax > 0 + l = size(csea,1); + r = size(cmap,1)*abs(zmin)/zmax/l; + cmap = cat(1,interp1(1:l,csea,linspace(1,l,round(l*r)),'*linear'),cmap); + end + + % normalisation of Z using CMAP and convertion to RGB + I = ind2rgb(uint16((z - zmin)*(length(cmap)/dz)),cmap); + + if c > 0 + % computes lighting from elevation gradient + [fx,fy] = gradient(z,x,y); + %fx = filter([1,0,0,0,-1],1,rf(z'))'; + %fy = filter([1,0,0,0,-1],1,rf(z)); + fxy = -fx*sind(a) - fy*cosd(a); + clear fx fy % free some memory... + + % lake option: zero gradient + if lake + dx = diff(z,1,2); + dy = diff(z,1,1); + u1 = ones(size(z,1),1); + u2 = ones(1,size(z,2)); + z(cat(1,u2,dy)==0 & cat(1,dy,u2)==0 & cat(2,dx,u1)==0 & cat(2,u1,dx)==0) = 0; + clear dx dy % free some memory... + end + + fxy(isnan(fxy)) = 0; + + % computes maximum absolute gradient (median-style), normalizes, saturates and duplicates in 3-D matrix + r = repmat(max(min(fxy/nmedian(abs(fxy),1 - scut/100),1),-1),[1,1,3]); + + % applies contrast using exponent + rp = (1 - abs(r)).^c; + I = I.*rp; + + % lighter for positive gradient + k = find(r > 0); + I(k) = I(k) + (1 - rp(k)); + + end + + % set novalues / NaN to black color + [i,j] = find(isnan(z)); + if ~isempty(i) + I(sub2ind(size(I),repmat(i,1,3),repmat(j,1,3),repmat(1:3,size(i,1),1))) = repmat(novalue_color,size(i,1),1); + end + % set the seacolor for 0 values + if ~isempty(csea) + [i,j] = find(z==0); + if ~isempty(i) + I(sub2ind(size(I),repmat(i,1,3),repmat(j,1,3),repmat(1:3,size(i,1),1))) = repmat(csea(end,:),size(i,1),1); + end + end + + hh = imagesc(x,y,I); +else + hh = imagesc(x,y,z); + colormap(cmap); + text(mean(x),mean(y),'SPLASH!','Color','c','FontWeight','bold','HorizontalAlignment','center') +end + +orient tall +axis xy, axis equal, axis tight + +xlim = [min(x),max(x)]; +ylim = [min(y),max(y)]; +zlim = [min(z(:)),max(z(:))]; + +% axis basemap style +if dec | dms + axis off + + if dms + % approximates X-Y aspect ratio for this latitude (< 20-m precision for 1x1° grid) + xyr = cos(mean(y)*pi/180); + else + xyr = 1; + end + set(gca,'DataAspectRatio',[1,xyr,1]) + bwy = 0.008*diff(ylim); % Y border width = 1% + bwx = bwy/xyr; % border width (in degree of longitude) + + % transparent borders + patch([xlim(1)-bwx,xlim(2)+bwx,xlim(2)+bwx,xlim(1)-bwx],ylim(1) - bwy*[0,0,1,1],'k','FaceColor','none','clipping','off') + patch([xlim(1)-bwx,xlim(2)+bwx,xlim(2)+bwx,xlim(1)-bwx],ylim(2) + bwy*[0,0,1,1],'k','FaceColor','none','clipping','off') + patch(xlim(1) - bwx*[0,0,1,1],[ylim(1)-bwy,ylim(2)+bwy,ylim(2)+bwy,ylim(1)-bwy],'k','FaceColor','none','clipping','off') + patch(xlim(2) + bwx*[0,0,1,1],[ylim(1)-bwy,ylim(2)+bwy,ylim(2)+bwy,ylim(1)-bwy],'k','FaceColor','none','clipping','off') + + dlon = {'E','W'}; + dlat = {'N','S'}; + + if dec + ddx = dtick(diff(xlim)); + ddy = dtick(diff(ylim)); + else + ddx = dtick(diff(xlim),1); + ddy = dtick(diff(ylim),1); + end + + xtick = (ddx*ceil(xlim(1)/ddx)):ddx:xlim(2); + for xt = xtick(1:2:end) + dt = ddx - max(0,xt + ddx - xlim(2)); + patch(repmat(xt + dt*[0,1,1,0]',[1,2]),[ylim(1) - bwy*[0,0,1,1];ylim(2) + bwy*[0,0,1,1]]','k','clipping','off') + text(xt,ylim(1) - bwy,deg2dms(xt,dlon,dec),'FontSize',fs,'HorizontalAlignment','center','VerticalAlignment','top'); + end + + ytick = (ddy*ceil(ylim(1)/ddy)):ddy:ylim(2); + for yt = ytick(1:2:end) + dt = ddy - max(0,yt + ddy - ylim(2)); + patch([xlim(1) - bwx*[0,0,1,1];xlim(2) + bwx*[0,0,1,1]]',repmat(yt + dt*[0,1,1,0]',[1,2]),'k','clipping','off') + text(xlim(1) - 1.1*bwx,yt,deg2dms(yt,dlat,dec),'FontSize',fs,'HorizontalAlignment','right','VerticalAlignment','middle'); + end +end + +% scale legend +if scale + %wsc = diff(xlim)*0.01; + wsc = bwx; + xsc = xlim(2) + wsc*4; + + % elevation scale (colorbar) + zscale = linspace(zlim(1),zlim(2),length(cmap)); + yscale = linspace(0,diff(ylim)/2,length(cmap)); + ysc = ylim(1); + ddz = dtick(dz*max(0.5*xyr*diff(xlim)/yscale(end),1)); + ztick = (ddz*ceil(zlim(1)/ddz)):ddz:zlim(2); + patch(xsc + repmat(wsc*[-1;1;1;-1],[1,length(cmap)]), ... + ysc + [repmat(yscale,[2,1]);repmat(yscale + diff(yscale(1:2)),[2,1])], ... + repmat(zscale,[4,1]), ... + 'EdgeColor','flat','LineWidth',.1,'FaceColor','flat','clipping','off') + colormap(cmap) + caxis([zmin,zmax]) + patch(xsc + wsc*[-1,1,1,-1],ysc + yscale(end)*[0,0,1,1],'k','FaceColor','none','Clipping','off') + text(xsc + 2*wsc + zeros(size(ztick)),ysc + (ztick - zlim(1))*0.5*diff(ylim)/diff(zlim),num2str(ztick'), ... + 'HorizontalAlignment','left','VerticalAlignment','middle','FontSize',8) + + % distance scale (in case of DMS only) + if dms + degkm = 6370*pi/180; + dkm = dtick(diff(ylim)*degkm); + ysc = ylim(2) - 0.5*dkm/degkm; + patch(xsc + wsc*[-1,-1,0,0],ysc + dkm*0.5*[-1,1,1,-1]/degkm,'k','FaceColor',grey,'clipping','off') + if dkm > 1 + skm = sprintf('%g km',dkm); + else + skm = sprintf('%g m',dkm*1000); + end + text(xsc,ysc,skm,'rotation',-90,'HorizontalAlignment','center','VerticalAlignment','bottom', ... + 'Color',grey,'FontWeight','bold') + end + +end + + +if nargout > 0 + h = hh; +end + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function y = nmedian(x,n) +%NMEDIAN Generalized median filter +% NMEDIAN(X,N) sorts elemets of X and returns N-th value (N normalized). +% So: +% N = 0 is minimum value +% N = 0.5 is median value +% N = 1 is maximum value + +if nargin < 2 + n = 0.5; +end +y = sort(x(:)); +y = interp1(sort(y),n*(length(y)-1) + 1); + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function dd = dtick(dlim,deg) +%DTICK Tick intervals + +if nargin < 2 + deg = 0; +end + +if deg & dlim <= 2/60 + % less than 2 minutes: base 36 + m = 10^floor(log10(dlim*36))/36; +elseif deg & dlim <= 2 + % less than 2 degrees: base 6 + m = 10^floor(log10(dlim*6))/6; +else + % more than few degrees or not degrees: decimal rules + m = 10^floor(log10(dlim)); +end +p = ceil(dlim/m); +if p <= 1 + dd = .1*m; +elseif p == 2 + dd = .2*m; +elseif p <= 5 + dd = .5*m; +else + dd = m; +end + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function s = deg2dms(x,ll,dec) +%DEG2DMS Degree/minute/second display + +if dec + s = sprintf('%7.7g',x); +else + xa = abs(x) + 1/360000; + sd = sprintf('%d%c',floor(xa),176); % ASCII char 176 is the degree sign + sm = ''; + ss = ''; + if mod(x,1) + sm = sprintf('%02d''',floor(mod(60*xa,60))); + sa = floor(mod(3600*xa,60)); + if sa + ss = sprintf('%02d"',sa); + else + if strcmp(sm,'00''') + sm = ''; + end + end + end + s = [sd,sm,ss,ll{1+int8(x<0)}]; +end + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function z = fillgap(x,y,z) +% GRIDDATA is not efficient for large arrays, but has great advantage to be +% included in Matlab core functions! To optimize interpolation, we +% reduce the number of relevant data by building a mask of surrounding +% pixels of novalue areas... playing with linear index! + +sz = size(z); +k = find(isnan(z)); +k(k == 1 | k == numel(z)) = []; % removes first and last index (if exist) +if ~isempty(k) + [xx,yy] = meshgrid(x,y); + mask = zeros(sz,'int8'); + k2 = ind90(sz,k); % k2 is linear index in the row order + % sets to 1 every previous and next index, both in column and row order + mask([k-1;k+1;ind90(fliplr(sz),[k2-1;k2+1])]) = 1; + mask(k) = 0; % removes the novalue index + kb = find(mask); % keeps only border values + z(k) = griddata(xx(kb),yy(kb),z(kb),xx(k),yy(k)); +end + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function k2 = ind90(sz,k) + +[i,j] = ind2sub(sz,k); +k2 = sub2ind(fliplr(sz),j,i); % switched i and j: k2 is linear index in row order Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dem/landcolor.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dem/landcolor.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dem/landcolor.m (revision 18231) @@ -0,0 +1,78 @@ +function y = landcolor(n) +%LANDCOLOR Land colormap +% +% Author: Francois Beauducel +% $Revision: 1.0.0 $ $Date: 2012/05/17 11:22:44 $ + +J = [ ... +0.095678 0.53427 0.21682 +0.15785 0.5979 0.23274 +0.21286 0.64673 0.2514 +0.26411 0.68789 0.27268 +0.32959 0.72416 0.31308 +0.39794 0.75695 0.36038 +0.46153 0.7871 0.40624 +0.52108 0.81516 0.45135 +0.57702 0.84152 0.49547 +0.62973 0.86645 0.53891 +0.67946 0.89016 0.58187 +0.72647 0.91282 0.62427 +0.77095 0.93455 0.66619 +0.81306 0.95546 0.70772 +0.85292 0.97563 0.7489 +0.89066 0.99514 0.78976 +0.88379 0.98595 0.77038 +0.86389 0.96758 0.73236 +0.84615 0.94972 0.69623 +0.8303 0.93233 0.66186 +0.81612 0.91536 0.6291 +0.80341 0.8988 0.59784 +0.79201 0.8826 0.56795 +0.78191 0.86676 0.53946 +0.7729 0.85123 0.51224 +0.76479 0.83602 0.48615 +0.75747 0.8211 0.46111 +0.75084 0.80645 0.43704 +0.74506 0.79206 0.41414 +0.73981 0.77792 0.39211 +0.73501 0.76401 0.37089 +0.73068 0.75033 0.35052 +0.72683 0.73685 0.33106 +0.72042 0.72074 0.31228 +0.71032 0.70085 0.29417 +0.69761 0.67821 0.27694 +0.68489 0.65558 0.26026 +0.67235 0.63313 0.24418 +0.65997 0.61082 0.22889 +0.64775 0.58874 0.21406 +0.63568 0.56689 0.19983 +0.62376 0.54527 0.18622 +0.61197 0.52391 0.17299 +0.60033 0.50283 0.16046 +0.58881 0.48203 0.14832 +0.57742 0.46151 0.13667 +0.56616 0.44133 0.12555 +0.55502 0.4214 0.11472 +0.54398 0.4019 0.10456 +0.53306 0.38266 0.094633 +0.52226 0.36382 0.085242 +0.51155 0.3453 0.076179 +0.50095 0.32714 0.067515 +0.49045 0.30938 0.059259 +0.48005 0.29193 0.051294 +0.46973 0.27495 0.043796 +0.45951 0.25823 0.0365 +0.44938 0.24206 0.029715 +0.43934 0.22609 0.023063 +0.42938 0.21074 0.016949 +0.41951 0.19556 0.010917 +0.40971 0.18105 0.0054326 +0.4 0.16667 0 +]; + +l = length(J); +if nargin < 1 + n = 256; +end +y = interp1(1:l,J,linspace(1,l,n),'*linear'); + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dem/license.txt =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dem/license.txt (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dem/license.txt (revision 18231) @@ -0,0 +1,24 @@ +Copyright (c) 2013, François Beauducel +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are +met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in + the documentation and/or other materials provided with the distribution + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE +LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dem/seacolor.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dem/seacolor.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dem/seacolor.m (revision 18231) @@ -0,0 +1,58 @@ +function y = seacolor(n) +%SEACOLOR Sea colormap adapted from NGDC ETOPO1 +% +% Author: Francois Beauducel + +J = [ ... + 0.0392 0 0.4745 + 0.1020 0 0.5373 + 0.1020 0 0.5373 + 0.1490 0 0.5961 + 0.1490 0 0.5961 + 0.1059 0.0118 0.6510 + 0.1059 0.0118 0.6510 + 0.0627 0.0235 0.7059 + 0.0627 0.0235 0.7059 + 0.0196 0.0353 0.7569 + 0.0196 0.0353 0.7569 + 0 0.0549 0.7961 + 0 0.0549 0.7961 + 0 0.0863 0.8235 + 0 0.0863 0.8235 + 0 0.1176 0.8471 + 0 0.1176 0.8471 + 0 0.1529 0.8745 + 0 0.1529 0.8745 + 0.0471 0.2667 0.9059 + 0.0471 0.2667 0.9059 + 0.1020 0.4000 0.9412 + 0.1020 0.4000 0.9412 + 0.0745 0.4588 0.9569 + 0.0745 0.4588 0.9569 + 0.0549 0.5216 0.9765 + 0.0549 0.5216 0.9765 + 0.0824 0.6196 0.9882 + 0.0824 0.6196 0.9882 + 0.1176 0.6980 1.0000 + 0.1176 0.6980 1.0000 + 0.1686 0.7294 1.0000 + 0.1686 0.7294 1.0000 + 0.2157 0.7569 1.0000 + 0.2157 0.7569 1.0000 + 0.2549 0.7843 1.0000 + 0.2549 0.7843 1.0000 + 0.3098 0.8235 1.0000 + 0.3098 0.8235 1.0000 + 0.3686 0.8745 1.0000 + 0.3686 0.8745 1.0000 + 0.5412 0.8902 1.0000 + 0.5412 0.8902 1.0000 + 0.7373 0.9020 1.0000 +]; + +l = length(J); +if nargin < 1 + n = 256; +end +y = interp1(1:l,J,linspace(1,l,n),'*linear'); + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/distribute/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/distribute/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/distribute/install.sh (revision 18231) @@ -0,0 +1,6 @@ +#!/bin/bash +set -eu + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://python-distribute.org/distribute_setup.py' 'distribute_setup.py' +python distribute_setup.py Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/doxygen/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/doxygen/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/doxygen/install.sh (revision 18231) @@ -0,0 +1,21 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +mkdir install + +#Download latest version +svn co https://svn.code.sf.net/p/doxygen/code/trunk src + +#Configure doxygen +cd src && ./configure --prefix "$ISSM_DIR/externalpackages/doxygen/install" +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi + +#Install doxygen +make install +make install_docs Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dyson/ldap.pl =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dyson/ldap.pl (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dyson/ldap.pl (revision 18231) @@ -0,0 +1,25 @@ +#!/usr/bin/perl +# +# LDAP.PL - Acquire JPL LDAP data and pare down to user IDs - 2011-08-01 +# +$cat="/bin/cat"; $srt="/bin/sort"; $ldb="/usr/bin/ldapsearch"; # Binary locations (change as needed) +$lds="ldap.jpl.nasa.gov"; $ou="ou=personnel,dc=dir,dc=jpl,dc=nasa,dc=gov"; # Define LDAP server & organization +$bn="jplbadgenumber"; $txt="$bn".".txt"; $db="jplusers.db"; # Initialize values +# +system(`$ldb -x -h $lds -b $ou uid=* uid > $txt`); # Execute LDAPsearch, write to file +# +open(I,"<$txt"); # Open input file handle + open(O,">badges.tmp"); # Open output file handle + while () { chomp($_); # Spool through input file + if ($_ =~ "^uid: ") { # If line begins with UID value, + $_=~s/uid: //; $_=~s/,(.*)$//; $_=~s/\n//; # strip line of extraneous data + if (!($_=~/^\d\d\d\d\d\d/)) { print O "$_\n"; } # If UID is non-numeric, print output + } # Close condition + } # Close spool + close(O); # Close output file handle +close(I); # Close input file handle +# +system(`$cat badges.tmp |$srt -u > $db 2>/dev/null`); # Sort output +unlink("badges.tmp"); unlink("$txt"); # Unlink temp files +# +# EOF - 2011-08-01 - Jay Dyson Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dyson/readme.txt =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dyson/readme.txt (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dyson/readme.txt (revision 18231) @@ -0,0 +1,38 @@ +-- ARCHIVE MANIFEST ------------------------------------------ 2011-08-19 -- + + Filename Description + -------------- ---------------------------------------------------------- + readme.txt This file: describes script functions. + ldap.pl PERL script for acquiring JPL user IDs via cron job. + source_seek.sh Code-scanning script. Surveys scripts for hard-coded IP + addresses, password callouts, and user IDs. + +-- SCRIPT INFORMATION ------------------------------------------------------ + + LDAP.PL (requires PERL, UNIX ldapsearch, and related utilities) + -------------------------------------------------------------------------- + The LDAP.PL script is intended solely for twice-daily invocation via cron. + This script should be run once at noon, once at midnight. This script + generates the jplusers.db file on which the SOURCE_SEEK.SH shell script + relies for its scanning of source files. + + SOURCE_SEEK.SH (requires UNIX shell and related utilities) + -------------------------------------------------------------------------- + The SOURCE_SEEK.SH shell script is intended for regular cron invocation, + but may be run at system administrator discretion. This script uses UNIX + 'find' and 'grep' utilities to scan code files for hard-coded JPL Internet + Protocol (IP) addresses, password callouts, and JPL user IDs. This script + accepts the path where source code files reside as a command line + argument (e.g., ./source_seek.sh /path/to/sourcecode/files). + +-- AUTHOR CONTACT INFO ----------------------------------------------------- + + Please direct questions regarding these files to the developer. + + Name : Jay Dyson, CISSP + Role : IT Security Engineer + Group : JPL IT Security + E-mail : jdyson@jpl.nasa.gov + Phone : 818-397-4960 + +------------------------------------------------ LAST UPDATED: 2011-08-19 -- Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dyson/source_seek.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dyson/source_seek.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/dyson/source_seek.sh (revision 18231) @@ -0,0 +1,26 @@ +#!/bin/sh +# +# SOURCE_SEEK.SH - Look for IP addresses and mention of 'password' in source files - 2009-10-05 +# +if [ -n "${1}" ]; then + clear + echo "Checking for IP addresses" + echo "--------------------------------------------" + find $1 -name "*" -exec grep -il "128\.149\." {} \; + find $1 -name "*" -exec grep -il "137\.78\." {} \; + find $1 -name "*" -exec grep -il "137\.79\." {} \; + find $1 -name "*" -exec grep -il "137\.228\." {} \; + echo "--------------------------------------------" + echo "\nChecking for 'password'" + echo "--------------------------------------------" + find $1 -name "*" -exec grep -il "password" {} \; + echo "--------------------------------------------" + echo "\nChecking for JPL user IDs" + echo "--------------------------------------------" + find $1 -name "*" -exec grep -ilf jplusers.db {} \; + echo "--------------------------------------------" +else + echo -e "\nUSE: $0 \n"; +fi +# +# EOF - 2011-08-05 - Jay Dyson Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/ec2ami/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/ec2ami/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/ec2ami/install.sh (revision 18231) @@ -0,0 +1,12 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf ec2-api-tools.zip +rm -rf ec2-api-tools-1.4.0.7 + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ec2-api-tools.zip' 'ec2-api-tools.zip' + +#Untar +unzip ec2-api-tools.zip Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/ec2api/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/ec2api/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/ec2api/install.sh (revision 18231) @@ -0,0 +1,13 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf ec2-api-tools.zip +rm -rf ec2-api-tools-1.6.3.1 + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ec2-api-tools.zip' 'ec2-api-tools.zip' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/docs/ec2-ug.pdf' 'ec2-ug.pdf' + +#Untar +unzip ec2-api-tools.zip Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/esmf/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/esmf/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/esmf/install.sh (revision 18231) @@ -0,0 +1,38 @@ +#!/bin/bash +set -eu + +export ESMF_DIR=$ISSM_DIR/externalpackages/esmf/esmf +export ESMF_COMPILER=gfortran +export ESMF_COMM=mpich2 + +#Some cleanup +rm -rf esmf_5_2_0rp2 +rm -rf esmf + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/esmf_5_2_0rp2_src.tar.gz' 'esmf_5_2_0rp2_src.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/docs/ESMF_refdoc.pdf' 'ESMF_refdoc.pdf' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/docs/ESMF_usrdoc.pdf' 'ESMF_usrdoc.pdf' + +#Untar +tar -zxvf esmf_5_2_0rp2_src.tar.gz + + +#Configure esmf +cd esmf + +#Compile and install esmf +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi + +cd esmf +if [ $# -eq 0 ]; then + make all_tests +else + make -j $1 all_tests +fi Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/copyfig.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/copyfig.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/copyfig.m (revision 18231) @@ -0,0 +1,33 @@ +%COPYFIG Create a copy of a figure, without changing the figure +% +% Examples: +% fh_new = copyfig(fh_old) +% +% This function will create a copy of a figure, but not change the figure, +% as copyobj sometimes does, e.g. by changing legends. +% +% IN: +% fh_old - The handle of the figure to be copied. Default: gcf. +% +% OUT: +% fh_new - The handle of the created figure. + +% Copyright (C) Oliver Woodford 2012 + +function fh = copyfig(fh) +% Set the default +if nargin == 0 + fh = gcf; +end +% Is there a legend? +if isempty(findobj(fh, 'Type', 'axes', 'Tag', 'legend')) + % Safe to copy using copyobj + fh = copyobj(fh, 0); +else + % copyobj will change the figure, so save and then load it instead + tmp_nam = [tempname '.fig']; + hgsave(fh, tmp_nam); + fh = hgload(tmp_nam); + delete(tmp_nam); +end +return Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/eps2pdf.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/eps2pdf.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/eps2pdf.m (revision 18231) @@ -0,0 +1,134 @@ +%EPS2PDF Convert an eps file to pdf format using ghostscript +% +% Examples: +% eps2pdf source dest +% eps2pdf(source, dest, crop) +% eps2pdf(source, dest, crop, append) +% eps2pdf(source, dest, crop, append, gray) +% eps2pdf(source, dest, crop, append, gray, quality) +% +% This function converts an eps file to pdf format. The output can be +% optionally cropped and also converted to grayscale. If the output pdf +% file already exists then the eps file can optionally be appended as a new +% page on the end of the eps file. The level of bitmap compression can also +% optionally be set. +% +% This function requires that you have ghostscript installed on your +% system. Ghostscript can be downloaded from: http://www.ghostscript.com +% +%IN: +% source - filename of the source eps file to convert. The filename is +% assumed to already have the extension ".eps". +% dest - filename of the destination pdf file. The filename is assumed to +% already have the extension ".pdf". +% crop - boolean indicating whether to crop the borders off the pdf. +% Default: true. +% append - boolean indicating whether the eps should be appended to the +% end of the pdf as a new page (if the pdf exists already). +% Default: false. +% gray - boolean indicating whether the output pdf should be grayscale or +% not. Default: false. +% quality - scalar indicating the level of image bitmap quality to +% output. A larger value gives a higher quality. quality > 100 +% gives lossless output. Default: ghostscript prepress default. + +% Copyright (C) Oliver Woodford 2009-2011 + +% Suggestion of appending pdf files provided by Matt C at: +% http://www.mathworks.com/matlabcentral/fileexchange/23629 + +% Thank you to Fabio Viola for pointing out compression artifacts, leading +% to the quality setting. +% Thank you to Scott for pointing out the subsampling of very small images, +% which was fixed for lossless compression settings. + +% 9/12/2011 Pass font path to ghostscript. + +function eps2pdf(source, dest, crop, append, gray, quality) +% Intialise the options string for ghostscript +options = ['-q -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -dPDFSETTINGS=/prepress -sOutputFile="' dest '"']; +% Set crop option +if nargin < 3 || crop + options = [options ' -dEPSCrop']; +end +% Set the font path +fp = font_path(); +if ~isempty(fp) + options = [options ' -sFONTPATH="' fp '"']; +end +% Set the grayscale option +if nargin > 4 && gray + options = [options ' -sColorConversionStrategy=Gray -dProcessColorModel=/DeviceGray']; +end +% Set the bitmap quality +if nargin > 5 && ~isempty(quality) + options = [options ' -dAutoFilterColorImages=false -dAutoFilterGrayImages=false']; + if quality > 100 + options = [options ' -dColorImageFilter=/FlateEncode -dGrayImageFilter=/FlateEncode -c ".setpdfwrite << /ColorImageDownsampleThreshold 10 /GrayImageDownsampleThreshold 10 >> setdistillerparams"']; + else + options = [options ' -dColorImageFilter=/DCTEncode -dGrayImageFilter=/DCTEncode']; + v = 1 + (quality < 80); + quality = 1 - quality / 100; + s = sprintf('<< /QFactor %.2f /Blend 1 /HSample [%d 1 1 %d] /VSample [%d 1 1 %d] >>', quality, v, v, v, v); + options = sprintf('%s -c ".setpdfwrite << /ColorImageDict %s /GrayImageDict %s >> setdistillerparams"', options, s, s); + end +end +% Check if the output file exists +if nargin > 3 && append && exist(dest, 'file') == 2 + % File exists - append current figure to the end + tmp_nam = tempname; + % Copy the file + copyfile(dest, tmp_nam); + % Add the output file names + options = [options ' -f "' tmp_nam '" "' source '"']; + try + % Convert to pdf using ghostscript + [status message] = ghostscript(options); + catch + % Delete the intermediate file + delete(tmp_nam); + rethrow(lasterror); + end + % Delete the intermediate file + delete(tmp_nam); +else + % File doesn't exist or should be over-written + % Add the output file names + options = [options ' -f "' source '"']; + % Convert to pdf using ghostscript + [status message] = ghostscript(options); +end +% Check for error +if status + % Report error + if isempty(message) + error('Unable to generate pdf. Check destination directory is writable.'); + else + error(message); + end +end +return + +% Function to return (and create, where necessary) the font path +function fp = font_path() +fp = user_string('gs_font_path'); +if ~isempty(fp) + return +end +% Create the path +% Start with the default path +fp = getenv('GS_FONTPATH'); +% Add on the typical directories for a given OS +if ispc + if ~isempty(fp) + fp = [fp ';']; + end + fp = [fp getenv('WINDIR') filesep 'Fonts']; +else + if ~isempty(fp) + fp = [fp ':']; + end + fp = [fp '/usr/share/fonts:/usr/local/share/fonts:/usr/share/fonts/X11:/usr/local/share/fonts/X11:/usr/share/fonts/truetype:/usr/local/share/fonts/truetype']; +end +user_string('gs_font_path', fp); +return Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/export_fig.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/export_fig.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/export_fig.m (revision 18231) @@ -0,0 +1,810 @@ +%EXPORT_FIG Exports figures suitable for publication +% +% Examples: +% im = export_fig +% [im alpha] = export_fig +% export_fig filename +% export_fig filename -format1 -format2 +% export_fig ... -nocrop +% export_fig ... -transparent +% export_fig ... -native +% export_fig ... -m +% export_fig ... -r +% export_fig ... -a +% export_fig ... -q +% export_fig ... - +% export_fig ... - +% export_fig ... -append +% export_fig ... -bookmark +% export_fig(..., handle) +% +% This function saves a figure or single axes to one or more vector and/or +% bitmap file formats, and/or outputs a rasterized version to the +% workspace, with the following properties: +% - Figure/axes reproduced as it appears on screen +% - Cropped borders (optional) +% - Embedded fonts (vector formats) +% - Improved line and grid line styles +% - Anti-aliased graphics (bitmap formats) +% - Render images at native resolution (optional for bitmap formats) +% - Transparent background supported (pdf, eps, png) +% - Semi-transparent patch objects supported (png only) +% - RGB, CMYK or grayscale output (CMYK only with pdf, eps, tiff) +% - Variable image compression, including lossless (pdf, eps, jpg) +% - Optionally append to file (pdf, tiff) +% - Vector formats: pdf, eps +% - Bitmap formats: png, tiff, jpg, bmp, export to workspace +% +% This function is especially suited to exporting figures for use in +% publications and presentations, because of the high quality and +% portability of media produced. +% +% Note that the background color and figure dimensions are reproduced +% (the latter approximately, and ignoring cropping & magnification) in the +% output file. For transparent background (and semi-transparent patch +% objects), use the -transparent option or set the figure 'Color' property +% to 'none'. To make axes transparent set the axes 'Color' property to +% 'none'. Pdf, eps and png are the only file formats to support a +% transparent background, whilst the png format alone supports transparency +% of patch objects. +% +% The choice of renderer (opengl, zbuffer or painters) has a large impact +% on the quality of output. Whilst the default value (opengl for bitmaps, +% painters for vector formats) generally gives good results, if you aren't +% satisfied then try another renderer. Notes: 1) For vector formats (eps, +% pdf), only painters generates vector graphics. 2) For bitmaps, only +% opengl can render transparent patch objects correctly. 3) For bitmaps, +% only painters will correctly scale line dash and dot lengths when +% magnifying or anti-aliasing. 4) Fonts may be substitued with Courier when +% using painters. +% +% When exporting to vector format (pdf & eps) and bitmap format using the +% painters renderer, this function requires that ghostscript is installed +% on your system. You can download this from: +% http://www.ghostscript.com +% When exporting to eps it additionally requires pdftops, from the Xpdf +% suite of functions. You can download this from: +% http://www.foolabs.com/xpdf +% +%IN: +% filename - string containing the name (optionally including full or +% relative path) of the file the figure is to be saved as. If +% a path is not specified, the figure is saved in the current +% directory. If no name and no output arguments are specified, +% the default name, 'export_fig_out', is used. If neither a +% file extension nor a format are specified, a ".png" is added +% and the figure saved in that format. +% -format1, -format2, etc. - strings containing the extensions of the +% file formats the figure is to be saved as. +% Valid options are: '-pdf', '-eps', '-png', +% '-tif', '-jpg' and '-bmp'. All combinations +% of formats are valid. +% -nocrop - option indicating that the borders of the output are not to +% be cropped. +% -transparent - option indicating that the figure background is to be +% made transparent (png, pdf and eps output only). +% -m - option where val indicates the factor to magnify the +% on-screen figure dimensions by when generating bitmap +% outputs. Default: '-m1'. +% -r - option val indicates the resolution (in pixels per inch) to +% export bitmap outputs at, keeping the dimensions of the +% on-screen figure. Default: sprintf('-r%g', get(0, +% 'ScreenPixelsPerInch')). Note that the -m and -r options +% change the same property. +% -native - option indicating that the output resolution (when outputting +% a bitmap format) should be such that the vertical resolution +% of the first suitable image found in the figure is at the +% native resolution of that image. To specify a particular +% image to use, give it the tag 'export_fig_native'. Notes: +% This overrides any value set with the -m and -r options. It +% also assumes that the image is displayed front-to-parallel +% with the screen. The output resolution is approximate and +% should not be relied upon. Anti-aliasing can have adverse +% effects on image quality (disable with the -a1 option). +% -a1, -a2, -a3, -a4 - option indicating the amount of anti-aliasing to +% use for bitmap outputs. '-a1' means no anti- +% aliasing; '-a4' is the maximum amount (default). +% - - option to force a particular renderer (painters, opengl +% or zbuffer) to be used over the default: opengl for +% bitmaps; painters for vector formats. +% - - option indicating which colorspace color figures should +% be saved in: RGB (default), CMYK or gray. CMYK is only +% supported in pdf, eps and tiff output. +% -q - option to vary bitmap image quality (in pdf, eps and jpg +% files only). Larger val, in the range 0-100, gives higher +% quality/lower compression. val > 100 gives lossless +% compression. Default: '-q95' for jpg, ghostscript prepress +% default for pdf & eps. Note: lossless compression can +% sometimes give a smaller file size than the default lossy +% compression, depending on the type of images. +% -append - option indicating that if the file (pdfs only) already +% exists, the figure is to be appended as a new page, instead +% of being overwritten (default). +% -bookmark - option to indicate that a bookmark with the name of the +% figure is to be created in the output file (pdf only). +% handle - The handle of the figure, axes or uipanels (can be an array of +% handles, but the objects must be in the same figure) to be +% saved. Default: gcf. +% +%OUT: +% im - MxNxC uint8 image array of the figure. +% alpha - MxN single array of alphamatte values in range [0,1], for the +% case when the background is transparent. +% +% Some helpful examples and tips can be found at: +% http://sites.google.com/site/oliverwoodford/software/export_fig +% +% See also PRINT, SAVEAS. + +% Copyright (C) Oliver Woodford 2008-2012 + +% The idea of using ghostscript is inspired by Peder Axensten's SAVEFIG +% (fex id: 10889) which is itself inspired by EPS2PDF (fex id: 5782). +% The idea for using pdftops came from the MATLAB newsgroup (id: 168171). +% The idea of editing the EPS file to change line styles comes from Jiro +% Doke's FIXPSLINESTYLE (fex id: 17928). +% The idea of changing dash length with line width came from comments on +% fex id: 5743, but the implementation is mine :) +% The idea of anti-aliasing bitmaps came from Anders Brun's MYAA (fex id: +% 20979). +% The idea of appending figures in pdfs came from Matt C in comments on the +% FEX (id: 23629) + +% Thanks to Roland Martin for pointing out the colour MATLAB +% bug/feature with colorbar axes and transparent backgrounds. +% Thanks also to Andrew Matthews for describing a bug to do with the figure +% size changing in -nodisplay mode. I couldn't reproduce it, but included a +% fix anyway. +% Thanks to Tammy Threadgill for reporting a bug where an axes is not +% isolated from gui objects. + +% 23/02/12: Ensure that axes limits don't change during printing +% 14/03/12: Fix bug in fixing the axes limits (thanks to Tobias Lamour for +% reporting it). +% 02/05/12: Incorporate patch of Petr Nechaev (many thanks), enabling +% bookmarking of figures in pdf files. +% 09/05/12: Incorporate patch of Arcelia Arrieta (many thanks), to keep +% tick marks fixed. +% 12/12/12: Add support for isolating uipanels. Thanks to michael for +% suggesting it. + +function [im, alpha] = export_fig(varargin) +% Make sure the figure is rendered correctly _now_ so that properties like +% axes limits are up-to-date. +drawnow; +% Parse the input arguments +[fig, options] = parse_args(nargout, varargin{:}); +% Isolate the subplot, if it is one +cls = all(ismember(get(fig, 'Type'), {'axes', 'uipanel'})); +if cls + % Given handles of one or more axes, so isolate them from the rest + fig = isolate_axes(fig); +else + % Check we have a figure + if ~isequal(get(fig, 'Type'), 'figure'); + error('Handle must be that of a figure, axes or uipanel'); + end + % Get the old InvertHardcopy mode + old_mode = get(fig, 'InvertHardcopy'); +end +% Hack the font units where necessary (due to a font rendering bug in +% print?). This may not work perfectly in all cases. Also it can change the +% figure layout if reverted, so use a copy. +magnify = options.magnify * options.aa_factor; +if isbitmap(options) && magnify ~= 1 + fontu = findobj(fig, 'FontUnits', 'normalized'); + if ~isempty(fontu) + % Some normalized font units found + if ~cls + fig = copyfig(fig); + set(fig, 'Visible', 'off'); + fontu = findobj(fig, 'FontUnits', 'normalized'); + cls = true; + end + set(fontu, 'FontUnits', 'points'); + end +end +% MATLAB "feature": axes limits and tick marks can change when printing +Hlims = findall(fig, 'Type', 'axes'); +if ~cls + % Record the old axes limit and tick modes + Xlims = make_cell(get(Hlims, 'XLimMode')); + Ylims = make_cell(get(Hlims, 'YLimMode')); + Zlims = make_cell(get(Hlims, 'ZLimMode')); + Xtick = make_cell(get(Hlims, 'XTickMode')); + Ytick = make_cell(get(Hlims, 'YTickMode')); + Ztick = make_cell(get(Hlims, 'ZTickMode')); +end +% Set all axes limit and tick modes to manual, so the limits and ticks can't change +set(Hlims, 'XLimMode', 'manual', 'YLimMode', 'manual', 'ZLimMode', 'manual', 'XTickMode', 'manual', 'YTickMode', 'manual', 'ZTickMode', 'manual'); +% Set to print exactly what is there +set(fig, 'InvertHardcopy', 'off'); +% Set the renderer +switch options.renderer + case 1 + renderer = '-opengl'; + case 2 + renderer = '-zbuffer'; + case 3 + renderer = '-painters'; + otherwise + renderer = '-opengl'; % Default for bitmaps +end +% Do the bitmap formats first +if isbitmap(options) + % Get the background colour + if options.transparent && (options.png || options.alpha) + % Get out an alpha channel + % MATLAB "feature": black colorbar axes can change to white and vice versa! + hCB = findobj(fig, 'Type', 'axes', 'Tag', 'Colorbar'); + if isempty(hCB) + yCol = []; + xCol = []; + else + yCol = get(hCB, 'YColor'); + xCol = get(hCB, 'XColor'); + if iscell(yCol) + yCol = cell2mat(yCol); + xCol = cell2mat(xCol); + end + yCol = sum(yCol, 2); + xCol = sum(xCol, 2); + end + % MATLAB "feature": apparently figure size can change when changing + % colour in -nodisplay mode + pos = get(fig, 'Position'); + % Set the background colour to black, and set size in case it was + % changed internally + tcol = get(fig, 'Color'); + set(fig, 'Color', 'k', 'Position', pos); + % Correct the colorbar axes colours + set(hCB(yCol==0), 'YColor', [0 0 0]); + set(hCB(xCol==0), 'XColor', [0 0 0]); + % Print large version to array + B = print2array(fig, magnify, renderer); + % Downscale the image + B = downsize(single(B), options.aa_factor); + % Set background to white (and set size) + set(fig, 'Color', 'w', 'Position', pos); + % Correct the colorbar axes colours + set(hCB(yCol==3), 'YColor', [1 1 1]); + set(hCB(xCol==3), 'XColor', [1 1 1]); + % Print large version to array + A = print2array(fig, magnify, renderer); + % Downscale the image + A = downsize(single(A), options.aa_factor); + % Set the background colour (and size) back to normal + set(fig, 'Color', tcol, 'Position', pos); + % Compute the alpha map + alpha = round(sum(B - A, 3)) / (255 * 3) + 1; + A = alpha; + A(A==0) = 1; + A = B ./ A(:,:,[1 1 1]); + clear B + % Convert to greyscale + if options.colourspace == 2 + A = rgb2grey(A); + end + A = uint8(A); + % Crop the background + if options.crop + [alpha, v] = crop_background(alpha, 0); + A = A(v(1):v(2),v(3):v(4),:); + end + if options.png + % Compute the resolution + res = options.magnify * get(0, 'ScreenPixelsPerInch') / 25.4e-3; + % Save the png + imwrite(A, [options.name '.png'], 'Alpha', double(alpha), 'ResolutionUnit', 'meter', 'XResolution', res, 'YResolution', res); + % Clear the png bit + options.png = false; + end + % Return only one channel for greyscale + if isbitmap(options) + A = check_greyscale(A); + end + if options.alpha + % Store the image + im = A; + % Clear the alpha bit + options.alpha = false; + end + % Get the non-alpha image + if isbitmap(options) + alph = alpha(:,:,ones(1, size(A, 3))); + A = uint8(single(A) .* alph + 255 * (1 - alph)); + clear alph + end + if options.im + % Store the new image + im = A; + end + else + % Print large version to array + if options.transparent + % MATLAB "feature": apparently figure size can change when changing + % colour in -nodisplay mode + pos = get(fig, 'Position'); + tcol = get(fig, 'Color'); + set(fig, 'Color', 'w', 'Position', pos); + A = print2array(fig, magnify, renderer); + set(fig, 'Color', tcol, 'Position', pos); + tcol = 255; + else + [A, tcol] = print2array(fig, magnify, renderer); + end + % Crop the background + if options.crop + A = crop_background(A, tcol); + end + % Downscale the image + A = downsize(A, options.aa_factor); + if options.colourspace == 2 + % Convert to greyscale + A = rgb2grey(A); + else + % Return only one channel for greyscale + A = check_greyscale(A); + end + % Outputs + if options.im + im = A; + end + if options.alpha + im = A; + alpha = zeros(size(A, 1), size(A, 2), 'single'); + end + end + % Save the images + if options.png + res = options.magnify * get(0, 'ScreenPixelsPerInch') / 25.4e-3; + imwrite(A, [options.name '.png'], 'ResolutionUnit', 'meter', 'XResolution', res, 'YResolution', res); + end + if options.bmp + imwrite(A, [options.name '.bmp']); + end + % Save jpeg with given quality + if options.jpg + quality = options.quality; + if isempty(quality) + quality = 95; + end + if quality > 100 + imwrite(A, [options.name '.jpg'], 'Mode', 'lossless'); + else + imwrite(A, [options.name '.jpg'], 'Quality', quality); + end + end + % Save tif images in cmyk if wanted (and possible) + if options.tif + if options.colourspace == 1 && size(A, 3) == 3 + A = double(255 - A); + K = min(A, [], 3); + K_ = 255 ./ max(255 - K, 1); + C = (A(:,:,1) - K) .* K_; + M = (A(:,:,2) - K) .* K_; + Y = (A(:,:,3) - K) .* K_; + A = uint8(cat(3, C, M, Y, K)); + clear C M Y K K_ + end + append_mode = {'overwrite', 'append'}; + imwrite(A, [options.name '.tif'], 'Resolution', options.magnify*get(0, 'ScreenPixelsPerInch'), 'WriteMode', append_mode{options.append+1}); + end +end +% Now do the vector formats +if isvector(options) + % Set the default renderer to painters + if ~options.renderer + renderer = '-painters'; + end + % Generate some filenames + tmp_nam = [tempname '.eps']; + if options.pdf + pdf_nam = [options.name '.pdf']; + else + pdf_nam = [tempname '.pdf']; + end + % Generate the options for print + p2eArgs = {renderer}; + if options.colourspace == 1 + p2eArgs = [p2eArgs {'-cmyk'}]; + end + if ~options.crop + p2eArgs = [p2eArgs {'-loose'}]; + end + try + % Generate an eps + print2eps(tmp_nam, fig, p2eArgs{:}); + % Remove the background, if desired + if options.transparent && ~isequal(get(fig, 'Color'), 'none') + eps_remove_background(tmp_nam); + end + % Add a bookmark to the PDF if desired + if options.bookmark + fig_nam = get(fig, 'Name'); + if isempty(fig_nam) + warning('export_fig:EmptyBookmark', 'Bookmark requested for figure with no name. Bookmark will be empty.'); + end + add_bookmark(tmp_nam, fig_nam); + end + % Generate a pdf + eps2pdf(tmp_nam, pdf_nam, 1, options.append, options.colourspace==2, options.quality); + catch ex + % Delete the eps + delete(tmp_nam); + rethrow(ex); + end + % Delete the eps + delete(tmp_nam); + if options.eps + try + % Generate an eps from the pdf + pdf2eps(pdf_nam, [options.name '.eps']); + catch ex + if ~options.pdf + % Delete the pdf + delete(pdf_nam); + end + rethrow(ex); + end + if ~options.pdf + % Delete the pdf + delete(pdf_nam); + end + end +end +if cls + % Close the created figure + close(fig); +else + % Reset the hardcopy mode + set(fig, 'InvertHardcopy', old_mode); + % Reset the axes limit and tick modes + for a = 1:numel(Hlims) + set(Hlims(a), 'XLimMode', Xlims{a}, 'YLimMode', Ylims{a}, 'ZLimMode', Zlims{a}, 'XTickMode', Xtick{a}, 'YTickMode', Ytick{a}, 'ZTickMode', Ztick{a}); + end +end +return + +function [fig, options] = parse_args(nout, varargin) +% Parse the input arguments +% Set the defaults +fig = get(0, 'CurrentFigure'); +options = struct('name', 'export_fig_out', ... + 'crop', true, ... + 'transparent', false, ... + 'renderer', 0, ... % 0: default, 1: OpenGL, 2: ZBuffer, 3: Painters + 'pdf', false, ... + 'eps', false, ... + 'png', false, ... + 'tif', false, ... + 'jpg', false, ... + 'bmp', false, ... + 'colourspace', 0, ... % 0: RGB/gray, 1: CMYK, 2: gray + 'append', false, ... + 'im', nout == 1, ... + 'alpha', nout == 2, ... + 'aa_factor', 3, ... + 'magnify', 1, ... + 'bookmark', false, ... + 'quality', []); +native = false; % Set resolution to native of an image + +% Go through the other arguments +for a = 1:nargin-1 + if all(ishandle(varargin{a})) + fig = varargin{a}; + elseif ischar(varargin{a}) && ~isempty(varargin{a}) + if varargin{a}(1) == '-' + switch lower(varargin{a}(2:end)) + case 'nocrop' + options.crop = false; + case {'trans', 'transparent'} + options.transparent = true; + case 'opengl' + options.renderer = 1; + case 'zbuffer' + options.renderer = 2; + case 'painters' + options.renderer = 3; + case 'pdf' + options.pdf = true; + case 'eps' + options.eps = true; + case 'png' + options.png = true; + case {'tif', 'tiff'} + options.tif = true; + case {'jpg', 'jpeg'} + options.jpg = true; + case 'bmp' + options.bmp = true; + case 'rgb' + options.colourspace = 0; + case 'cmyk' + options.colourspace = 1; + case {'gray', 'grey'} + options.colourspace = 2; + case {'a1', 'a2', 'a3', 'a4'} + options.aa_factor = str2double(varargin{a}(3)); + case 'append' + options.append = true; + case 'bookmark' + options.bookmark = true; + case 'native' + native = true; + otherwise + val = str2double(regexp(varargin{a}, '(?<=-(m|M|r|R|q|Q))(\d*\.)?\d+(e-?\d+)?', 'match')); + if ~isscalar(val) + error('option %s not recognised', varargin{a}); + end + switch lower(varargin{a}(2)) + case 'm' + options.magnify = val; + case 'r' + options.magnify = val ./ get(0, 'ScreenPixelsPerInch'); + case 'q' + options.quality = max(val, 0); + end + end + else + [p, options.name, ext] = fileparts(varargin{a}); + if ~isempty(p) + options.name = [p filesep options.name]; + end + switch lower(ext) + case {'.tif', '.tiff'} + options.tif = true; + case {'.jpg', '.jpeg'} + options.jpg = true; + case '.png' + options.png = true; + case '.bmp' + options.bmp = true; + case '.eps' + options.eps = true; + case '.pdf' + options.pdf = true; + otherwise + options.name = varargin{a}; + end + end + end +end + +% Check we have a figure handle +if isempty(fig) + error('No figure found'); +end + +% Set the default format +if ~isvector(options) && ~isbitmap(options) + options.png = true; +end + +% Check whether transparent background is wanted (old way) +if isequal(get(ancestor(fig, 'figure'), 'Color'), 'none') + options.transparent = true; +end + +% If requested, set the resolution to the native vertical resolution of the +% first suitable image found +if native && isbitmap(options) + % Find a suitable image + list = findobj(fig, 'Type', 'image', 'Tag', 'export_fig_native'); + if isempty(list) + list = findobj(fig, 'Type', 'image', 'Visible', 'on'); + end + for hIm = list(:)' + % Check height is >= 2 + height = size(get(hIm, 'CData'), 1); + if height < 2 + continue + end + % Account for the image filling only part of the axes, or vice + % versa + yl = get(hIm, 'YData'); + if isscalar(yl) + yl = [yl(1)-0.5 yl(1)+height+0.5]; + else + if ~diff(yl) + continue + end + yl = yl + [-0.5 0.5] * (diff(yl) / (height - 1)); + end + hAx = get(hIm, 'Parent'); + yl2 = get(hAx, 'YLim'); + % Find the pixel height of the axes + oldUnits = get(hAx, 'Units'); + set(hAx, 'Units', 'pixels'); + pos = get(hAx, 'Position'); + set(hAx, 'Units', oldUnits); + if ~pos(4) + continue + end + % Found a suitable image + % Account for stretch-to-fill being disabled + pbar = get(hAx, 'PlotBoxAspectRatio'); + pos = min(pos(4), pbar(2)*pos(3)/pbar(1)); + % Set the magnification to give native resolution + options.magnify = (height * diff(yl2)) / (pos * diff(yl)); + break + end +end +return + +function A = downsize(A, factor) +% Downsample an image +if factor == 1 + % Nothing to do + return +end +try + % Faster, but requires image processing toolbox + A = imresize(A, 1/factor, 'bilinear'); +catch + % No image processing toolbox - resize manually + % Lowpass filter - use Gaussian as is separable, so faster + % Compute the 1d Gaussian filter + filt = (-factor-1:factor+1) / (factor * 0.6); + filt = exp(-filt .* filt); + % Normalize the filter + filt = single(filt / sum(filt)); + % Filter the image + padding = floor(numel(filt) / 2); + for a = 1:size(A, 3) + A(:,:,a) = conv2(filt, filt', single(A([ones(1, padding) 1:end repmat(end, 1, padding)],[ones(1, padding) 1:end repmat(end, 1, padding)],a)), 'valid'); + end + % Subsample + A = A(1+floor(mod(end-1, factor)/2):factor:end,1+floor(mod(end-1, factor)/2):factor:end,:); +end +return + +function A = rgb2grey(A) +A = cast(reshape(reshape(single(A), [], 3) * single([0.299; 0.587; 0.114]), size(A, 1), size(A, 2)), class(A)); +return + +function A = check_greyscale(A) +% Check if the image is greyscale +if size(A, 3) == 3 && ... + all(reshape(A(:,:,1) == A(:,:,2), [], 1)) && ... + all(reshape(A(:,:,2) == A(:,:,3), [], 1)) + A = A(:,:,1); % Save only one channel for 8-bit output +end +return + +function [A, v] = crop_background(A, bcol) +% Map the foreground pixels +[h, w, c] = size(A); +if isscalar(bcol) && c > 1 + bcol = bcol(ones(1, c)); +end +bail = false; +for l = 1:w + for a = 1:c + if ~all(A(:,l,a) == bcol(a)) + bail = true; + break; + end + end + if bail + break; + end +end +bail = false; +for r = w:-1:l + for a = 1:c + if ~all(A(:,r,a) == bcol(a)) + bail = true; + break; + end + end + if bail + break; + end +end +bail = false; +for t = 1:h + for a = 1:c + if ~all(A(t,:,a) == bcol(a)) + bail = true; + break; + end + end + if bail + break; + end +end +bail = false; +for b = h:-1:t + for a = 1:c + if ~all(A(b,:,a) == bcol(a)) + bail = true; + break; + end + end + if bail + break; + end +end +% Crop the background, leaving one boundary pixel to avoid bleeding on +% resize +v = [max(t-1, 1) min(b+1, h) max(l-1, 1) min(r+1, w)]; +A = A(v(1):v(2),v(3):v(4),:); +return + +function eps_remove_background(fname) +% Remove the background of an eps file +% Open the file +fh = fopen(fname, 'r+'); +if fh == -1 + error('Not able to open file %s.', fname); +end +% Read the file line by line +while true + % Get the next line + l = fgets(fh); + if isequal(l, -1) + break; % Quit, no rectangle found + end + % Check if the line contains the background rectangle + if isequal(regexp(l, ' *0 +0 +\d+ +\d+ +rf *[\n\r]+', 'start'), 1) + % Set the line to whitespace and quit + l(1:regexp(l, '[\n\r]', 'start', 'once')-1) = ' '; + fseek(fh, -numel(l), 0); + fprintf(fh, l); + break; + end +end +% Close the file +fclose(fh); +return + +function b = isvector(options) +b = options.pdf || options.eps; +return + +function b = isbitmap(options) +b = options.png || options.tif || options.jpg || options.bmp || options.im || options.alpha; +return + +% Helper function +function A = make_cell(A) +if ~iscell(A) + A = {A}; +end +return + +function add_bookmark(fname, bookmark_text) +% Adds a bookmark to the temporary EPS file after %%EndPageSetup +% Read in the file +fh = fopen(fname, 'r'); +if fh == -1 + error('File %s not found.', fname); +end +try + fstrm = fread(fh, '*char')'; +catch ex + fclose(fh); + rethrow(ex); +end +fclose(fh); + +% Include standard pdfmark prolog to maximize compatibility +fstrm = strrep(fstrm, '%%BeginProlog', sprintf('%%%%BeginProlog\n/pdfmark where {pop} {userdict /pdfmark /cleartomark load put} ifelse')); +% Add page bookmark +fstrm = strrep(fstrm, '%%EndPageSetup', sprintf('%%%%EndPageSetup\n[ /Title (%s) /OUT pdfmark',bookmark_text)); + +% Write out the updated file +fh = fopen(fname, 'w'); +if fh == -1 + error('Unable to open %s for writing.', fname); +end +try + fwrite(fh, fstrm, 'char*1'); +catch ex + fclose(fh); + rethrow(ex); +end +fclose(fh); +return Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/fix_lines.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/fix_lines.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/fix_lines.m (revision 18231) @@ -0,0 +1,154 @@ +function fix_lines(fname, fname2) +%FIX_LINES Improves the line style of eps files generated by print +% +% Examples: +% fix_lines fname +% fix_lines fname fname2 +% +% This function improves the style of lines in eps files generated by +% MATLAB's print function, making them more similar to those seen on +% screen. Grid lines are also changed from a dashed style to a dotted +% style, for greater differentiation from dashed lines. +% +% The function also places embedded fonts after the postscript header, in +% versions of MATLAB which place the fonts first (R2006b and earlier), in +% order to allow programs such as Ghostscript to find the bounding box +% information. +% +% IN: +% fname - Name or path of source eps file. +% fname2 - Name or path of destination eps file. Default: same as fname. + +% Copyright: (C) Oliver Woodford, 2008-2010 + +% The idea of editing the EPS file to change line styles comes from Jiro +% Doke's FIXPSLINESTYLE (fex id: 17928) +% The idea of changing dash length with line width came from comments on +% fex id: 5743, but the implementation is mine :) + +% Thank you to Sylvain Favrot for bringing the embedded font/bounding box +% interaction in older versions of MATLAB to my attention. +% Thank you to D Ko for bringing an error with eps files with tiff previews +% to my attention. +% Thank you to Laurence K for suggesting the check to see if the file was +% opened. + +% Read in the file +fh = fopen(fname, 'r'); +if fh == -1 + error('File %s not found.', fname); +end +try + fstrm = fread(fh, '*char')'; +catch ex + fclose(fh); + rethrow(ex); +end +fclose(fh); + +% Move any embedded fonts after the postscript header +if strcmp(fstrm(1:15), '%!PS-AdobeFont-') + % Find the start and end of the header + ind = regexp(fstrm, '[\n\r]%!PS-Adobe-'); + [ind2 ind2] = regexp(fstrm, '[\n\r]%%EndComments[\n\r]+'); + % Put the header first + if ~isempty(ind) && ~isempty(ind2) && ind(1) < ind2(1) + fstrm = fstrm([ind(1)+1:ind2(1) 1:ind(1) ind2(1)+1:end]); + end +end + +% Make sure all line width commands come before the line style definitions, +% so that dash lengths can be based on the correct widths +% Find all line style sections +ind = [regexp(fstrm, '[\n\r]SO[\n\r]'),... % This needs to be here even though it doesn't have dots/dashes! + regexp(fstrm, '[\n\r]DO[\n\r]'),... + regexp(fstrm, '[\n\r]DA[\n\r]'),... + regexp(fstrm, '[\n\r]DD[\n\r]')]; +ind = sort(ind); +% Find line width commands +[ind2 ind3] = regexp(fstrm, '[\n\r]\d* w[\n\r]'); +% Go through each line style section and swap with any line width commands +% near by +b = 1; +m = numel(ind); +n = numel(ind2); +for a = 1:m + % Go forwards width commands until we pass the current line style + while b <= n && ind2(b) < ind(a) + b = b + 1; + end + if b > n + % No more width commands + break; + end + % Check we haven't gone past another line style (including SO!) + if a < m && ind2(b) > ind(a+1) + continue; + end + % Are the commands close enough to be confident we can swap them? + if (ind2(b) - ind(a)) > 8 + continue; + end + % Move the line style command below the line width command + fstrm(ind(a)+1:ind3(b)) = [fstrm(ind(a)+4:ind3(b)) fstrm(ind(a)+1:ind(a)+3)]; + b = b + 1; +end + +% Find any grid line definitions and change to GR format +% Find the DO sections again as they may have moved +ind = int32(regexp(fstrm, '[\n\r]DO[\n\r]')); +if ~isempty(ind) + % Find all occurrences of what are believed to be axes and grid lines + ind2 = int32(regexp(fstrm, '[\n\r] *\d* *\d* *mt *\d* *\d* *L[\n\r]')); + if ~isempty(ind2) + % Now see which DO sections come just before axes and grid lines + ind2 = repmat(ind2', [1 numel(ind)]) - repmat(ind, [numel(ind2) 1]); + ind2 = any(ind2 > 0 & ind2 < 12); % 12 chars seems about right + ind = ind(ind2); + % Change any regions we believe to be grid lines to GR + fstrm(ind+1) = 'G'; + fstrm(ind+2) = 'R'; + end +end + +% Isolate line style definition section +first_sec = strfind(fstrm, '% line types:'); +[second_sec remaining] = strtok(fstrm(first_sec+1:end), '/'); +[remaining remaining] = strtok(remaining, '%'); + +% Define the new styles, including the new GR format +% Dot and dash lengths have two parts: a constant amount plus a line width +% variable amount. The constant amount comes after dpi2point, and the +% variable amount comes after currentlinewidth. If you want to change +% dot/dash lengths for a one particular line style only, edit the numbers +% in the /DO (dotted lines), /DA (dashed lines), /DD (dot dash lines) and +% /GR (grid lines) lines for the style you want to change. +new_style = {'/dom { dpi2point 1 currentlinewidth 0.08 mul add mul mul } bdef',... % Dot length macro based on line width + '/dam { dpi2point 2 currentlinewidth 0.04 mul add mul mul } bdef',... % Dash length macro based on line width + '/SO { [] 0 setdash 0 setlinecap } bdef',... % Solid lines + '/DO { [1 dom 1.2 dom] 0 setdash 0 setlinecap } bdef',... % Dotted lines + '/DA { [4 dam 1.5 dam] 0 setdash 0 setlinecap } bdef',... % Dashed lines + '/DD { [1 dom 1.2 dom 4 dam 1.2 dom] 0 setdash 0 setlinecap } bdef',... % Dot dash lines + '/GR { [0 dpi2point mul 4 dpi2point mul] 0 setdash 1 setlinecap } bdef'}; % Grid lines - dot spacing remains constant + +if nargin < 2 + % Overwrite the input file + fname2 = fname; +end + +% Save the file with the section replaced +fh = fopen(fname2, 'w'); +if fh == -1 + error('Unable to open %s for writing.', fname2); +end +try + fwrite(fh, fstrm(1:first_sec), 'char*1'); + fwrite(fh, second_sec, 'char*1'); + fprintf(fh, '%s\r', new_style{:}); + fwrite(fh, remaining, 'char*1'); +catch ex + fclose(fh); + rethrow(ex); +end +fclose(fh); +return Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/ghostscript.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/ghostscript.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/ghostscript.m (revision 18231) @@ -0,0 +1,139 @@ +%GHOSTSCRIPT Calls a local GhostScript executable with the input command +% +% Example: +% [status result] = ghostscript(cmd) +% +% Attempts to locate a ghostscript executable, finally asking the user to +% specify the directory ghostcript was installed into. The resulting path +% is stored for future reference. +% +% Once found, the executable is called with the input command string. +% +% This function requires that you have Ghostscript installed on your +% system. You can download this from: http://www.ghostscript.com +% +% IN: +% cmd - Command string to be passed into ghostscript. +% +% OUT: +% status - 0 iff command ran without problem. +% result - Output from ghostscript. + +% Copyright: Oliver Woodford, 2009-2010 + +% Thanks to Jonas Dorn for the fix for the title of the uigetdir window on +% Mac OS. +% Thanks to Nathan Childress for the fix to the default location on 64-bit +% Windows systems. +% 27/4/11 - Find 64-bit Ghostscript on Windows. Thanks to Paul Durack and +% Shaun Kline for pointing out the issue +% 4/5/11 - Thanks to David Chorlian for pointing out an alternative +% location for gs on linux. +% 12/12/12 - Add extra executable name on Windows. Thanks to Ratish +% Punnoose for highlighting the issue. + +function varargout = ghostscript(cmd) +% Call ghostscript +[varargout{1:nargout}] = system(sprintf('"%s" %s', gs_path, cmd)); +return + +function path_ = gs_path +% Return a valid path +% Start with the currently set path +path_ = user_string('ghostscript'); +% Check the path works +if check_gs_path(path_) + return +end +% Check whether the binary is on the path +if ispc + bin = {'gswin32c.exe', 'gswin64c.exe', 'gs'}; +else + bin = {'gs'}; +end +for a = 1:numel(bin) + path_ = bin{a}; + if check_store_gs_path(path_) + return + end +end +% Search the obvious places +if ispc + default_location = 'C:\Program Files\gs\'; + dir_list = dir(default_location); + if isempty(dir_list) + default_location = 'C:\Program Files (x86)\gs\'; % Possible location on 64-bit systems + dir_list = dir(default_location); + end + executable = {'\bin\gswin32c.exe', '\bin\gswin64c.exe'}; + ver_num = 0; + % If there are multiple versions, use the newest + for a = 1:numel(dir_list) + ver_num2 = sscanf(dir_list(a).name, 'gs%g'); + if ~isempty(ver_num2) && ver_num2 > ver_num + for b = 1:numel(executable) + path2 = [default_location dir_list(a).name executable{b}]; + if exist(path2, 'file') == 2 + path_ = path2; + ver_num = ver_num2; + end + end + end + end + if check_store_gs_path(path_) + return + end +else + bin = {'/usr/bin/gs', '/usr/local/bin/gs'}; + for a = 1:numel(bin) + path_ = bin{a}; + if check_store_gs_path(path_) + return + end + end +end +% Ask the user to enter the path +while 1 + if strncmp(computer, 'MAC', 3) % Is a Mac + % Give separate warning as the uigetdir dialogue box doesn't have a + % title + uiwait(warndlg('Ghostscript not found. Please locate the program.')) + end + base = uigetdir('/', 'Ghostcript not found. Please locate the program.'); + if isequal(base, 0) + % User hit cancel or closed window + break; + end + base = [base filesep]; + bin_dir = {'', ['bin' filesep], ['lib' filesep]}; + for a = 1:numel(bin_dir) + for b = 1:numel(bin) + path_ = [base bin_dir{a} bin{b}]; + if exist(path_, 'file') == 2 + if check_store_gs_path(path_) + return + end + end + end + end +end +error('Ghostscript not found. Have you installed it from www.ghostscript.com?'); + +function good = check_store_gs_path(path_) +% Check the path is valid +good = check_gs_path(path_); +if ~good + return +end +% Update the current default path to the path found +if ~user_string('ghostscript', path_) + warning('Path to ghostscript installation could not be saved. Enter it manually in ghostscript.txt.'); + return +end +return + +function good = check_gs_path(path_) +% Check the path is valid +[good, message] = system(sprintf('"%s" -h', path_)); +good = good == 0; +return Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/isolate_axes.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/isolate_axes.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/isolate_axes.m (revision 18231) @@ -0,0 +1,113 @@ +%ISOLATE_AXES Isolate the specified axes in a figure on their own +% +% Examples: +% fh = isolate_axes(ah) +% fh = isolate_axes(ah, vis) +% +% This function will create a new figure containing the axes/uipanels +% specified, and also their associated legends and colorbars. The objects +% specified must all be in the same figure, but they will generally only be +% a subset of the objects in the figure. +% +% IN: +% ah - An array of axes and uipanel handles, which must come from the +% same figure. +% vis - A boolean indicating whether the new figure should be visible. +% Default: false. +% +% OUT: +% fh - The handle of the created figure. + +% Copyright (C) Oliver Woodford 2011-2012 + +% Thank you to Rosella Blatt for reporting a bug to do with axes in GUIs +% 16/3/2012 Moved copyfig to its own function. Thanks to Bob Fratantonio +% for pointing out that the function is also used in export_fig.m. +% 12/12/12 - Add support for isolating uipanels. Thanks to michael for +% suggesting it. + +function fh = isolate_axes(ah, vis) +% Make sure we have an array of handles +if ~all(ishandle(ah)) + error('ah must be an array of handles'); +end +% Check that the handles are all for axes or uipanels, and are all in the same figure +fh = ancestor(ah(1), 'figure'); +nAx = numel(ah); +for a = 1:nAx + if ~ismember(get(ah(a), 'Type'), {'axes', 'uipanel'}) + error('All handles must be axes or uipanel handles.'); + end + if ~isequal(ancestor(ah(a), 'figure'), fh) + error('Axes must all come from the same figure.'); + end +end +% Tag the objects so we can find them in the copy +old_tag = get(ah, 'Tag'); +if nAx == 1 + old_tag = {old_tag}; +end +set(ah, 'Tag', 'ObjectToCopy'); +% Create a new figure exactly the same as the old one +fh = copyfig(fh); %copyobj(fh, 0); +if nargin < 2 || ~vis + set(fh, 'Visible', 'off'); +end +% Reset the object tags +for a = 1:nAx + set(ah(a), 'Tag', old_tag{a}); +end +% Find the objects to save +ah = findall(fh, 'Tag', 'ObjectToCopy'); +if numel(ah) ~= nAx + close(fh); + error('Incorrect number of objects found.'); +end +% Set the axes tags to what they should be +for a = 1:nAx + set(ah(a), 'Tag', old_tag{a}); +end +% Keep any legends and colorbars which overlap the subplots +lh = findall(fh, 'Type', 'axes', '-and', {'Tag', 'legend', '-or', 'Tag', 'Colorbar'}); +nLeg = numel(lh); +if nLeg > 0 + ax_pos = get(ah, 'OuterPosition'); + if nAx > 1 + ax_pos = cell2mat(ax_pos(:)); + end + ax_pos(:,3:4) = ax_pos(:,3:4) + ax_pos(:,1:2); + leg_pos = get(lh, 'OuterPosition'); + if nLeg > 1; + leg_pos = cell2mat(leg_pos); + end + leg_pos(:,3:4) = leg_pos(:,3:4) + leg_pos(:,1:2); + for a = 1:nAx + % Overlap test + ah = [ah; lh(leg_pos(:,1) < ax_pos(a,3) & leg_pos(:,2) < ax_pos(a,4) &... + leg_pos(:,3) > ax_pos(a,1) & leg_pos(:,4) > ax_pos(a,2))]; + end +end +% Get all the objects in the figure +axs = findall(fh); +% Delete everything except for the input objects and associated items +delete(axs(~ismember(axs, [ah; allchildren(ah); allancestors(ah)]))); +return + +function ah = allchildren(ah) +ah = allchild(ah); +if iscell(ah) + ah = cell2mat(ah); +end +ah = ah(:); +return + +function ph = allancestors(ah) +ph = []; +for a = 1:numel(ah) + h = get(ah(a), 'parent'); + while h ~= 0 + ph = [ph; h]; + h = get(h, 'parent'); + end +end +return Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/license.txt =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/license.txt (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/license.txt (revision 18231) @@ -0,0 +1,24 @@ +Copyright (c) 2012, Oliver Woodford +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are +met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in + the documentation and/or other materials provided with the distribution + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE +LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/pdf2eps.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/pdf2eps.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/pdf2eps.m (revision 18231) @@ -0,0 +1,51 @@ +%PDF2EPS Convert a pdf file to eps format using pdftops +% +% Examples: +% pdf2eps source dest +% +% This function converts a pdf file to eps format. +% +% This function requires that you have pdftops, from the Xpdf suite of +% functions, installed on your system. This can be downloaded from: +% http://www.foolabs.com/xpdf +% +%IN: +% source - filename of the source pdf file to convert. The filename is +% assumed to already have the extension ".pdf". +% dest - filename of the destination eps file. The filename is assumed to +% already have the extension ".eps". + +% Copyright (C) Oliver Woodford 2009-2010 + +% Thanks to Aldebaro Klautau for reporting a bug when saving to +% non-existant directories. + +function pdf2eps(source, dest) +% Construct the options string for pdftops +options = ['-q -paper match -eps -level2 "' source '" "' dest '"']; +% Convert to eps using pdftops +[status message] = pdftops(options); +% Check for error +if status + % Report error + if isempty(message) + error('Unable to generate eps. Check destination directory is writable.'); + else + error(message); + end +end +% Fix the DSC error created by pdftops +fid = fopen(dest, 'r+'); +if fid == -1 + % Cannot open the file + return +end +fgetl(fid); % Get the first line +str = fgetl(fid); % Get the second line +if strcmp(str(1:min(13, end)), '% Produced by') + fseek(fid, -numel(str)-1, 'cof'); + fwrite(fid, '%'); % Turn ' ' into '%' +end +fclose(fid); +return + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/pdftops.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/pdftops.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/pdftops.m (revision 18231) @@ -0,0 +1,107 @@ +function varargout = pdftops(cmd) +%PDFTOPS Calls a local pdftops executable with the input command +% +% Example: +% [status result] = pdftops(cmd) +% +% Attempts to locate a pdftops executable, finally asking the user to +% specify the directory pdftops was installed into. The resulting path is +% stored for future reference. +% +% Once found, the executable is called with the input command string. +% +% This function requires that you have pdftops (from the Xpdf package) +% installed on your system. You can download this from: +% http://www.foolabs.com/xpdf +% +% IN: +% cmd - Command string to be passed into pdftops. +% +% OUT: +% status - 0 iff command ran without problem. +% result - Output from pdftops. + +% Copyright: Oliver Woodford, 2009-2010 + +% Thanks to Jonas Dorn for the fix for the title of the uigetdir window on +% Mac OS. +% Thanks to Christoph Hertel for pointing out a bug in check_xpdf_path +% under linux. + +% Call pdftops +[varargout{1:nargout}] = system(sprintf('"%s" %s', xpdf_path, cmd)); +return + +function path_ = xpdf_path +% Return a valid path +% Start with the currently set path +path_ = user_string('pdftops'); +% Check the path works +if check_xpdf_path(path_) + return +end +% Check whether the binary is on the path +if ispc + bin = 'pdftops.exe'; +else + bin = 'pdftops'; +end +if check_store_xpdf_path(bin) + path_ = bin; + return +end +% Search the obvious places +if ispc + path_ = 'C:\Program Files\xpdf\pdftops.exe'; +else + path_ = '/usr/local/bin/pdftops'; +end +if check_store_xpdf_path(path_) + return +end +% Ask the user to enter the path +while 1 + if strncmp(computer,'MAC',3) % Is a Mac + % Give separate warning as the uigetdir dialogue box doesn't have a + % title + uiwait(warndlg('Pdftops not found. Please locate the program, or install xpdf-tools from http://users.phg-online.de/tk/MOSXS/.')) + end + base = uigetdir('/', 'Pdftops not found. Please locate the program.'); + if isequal(base, 0) + % User hit cancel or closed window + break; + end + base = [base filesep]; + bin_dir = {'', ['bin' filesep], ['lib' filesep]}; + for a = 1:numel(bin_dir) + path_ = [base bin_dir{a} bin]; + if exist(path_, 'file') == 2 + break; + end + end + if check_store_xpdf_path(path_) + return + end +end +error('pdftops executable not found.'); + +function good = check_store_xpdf_path(path_) +% Check the path is valid +good = check_xpdf_path(path_); +if ~good + return +end +% Update the current default path to the path found +if ~user_string('pdftops', path_) + warning('Path to pdftops executable could not be saved. Enter it manually in pdftops.txt.'); + return +end +return + +function good = check_xpdf_path(path_) +% Check the path is valid +[good message] = system(sprintf('"%s" -h', path_)); +% system returns good = 1 even when the command runs +% Look for something distinct in the help text +good = ~isempty(strfind(message, 'PostScript')); +return Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/print2array.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/print2array.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/print2array.m (revision 18231) @@ -0,0 +1,198 @@ +%PRINT2ARRAY Exports a figure to an image array +% +% Examples: +% A = print2array +% A = print2array(figure_handle) +% A = print2array(figure_handle, resolution) +% A = print2array(figure_handle, resolution, renderer) +% [A bcol] = print2array(...) +% +% This function outputs a bitmap image of the given figure, at the desired +% resolution. +% +% If renderer is '-painters' then ghostcript needs to be installed. This +% can be downloaded from: http://www.ghostscript.com +% +% IN: +% figure_handle - The handle of the figure to be exported. Default: gcf. +% resolution - Resolution of the output, as a factor of screen +% resolution. Default: 1. +% renderer - string containing the renderer paramater to be passed to +% print. Default: '-opengl'. +% +% OUT: +% A - MxNx3 uint8 image of the figure. +% bcol - 1x3 uint8 vector of the background color + +% Copyright (C) Oliver Woodford 2008-2012 + +% 05/09/11: Set EraseModes to normal when using opengl or zbuffer +% renderers. Thanks to Pawel Kocieniewski for reporting the +% issue. +% 21/09/11: Bug fix: unit8 -> uint8! Thanks to Tobias Lamour for reporting +% the issue. +% 14/11/11: Bug fix: stop using hardcopy(), as it interfered with figure +% size and erasemode settings. Makes it a bit slower, but more +% reliable. Thanks to Phil Trinh and Meelis Lootus for reporting +% the issues. +% 09/12/11: Pass font path to ghostscript. +% 27/01/12: Bug fix affecting painters rendering tall figures. Thanks to +% Ken Campbell for reporting it. +% 03/04/12: Bug fix to median input. Thanks to Andy Matthews for reporting +% it. +% 26/10/12: Set PaperOrientation to portrait. Thanks to Michael Watts for +% reporting the issue. + +function [A, bcol] = print2array(fig, res, renderer) +% Generate default input arguments, if needed +if nargin < 2 + res = 1; + if nargin < 1 + fig = gcf; + end +end +% Warn if output is large +old_mode = get(fig, 'Units'); +set(fig, 'Units', 'pixels'); +px = get(fig, 'Position'); +set(fig, 'Units', old_mode); +npx = prod(px(3:4)*res)/1e6; +if npx > 30 + % 30M pixels or larger! + warning('MATLAB:LargeImage', 'print2array generating a %.1fM pixel image. This could be slow and might also cause memory problems.', npx); +end +% Retrieve the background colour +bcol = get(fig, 'Color'); +% Set the resolution parameter +res_str = ['-r' num2str(ceil(get(0, 'ScreenPixelsPerInch')*res))]; +% Generate temporary file name +tmp_nam = [tempname '.tif']; +if nargin > 2 && strcmp(renderer, '-painters') + % Print to eps file + tmp_eps = [tempname '.eps']; + print2eps(tmp_eps, fig, renderer, '-loose'); + try + % Initialize the command to export to tiff using ghostscript + cmd_str = ['-dEPSCrop -q -dNOPAUSE -dBATCH ' res_str ' -sDEVICE=tiff24nc']; + % Set the font path + fp = font_path(); + if ~isempty(fp) + cmd_str = [cmd_str ' -sFONTPATH="' fp '"']; + end + % Add the filenames + cmd_str = [cmd_str ' -sOutputFile="' tmp_nam '" "' tmp_eps '"']; + % Execute the ghostscript command + ghostscript(cmd_str); + catch me + % Delete the intermediate file + delete(tmp_eps); + rethrow(me); + end + % Delete the intermediate file + delete(tmp_eps); + % Read in the generated bitmap + A = imread(tmp_nam); + % Delete the temporary bitmap file + delete(tmp_nam); + % Set border pixels to the correct colour + if isequal(bcol, 'none') + bcol = []; + elseif isequal(bcol, [1 1 1]) + bcol = uint8([255 255 255]); + else + for l = 1:size(A, 2) + if ~all(reshape(A(:,l,:) == 255, [], 1)) + break; + end + end + for r = size(A, 2):-1:l + if ~all(reshape(A(:,r,:) == 255, [], 1)) + break; + end + end + for t = 1:size(A, 1) + if ~all(reshape(A(t,:,:) == 255, [], 1)) + break; + end + end + for b = size(A, 1):-1:t + if ~all(reshape(A(b,:,:) == 255, [], 1)) + break; + end + end + bcol = uint8(median(single([reshape(A(:,[l r],:), [], size(A, 3)); reshape(A([t b],:,:), [], size(A, 3))]), 1)); + for c = 1:size(A, 3) + A(:,[1:l-1, r+1:end],c) = bcol(c); + A([1:t-1, b+1:end],:,c) = bcol(c); + end + end +else + if nargin < 3 + renderer = '-opengl'; + end + err = false; + % Set paper size + old_pos_mode = get(fig, 'PaperPositionMode'); + old_orientation = get(fig, 'PaperOrientation'); + set(fig, 'PaperPositionMode', 'auto', 'PaperOrientation', 'portrait'); + try + % Print to tiff file + print(fig, renderer, res_str, '-dtiff', tmp_nam); + % Read in the printed file + A = imread(tmp_nam); + % Delete the temporary file + delete(tmp_nam); + catch ex + err = true; + end + % Reset paper size + set(fig, 'PaperPositionMode', old_pos_mode, 'PaperOrientation', old_orientation); + % Throw any error that occurred + if err + rethrow(ex); + end + % Set the background color + if isequal(bcol, 'none') + bcol = []; + else + bcol = bcol * 255; + if isequal(bcol, round(bcol)) + bcol = uint8(bcol); + else + bcol = squeeze(A(1,1,:)); + end + end +end +% Check the output size is correct +if isequal(res, round(res)) + px = [px([4 3])*res 3]; + if ~isequal(size(A), px) + % Correct the output size + A = A(1:min(end,px(1)),1:min(end,px(2)),:); + end +end +return + +% Function to return (and create, where necessary) the font path +function fp = font_path() +fp = user_string('gs_font_path'); +if ~isempty(fp) + return +end +% Create the path +% Start with the default path +fp = getenv('GS_FONTPATH'); +% Add on the typical directories for a given OS +if ispc + if ~isempty(fp) + fp = [fp ';']; + end + fp = [fp getenv('WINDIR') filesep 'Fonts']; +else + if ~isempty(fp) + fp = [fp ':']; + end + fp = [fp '/usr/share/fonts:/usr/local/share/fonts:/usr/share/fonts/X11:/usr/local/share/fonts/X11:/usr/share/fonts/truetype:/usr/local/share/fonts/truetype']; +end +user_string('gs_font_path', fp); +return Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/print2eps.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/print2eps.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/print2eps.m (revision 18231) @@ -0,0 +1,206 @@ +%PRINT2EPS Prints figures to eps with improved line styles +% +% Examples: +% print2eps filename +% print2eps(filename, fig_handle) +% print2eps(filename, fig_handle, options) +% +% This function saves a figure as an eps file, with two improvements over +% MATLAB's print command. First, it improves the line style, making dashed +% lines more like those on screen and giving grid lines their own dotted +% style. Secondly, it substitutes original font names back into the eps +% file, where these have been changed by MATLAB, for up to 11 different +% fonts. +% +%IN: +% filename - string containing the name (optionally including full or +% relative path) of the file the figure is to be saved as. A +% ".eps" extension is added if not there already. If a path is +% not specified, the figure is saved in the current directory. +% fig_handle - The handle of the figure to be saved. Default: gcf. +% options - Additional parameter strings to be passed to print. + +% Copyright (C) Oliver Woodford 2008-2013 + +% The idea of editing the EPS file to change line styles comes from Jiro +% Doke's FIXPSLINESTYLE (fex id: 17928) +% The idea of changing dash length with line width came from comments on +% fex id: 5743, but the implementation is mine :) + +% 14/11/2011: Fix a MATLAB bug rendering black or white text incorrectly. +% Thanks to Mathieu Morlighem for reporting the issue and +% obtaining a fix from TMW. +% 08/12/11: Added ability to correct fonts. Several people have requested +% this at one time or another, and also pointed me to printeps +% (fex id: 7501), so thank you to them. My implementation (which +% was not inspired by printeps - I'd already had the idea for my +% approach) goes slightly further in that it allows multiple +% fonts to be swapped. +% 14/12/11: Fix bug affecting font names containing spaces. Thanks to David +% Szwer for reporting the issue. +% 25/01/12: Add a font not to be swapped. Thanks to Anna Rafferty and Adam +% Jackson for reporting the issue. Also fix a bug whereby using a +% font alias can lead to another font being swapped in. +% 10/04/12: Make the font swapping case insensitive. +% 26/10/12: Set PaperOrientation to portrait. Thanks to Michael Watts for +% reporting the issue. +% 26/10/12: Fix issue to do with swapping fonts changing other fonts and +% sizes we don't want, due to listeners. Thanks to Malcolm Hudson +% for reporting the issue. +% 22/03/13: Extend font swapping to axes labels. Thanks to Rasmus Ischebeck +% for reporting the issue. + +function print2eps(name, fig, varargin) +options = {'-depsc2'}; +if nargin < 2 + fig = gcf; +elseif nargin > 2 + options = [options varargin]; +end +% Construct the filename +if numel(name) < 5 || ~strcmpi(name(end-3:end), '.eps') + name = [name '.eps']; % Add the missing extension +end +% Find all the used fonts in the figure +font_handles = findall(fig, '-property', 'FontName'); +fonts = get(font_handles, 'FontName'); +if ~iscell(fonts) + fonts = {fonts}; +end +% Map supported font aliases onto the correct name +fontsl = lower(fonts); +for a = 1:numel(fonts) + f = fontsl{a}; + f(f==' ') = []; + switch f + case {'times', 'timesnewroman', 'times-roman'} + fontsl{a} = 'times-roman'; + case {'arial', 'helvetica'} + fontsl{a} = 'helvetica'; + case {'newcenturyschoolbook', 'newcenturyschlbk'} + fontsl{a} = 'newcenturyschlbk'; + otherwise + end +end +fontslu = unique(fontsl); +% Determine the font swap table +matlab_fonts = {'Helvetica', 'Times-Roman', 'Palatino', 'Bookman', 'Helvetica-Narrow', 'Symbol', ... + 'AvantGarde', 'NewCenturySchlbk', 'Courier', 'ZapfChancery', 'ZapfDingbats'}; +matlab_fontsl = lower(matlab_fonts); +require_swap = find(~ismember(fontslu, matlab_fontsl)); +unused_fonts = find(~ismember(matlab_fontsl, fontslu)); +font_swap = cell(3, min(numel(require_swap), numel(unused_fonts))); +fonts_new = fonts; +for a = 1:size(font_swap, 2) + font_swap{1,a} = find(strcmp(fontslu{require_swap(a)}, fontsl)); + font_swap{2,a} = matlab_fonts{unused_fonts(a)}; + font_swap{3,a} = fonts{font_swap{1,end}(1)}; + fonts_new(font_swap{1,a}) = {font_swap{2,a}}; +end +% Swap the fonts +if ~isempty(font_swap) + fonts_size = get(font_handles, 'FontSize'); + if iscell(fonts_size) + fonts_size = cell2mat(fonts_size); + end + M = false(size(font_handles)); + % Loop because some changes may not stick first time, due to listeners + c = 0; + update = zeros(1000, 1); + for b = 1:10 % Limit number of loops to avoid infinite loop case + for a = 1:numel(M) + M(a) = ~isequal(get(font_handles(a), 'FontName'), fonts_new{a}) || ~isequal(get(font_handles(a), 'FontSize'), fonts_size(a)); + if M(a) + set(font_handles(a), 'FontName', fonts_new{a}, 'FontSize', fonts_size(a)); + c = c + 1; + update(c) = a; + end + end + if ~any(M) + break; + end + end + % Compute the order to revert fonts later, without the need of a loop + [update, M] = unique(update(1:c)); + [M, M] = sort(M); + update = reshape(update(M), 1, []); +end +% Set paper size +old_pos_mode = get(fig, 'PaperPositionMode'); +old_orientation = get(fig, 'PaperOrientation'); +set(fig, 'PaperPositionMode', 'auto', 'PaperOrientation', 'portrait'); +% MATLAB bug fix - black and white text can come out inverted sometimes +% Find the white and black text +white_text_handles = findobj(fig, 'Type', 'text'); +M = get(white_text_handles, 'Color'); +if iscell(M) + M = cell2mat(M); +end +M = sum(M, 2); +black_text_handles = white_text_handles(M == 0); +white_text_handles = white_text_handles(M == 3); +% Set the font colors slightly off their correct values +set(black_text_handles, 'Color', [0 0 0] + eps); +set(white_text_handles, 'Color', [1 1 1] - eps); +% Print to eps file +print(fig, options{:}, name); +% Reset the font colors +set(black_text_handles, 'Color', [0 0 0]); +set(white_text_handles, 'Color', [1 1 1]); +% Reset paper size +set(fig, 'PaperPositionMode', old_pos_mode, 'PaperOrientation', old_orientation); +% Correct the fonts +if ~isempty(font_swap) + % Reset the font names in the figure + for a = update + set(font_handles(a), 'FontName', fonts{a}, 'FontSize', fonts_size(a)); + end + % Replace the font names in the eps file + font_swap = font_swap(2:3,:); + try + swap_fonts(name, font_swap{:}); + catch + warning('swap_fonts() failed. This is usually because the figure contains a large number of patch objects. Consider exporting to a bitmap format in this case.'); + return + end +end +% Fix the line styles +try + fix_lines(name); +catch + warning('fix_lines() failed. This is usually because the figure contains a large number of patch objects. Consider exporting to a bitmap format in this case.'); +end +return + +function swap_fonts(fname, varargin) +% Read in the file +fh = fopen(fname, 'r'); +if fh == -1 + error('File %s not found.', fname); +end +try + fstrm = fread(fh, '*char')'; +catch ex + fclose(fh); + rethrow(ex); +end +fclose(fh); + +% Replace the font names +for a = 1:2:numel(varargin) + fstrm = regexprep(fstrm, [varargin{a} '-?[a-zA-Z]*\>'], varargin{a+1}(~isspace(varargin{a+1}))); +end + +% Write out the updated file +fh = fopen(fname, 'w'); +if fh == -1 + error('Unable to open %s for writing.', fname2); +end +try + fwrite(fh, fstrm, 'char*1'); +catch ex + fclose(fh); + rethrow(ex); +end +fclose(fh); +return Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/user_string.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/user_string.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/export_fig/user_string.m (revision 18231) @@ -0,0 +1,87 @@ +%USER_STRING Get/set a user specific string +% +% Examples: +% string = user_string(string_name) +% saved = user_string(string_name, new_string) +% +% Function to get and set a string in a system or user specific file. This +% enables, for example, system specific paths to binaries to be saved. +% +% IN: +% string_name - String containing the name of the string required. The +% string is extracted from a file called (string_name).txt, +% stored in the same directory as user_string.m. +% new_string - The new string to be saved under the name given by +% string_name. +% +% OUT: +% string - The currently saved string. Default: ''. +% saved - Boolean indicating whether the save was succesful + +% Copyright (C) Oliver Woodford 2011-2013 + +% This method of saving paths avoids changing .m files which might be in a +% version control system. Instead it saves the user dependent paths in +% separate files with a .txt extension, which need not be checked in to +% the version control system. Thank you to Jonas Dorn for suggesting this +% approach. + +% 10/01/2013 - Access files in text, not binary mode, as latter can cause +% errors. Thanks to Christian for pointing this out. + +function string = user_string(string_name, string) +if ~ischar(string_name) + error('string_name must be a string.'); +end +% Create the full filename +string_name = fullfile(fileparts(mfilename('fullpath')), '.ignore', [string_name '.txt']); +if nargin > 1 + % Set string + if ~ischar(string) + error('new_string must be a string.'); + end + % Make sure the save directory exists + dname = fileparts(string_name); + if ~exist(dname, 'dir') + % Create the directory + try + if ~mkdir(dname) + string = false; + return + end + catch + string = false; + return + end + % Make it hidden + try + fileattrib(dname, '+h'); + catch + end + end + % Write the file + fid = fopen(string_name, 'wt'); + if fid == -1 + string = false; + return + end + try + fprintf(fid, '%s', string); + catch + fclose(fid); + string = false; + return + end + fclose(fid); + string = true; +else + % Get string + fid = fopen(string_name, 'rt'); + if fid == -1 + string = ''; + return + end + string = fgetl(fid); + fclose(fid); +end +return Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/ffmpeg/install-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/ffmpeg/install-macosx64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/ffmpeg/install-macosx64.sh (revision 18231) @@ -0,0 +1,31 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install ffmpeg-1.1.2 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ffmpeg-1.1.2.tar.gz' 'ffmpeg-1.1.2.tar.gz' + +#Untar +tar -zxvf ffmpeg-1.1.2.tar.gz + +#Move ffmpeg into src directory +mv ffmpeg-1.1.2/* src +rm -rf ffmpeg-1.1.2 + +#Configure ffmpeg +cd src + +export CFLAGS=" -arch x86_64" + +./configure --prefix="$ISSM_DIR/externalpackages/ffmpeg/install" --disable-yasm + +#Compile ffmpeg +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/findbugs/README =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/findbugs/README (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/findbugs/README (revision 18231) @@ -0,0 +1,2 @@ +Fingbugs for Java programs. +Downloaded from http://findbugs.sourceforge.net/downloads.html Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/findbugs/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/findbugs/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/findbugs/install.sh (revision 18231) @@ -0,0 +1,13 @@ +#!/bin/bash +set -eu + +#Erase install +rm -rf install findbugs-1.3.9 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/findbugs-1.3.9.tar.gz' 'findbugs-1.3.9.tar.gz' +tar -zxvf findbugs-1.3.9.tar.gz + +mv findbugs-1.3.9/* install +rm -rf findbugs-1.3.9 Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/flaim/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/flaim/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/flaim/install.sh (revision 18231) @@ -0,0 +1,8 @@ +#!/bin/bash +set -eu + +#Erase symlink +rm -rf install + +#symlink to flaim directory +ln -s /home/jschierm/flaim/svn/trunk ./install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/freetype/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/freetype/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/freetype/install.sh (revision 18231) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf freetype-2.5.0 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/freetype-2.5.0.tar.gz' 'freetype-2.5.0.tar.gz' + +#Untar +tar -zxvf freetype-2.5.0.tar.gz + +#Move freetype into src directory +mv freetype-2.5.0/* src +rm -rf freetype-2.5.0 + +#Configure freetype +cd src +sudo ./configure + +#Compile and install freetype +if [ $# -eq 0 ]; then + sudo make +else + sudo make -j $1 +fi +sudo make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/fti/Makefile =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/fti/Makefile (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/fti/Makefile (revision 18231) @@ -0,0 +1,90 @@ +## * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * +##* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * +##======================================================================= +##Copyright (C) 2010-2013 Leonardo A. BAUTISTA GOMEZ +##This program is free software; you can redistribute it and/or modify +##it under the terms of the GNU General Public License (GPL) as published +##of the License, or (at your option) any later version. +## +##This program is distributed in the hope that it will be useful, +##but WITHOUT ANY WARRANTY; without even the implied warranty of +##MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +##GNU General Public License for more details. +## +##To read the license please visit http://www.gnu.org/copyleft/gpl.html +##======================================================================= + +##======================================================================= +## PLEASE SET THESE VARIABLES BEFORE COMPILING +##======================================================================= + +FTIPATH = $(ISSM_DIR)/externalpackages/fti/install +MPIPATH = $(ISSM_DIR)/externalpackages/mpich/install + +##======================================================================= +## DIRECTORY TREE +##======================================================================= + +LIB = lib +OBJ = obj +SRC = src +DOC = doc +INC = include + +##======================================================================= +## COMPILERS +##======================================================================= + +CC = gcc +MPICC = mpicc + +##======================================================================= +## FLAGS +##======================================================================= + +FTIFLAGS = -fPIC -g -Iinclude/ -c +MPIFLAGS = -I$(MPIPATH)/include -L$(MPIPATH)/lib -lmpich -lpmpich + +##======================================================================= +## TARGETS +##======================================================================= + + +OBJS = $(OBJ)/galois.o $(OBJ)/jerasure.o $(OBJ)/dictionary.o $(OBJ)/iniparser.o \ + $(OBJ)/recover.o $(OBJ)/tools.o $(OBJ)/checkpoint.o $(OBJ)/topo.o \ + $(OBJ)/api.o + +SHARED = libfti.so +STATIC = libfti.a + +all: $(SHARED) $(STATIC) + +doc: + doxygen $(DOC)/Doxyfile + +$(OBJ)/%.o: $(SRC)/%.c + $(MPICC) $(FTIFLAGS) $< -o $@ + +$(SHARED): $(OBJS) + $(CC) $(MPIFLAGS) -shared -o $(LIB)/$(SHARED) $(OBJS) -lc + +$(STATIC): $(OBJS) + $(AR) -cvq $(LIB)/$(STATIC) $(OBJS) +install: + if [ ! -d "$(FTIPATH)/FTI" ]; then mkdir $(FTIPATH)/FTI; fi + if [ ! -d "$(FTIPATH)/FTI/$(LIB)" ]; then mkdir $(FTIPATH)/FTI/$(LIB); fi + if [ ! -d "$(FTIPATH)/FTI/$(INC)" ]; then mkdir $(FTIPATH)/FTI/$(INC); fi + rm -f $(FTIPATH)/FTI/$(LIB)/* $(FTIPATH)/FTI/$(INC)/* + cp $(INC)/* $(FTIPATH)/FTI/$(INC)/ + cp $(LIB)/* $(FTIPATH)/FTI/$(LIB)/ + +uninstall: + rm -f $(FTIPATH)/FTI/$(LIB)/* $(FTIPATH)/FTI/$(INC)/* + if [ -d "$(FTIPATH)/FTI/$(LIB)" ]; then rmdir $(FTIPATH)/FTI/$(LIB); fi + if [ -d "$(FTIPATH)/FTI/$(INC)" ]; then rmdir $(FTIPATH)/FTI/$(INC); fi + if [ -d "$(FTIPATH)/FTI" ]; then rmdir $(FTIPATH)/FTI; fi + +clean: + rm -f $(OBJ)/* $(LIB)/* + +.PHONY: $(SHARED) $(STATIC) doc install uninstall clean Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/fti/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/fti/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/fti/install.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install fti-0.9.2 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/fti-0.9.2.tgz' 'fti-0.9.2.tgz' + +#Untar +tar -zxvf fti-0.9.2.tgz + +#Move mpich into src directory +mv fti/* install +rm -rf fti + +#Configure mpich +cd install +cp ../Makefile . + +#Compile mpich (this new version supports parallel make) +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gdal/configs/GDALmake.opt.patch.murdo =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gdal/configs/GDALmake.opt.patch.murdo (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gdal/configs/GDALmake.opt.patch.murdo (revision 18231) @@ -0,0 +1,8 @@ +31c31 +< LIBS = $(SDE_LIB) -I/usr/include -lsqlite3 -L/usr/lib -lexpat -ljpeg -lpng -lz -lm -lrt -ldl $(KAK_LIBS) $(DWG_LIBS) $(CURL_LIB) \ +--- +> LIBS = $(SDE_LIB) -I/usr/include -lsqlite3 -L/usr/lib64 -lexpat -ljpeg -lpng -lz -lm -lrt -ldl $(KAK_LIBS) $(DWG_LIBS) $(CURL_LIB) \ +225c225 +< CURL_LIB = -L/usr/kerberos/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz +--- +> CURL_LIB = -L/usr/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gdal/install-1.10-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gdal/install-1.10-linux64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gdal/install-1.10-linux64.sh (revision 18231) @@ -0,0 +1,37 @@ +#!/bin/bash +set -eu + +#WARNING: you need to have python installed in externalpackages + +#Some cleanup +rm -rf src +rm -rf install +rm -rf gdal-1.10.0 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.10.0.tar.gz' 'gdal-1.10.0.tar.gz' + +#Untar +tar -zxvf gdal-1.10.0.tar.gz + +#Move gdal into src directory +mv gdal-1.10.0/* src +rm -rf gdal-1.10.0 + +#Configure gdal +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/gdal/install" \ + --with-python \ + --with-netcdf=no \ + --with-jasper=no \ + --without-hdf5 + +#Compile and install gdal +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gdal/install-1.10-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gdal/install-1.10-macosx64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gdal/install-1.10-macosx64.sh (revision 18231) @@ -0,0 +1,38 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf gdal-1.10.0 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.10.0.tar.gz' 'gdal-1.10.0.tar.gz' + +#Untar +tar -zxvf gdal-1.10.0.tar.gz + +#Move gdal into src directory +mv gdal-1.10.0/* src +rm -rf gdal-1.10.0 + +#Configure gdal +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/gdal/install" \ + --with-python \ + --with-netcdf=no \ + --with-libiconv-prefix="/usr/lib/" \ + --without-hdf5 \ + --with-expat=$ISSM_DIR/externalpackages/expat/install +#Note: +# look for libiconv in /usr/lib/ because there seemed to be a conflict with port's library + +#Compile and install gdal +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gdal/install-1.6-linux64-murdo.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gdal/install-1.6-linux64-murdo.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gdal/install-1.6-linux64-murdo.sh (revision 18231) @@ -0,0 +1,39 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf gdal-1.6.0 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz' + +#Untar +tar -zxvf gdal-1.6.0.tar.gz + +#Move gdal into src directory +mv gdal-1.6.0/* src +rm -rf gdal-1.6.0 + +#Configure gdal +cd src +./configure --prefix="$ISSM_DIR/externalpackages/gdal/install" \ + --without-python \ + --without-png \ + --with-netcdf=no \ + --with-jasper=no \ + --without-ld-shared \ + --with-unix-stdio-64=no + +#Patch GDALmake.opt +patch GDALmake.opt ../configs/GDALmake.opt.patch + +#Compile and install gdal +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gdal/install-1.6-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gdal/install-1.6-macosx64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gdal/install-1.6-macosx64.sh (revision 18231) @@ -0,0 +1,39 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf gdal-1.6.0 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz' + +#Untar +tar -zxvf gdal-1.6.0.tar.gz + +#Move gdal into src directory +mv gdal-1.6.0/* src +rm -rf gdal-1.6.0 + +#Configure gdal +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/gdal/install" \ + --without-python \ + --without-png \ + --with-netcdf=no \ + --with-jasper=no \ + --without-ld-shared \ + --without-hdf5 \ + --with-unix-stdio-64=no \ + --with-expat=$ISSM_DIR/externalpackages/expat/install + +#Compile and install gdal +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/geos5/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/geos5/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/geos5/install.sh (revision 18231) @@ -0,0 +1,7 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf GEOSagcm +#svn download +svn --username eric.larour@jpl.nasa.gov checkout http://geos5.org/svn/branches/Fortuna-2_5_p1 GEOSagcm Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gfortran/README =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gfortran/README (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gfortran/README (revision 18231) @@ -0,0 +1,7 @@ +For Mac users, you can download a fortran compiler on: +http://gcc.gnu.org/wiki/GFortranBinaries + +Other websites: +http://www.macresearch.org/gfortran-leopard +http://hpc.sourceforge.net/ +http://r.research.att.com/tools/ or http://cran.r-project.org/bin/macosx/tools/ Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/git/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/git/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/git/install.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install git-1.7.10.2 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/git-1.7.10.2.tar.gz' 'git-1.7.10.2.tar.gz' + +#Untar +tar -zxvf git-1.7.10.2.tar.gz + +#Move git into install directory +mv git-1.7.10.2/* src +rm -rf git-1.7.10.2 + +#install +cd src +./configure --prefix="$ISSM_DIR/externalpackages/git/install" +#--with-python="$ISSM_DIR/externalpackages/python/install/bin/python" #Do we really need this line? + +#Compile +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gmake/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gmake/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gmake/install.sh (revision 18231) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src make-3.82 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/make-3.82.tar.gz' 'make-3.82.tar.gz' + +#Untar +tar -zxvf make-3.82.tar.gz + +#Move make into install directory +mv make-3.82/* src +rm -rf make-3.82 + +#Apply patches +cd src + +#Configure and compile: +./configure --prefix=$ISSM_DIR/externalpackages/gmake/install + +if [ $# -eq 0 ]; then + make + make install +else + make -j $1; + make -j $1 install; +fi Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gmp/install-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gmp/install-linux64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gmp/install-linux64.sh (revision 18231) @@ -0,0 +1,29 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install gmp-5.0.5 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gmp-5.0.5.tar.bz2' 'gmp-5.0.5.tar.bz2' + +#Untar +bunzip2 gmp-5.0.5.tar.bz2 +tar -xvf gmp-5.0.5.tar + +#Move gmp into install directory +mv gmp-5.0.5/* src +rm -rf gmp-5.0.5 + +#install +cd src +./configure --prefix="$ISSM_DIR/externalpackages/gmp/install" + +#Compile and install gmp +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gmsh/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gmsh/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gmsh/install.sh (revision 18231) @@ -0,0 +1,21 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +mkdir install + +#Download latest version +svn --username gmsh --password gmsh co https://geuz.org/svn/gmsh/trunk src + +#Configure +cd install +cmake ../src -DCMAKE_INSTALL_PREFIX="$ISSM_DIR/externalpackages/gmsh/install" + +#Compile and install +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/googleearthtoolbox/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/googleearthtoolbox/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/googleearthtoolbox/install.sh (revision 18231) @@ -0,0 +1,8 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install + +#Download code: +svn checkout http://googleearthtoolbox.googlecode.com/svn/trunk/ install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/graphviz/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/graphviz/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/graphviz/install.sh (revision 18231) @@ -0,0 +1,31 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/graphviz-2.24.0.tar.gz' 'graphviz-2.24.0.tar.gz' + +#Untar +tar -zxvf graphviz-2.24.0.tar.gz + +#Move Dakota to src directory +mv graphviz-2.24.0/* src/ +rm -rf graphviz-2.24.0 + +#Configure dakota +cd src +./configure --prefix="$ISSM_DIR/externalpackages/graphviz/install" +cd .. + +#Compile and install +cd src +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install +cd .. Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/Makefile.am.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/Makefile.am.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/Makefile.am.patch (revision 18231) @@ -0,0 +1,27 @@ +--- Makefile.am 2011-04-14 08:13:48.000000000 -0700 ++++ Makefile.am_tmp 2012-11-12 14:54:02.000000000 -0800 +@@ -24,10 +24,22 @@ + noinst_HEADERS = templates_on.h templates_off.h build.h + + MINGW32_HOST = @MINGW32_HOST@ +-if MINGW32_HOST ++ ++# Origional 'Makefile.am' sets 'libgslcblas.la' as a requirement for ++#'libgsl.ls' only if the host system is detected to be MingW32. This ++# is unfortunate as 'libgsl.la' has undefined 'cblas' symbols the ++# result is linking errors at run time. This patch sets the 'cblas' ++# library as a requirement for linking 'libgsl'. ++# ++# Origional script: ++# ++# if MINGW32_HOST ++# libgsl_la_LIBADD += cblas/libgslcblas.la ++# libgsl_la_LDFLAGS += -no-undefined ++# endif ++ + libgsl_la_LIBADD += cblas/libgslcblas.la + libgsl_la_LDFLAGS += -no-undefined +-endif + + m4datadir = $(datadir)/aclocal + m4data_DATA = gsl.m4 Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/README =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/README (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/README (revision 18231) @@ -0,0 +1,1 @@ +GNU Scientfic Library, obtained from: http://www.gnu.org/software/gsl/ Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/install-android.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/install-android.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/install-android.sh (revision 18231) @@ -0,0 +1,49 @@ +#!/bin/bash +set -eu + +source $ANDROID_DIR/android_aux.sh + +if [[ $step == "1" || $step == "0" ]]; then + + #Some cleanup + rm -rf src install gsl-1.15 + mkdir src install + + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.' 'gsl-1.15.tar.gz' + + #Untar + tar -zxvf gsl-1.15.tar.gz + + #Move gsl into src directory + mv gsl-1.15/* src + rm -rf gsl-1.15 +fi + +#Configure gsl +if [[ $step == "2" || $step == "0" ]]; then + cd src + + patch Makefile.am < ./../Makefile.am.patch + + autoreconf -if + + ./configure \ + --build="i386-apple-darwin10.8.0" \ + --host=$host_triplet \ + --prefix="$ISSM_DIR/externalpackages/gsl/install" +fi + +#Compile gsl +if [[ $step == "3" || $step == "0" ]]; then + cd $ISSM_DIR/externalpackages/gsl/src + + if [ $# -eq 0 ]; then + make + else + make -j $j + fi + + make install +fi + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/install-greenplanet.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/install-greenplanet.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/install-greenplanet.sh (revision 18231) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install gsl-1.15 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz' + +#Untar +tar -zxvf gsl-1.15.tar.gz + +#Move gsl into src directory +mv gsl-1.15/* src +rm -rf gsl-1.15 + +#Configure gsl +cd src + +./configure \ + --prefix="$ISSM_DIR/externalpackages/gsl/install" + +#Compile gsl +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/install-ios.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/install-ios.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/install-ios.sh (revision 18231) @@ -0,0 +1,63 @@ +#!/bin/bash +set -eu + +source $ANDROID_DIR/android_aux.sh +export DEVROOT="/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/" +export SDKROOT="$DEVROOT/SDKs/iPhoneOS6.0.sdk/" +export CC="$DEVROOT/usr/bin/gcc -arch armv7" +export CFLAGS="-O -arch armv7 -isysroot $SDKROOT" +export CXXFLAGS="-O -arch armv7 -isysroot $SDKROOT" +export CPP=$DEVROOT/usr/bin/cpp +export CXX=$DEVROOT/usr/bin/g++ +export AR=$DEVROOT/usr/bin/ar +export AS=$DEVROOT/usr/bin/as +export LIBTOOL=$DEVROOT/usr/bin/libtool +export LDFLAGS="-lstdc++ -arch armv7 -isysroot $SDKROOT" +export STRIP=$DEVROOT/usr/bin/strip +export RANLIB=$DEVROOT/usr/bin/ranlib + + +if [[ $step == "1" || $step == "0" ]]; then + + #Some cleanup + rm -rf src install gsl-1.15 + mkdir src install + + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.' 'gsl-1.15.tar.gz' + + #Untar + tar -zxvf gsl-1.15.tar.gz + + #Move gsl into src directory + mv gsl-1.15/* src + rm -rf gsl-1.15 +fi + +#Configure gsl +if [[ $step == "2" || $step == "0" ]]; then + cd src + + patch Makefile.am < ./../Makefile.am.patch + + autoreconf -if + + ./configure \ + --build="i386-apple-darwin10.8.0" \ + --host="arm-apple-darwin10" \ + --prefix="$ISSM_DIR/externalpackages/gsl/install" +fi + +#Compile gsl +if [[ $step == "3" || $step == "0" ]]; then + cd $ISSM_DIR/externalpackages/gsl/src + + if [ $# -eq 0 ]; then + make + else + make -j $j + fi + + make install +fi + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/install-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/install-linux64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/install-linux64.sh (revision 18231) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install gsl-1.15 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz' + +#Untar +tar -zxvf gsl-1.15.tar.gz + +#Move gsl into src directory +mv gsl-1.15/* src +rm -rf gsl-1.15 + +#Configure gsl +cd src + +./configure \ + --prefix="$ISSM_DIR/externalpackages/gsl/install" + +#Compile gsl +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/install-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/install-macosx64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/install-macosx64.sh (revision 18231) @@ -0,0 +1,32 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install gsl-1.15 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz' + +#Untar +tar -zxvf gsl-1.15.tar.gz + +#Move gsl into src directory +mv gsl-1.15/* src +rm -rf gsl-1.15 + +#Configure gsl +cd src + +export CFLAGS=" -arch x86_64" + +./configure \ + --prefix="$ISSM_DIR/externalpackages/gsl/install" + +#Compile gsl +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/install-pleiades.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/install-pleiades.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/install-pleiades.sh (revision 18231) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install gsl-1.15 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz' + +#Untar +tar -zxvf gsl-1.15.tar.gz + +#Move gsl into src directory +mv gsl-1.15/* src +rm -rf gsl-1.15 + +#Configure gsl +cd src + +./configure \ + --prefix="$ISSM_DIR/externalpackages/gsl/install" + +#Compile gsl +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/install-walgreen.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/install-walgreen.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gsl/install-walgreen.sh (revision 18231) @@ -0,0 +1,31 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install gsl-1.15 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz' + +#Untar +tar -zxvf gsl-1.15.tar.gz + +#Move gsl into src directory +mv gsl-1.15/* src +rm -rf gsl-1.15 + +#Configure gsl +cd src + +export CC=icc +./configure \ + --prefix="$ISSM_DIR/externalpackages/gsl/install" + +#Compile gsl +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gslib/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gslib/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/gslib/install.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gslib90_ls.tar.gz' 'gslib90_ls.tar.gz' + +#Untar +tar -zxvf gslib90_ls.tar.gz + +#Move gslib into install directory +mv gslib90/* install +rm -rf gslib90 + +#Change compiler to gfortran +cd install +cat Makefile | sed -e "s/FC=g95/FC=gfortran/g" > Makefile.bak +mv Makefile.bak Makefile +cat gslib/Makefile | sed -e "s/FC=g95/FC=gfortran/g" > Makefile.bak +mv Makefile.bak gslib/Makefile +make Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/h5py/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/h5py/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/h5py/install.sh (revision 18231) @@ -0,0 +1,25 @@ +#!/bin/bash +set -eu + +#needed further along +export HDF5_DIR=$ISSM_DIR/externalpackages/hdf5/install + +#Some cleanup +rm -rf install h5py-2.0.1 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/h5py-2.0.1.tar.gz' 'h5py-2.0.1.tar.gz' + +#Untar +tar -zxvf h5py-2.0.1.tar.gz + +#Move h5py to install directory +rm -rf install/* +mv h5py-2.0.1/* install/ +rm -rf h5py-2.0.1 + +#Configure and compile +cd install +python setup.py build –hdf5=$ISSM_DIR/externalpackages/hdf5/install +python setup.py install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/hdf5/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/hdf5/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/hdf5/install.sh (revision 18231) @@ -0,0 +1,28 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install hdf5-1.8.9 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/hdf5-1.8.9.tar.gz' 'hdf5-1.8.9.tar.gz' + +#Untar +tar -zxvf hdf5-1.8.9.tar.gz + +#Move hdf5 to src directory +rm -rf src/* +mv hdf5-1.8.9/* src/ +rm -rf hdf5-1.8.9 + +#Configure and compile +cd src +./configure --prefix="$ISSM_DIR/externalpackages/hdf5/install" +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/howatmask/enviread.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/howatmask/enviread.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/howatmask/enviread.m (revision 18231) @@ -0,0 +1,323 @@ +function I=enviread(varargin) +%enviread: Read binary image files using ENVI header information +% +%I=enviread('filename') where the header file is named filename.hdr +%and exists in the same directory. Otherwise use +% +%I=enviread('filename','hdrfilename') +% +%The output structure I contains fields I.x, I.y, I.z and I.info +%containing the x-coordinate vector, y-coordinate vector, +%images data and header info, respectively. I.z will be in whatever +%number format (double, int, etc.) as in the envi file. +% +%Original version by Ian Howat, Ohio State Universtiy, ihowat@gmail.com +%Thanks to Yushin Ahn and Ray Jung +% +%% Current version 3 - adding subsetting feature to read only parts of +%% files. + +file=varargin{1}; +hdrfile=[deblank(file),'.hdr']; +info=read_envihdr(hdrfile); +sub = [1, info.samples, 1, info.lines]; +if nargin==2 + if varargin{2}=='date' + [pathstr, name, ext, versn] = fileparts(file); + info.hdrname=hdrfile; + info.ipath=pathstr; + info.iname=name; + info.ipname=file; + info.year =name(1:4); + info.month=name(5:6); + info.day =name(7:8); + info.date =name(1:8); + info.sfname=name(1:14); + info.datenum=datenum(str2double(info.year),... + str2double(info.month),str2double(info.day)); + end +end + +% subset +if nargin == 3; + if strcmp(varargin{2},'pixel_subset'); + sub = varargin{3}; + elseif strcmp(varargin{2},'map_subset'); + sub = varargin{3}; + subx = (sub(1:2)-info.map_info.mapx)./info.map_info.dx; + suby = (info.map_info.mapy - sub(3:4))./info.map_info.dy; + subx = round(subx); + suby = round(suby); + + subx(subx < 1) = 1; + suby(suby < 1) = 1; + subx(subx > info.samples) = info.samples; + suby(suby > info.lines) = info.lines; + + sub = [subx,suby]; + end +end + +sub(1:2) = sort(sub(1:2)); +sub(3:4) = sort(sub(3:4)); + + +%% Make geo-location vectors +if isfield(info.map_info,'mapx') && isfield(info.map_info,'mapy') + xi = info.map_info.image_coords(1); + yi = info.map_info.image_coords(2); + xm = info.map_info.mapx; + ym = info.map_info.mapy; + %adjust points to corner (1.5,1.5) + if yi > 1.5 + ym = ym + ((yi*info.map_info.dy)-info.map_info.dy); + end + if xi > 1.5 + xm = xm - ((xi*info.map_info.dy)-info.map_info.dx); + end + + I.x = xm + ((0:info.samples-1).*info.map_info.dx); + I.y = ym - ((0:info.lines-1).* info.map_info.dy); + %I.x = xm + (subE(1):subE(2)-1).*info.map_info.dx; + %I.y = ym - (subE(3):subE(4)-1).*info.map_info.dy; +end + + +I.x = I.x(sub(1):sub(2)); +I.y = I.y(sub(3):sub(4)); + + +%% Set binary format parameters +switch info.byte_order + case {0} + machine = 'ieee-le'; + case {1} + machine = 'ieee-be'; + otherwise + machine = 'n'; +end +switch info.data_type + case {1} + format = 'uint8'; + case {2} + format= 'int16'; + case{3} + format= 'int32'; + case {4} + format= 'single'; + case {5} + format= 'double'; + case {6} + disp('>> Sorry, Complex (2x32 bits)data currently not supported'); + disp('>> Importing as double-precision instead'); + format= 'double'; + case {9} + error('Sorry, double-precision complex (2x64 bits) data currently not supported'); + case {12} + format= 'uint16'; + case {13} + format= 'uint32'; + case {14} + format= 'int64'; + case {15} + format= 'uint64'; + otherwise + error(['File type number: ',num2str(dtype),' not supported']); +end + +%% file read +% Version 2 code by Yushin Ahn - replaces resize calls with loops (except +% for BIP formats) to work on big arrays. + + %tmp=zeros(info.lines, info.samples,info.bands,format); + tmp=zeros(sub(4)-sub(3)+1,sub(2)-sub(1)+1,info.bands,format); + fid=fopen(file,'r'); + +switch lower(info.interleave) + + case {'bsq'} + % Format: + % [Band 1] + % R1: C1, C2, C3, ... + % R2: C1, C2, C3, ... + % ... + % RN: C1, C2, C3, ... + % + % [Band 2] + % ... + % [Band N] + +%% Old Script w/out subsetting +% for b=1:info.bands +% for i=1:info.lines +% t=fread(fid,info.samples,format); +% tmp(i,:,b)=t; +% end +% end + +%% New Subsetting script - IMH + offset1=(sub(3)-1)*info.samples; + fseek(fid,offset1,'bof'); + for b=1:info.bands + for i=sub(3):sub(4) + t=fread(fid,info.samples,format); + %if i >= sub(3) && i <= sub(4) + tmp(i-sub(3)+1,:,b)=t(sub(1):sub(2)); + %end + end + offset2 = info.samples*info.lines*b+offset1; + fseek(fid,offset2,'bof'); + end + + case {'bil'} + % Format: + % [Row 1] + % B1: C1, C2, C3, ... + % B2: C1, C2, C3, ... + % + % ... + % [Row N] + +% for i=1:info.lines +% for b=1:info.bands +% t=fread(fid,info.samples,format); +% tmp(i,:,b)=t; +% end +% end + +%% New Subsetting script - IMH + for i=1:sub(4) + for b=1:info.bands + t=fread(fid,info.samples,format); + if i >= sub(3) && i <= sub(4) + tmp(i-sub(3)+1,:,b)=t(sub(1):sub(2)); + end + end + end + + + + case {'bip'} + + % Row 1 + % C1: B1 B2 B3, ... + % C2: B1 B2 B3, ... + % ... + % Row N + %This section authored by Ray Jung, APL-Johns Hopkins + Z = fread(fid,info.samples*info.lines*info.bands,format,0,machine); + Z = reshape(Z, [info.bands, info.samples, info.lines]); + + for k=1:info.bands + tmp(:,:,k) = squeeze(Z(k,:,:))'; + end +end +fclose(fid); + +% tmp2=zeros(subE(4)-subE(3)+1,subE(2)-subE(1)+1,info.bands,format); +% [a,b]=size(tmp); +% for i=1:info.bands +% tmp2(xoff+1:a,yoff+1:b,1)=tmp(1:a,1:b,1); +% end +I.z=tmp; +I.info =info; + + + +%% sub function +function info = read_envihdr(hdrfile) +% READ_ENVIHDR read and return ENVI image file header information. +% INFO = READ_ENVIHDR('HDR_FILE') reads the ASCII ENVI-generated image +% header file and returns all the information in a structure of +% parameters. +% +% Example: +% >> info = read_envihdr('my_envi_image.hdr') +% info = +% description: [1x101 char] +% samples: 658 +% lines: 749 +% bands: 3 +% header_offset: 0 +% file_type: 'ENVI Standard' +% data_type: 4 +% interleave: 'bsq' +% sensor_type: 'Unknown' +% byte_order: 0 +% map_info: [1x1 struct] +% projection_info: [1x102 char] +% wavelength_units: 'Unknown' +% pixel_size: [1x1 struct] +% band_names: [1x154 char] +% +% NOTE: This function is used by ENVIREAD to import data. +% Ian M. Howat, Applied Physics Lab, University of Washington +% ihowat@apl.washington.edu +% Version 1: 19-Jul-2007 00:50:57 +fid = fopen(hdrfile); +while fid; + line = fgetl(fid); + if line == -1 + break + else + eqsn = findstr(line,'='); + if ~isempty(eqsn) + param = strtrim(line(1:eqsn-1)); + param(findstr(param,' ')) = '_'; + value = strtrim(line(eqsn+1:end)); + if isempty(str2num(value)) + if ~isempty(findstr(value,'{')) && isempty(findstr(value,'}')) + while isempty(findstr(value,'}')) + line = fgetl(fid); + value = [value,strtrim(line)]; + end + end + eval(['info.',param,' = ''',value,''';']) + else + eval(['info.',param,' = ',value,';']) + end + end + end +end +fclose(fid); + +if isfield(info,'map_info') + line = info.map_info; + line(line == '{' | line == '}') = []; + line = strtrim(split(line,',')); + info.map_info = []; + info.map_info.projection = line{1}; + info.map_info.image_coords = [str2num(line{2}),str2num(line{3})]; + info.map_info.mapx = str2num(line{4}); + info.map_info.mapy = str2num(line{5}); + info.map_info.dx = str2num(line{6}); + info.map_info.dy = str2num(line{7}); + if length(line) == 9 + info.map_info.datum = line{8}; + info.map_info.units = line{9}(7:end); + elseif length(line) == 11 + info.map_info.zone = str2num(line{8}); + info.map_info.hemi = line{9}; + info.map_info.datum = line{10}; + info.map_info.units = line{11}(7:end); + end +end + +if isfield(info,'pixel_size') + line = info.pixel_size; + line(line == '{' | line == '}') = []; + line = strtrim(split(line,',')); + info.pixel_size = []; + info.pixel_size.x = str2num(line{1}); + info.pixel_size.y = str2num(line{2}); + info.pixel_size.units = line{3}(7:end); +end + +%% +function A = split(s,d) +%This function by Gerald Dalley (dalleyg@mit.edu), 2004 +A = {}; +while (length(s) > 0) + [t,s] = strtok(s,d); + A = {A{:}, t}; +end Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/howatmask/subsetGimpIceMask.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/howatmask/subsetGimpIceMask.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/howatmask/subsetGimpIceMask.m (revision 18231) @@ -0,0 +1,282 @@ +function [M,Mx,My] = subsetGimpIceMask(x0,x1,y0,y1) +% subsetGimpIceMask samples mask tiles for a given coordinate range +% +% [M,Mx,My] = subsetGimpIceMask(x0,x1,y0,y1) returns the mask in array M +% with map vectors Mx and My within the bounding box specified by +% coordinate ranges x0 < x1 and y0 < y1. The function finds tiles +% overlappimg the box, samples the tiles and mosaics the samples into one +% array. +% +% Example: Specify the following coordinate range and map the result. +% >> x0 = 260000; x1 = 377900; y0 = -2609400; y1 = -2543000; +% >> [M,Mx,My] = subsetGimpIceMask(x0,x1,y0,y1); +% >> imagesc(Mx,My,M); axis equal xy; colormap gray; +% +% Ian Howat, Ohio State University, ihowat@gmail.com +% The Greenland Ice Mapping Project is funded by NASA. +% $Revision: 0 $ $Date: 09-Nov-2011 14:48:24$ +% + +%make coordinate index +nt = 6; +ps = 15; +xn0 = -640000 ; %xn1 = 857550; +yn0 = -3313350; %yn1 = -665450; + +c = 16640; +r = 29420; + +x = xn0:ps:xn0 + c.*ps.*nt; +y = yn0:ps:yn0 + r.*ps.*nt; + +X = cell(1,nt); +Y = cell(nt,1); +i=1; +for i=1:nt; + + X{i} = [x((i-1)*c+1),x(i*c)]; + Y{i} = [y((i-1)*r+1),y(i*r)]; + +end + +X = repmat(X,[nt,1]); +Y = repmat(Y,[1,nt]); +N = cell(size(X)); + + +i=1; +for i=1:numel(X) + N{i} = [[X{i}(1),Y{i}(2)];... + [X{i}(2),Y{i}(2)];... + [X{i}(2),Y{i}(1)];... + [X{i}(1),Y{i}(1)]]; +end + + +%% find overlapping tiles +p = [[x0,y1];[x1,y1];[x1,y0];[x0,y0]]; + +n = zeros(size(N)); + +i=1; +for i=1:numel(N) + n(i) = any(inpolygon(p(:,1),p(:,2),N{i}(:,1),N{i}(:,2))); +end +i=1; +for i=1:size(n,1) + n(i,find(n(i,:),1,'first'):find(n(i,:),1,'last')) = 1; +end +i=1; +for i=1:size(n,2) + n(find(n(:,i),1,'first'):find(n(:,i),1,'last'),i) = 1; +end + +[i,j] = find(n); +row = (min(i):max(i))'; +col = min(j):max(j); +col = repmat(col,[length(row),1])-1; +row = repmat(row,[1,size(col,2)])-1; + +% make output cells +M = cell(size(row)); +Mx = M; +My = M; + +% read each overlapping file and populate output cell +j=1; +for j=1:size(col,2) + i=1; + for i=1:size(row,1); + m = enviread(['GimpIceMask_15m_tile',num2str(col(i,j)),'_',... + num2str(row(i,j))],'map_subset',[x0 x1 y0 y1]); + M{end-i+1,j} = m.z; + Mx{end-i+1,j} = m.x; + My{end-i+1,j} = m.y'; + + + end +end + +% put together cells +M = cell2mat(M); +Mx =cell2mat(Mx(1,:)); +My =cell2mat(My(:,1)); + + +function I=enviread(varargin) + +file=varargin{1}; +hdrfile=[deblank(file),'.hdr']; +info=read_envihdr(hdrfile); +sub = [1, info.samples, 1, info.lines]; + +sub = varargin{3}; +subx = (sub(1:2)-info.map_info.mapx)./info.map_info.dx; +suby = (info.map_info.mapy - sub(3:4))./info.map_info.dy; +subx = round(subx); +suby = round(suby); + +subx(subx < 1) = 1; +suby(suby < 1) = 1; +subx(subx > info.samples) = info.samples; +suby(suby > info.lines) = info.lines; + +sub = [subx,suby]; + +sub(1:2) = sort(sub(1:2)); +sub(3:4) = sort(sub(3:4)); + +%% Make geo-location vectors +if isfield(info.map_info,'mapx') && isfield(info.map_info,'mapy') + xi = info.map_info.image_coords(1); + yi = info.map_info.image_coords(2); + xm = info.map_info.mapx; + ym = info.map_info.mapy; + %adjust points to corner (1.5,1.5) + if yi > 1.5 + ym = ym + ((yi*info.map_info.dy)-info.map_info.dy); + end + if xi > 1.5 + xm = xm - ((xi*info.map_info.dy)-info.map_info.dx); + end + + I.x = xm + ((0:info.samples-1).*info.map_info.dx); + I.y = ym - ((0:info.lines-1).* info.map_info.dy); + +end + +I.x = I.x(sub(1):sub(2)); +I.y = I.y(sub(3):sub(4)); + +%% Set binary format parameters +switch info.byte_order + case {0} + machine = 'ieee-le'; + case {1} + machine = 'ieee-be'; + otherwise + machine = 'n'; +end + +format = 'uint8'; + +tmp=zeros(sub(4)-sub(3)+1,sub(2)-sub(1)+1,info.bands,format); +fid=fopen(file,'r'); + +offset1=(sub(3)-1)*info.samples; +fseek(fid,offset1,'bof'); +for b=1:info.bands + for i=sub(3):sub(4) + t=fread(fid,info.samples,format); + tmp(i-sub(3)+1,:,b)=t(sub(1):sub(2)); + end + offset2 = info.samples*info.lines*b+offset1; + fseek(fid,offset2,'bof'); +end + +fclose(fid); + +I.z=tmp; +I.info =info; + +%% sub function +function info = read_envihdr(hdrfile) +% READ_ENVIHDR read and return ENVI image file header information. +% INFO = READ_ENVIHDR('HDR_FILE') reads the ASCII ENVI-generated image +% header file and returns all the information in a structure of +% parameters. +% +% Example: +% >> info = read_envihdr('my_envi_image.hdr') +% info = +% description: [1x101 char] +% samples: 658 +% lines: 749 +% bands: 3 +% header_offset: 0 +% file_type: 'ENVI Standard' +% data_type: 4 +% interleave: 'bsq' +% sensor_type: 'Unknown' +% byte_order: 0 +% map_info: [1x1 struct] +% projection_info: [1x102 char] +% wavelength_units: 'Unknown' +% pixel_size: [1x1 struct] +% band_names: [1x154 char] +% +% NOTE: This function is used by ENVIREAD to import data. +% Ian M. Howat, Applied Physics Lab, University of Washington +% ihowat@apl.washington.edu +% Version 1: 19-Jul-2007 00:50:57 +fid = fopen(hdrfile); +while fid; + line = fgetl(fid); + if line == -1 + break + else + eqsn = findstr(line,'='); + if ~isempty(eqsn) + param = strtrim(line(1:eqsn-1)); + param(findstr(param,' ')) = '_'; + value = strtrim(line(eqsn+1:end)); + if isempty(str2num(value)) + if ~isempty(findstr(value,'{')) && isempty(findstr(value,'}')) + while isempty(findstr(value,'}')) + line = fgetl(fid); + value = [value,strtrim(line)]; + end + end + eval(['info.',param,' = ''',value,''';']) + else + eval(['info.',param,' = ',value,';']) + end + end + end +end +fclose(fid); + +if isfield(info,'map_info') + line = info.map_info; + line(line == '{' | line == '}') = []; + line = strtrim(split(line,',')); + info.map_info = []; + info.map_info.projection = line{1}; + info.map_info.image_coords = [str2num(line{2}),str2num(line{3})]; + info.map_info.mapx = str2num(line{4}); + info.map_info.mapy = str2num(line{5}); + info.map_info.dx = str2num(line{6}); + info.map_info.dy = str2num(line{7}); + if length(line) == 9 + info.map_info.datum = line{8}; + info.map_info.units = line{9}(7:end); + elseif length(line) == 11 + info.map_info.zone = str2num(line{8}); + info.map_info.hemi = line{9}; + info.map_info.datum = line{10}; + info.map_info.units = line{11}(7:end); + end +end + +if isfield(info,'pixel_size') + line = info.pixel_size; + line(line == '{' | line == '}') = []; + line = strtrim(split(line,',')); + info.pixel_size = []; + info.pixel_size.x = str2num(line{1}); + info.pixel_size.y = str2num(line{2}); + info.pixel_size.units = line{3}(7:end); +end + +%% +function A = split(s,d) +%This function by Gerald Dalley (dalleyg@mit.edu), 2004 +A = {}; +while (length(s) > 0) + [t,s] = strtok(s,d); + A = {A{:}, t}; +end + + + + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/inishell/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/inishell/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/inishell/install.sh (revision 18231) @@ -0,0 +1,40 @@ +#!/bin/bash +#inishell install package: this package is not distributed by ISSM. Please request access to the code by +#contacting Mathias Bavay () or logging onto http://models.slf.ch/ and registering. Once you have a tarball +#of the code, please use this script to install. + +#we assume you have a inishell-src-*.tgz tarball +set -eu + +#Do some inquiry about the names of the tar balls: +source_tar=`ls inishell-src-*.tgz` +source_version=`echo $source_tar | sed 's/inishell-src-//g' | sed 's/.tgz//g'` + +if [[ $source_tar == "" ]]; then + echo "Could not identify a tar ball for the source code, name should be inishell-src-*.tgz" + exit 1 +fi +if [[ $source_version == "" ]]; then + echo "Could not identify a tar ball version for the source code" + exit 1 +fi + + +#Some cleanup +rm -rf src install inishell-$source_version +mkdir install + +#First deal with source code +tar -zxvf $source_tar +mv inishell-$source_version src +rm -rf inishell-$source_version + +#Build inishell +cd src && ant snowpack + +#Put the .jar in the install directory +cp dist/inishell.jar ../install + +#Install script to launch inishell jar file directly +cd .. +cp scripts/inishell install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/inishell/scripts/inishell =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/inishell/scripts/inishell (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/inishell/scripts/inishell (revision 18231) @@ -0,0 +1,3 @@ +#/bin/bash + +java -jar $ISSM_DIR/externalpackages/inishell/install/inishell.jar Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/ipython/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/ipython/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/ipython/install.sh (revision 18231) @@ -0,0 +1,22 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf ipython-1.0.0 +mkdir src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ipython-1.0.0.tar.gz' 'ipython-1.0.0.tar.gz' + +#Untar +tar -zxvf ipython-1.0.0.tar.gz + +#Move ipython into src directory +mv ipython-1.0.0/* src +rm -rf ipython-1.0.0 + +#install ipython +cd src +python setup.py build +python setup.py install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/kml/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/kml/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/kml/install.sh (revision 18231) @@ -0,0 +1,5 @@ +#!/bin/bash +set -eu + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/kml_shapefile.zip' 'kml_shapefile.zip' Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/lapack/configs/linux64/make.inc =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/lapack/configs/linux64/make.inc (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/lapack/configs/linux64/make.inc (revision 18231) @@ -0,0 +1,71 @@ +#################################################################### +# LAPACK make include file. # +# LAPACK, Version 3.4.0 # +# April 2012 # +#################################################################### +# +SHELL = /bin/sh +# +# Modify the FORTRAN and OPTS definitions to refer to the +# compiler and desired compiler options for your machine. NOOPT +# refers to the compiler options desired when NO OPTIMIZATION is +# selected. Define LOADER and LOADOPTS to refer to the loader and +# desired load options for your machine. +# +FORTRAN = gfortran +OPTS = -fPIC -O2 +DRVOPTS = $(OPTS) +NOOPT = -fPIC -O0 +LOADER = gfortran +LOADOPTS = +# +# Timer for the SECOND and DSECND routines +# +# Default : SECOND and DSECND will use a call to the EXTERNAL FUNCTION ETIME +#TIMER = EXT_ETIME +# For RS6K : SECOND and DSECND will use a call to the EXTERNAL FUNCTION ETIME_ +# TIMER = EXT_ETIME_ +# For gfortran compiler: SECOND and DSECND will use a call to the INTERNAL FUNCTION ETIME +TIMER = INT_ETIME +# If your Fortran compiler does not provide etime (like Nag Fortran Compiler, etc...) +# SECOND and DSECND will use a call to the INTERNAL FUNCTION CPU_TIME +# TIMER = INT_CPU_TIME +# If neither of this works...you can use the NONE value... In that case, SECOND and DSECND will always return 0 +# TIMER = NONE +# +# Configuration LAPACKE: Native C interface to LAPACK +# To generate LAPACKE library: type 'make lapackelib' +# Configuration file: turned off (default) +# Complex types: C99 (default) +# Name pattern: mixed case (default) +# (64-bit) Data model: LP64 (default) +# +# CC is the C compiler, normally invoked with options CFLAGS. +# +CC = gcc +CFLAGS = -O3 +# +# The archiver and the flag(s) to use when building archive (library) +# If you system has no ranlib, set RANLIB = echo. +# +ARCH = ar +ARCHFLAGS= cr +RANLIB = ranlib +# +# Location of the extended-precision BLAS (XBLAS) Fortran library +# used for building and testing extended-precision routines. The +# relevant routines will be compiled and XBLAS will be linked only if +# USEXBLAS is defined. +# +# USEXBLAS = Yes +XBLASLIB = +# XBLASLIB = -lxblas +# +# The location of the libraries to which you will link. (The +# machine-specific, optimized BLAS library should be used whenever +# possible.) +# +BLASLIB = ../../librefblas.a +LAPACKLIB = liblapack.a +TMGLIB = libtmglib.a +LAPACKELIB = liblapacke.a Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/lapack/configs/macosx64/make.inc =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/lapack/configs/macosx64/make.inc (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/lapack/configs/macosx64/make.inc (revision 18231) @@ -0,0 +1,71 @@ +#################################################################### +# LAPACK make include file. # +# LAPACK, Version 3.4.0 # +# April 2012 # +#################################################################### +# +SHELL = /bin/sh +# +# Modify the FORTRAN and OPTS definitions to refer to the +# compiler and desired compiler options for your machine. NOOPT +# refers to the compiler options desired when NO OPTIMIZATION is +# selected. Define LOADER and LOADOPTS to refer to the loader and +# desired load options for your machine. +# +FORTRAN = gfortran +OPTS = -fPIC -O2 +DRVOPTS = $(OPTS) +NOOPT = -fPIC -O0 +LOADER = gfortran +LOADOPTS = +# +# Timer for the SECOND and DSECND routines +# +# Default : SECOND and DSECND will use a call to the EXTERNAL FUNCTION ETIME +#TIMER = EXT_ETIME +# For RS6K : SECOND and DSECND will use a call to the EXTERNAL FUNCTION ETIME_ +# TIMER = EXT_ETIME_ +# For gfortran compiler: SECOND and DSECND will use a call to the INTERNAL FUNCTION ETIME +TIMER = INT_ETIME +# If your Fortran compiler does not provide etime (like Nag Fortran Compiler, etc...) +# SECOND and DSECND will use a call to the INTERNAL FUNCTION CPU_TIME +# TIMER = INT_CPU_TIME +# If neither of this works...you can use the NONE value... In that case, SECOND and DSECND will always return 0 +# TIMER = NONE +# +# Configuration LAPACKE: Native C interface to LAPACK +# To generate LAPACKE library: type 'make lapackelib' +# Configuration file: turned off (default) +# Complex types: C99 (default) +# Name pattern: mixed case (default) +# (64-bit) Data model: LP64 (default) +# +# CC is the C compiler, normally invoked with options CFLAGS. +# +CC = gcc +CFLAGS = -O3 +# +# The archiver and the flag(s) to use when building archive (library) +# If you system has no ranlib, set RANLIB = echo. +# +ARCH = ar +ARCHFLAGS= cr +RANLIB = ranlib +# +# Location of the extended-precision BLAS (XBLAS) Fortran library +# used for building and testing extended-precision routines. The +# relevant routines will be compiled and XBLAS will be linked only if +# USEXBLAS is defined. +# +# USEXBLAS = Yes +XBLASLIB = +# XBLASLIB = -lxblas +# +# The location of the libraries to which you will link. (The +# machine-specific, optimized BLAS library should be used whenever +# possible.) +# +BLASLIB = ../../librefblas.a +LAPACKLIB = liblapack.a +TMGLIB = libtmglib.a +LAPACKELIB = liblapacke.a Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/lapack/install-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/lapack/install-linux64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/lapack/install-linux64.sh (revision 18231) @@ -0,0 +1,33 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install lapack-3.4.1 lapack-3.4.1.tgz +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/lapack-3.4.1.tgz' 'lapack-3.4.1.tgz' + +#Untar +tar -zxvf lapack-3.4.1.tgz + +#Move lapack into install directory +mv lapack-3.4.1/* src +rm -rf lapack-3.4.1 + +#install +cd src +cp ../configs/linux64/make.inc ./ + +#Compile and install lapack +if [ $# -eq 0 ]; then + make lib +else + make -j $1 lib +fi + +#Compile +cd ../install +mkdir lib +cd lib +cp ../../src/liblapack.a . Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/lapack/install-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/lapack/install-macosx64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/lapack/install-macosx64.sh (revision 18231) @@ -0,0 +1,33 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install lapack-3.4.1 lapack-3.4.1.tgz +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/lapack-3.4.1.tgz' 'lapack-3.4.1.tgz' + +#Untar +tar -zxvf lapack-3.4.1.tgz + +#Move lapack into install directory +mv lapack-3.4.1/* src +rm -rf lapack-3.4.1 + +#install +cd src +cp ../configs/macosx64/make.inc ./ + +#Compile and install lapack +if [ $# -eq 0 ]; then + make lib +else + make -j $1 lib +fi + +#Compile +cd ../install +mkdir lib +cd lib +cp ../../src/liblapack.a . Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/latex2rtf/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/latex2rtf/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/latex2rtf/install.sh (revision 18231) @@ -0,0 +1,17 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf latex2rtf-2.0.0 cfg install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/latex2rtf-2.0.0.tar.gz' 'latex2rtf-2.0.0.tar.gz' + +#untar +tar -zxvf latex2rtf-2.0.0.tar.gz +mv latex2rtf-2.0.0 install + +#Compile +cd install +export PREFIX="$ISSM_DIR/externalpackages/latex2rtf/install/" +make Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/libermate/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/libermate/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/libermate/install.sh (revision 18231) @@ -0,0 +1,17 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install +rm -rf libermate-0.4 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libermate-0.4.tgz' 'libermate-0.4.tgz' + +#Untar +tar -zxvf libermate-0.4.tgz + +#Move libermate into install directory +mv libermate-0.4/* install +rm -rf libermate-0.4 Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/libpng/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/libpng/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/libpng/install.sh (revision 18231) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf libpng-1.5.10 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libpng-1.5.10.tar.gz' 'libpng-1.5.10.tar.gz' + +#Untar +tar -zxvf libpng-1.5.10.tar.gz + +#Move libpng into src directory +mv libpng-1.5.10/* src +rm -rf libpng-1.5.10 + +#Configure libpng +cd src +sudo ./configure + +#Compile and install libpng +if [ $# -eq 0 ]; then + sudo make +else + sudo make -j $1 +fi +sudo make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/m1qn3/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/m1qn3/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/m1qn3/install.sh (revision 18231) @@ -0,0 +1,59 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src m1qn3-3.3-distrib +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/m1qn3-3.3-distrib.tgz' 'm1qn3-3.3-distrib.tgz' + +#Untar +tar -xzf m1qn3-3.3-distrib.tgz +mv m1qn3-3.3-distrib src + +if which ifort >/dev/null; then + FC="ifort" +else + FC="gfortran" +fi + +#Compile m1qn3 +cd src/src/ +( +cat << EOF +LIB_EXT=a +FC=$FC +install: libm1qn3.\$(LIB_EXT) + cp libm1qn3.\$(LIB_EXT) ../../install/ +OBJECTS= m1qn3.o +libm1qn3.\$(LIB_EXT): \$(OBJECTS) + ar -r libm1qn3.\$(LIB_EXT) \$(OBJECTS) + ranlib libm1qn3.\$(LIB_EXT) +%.o: %.f + \$(FC) \$(FFLAGS) -c $< -o \$@ +clean: + rm -rf *.o *.\$(LIB_EXT) +EOF +) > Makefile +make + +#compile ddot +cd ../blas +( +cat << EOF +LIB_EXT=a +FC=$FC +install: libddot.\$(LIB_EXT) + cp libddot.\$(LIB_EXT) ../../install/ +OBJECTS= ddot.o +libddot.\$(LIB_EXT): \$(OBJECTS) + ar -r libddot.\$(LIB_EXT) \$(OBJECTS) + ranlib libddot.\$(LIB_EXT) +%.o: %.f + \$(FC) \$(FFLAGS) -c $< -o \$@ +clean: + rm -rf *.o *.\$(LIB_EXT) +EOF +) > Makefile +make Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/m2html/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/m2html/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/m2html/install.sh (revision 18231) @@ -0,0 +1,21 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install m2html +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/m2html.zip' 'm2html.zip' + +#uncompress +unzip m2html.zip + +#move to install directory +mv m2html/* install +rm -rf m2html + +#patch m2html +cd install +patch m2html.m ../m2html.m.patch +cd .. Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/m2html/m2html.m.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/m2html/m2html.m.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/m2html/m2html.m.patch (revision 18231) @@ -0,0 +1,114 @@ +*** m2html.m 2011-08-12 10:57:45.000000000 -0700 +--- install/m2html.m 2011-08-12 10:58:26.000000000 -0700 +*************** +*** 306,311 **** +--- 306,325 ---- + end + + mdir = unique(mdirs); ++ ++ %add root directories ++ for i=1:length(mdir) ++ path=strsplit(mdir{i},'/'); ++ string=path{1}; ++ mdir{end+1}=string; ++ for j=2:length(path), ++ string=[string '/' path{j}]; ++ mdir{end+1}=string; ++ end ++ end ++ ++ mdir=unique(mdir); ++ + if options.verbose, + fprintf('Found %d unique Matlab directories.\n',length(mdir)); + end +*************** +*** 423,429 **** + %- Set some template variables + tpl = set(tpl,'var','DATE',[datestr(now,8) ' ' datestr(now,1) ' ' ... + datestr(now,13)]); +! tpl = set(tpl,'var','MASTERPATH', './'); + tpl = set(tpl,'var','DIRS', sprintf('%s ',mdir{:})); + + %- Print list of unique directories +--- 437,443 ---- + %- Set some template variables + tpl = set(tpl,'var','DATE',[datestr(now,8) ' ' datestr(now,1) ' ' ... + datestr(now,13)]); +! tpl = set(tpl,'var','MASTERPATH', ''); + tpl = set(tpl,'var','DIRS', sprintf('%s ',mdir{:})); + + %- Print list of unique directories +*************** +*** 555,561 **** + tpl = set(tpl,'var','subfold',''); + d = dir(mdir{i}); + d = {d([d.isdir]).name}; +! d = {d{~ismember(d,{'.' '..'})}}; + for j=1:length(d) + if ismember(fullfile(mdir{i},d{j}),mdir) + tpl = set(tpl,'var','SUBDIRECTORY',... +--- 569,575 ---- + tpl = set(tpl,'var','subfold',''); + d = dir(mdir{i}); + d = {d([d.isdir]).name}; +! d = {d{~ismember(d,{'.' '..' 'CVS' '.svn'})}}; + for j=1:length(d) + if ismember(fullfile(mdir{i},d{j}),mdir) + tpl = set(tpl,'var','SUBDIRECTORY',... +*************** +*** 687,695 **** + % Path should look like: ...;C:\WINNT\System32;...;C:\GraphViz\bin + % (Note that this should have been done automatically during GraphViz installation) + +! eval(['!' dot_exec ' -Tcmap -Tpng ' mdotfile ... + ' -o ' fullfile(options.htmlDir,mdir{i},[dotbase '.map']) ... +! ' -o ' fullfile(options.htmlDir,mdir{i},[dotbase '.png'])]) + % use '!' rather than 'system' for backward compability + catch + fprintf('failed.'); +--- 701,709 ---- + % Path should look like: ...;C:\WINNT\System32;...;C:\GraphViz\bin + % (Note that this should have been done automatically during GraphViz installation) + +! eval(['!' dot_exec ' -Tcmap -Tgif ' mdotfile ... + ' -o ' fullfile(options.htmlDir,mdir{i},[dotbase '.map']) ... +! ' -o ' fullfile(options.htmlDir,mdir{i},[dotbase '.gif'])]) + % use '!' rather than 'system' for backward compability + catch + fprintf('failed.'); +*************** +*** 700,706 **** + tpl = set(tpl,'var','INDEX',[options.indexFile options.extension]); + tpl = set(tpl,'var','MASTERPATH', backtomaster(mdir{i})); + tpl = set(tpl,'var','MDIR', mdir{i}); +! tpl = set(tpl,'var','GRAPH_IMG', [dotbase '.png']); + fmap = openfile(fullfile(options.htmlDir,mdir{i},[dotbase '.map']),'r'); + tpl = set(tpl,'var','GRAPH_MAP', fscanf(fmap,'%c')); + fclose(fmap); +--- 714,720 ---- + tpl = set(tpl,'var','INDEX',[options.indexFile options.extension]); + tpl = set(tpl,'var','MASTERPATH', backtomaster(mdir{i})); + tpl = set(tpl,'var','MDIR', mdir{i}); +! tpl = set(tpl,'var','GRAPH_IMG', [dotbase '.gif']); + fmap = openfile(fullfile(options.htmlDir,mdir{i},[dotbase '.map']),'r'); + tpl = set(tpl,'var','GRAPH_MAP', fscanf(fmap,'%c')); + fclose(fmap); +*************** +*** 1032,1038 **** + if recursive + d = dir(mdirs{i}); + d = {d([d.isdir]).name}; +! d = {d{~ismember(d,{'.' '..'})}}; + for j=1:length(d) + mfiles = getmfiles(cellstr(fullfile(mdirs{i},d{j})),... + mfiles,recursive); +--- 1046,1052 ---- + if recursive + d = dir(mdirs{i}); + d = {d([d.isdir]).name}; +! d = {d{~ismember(d,{'.' '..' 'CVS' '.svn'})}}; + for j=1:length(d) + mfiles = getmfiles(cellstr(fullfile(mdirs{i},d{j})),... + mfiles,recursive); Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/math77/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/math77/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/math77/install.sh (revision 18231) @@ -0,0 +1,27 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install math77 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/math77.tar.gz' 'math77.tar.gz' + +#Untar +tar -zxvf math77.tar.gz + +#Move math77 into src directory +mv math77/* src +rm -rf math77 + +#Configure math77 +cd src + +#Compile math77 +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/matlab/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/matlab/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/matlab/install.sh (revision 18231) @@ -0,0 +1,35 @@ +#!/bin/bash +set -eu + +if [ ! -h install ]; +then + echo " ****************************************************************" + echo " * *" + echo " * you need create a symbolic link from matlab's root directory *" + echo " * *" + echo " * First, you need to locate matlab's root directory *" + echo " * The easiest way to find it is to launch matlab and run the *" + echo " * following command: matlabroot *" + echo " * Then, create a symbolic link using the command 'ln -s ' the *" + echo " * target directory should be named 'install' *" + echo " * *" + echo " * Examples: *" + echo " * ln -s /usr/local/matlab712/ install *" + echo " * ln -s /Applications/MATLAB_R2012a.app/ install *" + echo " * *" + echo " * run ./install.sh again to check that the link is correct *" + echo " * *" + echo " ****************************************************************" +else + + #Read link + DIR=$(readlink install) + if [ -d $DIR ] + then + echo "Symbolic link correctly set" + else + rm -rf install + echo "Incorrect symbolic link:" + echo "provided target ($DIR) does not exist or is not a directory" + fi +fi Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/matplotlib/install-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/matplotlib/install-linux64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/matplotlib/install-linux64.sh (revision 18231) @@ -0,0 +1,14 @@ +#/bin/bash +set -eu +export GIT_SSL_NO_VERIFY=true +export CC="gcc -fPIC " +export CXX="g++ -fPIC -L$ISSM_DIR/externalpackages/tcl/install/lib" +export F77="gfortran -fPIC" +export FC="gfortran -fPIC" +export FFLAGS=-ff2c + +git clone https://github.com/matplotlib/matplotlib +mv matplotlib src +cd src +python setup.py build +python setup.py install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/matplotlib/install-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/matplotlib/install-macosx64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/matplotlib/install-macosx64.sh (revision 18231) @@ -0,0 +1,32 @@ +#/bin/bash +set -eu + +rm -rf src deps + +export C_INCLUDE_PATH="$C_INCLUDE_PATH:/usr/include/c++/4.2.1" +export GIT_SSL_NO_VERIFY=true +export CC="gcc -fPIC -arch x86_64 -I/usr/include/c++/4.2.1" +export CXX="g++ -fPIC -arch x86_64 -I/usr/include/c++/4.2.1" +export F77="gfortran -fPIC -arch x86_64 -I/usr/include/c++/4.2.1" +export FC="gfortran -fPIC -arch x86_64 -I/usr/include/c++/4.2.1" +export FFLAGS="-ff2c -arch x86_64 -I/usr/include/c++/4.2.1" +export ARCHFLAGS="-arch x86_64 -I/usr/include/c++/4.2.1" + +git clone https://github.com/matplotlib/matplotlib +mv matplotlib src +mkdir deps +cd src + +#only try this if the classic python setup.py build approach does not work. The approach in the next 3 lines can +#trigger issues of permissions with freetype. Sometimes it is better to independently install freetype2 (from the +#issm externalpackages) as sudo (or root), so that the python script can detect its existence automatically. +#sudo make -f make.osx PREFIX=$ISSM_DIR/externalpackages/matplotlib/deps PYVERSION=$pythonversion fetch deps mpl_install_std +#sudo make -f make.osx PREFIX=$ISSM_DIR/externalpackages/matplotlib/deps PYVERSION=$pythonversion mpl_install_std +#python -c "import matplotlib; print 'Installed matplotlib', matplotlib.__version__, matplotlib.__file__" + +#comments: try exporting this first before calling python setup.py build +CFLAGS=-mmacosx-version-min=10.7 + +#to be tried: first get freetype and zlib and libpng installed in sudo mode +python setup.py build +python setup.py install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mercurial/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mercurial/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mercurial/install.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install mercurial-1.7.3 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mercurial-1.7.3.tar.gz' 'mercurial-1.7.3.tar.gz' + +#Untar +tar -zxvf mercurial-1.7.3.tar.gz + +#Move mercurial into install directory +mv mercurial-1.7.3/* install +rm -rf mercurial-1.7.3 + +#Apply patches +cd install +#patch Lib/Makefile ../lib_Makefile.patch +exit + +#Compile mercurial +make Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/meteoio/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/meteoio/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/meteoio/install.sh (revision 18231) @@ -0,0 +1,39 @@ +#!/bin/bash +#METEOIO install package: this package is not distributed by ISSM. Please request access to the code by +#contacting Mathias Bavay () or logging onto http://models.slf.ch/ and registering. Once you have a tarball +#of the code, please use this script to install. + +#we assume you have a MeteoIO-*-tar.gz tarball +set -eu + +#Do some inquiry about the names of the tar balls: +source_tar=`ls MeteoIO-*.tar.gz` +source_version=`echo $source_tar | sed 's/MeteoIO-//g' | sed 's/.tar.gz//g'` + +if [[ $source_tar == "" ]]; then + echo "Could not identify a tar ball for the source code, name should be MeteoIO-*-tar.gz" + exit 1 +fi +if [[ $source_version == "" ]]; then + echo "Could not identify a tar ball version for the source code" + exit 1 +fi + +#Some cleanup +rm -rf src install MeteoIO-$source_version + +#First deal with source code +tar -zxvf $source_tar +mv MeteoIO-$source_version/usr src +rm -rf MeteoIO-$source_version + +#Reset makefile: +cd src && rm -rf CMakeCache.txt +cmake -DCMAKE_INSTALL_PREFIX:PATH=$ISSM_DIR/externalpackages/meteoio/install . + +#Compile +if [ $# -eq 0 ]; then + make all install +else + make -j $1 all install +fi Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/altix64/Makefile.in.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/altix64/Makefile.in.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/altix64/Makefile.in.patch (revision 18231) @@ -0,0 +1,10 @@ +3c3,5 +< CC = cc +--- +> CC = gcc +> OBJ_EXT=o +> LIB_EXT=a +6c8 +< OPTFLAGS = -O2 +--- +> OPTFLAGS = -DLINUX -fPIC Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/cosmos/Makefile.in.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/cosmos/Makefile.in.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/cosmos/Makefile.in.patch (revision 18231) @@ -0,0 +1,10 @@ +3c3,5 +< CC = cc +--- +> CC = icc +> OBJ_EXT=o +> LIB_EXT=a +6c8 +< OPTFLAGS = -O2 +--- +> OPTFLAGS = -DLINUX -fPIC Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/discover/Makefile.in.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/discover/Makefile.in.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/discover/Makefile.in.patch (revision 18231) @@ -0,0 +1,10 @@ +3c3,5 +< CC = cc +--- +> CC = icc +> OBJ_EXT=o +> LIB_EXT=a +6c8 +< OPTFLAGS = -O2 +--- +> OPTFLAGS = -DLINUX -fPIC Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/greenplanet/Makefile.in.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/greenplanet/Makefile.in.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/greenplanet/Makefile.in.patch (revision 18231) @@ -0,0 +1,10 @@ +3c3,5 +< CC = cc +--- +> CC = icc +> OBJ_EXT=o +> LIB_EXT=a +6c8 +< OPTFLAGS = -O2 +--- +> OPTFLAGS = -DLINUX -fPIC Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/linux64/Makefile.in.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/linux64/Makefile.in.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/linux64/Makefile.in.patch (revision 18231) @@ -0,0 +1,10 @@ +3c3,5 +< CC = cc +--- +> CC = gcc +> OBJ_EXT=o +> LIB_EXT=a +6c8 +< OPTFLAGS = -O2 +--- +> OPTFLAGS = -DLINUX -fPIC Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/macosx32/Makefile.in.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/macosx32/Makefile.in.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/macosx32/Makefile.in.patch (revision 18231) @@ -0,0 +1,10 @@ +3c3,5 +< CC = cc +--- +> CC = gcc +> OBJ_EXT=o +> LIB_EXT=a +6c8 +< OPTFLAGS = -O2 +--- +> OPTFLAGS = -O2 -m32 Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/macosx64/Makefile.in.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/macosx64/Makefile.in.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/macosx64/Makefile.in.patch (revision 18231) @@ -0,0 +1,10 @@ +3c3,5 +< CC = cc +--- +> CC = gcc +> OBJ_EXT=o +> LIB_EXT=a +6c8 +< OPTFLAGS = -O2 +--- +> OPTFLAGS = -O2 -m64 Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/pleiades/Makefile.in.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/pleiades/Makefile.in.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/pleiades/Makefile.in.patch (revision 18231) @@ -0,0 +1,10 @@ +3c3,5 +< CC = cc +--- +> CC = icc +> OBJ_EXT=o +> LIB_EXT=a +6c8 +< OPTFLAGS = -O2 +--- +> OPTFLAGS = -DLINUX -fPIC Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/win32/Makefile.in.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/win32/Makefile.in.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/win32/Makefile.in.patch (revision 18231) @@ -0,0 +1,10 @@ +3c3,5 +< CC = cc +--- +> CC = icl +> OBJ_EXT=obj +> LIB_EXT=lib +6c8 +< OPTFLAGS = -O2 +--- +> OPTFLAGS = -DWIN32 -D__VC__ Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/win7/Makefile.in.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/win7/Makefile.in.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/win7/Makefile.in.patch (revision 18231) @@ -0,0 +1,21 @@ +3c3,5 +< CC = cc +--- +> CC = cl +> OBJ_EXT=obj +> LIB_EXT=lib +6c8 +< OPTFLAGS = -O2 +--- +> OPTFLAGS = -DWIN32 -D__VC__ +14,20c16,17 +< # What archiving to use +< AR = ar rv +< +< # What to use for indexing the archive +< RANLIB = ranlib +< #RANLIB = ar -ts +< #RANLIB = +--- +> # What tool to use to create library +> LIB=lib.exe Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/win7/Makefile.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/win7/Makefile.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/configs/4.0/win7/Makefile.patch (revision 18231) @@ -0,0 +1,5 @@ +24c24,25 +< $(LIB) -out:$@ $(OBJS) +--- +> $(AR) $@ $(OBJS) +> $(RANLIB) $@ Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-altix64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-altix64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-altix64.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install metis-4.0 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz' + +#Untar +tar -zxvf metis-4.0.tar.gz + +#Move metis into install directory +mv metis-4.0/* install +rm -rf metis-4.0 + +#Apply patches +cd install +patch -p1 < ../metis-4.0.patch +patch Makefile.in ../configs/4.0/altix64/Makefile.in.patch + +#Compile +make Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-cosmos.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-cosmos.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-cosmos.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install metis-4.0 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz' + +#Untar +tar -zxvf metis-4.0.tar.gz + +#Move metis into install directory +mv metis-4.0/* install +rm -rf metis-4.0 + +#Apply patches +cd install +patch -p1 < ../metis-4.0.patch +patch Makefile.in ../configs/4.0/cosmos/Makefile.in.patch + +#Compile +make Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-discover.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-discover.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-discover.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install metis-4.0 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz' + +#Untar +tar -zxvf metis-4.0.tar.gz + +#Move metis into install directory +mv metis-4.0/* install +rm -rf metis-4.0 + +#Apply patches +cd install +patch -p1 < ../metis-4.0.patch +patch Makefile.in ../configs/4.0/discover/Makefile.in.patch + +#Compile +make Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-greenplanet.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-greenplanet.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-greenplanet.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install metis-4.0 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz' + +#Untar +tar -zxvf metis-4.0.tar.gz + +#Move metis into install directory +mv metis-4.0/* install +rm -rf metis-4.0 + +#Apply patches +cd install +patch -p1 < ../metis-4.0.patch +patch Makefile.in ../configs/4.0/greenplanet/Makefile.in.patch + +#Compile +make Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-hoffman2.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-hoffman2.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-hoffman2.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install metis-4.0 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz' + +#Untar +tar -zxvf metis-4.0.tar.gz + +#Move metis into install directory +mv metis-4.0/* install +rm -rf metis-4.0 + +#Apply patches +cd install +patch -p1 < ../metis-4.0.patch +patch Makefile.in ../configs/4.0/pleiades/Makefile.in.patch + +#Compile +make Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-linux64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-linux64.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install metis-4.0 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz' + +#Untar +tar -zxvf metis-4.0.tar.gz + +#Move metis into install directory +mv metis-4.0/* install +rm -rf metis-4.0 + +#Apply patches +cd install +patch -p1 < ../metis-4.0.patch +patch Makefile.in ../configs/4.0/linux64/Makefile.in.patch + +#Compile +make Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-macosx32.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-macosx32.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-macosx32.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install metis-4.0 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz' + +#Untar +tar -zxvf metis-4.0.tar.gz + +#Move metis into install directory +mv metis-4.0/* install +rm -rf metis-4.0 + +#Apply patches +cd install +patch -p1 < ../metis-4.0.patch +patch Makefile.in ../configs/4.0/macosx32/Makefile.in.patch + +#Compile +make Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-macosx64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-macosx64.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install metis-4.0 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz' + +#Untar +tar -zxvf metis-4.0.tar.gz + +#Move metis into install directory +mv metis-4.0/* install +rm -rf metis-4.0 + +#Apply patches +cd install +patch -p1 < ../metis-4.0.patch +patch Makefile.in ../configs/4.0/macosx64/Makefile.in.patch + +#Compile +make Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-pleiades.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-pleiades.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-pleiades.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install metis-4.0 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz' + +#Untar +tar -zxvf metis-4.0.tar.gz + +#Move metis into install directory +mv metis-4.0/* install +rm -rf metis-4.0 + +#Apply patches +cd install +patch -p1 < ../metis-4.0.patch +patch Makefile.in ../configs/4.0/pleiades/Makefile.in.patch + +#Compile +make Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-win32.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-win32.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-win32.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install metis-4.0 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz' + +#Untar +tar -zxvf metis-4.0.tar.gz + +#Move metis into install directory +mv metis-4.0/* install +rm -rf metis-4.0 + +#Apply patches +cd install +patch -p1 < ../metis-4.0.patch +patch Makefile.in ../configs/4.0/win32/Makefile.in.patch + +#Compile +make Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-win7.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-win7.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-4.0-win7.sh (revision 18231) @@ -0,0 +1,25 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install metis-4.0 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz' + +#Untar +tar -zxvf metis-4.0.tar.gz + +#Move metis into install directory +mv metis-4.0/* install +rm -rf metis-4.0 + +#Apply patches +cd install +patch -p1 < ../metis-4.0.patch +patch -R Lib/Makefile ../configs/4.0/win7/Makefile.patch +patch Makefile.in ../configs/4.0/win7/Makefile.in.patch + +#Compile +make Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-5.0.1-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-5.0.1-linux64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/install-5.0.1-linux64.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu +#metis 5.0 should be used: srand48 and drand48 are being redefined in conflict to the stdlib equivalent functions. + +#Some cleanup +rm -rf install metis-5.0.1 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-5.0.1.tar.gz' 'metis-5.0.1.tar.gz' + +#Untar +tar -zxvf metis-5.0.1.tar.gz + +#Move metis into install directory +mv metis-5.0.1/* install +rm -rf metis-5.0.1 + +#Apply patches +cd install + +#Compile metis +make config prefix="$ISSM_DIR/externalpackages/metis/install" +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/metis-4.0.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/metis-4.0.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/metis/metis-4.0.patch (revision 18231) @@ -0,0 +1,237 @@ +diff -crB install/Lib/kmetis.c install2/Lib/kmetis.c +*** install/Lib/kmetis.c 1998-11-30 08:26:47.000000000 -0800 +--- install2/Lib/kmetis.c 2011-06-08 15:47:33.911358942 -0700 +*************** +*** 66,72 **** + ctrl.dbglvl = options[OPTION_DBGLVL]; + } + ctrl.optype = OP_KMETIS; +! ctrl.CoarsenTo = amax((*nvtxs)/(40*log2(*nparts)), 20*(*nparts)); + ctrl.maxvwgt = 1.5*((graph.vwgt ? idxsum(*nvtxs, graph.vwgt) : (*nvtxs))/ctrl.CoarsenTo); + + InitRandom(-1); +--- 66,72 ---- + ctrl.dbglvl = options[OPTION_DBGLVL]; + } + ctrl.optype = OP_KMETIS; +! ctrl.CoarsenTo = amax((*nvtxs)/(40*log2_function(*nparts)), 20*(*nparts)); + ctrl.maxvwgt = 1.5*((graph.vwgt ? idxsum(*nvtxs, graph.vwgt) : (*nvtxs))/ctrl.CoarsenTo); + + InitRandom(-1); +diff -crB install/Lib/kvmetis.c install2/Lib/kvmetis.c +*** install/Lib/kvmetis.c 1998-11-30 08:26:47.000000000 -0800 +--- install2/Lib/kvmetis.c 2011-06-08 15:47:33.916358976 -0700 +*************** +*** 66,72 **** + ctrl.dbglvl = options[OPTION_DBGLVL]; + } + ctrl.optype = OP_KVMETIS; +! ctrl.CoarsenTo = amax((*nvtxs)/(40*log2(*nparts)), 20*(*nparts)); + ctrl.maxvwgt = 1.5*((graph.vwgt ? idxsum(*nvtxs, graph.vwgt) : (*nvtxs))/ctrl.CoarsenTo); + + InitRandom(-1); +--- 66,72 ---- + ctrl.dbglvl = options[OPTION_DBGLVL]; + } + ctrl.optype = OP_KVMETIS; +! ctrl.CoarsenTo = amax((*nvtxs)/(40*log2_function(*nparts)), 20*(*nparts)); + ctrl.maxvwgt = 1.5*((graph.vwgt ? idxsum(*nvtxs, graph.vwgt) : (*nvtxs))/ctrl.CoarsenTo); + + InitRandom(-1); +diff -crB install/Lib/Makefile install2/Lib/Makefile +*** install/Lib/Makefile 1998-09-22 05:08:29.000000000 -0700 +--- install2/Lib/Makefile 2011-06-08 15:19:00.551540482 -0700 +*************** +*** 6,31 **** + LD = $(CC) -L. + + +! OBJS = coarsen.o fm.o initpart.o match.o ccgraph.o memory.o \ +! pmetis.o pqueue.o refine.o util.o timing.o debug.o \ +! bucketsort.o graph.o stat.o kmetis.o kwayrefine.o \ +! kwayfm.o balance.o ometis.o srefine.o sfm.o separator.o \ +! mincover.o mmd.o mesh.o meshpart.o frename.o fortran.o \ +! myqsort.o compress.o parmetis.o estmem.o \ +! mpmetis.o mcoarsen.o mmatch.o minitpart.o mbalance.o \ +! mrefine.o mutil.o mfm.o mkmetis.o mkwayrefine.o mkwayfmh.o \ +! mrefine2.o minitpart2.o mbalance2.o mfm2.o \ +! kvmetis.o kwayvolrefine.o kwayvolfm.o subdomains.o + +! .c.o: +! $(CC) $(CFLAGS) -c $*.c + +! ../libmetis.a: $(OBJS) + $(AR) $@ $(OBJS) + $(RANLIB) $@ + + clean: +! rm -f *.o + + realclean: +! rm -f *.o ; rm -f ../libmetis.a +--- 6,31 ---- + LD = $(CC) -L. + + +! OBJS = coarsen.$(OBJ_EXT) fm.$(OBJ_EXT) initpart.$(OBJ_EXT) match.$(OBJ_EXT) ccgraph.$(OBJ_EXT) memory.$(OBJ_EXT) \ +! pmetis.$(OBJ_EXT) pqueue.$(OBJ_EXT) refine.$(OBJ_EXT) util.$(OBJ_EXT) timing.$(OBJ_EXT) debug.$(OBJ_EXT) \ +! bucketsort.$(OBJ_EXT) graph.$(OBJ_EXT) stat.$(OBJ_EXT) kmetis.$(OBJ_EXT) kwayrefine.$(OBJ_EXT) \ +! kwayfm.$(OBJ_EXT) balance.$(OBJ_EXT) ometis.$(OBJ_EXT) srefine.$(OBJ_EXT) sfm.$(OBJ_EXT) separator.$(OBJ_EXT) \ +! mincover.$(OBJ_EXT) mmd.$(OBJ_EXT) mesh.$(OBJ_EXT) meshpart.$(OBJ_EXT) frename.$(OBJ_EXT) fortran.$(OBJ_EXT) \ +! myqsort.$(OBJ_EXT) compress.$(OBJ_EXT) parmetis.$(OBJ_EXT) estmem.$(OBJ_EXT) \ +! mpmetis.$(OBJ_EXT) mcoarsen.$(OBJ_EXT) mmatch.$(OBJ_EXT) minitpart.$(OBJ_EXT) mbalance.$(OBJ_EXT) \ +! mrefine.$(OBJ_EXT) mutil.$(OBJ_EXT) mfm.$(OBJ_EXT) mkmetis.$(OBJ_EXT) mkwayrefine.$(OBJ_EXT) mkwayfmh.$(OBJ_EXT) \ +! mrefine2.$(OBJ_EXT) minitpart2.$(OBJ_EXT) mbalance2.$(OBJ_EXT) mfm2.$(OBJ_EXT) \ +! kvmetis.$(OBJ_EXT) kwayvolrefine.$(OBJ_EXT) kwayvolfm.$(OBJ_EXT) subdomains.$(OBJ_EXT) + +! %.$(OBJ_EXT) : %.c +! $(CC) -c $(CFLAGS) -o $@ $< + +! ../libmetis.$(LIB_EXT): $(OBJS) + $(AR) $@ $(OBJS) + $(RANLIB) $@ + + clean: +! rm -f *.$(OBJ_EXT) + + realclean: +! rm -f *.$(OBJ_EXT) ; rm -f ../libmetis.$(LIB_EXT) +diff -crB install/Lib/metis.h install2/Lib/metis.h +*** install/Lib/metis.h 1998-11-30 08:26:50.000000000 -0800 +--- install2/Lib/metis.h 2011-06-08 15:19:00.544540433 -0700 +*************** +*** 18,24 **** +--- 18,26 ---- + #else + #include + #endif ++ #ifndef WIN32 + #include ++ #endif + #include + #include + #include +diff -crB install/Lib/mkmetis.c install2/Lib/mkmetis.c +*** install/Lib/mkmetis.c 1998-11-30 08:26:48.000000000 -0800 +--- install2/Lib/mkmetis.c 2011-06-08 15:47:33.921359010 -0700 +*************** +*** 47,53 **** + ctrl.dbglvl = options[OPTION_DBGLVL]; + } + ctrl.optype = OP_KMETIS; +! ctrl.CoarsenTo = amax((*nvtxs)/(20*log2(*nparts)), 30*(*nparts)); + + ctrl.nmaxvwgt = 1.5/(1.0*ctrl.CoarsenTo); + +--- 47,53 ---- + ctrl.dbglvl = options[OPTION_DBGLVL]; + } + ctrl.optype = OP_KMETIS; +! ctrl.CoarsenTo = amax((*nvtxs)/(20*log2_function(*nparts)), 30*(*nparts)); + + ctrl.nmaxvwgt = 1.5/(1.0*ctrl.CoarsenTo); + +diff -crB install/Lib/proto.h install2/Lib/proto.h +*** install/Lib/proto.h 1998-11-30 08:26:50.000000000 -0800 +--- install2/Lib/proto.h 2011-06-08 15:47:34.009359613 -0700 +*************** +*** 230,237 **** +--- 230,243 ---- + void QUADNODALMETIS(int, int, idxtype *, idxtype *, idxtype *adjncy); + + /* meshpart.c */ ++ #ifdef __cplusplus ++ extern "C" { ++ #endif + void METIS_PartMeshNodal(int *, int *, idxtype *, int *, int *, int *, int *, idxtype *, idxtype *); + void METIS_PartMeshDual(int *, int *, idxtype *, int *, int *, int *, int *, idxtype *, idxtype *); ++ #ifdef __cplusplus ++ } ++ #endif + + /* mfm.c */ + void MocFM_2WayEdgeRefine(CtrlType *, GraphType *, float *, int); +*************** +*** 459,465 **** + void srand48(long); + int ispow2(int); + void InitRandom(int); +! int log2(int); + + + +--- 465,471 ---- + void srand48(long); + int ispow2(int); + void InitRandom(int); +! int log2_function(int); + + + +diff -crB install/Lib/rename.h install2/Lib/rename.h +*** install/Lib/rename.h 1998-11-30 08:26:50.000000000 -0800 +--- install2/Lib/rename.h 2011-06-08 15:47:34.014359647 -0700 +*************** +*** 410,416 **** + #define RandomPermute __RandomPermute + #define ispow2 __ispow2 + #define InitRandom __InitRandom +! #define log2 __log2 + + + +--- 410,417 ---- + #define RandomPermute __RandomPermute + #define ispow2 __ispow2 + #define InitRandom __InitRandom +! /* Correction bug Nadir SOUALEM*/ +! #define log2_function __log2_function + + + +diff -crB install/Lib/util.c install2/Lib/util.c +*** install/Lib/util.c 1998-11-30 08:26:50.000000000 -0800 +--- install2/Lib/util.c 2011-06-08 15:47:34.018359675 -0700 +*************** +*** 507,515 **** + } + + /************************************************************************* +! * This function returns the log2(x) + **************************************************************************/ +! int log2(int a) + { + int i; + +--- 507,515 ---- + } + + /************************************************************************* +! * This function returns the log2_function(x) + **************************************************************************/ +! int log2_function(int a) + { + int i; + +diff -crB install/Makefile install2/Makefile +*** install/Makefile 1998-09-20 11:15:31.000000000 -0700 +--- install2/Makefile 2011-06-08 15:19:00.511540204 -0700 +*************** +*** 2,9 **** + + default: + (cd Lib ; make ) +! (cd Programs ; make ) +! (cd Test ; make ) + + clean: + (cd Lib ; make clean ) +--- 2,9 ---- + + default: + (cd Lib ; make ) +! # (cd Programs ; make ) +! # (cd Test ; make ) + + clean: + (cd Lib ; make clean ) Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mitgcm/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mitgcm/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mitgcm/install.sh (revision 18231) @@ -0,0 +1,34 @@ +#!/bin/bash +set -eu + +#Do these commands once: +# cvs -d:pserver:cvsanon@mitgcm.org:/u/gcmpack login +# ( enter the CVS password: "cvsanon" ) + +#Some cleanup +rm -rf install bin exe + +#add cvs repository +export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack' + +echo loging into MITgcm cvs: provide password, which is cvsanon +cvs login + +#Download code from server +cvs login +cvs co -P MITgcm + +#move +mv MITgcm install + + +#compile code +cd install +mkdir bin exe +cd bin +../tools/genmake2 -mods=../../code +make depend +make -j 8 + + + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mitgcm/notes =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mitgcm/notes (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mitgcm/notes (revision 18231) @@ -0,0 +1,112 @@ +Explanations of the code: {{{1 +doc: call Dimitris. + +Main code of MITgcm in 3 dir: + +eesupp: running the code on parallel clusters. infrastructure for running MPI, shared memory, non-physics part of the code. + src: main.F: eeboo (wrapper initialization) + check_threads + the_model_main + eedie (wrapper termination) + inc + + +model: here is the model main. + src: the_model_main.F includes the base MITgcm code. + inc: + +pkg: do various physics. packages will not be compiled. + kpp: vertical mixing parametization + gmred: isopicnel mixing parameterization. + + thice: + seaice: sea ice models + + shelfice: interacting with ice sheets + icefront + + cal: calendar correspondance between model time step and calendar time. + + diagnostics: any physical variable that you want to look at. get output variables into output of the model. + + debug: other kind of diagnostics, various levels of debug. + + frazil: frazil ice. + + atmospherics packages: fizhi, cheapaml + + exch2: fancier way of exchanging data and tiling. + + +jobs: forget about it. + + +lsopt: forget it. + +optim: forget it. + + +utils: + matlab: bunch of matlab scripts. + +tools: build_options: platform dependent run files to be run with gene_make to generate the correct Makefile. +}}} +How to run : {{{1 +All the verification tests are downloaded if you checkout the MITgcm repository instead of the +MITgcm_code: +cvs co -P MITgcm + +The verification tests are downloaded in MITgcm/verification. They can be run using +the testreport utility. Only a subset of the tests can be run if needed, by supplying +an option flag to tesstreport. + + +For our work, the relevant tests are: +labsea: sea ice +ismip: shelf ice + +If you run a test like lab_sea: + +./code/packages.conf: list of packages that we want to compile for this specific run. +For each package, you at least need to modify code/size.h + +You can find the runtime parameters in: +input/data: runtime parameters for model source +input/eedata:runtime parameters for eesupp source +input/data.: runtime parameters for all packages +intput/data.pkg: runtime parameters for packages that need to be run. subset of packages.conf + +The build directory holds the source and objects for the current test, with symlinks + +If errors appear during the run, go into: +./run and find the STDERR file. + +To supply different Makefile templates for testreport: +testreport -ef -opt Makefile_amd64_gfortran + +You can use matlab to plot the results: +use readbin from the labsea experiment or MITgcm/tools/matlab/rdmds + +There is an MITgcm_contrib repository for code that is not in the main trunk yet: +MITgcm_contrib/MPMice/beaufort presents a scenario for a quick coupler. + +}}} +Extra nodes{{{ +cd install/verification/ +./testreport -of ../tools/build_options/linux_amd64_gfortran + +( results for baseline lab_sea verification + experiment are in verification/lab_sea/run ) + +cd lab_sea/run +there is routines in lab_sea/matlab + +ma +addpath('../matlab') +eta=readbin('Eta.0000000001.data',[20 16],1); +pcolor(eta') +colorbar + +addpath('../../../utils/matlab') +eta=rdmds('Eta.0000000001'); +}}} Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mitgcm/readme_mitgcm.txt =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mitgcm/readme_mitgcm.txt (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mitgcm/readme_mitgcm.txt (revision 18231) @@ -0,0 +1,84 @@ +Instructions for getting MITgcm: http://mitgcm.org/ + + +(1) +add to your .bashrc file +# CVS +export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack' + +source .bashrc + +cvs login + ( enter the CVS password: "cvsanon" ) + +cvs co -P MITgcm + +( +or if you don't want the verification packages +cvs co -P MITgcm_code +) + + +(2) +and if you don't like CVS go to : + +http://mitgcm.org/download/ + +and download the most recent checkpoint: +e.g. + MITgcm_c62w.tar.gz + + + + + +========================================================== +Instructions for generating and running a 1-CPU experiment +========================================================== + + cd MITgcm/verification/lab_sea + cd build + cp ../code/*.h ../code/packages.conf . + ../../../tools/genmake2 + make depend + make + cd ../input + ../build/mitgcmuv > output.txt + +Use matlab script to look at the output + cd ../../../verification/lab_sea/matlab + matlab + lookat_ice (you might have to modify the script) + + + +================================================================ +Instructions for running the "weddell" 200x160x50 configuration +================================================================ +face=6; ix=101:300; jx=290:449; kx=1:50; + +1. Obtain copies of following directories: + ftp://ecco2.jpl.nasa.gov/data1/weddell/code + ftp://ecco2.jpl.nasa.gov/data1/weddell/run_template + ftp://ecco2.jpl.nasa.gov/data1/data/era40/era40_ecmwf_blend + ftp://ecco2.jpl.nasa.gov/data1/data/blend_forcing/cube59_GPCP + +2. Get and compile code: + cvs co MITgcm_code + cd MITgcm + mkdir bin exe + cd bin + ../tools/genmake2 -mods=../../code + make depend + make -j + +3. Model execution: + cd ../exe + cp ../../run_template/* . + cp ../bin/mitgcmuv . + ./mitgcmuv >& output.txt & + + + + + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/modelE/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/modelE/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/modelE/install.sh (revision 18231) @@ -0,0 +1,21 @@ +#!/bin/bash +set -eu +#modelE downloaded from the gis repository of the GISS (Goddard Institute for Space Studies) +#at http://www.giss.nasa.gov/tools/modelE/ + +#Some cleanup +rm -rf src install modelE_AR5_branch +mkdir src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/modelE_AR5_branch.2012.03.13_10.12.21.tgz' 'modelE_AR5_branch.2012.03.13_10.12.21.tgz' + +#Untar +tar -zxvf modelE_AR5_branch.2012.03.13_10.12.21.tgz + +#Move modelE into install directory +mv modelE_AR5_branch/* src +rm -rf modelE_AR5_branch + +#Apply patches +cd src Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/modules/install-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/modules/install-macosx64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/modules/install-macosx64.sh (revision 18231) @@ -0,0 +1,39 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install +rm -rf modules-3.2.10 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/modules-3.2.10.tar.gz' 'modules-3.2.10.tar.gz' + +#Untar +tar -zxvf modules-3.2.10.tar.gz + +#Move modules into src directory + +#Configure modules +cd modules-3.2.10 +sudo ./configure \ + --prefix=/usr/local/modules \ + --with-tcl-lib=$ISSM_DIR/externalpackages/tcl/install/Library/Frameworks/Tcl.framework/Versions/8.5\ + --with-tcl-inc=$ISSM_DIR/externalpackages/tcl/install/Library/Frameworks/Tcl.framework/Versions/8.5/Headers\ + --with-tcl-ver=8.5 \ + --with-tclx-lib=$ISSM_DIR/externalpackages/tclx/install/lib/tclx8.4\ + --with-tclx-inc=$ISSM_DIR/externalpackages/tclx/install/include\ + --with-tclx-ver=8.4 \ + --with-version-path=/usr/local/modules/versions \ + --with-skel-path=/usr/local/modules/etc/skel \ + --with-etc-path=/usr/local/modules/etc \ + --with-module-path=/usr/local/modules/files \ + --disable-dependency-tracking + +#Compile and install modules +if [ $# -eq 0 ]; then + sudo make +else + sudo make -j $1 +fi +sudo make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/modules/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/modules/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/modules/install.sh (revision 18231) @@ -0,0 +1,22 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/modules-3.2.9c.tar.gz modules-3.2.9c.tar.gz + +#Untar and move python into install directory +tar -zxvf modules-3.2.9c.tar.gz +mv modules-3.2.9 install + +#Configure doxygen +cd install +./configure \ + --prefix "$ISSM_DIR/externalpackages/modules/install" \ + --without-x + +#compile and install +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-2_1.4-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-2_1.4-linux64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-2_1.4-linux64.sh (revision 18231) @@ -0,0 +1,30 @@ +#!/bin/bash + +#Some cleanup +rm -rf src install mpich2-1.4 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich2-1.4.tar.gz' 'mpich2-1.4.tar.gz' + +#Untar +tar -zxvf mpich2-1.4.tar.gz + +#Move mpich2 into src directory +mv mpich2-1.4/* src +rm -rf mpich2-1.4 + +#Configure mpich2 +cd src +export -n F90 +export CFLAGS="$CFLAGS -fPIC" +export FFLAGS="$FFLAGS -fPIC" +./configure \ + --prefix="$ISSM_DIR/externalpackages/mpich/install" \ + --enable-shared \ + --enable-sharedlibs=gcc \ + --enable-f91=gfortran + +#Compile mpich2 (parallel make not supported) +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-2_1.4-macosx32.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-2_1.4-macosx32.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-2_1.4-macosx32.sh (revision 18231) @@ -0,0 +1,32 @@ +#!/bin/bash + +#Some cleanup +rm -rf src install mpich2-1.4 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich2-1.4.tar.gz' 'mpich2-1.4.tar.gz' + +#Untar +tar -zxvf mpich2-1.4.tar.gz + +#Move mpich2 into src directory +mv mpich2-1.4/* src +rm -rf mpich2-1.4 + +#Configure mpich2 +cd src +export FFLAGS=" -m32" +export CFLAGS=" -m32" +export CXXFLAGS=" -arch i386" +export CPPFLAGS=" -arch i386" +./configure \ + --prefix="$ISSM_DIR/externalpackages/mpich/install" \ + --enable-f91=gfortran \ + --enable-sharedlibs=osx-gcc \ + --enable-shared \ + --enable-fc + +#Compile mpich2 (parallel make not supported) +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-2_1.4-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-2_1.4-macosx64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-2_1.4-macosx64.sh (revision 18231) @@ -0,0 +1,32 @@ +#!/bin/bash + +#Some cleanup +rm -rf src install mpich2-1.4 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich2-1.4.tar.gz' 'mpich2-1.4.tar.gz' + +#Untar +tar -zxvf mpich2-1.4.tar.gz + +#Move mpich2 into src directory +mv mpich2-1.4/* src +rm -rf mpich2-1.4 + +#Configure mpich2 +cd src +export FCFLAGS=" -m64" +export FFLAGS=" -m64" +export CFLAGS=" -arch x86_64" +export CXXFLAGS=" -arch x86_64" +./configure \ + --prefix="$ISSM_DIR/externalpackages/mpich/install" \ + --enable-f91 \ + --enable-sharedlibs=osx-gcc \ + --enable-shared \ + --enable-fc + +#Compile mpich2 (parallel make not supported) +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-2_1.4.1-p1-win7.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-2_1.4.1-p1-win7.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-2_1.4.1-p1-win7.sh (revision 18231) @@ -0,0 +1,13 @@ +#!/bin/bash + +#In order to install MPICH2 on your platform, go to www.mpich.org/downloads +#and download the following file (Windows x86_64 for the Windows distribution): +#mpich2-1.4.1p1-win-x86-64.msi. This file is also hosted on the ISSM website. + + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich2-1.4.1p1-win-x86-64.msi' 'mpich2-1.4.1p1-win-x86-64.msi' + +#once installed, create a symbolic link between the MPICH2 directory +#and the install directory. For example: +#ln -s /cygdrive/c/Program\ Files/MPICH2 install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-2_1.5-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-2_1.5-linux64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-2_1.5-linux64.sh (revision 18231) @@ -0,0 +1,32 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install mpich2-1.5 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich2-1.5.tar.gz' 'mpich2-1.5.tar.gz' + +#Untar +tar -zxvf mpich2-1.5.tar.gz + +#Move mpich2 into src directory +mv mpich2-1.5/* src +rm -rf mpich2-1.5 + +#Configure mpich2 +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/mpich/install" \ + --enable-shared \ + --enable-sharedlibs=gcc \ + --enable-f91=gfortran CC=gcc FC=gfortran + +#Compile mpich2 (this new version supports parallel make) +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-2_1.5-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-2_1.5-macosx64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-2_1.5-macosx64.sh (revision 18231) @@ -0,0 +1,32 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install mpich2-1.5 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich2-1.5.tar.gz' 'mpich2-1.5.tar.gz' + +#Untar +tar -zxvf mpich2-1.5.tar.gz + +#Move mpich2 into src directory +mv mpich2-1.5/* src +rm -rf mpich2-1.5 + +#Configure mpich2 +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/mpich/install" \ + --enable-shared \ + --enable-sharedlibs=gcc \ + --enable-f91=gfortran + +#Compile mpich2 (this new version supports parallel make) +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-2_1.5-walgreen.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-2_1.5-walgreen.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-2_1.5-walgreen.sh (revision 18231) @@ -0,0 +1,31 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install mpich2-1.5 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich2-1.5.tar.gz' 'mpich2-1.5.tar.gz' + +#Untar +tar -zxvf mpich2-1.5.tar.gz + +#Move mpich2 into src directory +mv mpich2-1.5/* src +rm -rf mpich2-1.5 + +#Configure mpich2 +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/mpich/install" \ + --enable-shared \ + --with-device=ch3:sock + +#Compile mpich2 (this new version supports parallel make) +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-3.0-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-3.0-linux64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-3.0-linux64.sh (revision 18231) @@ -0,0 +1,31 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install mpich-3.0.4 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich-3.0.4.tar.gz' 'mpich-3.0.4.tar.gz' + +#Untar +tar -zxvf mpich-3.0.4.tar.gz + +#Move mpich into src directory +mv mpich-3.0.4/* src +rm -rf mpich-3.0.4 + +#Configure mpich +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/mpich/install" \ + --enable-shared \ + --enable-sharedlibs=gcc + +#Compile mpich (this new version supports parallel make) +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-3.0-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-3.0-macosx64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mpich/install-3.0-macosx64.sh (revision 18231) @@ -0,0 +1,32 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install mpich-3.0.4 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich-3.0.4.tar.gz' 'mpich-3.0.4.tar.gz' + +#Untar +tar -zxvf mpich-3.0.4.tar.gz + +#Move mpich into src directory +mv mpich-3.0.4/* src +rm -rf mpich-3.0.4 + +#Configure mpich +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/mpich/install" \ + --enable-shared + + #CC=llvm-gcc \ + +#Compile mpich (this new version supports parallel make) +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mumps/README =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mumps/README (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mumps/README (revision 18231) @@ -0,0 +1,1 @@ +MUMPS install package. Better rely on Petsc to install this, but feel free to try. Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mumps/configs/Makefile-macosx64.inc =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mumps/configs/Makefile-macosx64.inc (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mumps/configs/Makefile-macosx64.inc (revision 18231) @@ -0,0 +1,32 @@ +LPORDDIR = $(topdir)/PORD/lib/ +IPORD = -I$(topdir)/PORD/include/ +LPORD = -L$(LPORDDIR) -lpord +IMETIS = -I$(ISSM_DIR)/externalpackages/petsc/install/include/ +LMETIS = -L$(ISSM_DIR)/externalpackages/petsc/src/macosx-gnu/lib -L$(ISSM_DIR)/externalpackages/petsc/src/macosx-gnu/lib -lparmetis +ORDERINGSC = -Dpord -Dmetis -Dparmetis +ORDERINGSF = -Dprod -Dmetis -Dparmetis +LORDERINGS = $(LMETIS) $(LPORD) $(LSCOTCH) +IORDERINGSC = $(IMETIS) $(IPORD) $(ISCOTCH) +IORDERINGSF = $(ISCOTCH) +RM = /bin/rm -f +CC = $(ISSM_DIR)/externalpackages/mpich2/install/bin/mpicc +OPTC = -PIC -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -O +OUTC = -o +FC = $(ISSM_DIR)/externalpackages/mpich2/install/bin/mpif90 +FL = $(ISSM_DIR)/externalpackages/mpich2/install/bin/mpif90 +OPTF = -fPIC -Wno-unused-variable -Wno-unused-dummy-argument -O +OUTF = -o +CDEFS = -DAdd_ +AR = /usr/bin/ar cr +LIBEXT = .a +RANLIB = /usr/bin/ranlib -c +SCALAP = -L$(ISSM_DIR)/externalpackages/petsc/src/macosx-gnu/lib -L$(ISSM_DIR)/externalpackages/petsc/src/macosx-gnu/lib -lscalapack -L$(ISSM_DIR)/externalpackages/petsc/src/macosx-gnu/lib -L$(ISSM_DIR)/externalpackages/petsc/src/macosx-gnu/lib -lblacs +INCPAR = -I$(ISSM_DIR)/externalpackages/mpich2/install/include -I$(ISSM_DIR)/externalpackages/mpich2/install/include +LIBPAR = $(SCALAP) +INCSEQ = -I$(topdir)/libseq +LIBSEQ = $(LAPACK) -L$(topdir)/libseq -lmpiseq +LIBBLAS = -L$(ISSM_DIR)/externalpackages/petsc/src/macosx-gnu/lib -L$(ISSM_DIR)/externalpackages/petsc/src/macosx-gnu/lib -lflapack -L$(ISSM_DIR)/externalpackages/petsc/src/macosx-gnu/lib -L$(ISSM_DIR)/externalpackages/petsc/src/macosx-gnu/lib -lfblas -L$(ISSM_DIR)/externalpackages/mpich2/install/lib -L/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/x86_64 -L/Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1/x86_64 -L/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1 -L/usr/llvm-gcc-4.2/lib/gcc -L$(ISSM_DIR)/externalpackages/petsc/src -L$(ISSM_DIR)/externalpackages/hdf5/install/lib -L$(ISSM_DIR)/externalpackages/netcdf/install/lib -L/Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib/gcc/i686-apple-darwin11/4.2.1 -L/usr/llvm-gcc-4.2/lib -L/Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2/lib -lmpichf90 -lgfortran -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin11/4.6.2 -L/usr/local/gfortran/lib -lgfortran -lgcc_ext.10.5 -lquadmath -lm -lm +OPTL = -O -I. +INCS = $(INCPAR) +LIBS = $(LIBPAR) +LIBSEQNEEDED = Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mumps/install-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mumps/install-macosx64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/mumps/install-macosx64.sh (revision 18231) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install mumps-4.10.0-p3 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mumps-4.10.0-p3.tar.gz' 'mumps-4.10.0-p3.tar.gz' + +#Untar +tar -zxvf mumps-4.10.0-p3.tar.gz + +#Move mumps into src directory +mv mumps-4.10.0-p3/* src +rm -rf mumps-4.10.0-p3 + +#configuration: +cp configs/Makefile-macosx64.inc src/Makefile.inc + +#Configure mumps +cd src + +#Compile mumps +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/ncview/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/ncview/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/ncview/install.sh (revision 18231) @@ -0,0 +1,28 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ncview-1.93g.tar.gz' 'ncview-1.93g.tar.gz' + +#Untar +tar -zxvf ncview-1.93g.tar.gz + +#Move doxygen into src directory +mv ncview-1.93g/* install +rmdir ncview-1.93g + +#Configure doxygen +cd install +./configure \ + --prefix="$ISSM_DIR/externalpackages/ncview/install" \ + --x-libraries=/usr/X11/lib/ \ + --x-includes=/usr/X11/include/ \ + --with-netcdf_incdir="$ISSM_DIR/externalpackages/netcdf/install/include/" \ + --with-netcdf_libdir="$ISSM_DIR/externalpackages/netcdf/install/lib/" + +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/netcdf-cxx/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/netcdf-cxx/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/netcdf-cxx/install.sh (revision 18231) @@ -0,0 +1,23 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install netcdf-cxx-4.2 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/netcdf-cxx-4.2.tar.gz' 'netcdf-cxx-4.2.tar.gz' + +#Untar +tar -zxvf netcdf-cxx-4.2.tar.gz + +#Move metis into install directory +mv netcdf-cxx-4.2/* install +rm -rf netcdf-cxx-4.2 + +#Compile +export CXXFLAGS="-I$ISSM_DIR/externalpackages/netcdf/install/include " +cd install +./configure --prefix="$ISSM_DIR/externalpackages/netcdf-cxx/install" +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/netcdf-python/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/netcdf-python/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/netcdf-python/install.sh (revision 18231) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install netCDF4-1.0 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/netCDF4-1.0.tar.gz" "netCDF4-1.0.tar.gz" + +#Untar +tar -zxvf netCDF4-1.0.tar.gz + +#for later: +rm -rf ISSMDIR +echo $ISSM_DIR | sed 's/\//\\\//g' > ISSMDIR +ISSMDIR=`cat ISSMDIR` && rm -rf ISSMDIR + +#Move netCDF4 to install directory +rm -rf install/* +mv netCDF4-1.0/* install/ +rm -rf netCDF4-1.0 + +#Configur and compile +cd install +#edit setup.cfg to point to hdf5 and netcdf +cat setup.cfg.template | sed "s/\#netCDF4_dir = \/usr\/local/netCDF4_dir = $ISSMDIR\/externalpackages\/netcdf\/install/g" | sed "s/\#HDF5_dir = \/usr\/local/HDF5_DIR = $ISSMDIR\/externalpackages\/hdf5\/install/g" > setup.cfg + +python setup.py build +python setup.py install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/netcdf/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/netcdf/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/netcdf/install.sh (revision 18231) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu +#you need hdf5 compiled + +#Some cleanup +rm -rf src install netcdf-4.2 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/netcdf-4.2.tar.gz" "netcdf-4.2.tar.gz" + +#Untar +tar -zxvf netcdf-4.2.tar.gz + +#Move netcdf to install directory +rm -rf src/* +mv netcdf-4.2/* src/ +rm -rf netcdf-4.2 + +#Configure and compile +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/netcdf/install" \ + --disable-doxygen +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/nose/install-linux64-python2.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/nose/install-linux64-python2.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/nose/install-linux64-python2.sh (revision 18231) @@ -0,0 +1,20 @@ +#!/bin/bash +#Install Python nose module + +rm -rf src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/nose-1.1.2.tar.gz' 'nose-1.1.2.tar.gz' +tar -zxvf nose-1.1.2.tar.gz +mv nose-1.1.2 src +rm -rf nose-1.1.2 + +cd src +python ./setup.py build +python ./setup.py install + +#to be flagged by jenkins, we create an empty install dir: +cd ../ +mkdir install +touch install/emptyfile + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/nose/install-linux64-python3.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/nose/install-linux64-python3.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/nose/install-linux64-python3.sh (revision 18231) @@ -0,0 +1,16 @@ +#!/bin/bash +#Install Python nose module + +rm -rf src install + +svn checkout http://python-nose.googlecode.com/svn/branches/py3k +mv py3k src + +cd src +python ./setup.py build +python ./setup.py install + +#to be flagged by jenkins, we create an empty install dir: +cd ../ +mkdir install +touch install/emptyfile Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/nose/install-macosx64-python2.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/nose/install-macosx64-python2.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/nose/install-macosx64-python2.sh (revision 18231) @@ -0,0 +1,19 @@ +#!/bin/bash +#Install Python nose module + +rm -rf src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/nose-1.1.2.tar.gz' 'nose-1.1.2.tar.gz' +tar -zxvf nose-1.1.2.tar.gz +mv nose-1.1.2 src +rm -rf nose-1.1.2 + +cd src +python ./setup.py build +python ./setup.py install + +#to be flagged by jenkins, we create an empty install dir: +cd ../ +mkdir install +touch install/emptyfile Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/nose/install-macosx64-python3.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/nose/install-macosx64-python3.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/nose/install-macosx64-python3.sh (revision 18231) @@ -0,0 +1,16 @@ +#!/bin/bash +#Install Python nose module + +rm -rf src install + +svn checkout http://python-nose.googlecode.com/svn/branches/py3k +mv py3k src + +cd src +python ./setup.py build +python ./setup.py install + +#to be flagged by jenkins, we create an empty install dir: +cd ../ +mkdir install +touch install/emptyfile Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/numpy/README =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/numpy/README (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/numpy/README (revision 18231) @@ -0,0 +1,9 @@ +For OSX 10.7 (Lion), the instructions here can be followed: +http://www.scipy.org/Installing_SciPy/Mac_OS_X + +For OSX 10.6 (Snow Leopard), the scipy folks recommend gcc and g++ version 4.0. +However, ISSM needs the gfortran version recommended in $ISSM_DIR/externalpackages/gfortran. +On the webpage listed above, make sure the "export CC" and "export CXX" commands point to the +binaries associated with this gfortran version (likely in /usr/local/gfortran/bin by default). +Once this gfortran is installed, the install script in this directory for Snow Leopard should +work. Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/numpy/install-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/numpy/install-linux64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/numpy/install-linux64.sh (revision 18231) @@ -0,0 +1,33 @@ +#!/bin/bash +set -eu + +rm -rf install + +export CC="gcc -fPIC" +export CXX="g++ -fPIC" +export F77="gfortran -fPIC" +export FC="gfortran -fPIC" +export FFLAGS=-ff2c + +#clean up +rm -rf numpy +rm -rf numpy-1.7.0b2 + +#download numpy first +#export GIT_SSL_NO_VERIFY=true +#git clone https://github.com/numpy/numpy.git +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/numpy-1.7.0b2.tar.gz' 'numpy-1.7.0b2.tar.gz' + +#install numpy +tar -zxvf numpy-1.7.0b2.tar.gz +cd numpy-1.7.0b2 +python setup.py build +python setup.py install +cd .. +python -c "import numpy; print 'Installed NumPy', numpy.__version__" +python -c "import numpy; numpy.test()" + +#to be flagged by jenkins, we create an empty install dir: +mkdir install +touch install/emptyfile + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/numpy/install-macosx-lion.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/numpy/install-macosx-lion.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/numpy/install-macosx-lion.sh (revision 18231) @@ -0,0 +1,31 @@ +#!/bin/bash +set -eu + +rm -rf install + +export CC=gcc +export CXX=g++ +export FFLAGS=-ff2c + +#clean up +rm -rf numpy +rm -rf numpy-1.7.0b2 + +#download numpy first +#export GIT_SSL_NO_VERIFY=true +#git clone https://github.com/numpy/numpy.git +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/numpy-1.7.0b2.tar.gz' 'numpy-1.7.0b2.tar.gz' + +#install numpy +tar -zxvf numpy-1.7.0b2.tar.gz +cd numpy-1.7.0b2 +python setup.py build +python setup.py install +cd .. +python -c "import numpy; print 'Installed NumPy', numpy.__version__" +python -c "import numpy; numpy.test()" + +#to be flagged by jenkins, we create an empty install dir: +mkdir install +touch install/emptyfile + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/numpy/install-macosx-mlion.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/numpy/install-macosx-mlion.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/numpy/install-macosx-mlion.sh (revision 18231) @@ -0,0 +1,31 @@ +#!/bin/bash +set -eu + +rm -rf install + +export CC=gcc +export CXX=g++ +export FFLAGS=-ff2c + +#clean up +rm -rf numpy +rm -rf numpy-1.7.0b2 + +#download numpy first +#export GIT_SSL_NO_VERIFY=true +#git clone https://github.com/numpy/numpy.git +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/numpy-1.7.0b2.tar.gz' 'numpy-1.7.0b2.tar.gz' + +#install numpy +tar -zxvf numpy-1.7.0b2.tar.gz +cd numpy-1.7.0b2 +python setup.py build +python setup.py install +cd .. +python -c "import numpy; print 'Installed NumPy', numpy.__version__" +python -c "import numpy; numpy.test()" + +#to be flagged by jenkins, we create an empty install dir: +mkdir install +touch install/emptyfile + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/numpy/install-macosx-snowleopard.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/numpy/install-macosx-snowleopard.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/numpy/install-macosx-snowleopard.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +rm -rf install + +# On OSX 10.6, gfortran gets installed in /usr/local/gfortran +export CC="/usr/local/gfortran/bin/gcc" +export CXX="/usr/local/gfortran/bin/g++" + +#download numpy first +git clone https://github.com/numpy/numpy.git + +#install numpy +cd numpy +python setup.py build +python setup.py install +cd .. +python -c "import numpy; print 'Installed NumPy', numpy.__version__" +python -c "import numpy; numpy.test()" + +#to be flagged by jenkins, we create an empty install dir: +mkdir install +touch install/emptyfile + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/octave/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/octave/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/octave/install.sh (revision 18231) @@ -0,0 +1,31 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install octave-3.6.2 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/octave-3.6.2.tar.gz" "octave-3.6.2.tar.gz" + +#Untar +tar -zxvf octave-3.6.2.tar.gz + +#Move octave into install directory +mv octave-3.6.2/* src +rm -rf octave-3.6.2 + +#install +cd src +./configure \ + --prefix=$ISSM_DIR/externalpackages/octave/install \ + --disable-readline + +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/oofem/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/oofem/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/oofem/install.sh (revision 18231) @@ -0,0 +1,36 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf oofem-2.0 +mkdir src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/oofem-2.0.tar.gz' 'oofem-2.0.tar.gz' + +#Untar +tar -zxvf oofem-2.0.tar.gz + +#Move oofem into src directory +mv oofem-2.0/* src +rm -rf oofem-2.0 + +# currently a basic serial configuration, see http://www.oofem.org/wiki/doku.php?id=installation +# for details on enabling the IML++ and PETSc libraries, and for configuring the parallel version +cd src +./configure OOFEM_TARGET=oofem-2.0 --enable-dss + +#Compile oofem +cd targets/oofem-2.0 +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi + +# build verification tools +cd ../../tools && make all + +# testing solver +cd ../targets/oofem-2.0 && make tests && less ./test_results Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/openanalysis/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/openanalysis/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/openanalysis/install.sh (revision 18231) @@ -0,0 +1,14 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf openanalysis + +#download openanalysis +svn co http://svn.berlios.de/svnroot/repos/openanalysis/OpenAnalysis/trunk openanalysis + +#Configure +cd openanalysis + +make -f Makefile.quick all +make -f Makefile.quick install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/openssl/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/openssl/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/openssl/install.sh (revision 18231) @@ -0,0 +1,23 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src + +#Download latest version +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/openssl-0.9.8x.tar.gz' 'openssl-0.9.8x.tar.gz' + +#Untar +tar -xzf openssl-0.9.8x.tar.gz +mv openssl-0.9.8x src +mkdir install + +#Configure openssl +cd src +./config --prefix="$ISSM_DIR/externalpackages/openssl/install" shared +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/packagemaker/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/packagemaker/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/packagemaker/install.sh (revision 18231) @@ -0,0 +1,8 @@ +#!/bin/bash +set -eu + +#Erase symlink +rm -rf install + +#Select or create a new simlink +ln -s /Developer/Applications/Utilities/PackageMaker.app/Contents/MacOS/ install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/pcre/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/pcre/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/pcre/install.sh (revision 18231) @@ -0,0 +1,21 @@ +#!/bin/bash +set -eu + +#Cleaning +rm -rf install +rm -rf pcre-8.21 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/pcre-8.21.tar.gz' 'pcre-8.21.tar.gz' + +#Untar and move python into install directory +tar -zxvf pcre-8.21.tar.gz +mv pcre-8.21/* install +rm -rf pcre-8.21 + +#Configure doxygen +cd install +./configure --prefix "$ISSM_DIR/externalpackages/python/install" +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/README =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/README (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/README (revision 18231) @@ -0,0 +1,27 @@ +petsc carries a version of Blas that uses int arguments (int32) type, while +Matlab carries a version of Blas that uses int64_t arguments (hidden behing +a ptrdiff_t type (check MATLAB_DIR/extern/include/blas.h). +In serial mode, Matlab discards the Petsc Blas library (even when it was statically +linked against the mex files!) symbols, and replaces them with its version. +Because the prototypes conflict (32 vs 64), crashes ensue whenever using a Blas +routine (for ex: VecAXPY calls BLASaxpy_, which calls daxpy). + +To avoid that, we have to recompile Petsc with a 64 bit prototype. Luckily, +Petsc did a good job, and hid the Blas int type into the typedef BLASint (check +in include/petsc.h). Just typedef it back from int to int64_t, and recompile, +and that does the trick. Don't forget the #include "inttypes.h" at the top of petsc.h, +otherwise, crashes during the compile. + +Same problem may arise for using the lapack library. + +Now, Petsc pretends it can compile in --with-64-bit-pointers. That sets PetscInt to long long +The only problem, it says MUMPS, Scalapack, blacs, Plapack don't support 64 bit indexing. +Mumps looks like it might. + +If compiling --with-64-bit-pointers, all prototypes in Petsc ask for PetscInt = long long +which Issm does not know. Can't compile with this option. Unless we switch to 64 bit integers +in ISSM. Started to put this framework into place: we now have IssmInt, IssmDouble, IssmChar +in types.h. They rely on ISSM_USE_64_BIT_INDEXING symbol, define in config.h, instantiated by +autotools with --with-64bit-pointers=1 in configure.sh + +Recomendation: wait until MUMPS implements 64 bit indexing. Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/configs/3.1/win7/petscfix.h.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/configs/3.1/win7/petscfix.h.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/configs/3.1/win7/petscfix.h.patch (revision 18231) @@ -0,0 +1,8 @@ +10c10 +< extern "C" { +--- +> //extern "C" { +14c14 +< } +--- +> //} Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-altix64-castor.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-altix64-castor.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-altix64-castor.sh (revision 18231) @@ -0,0 +1,66 @@ +#!/bin/bash +set -eu +#Step 1: unzip and install +#Step 2: After Plapack implodes +STEP=0 + +if [ $STEP -eq 1 ]; then + #Some cleanup + rm -rf install petsc-3.1-p7 src + mkdir install src + + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz' + + #Untar and move petsc to install directory + tar -zxvf petsc-3.1-p7.tar.gz + mv petsc-3.1-p7/* install/ + rm -rf petsc-3.1-p7 + + #configure + cd src + ./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --ISSM_ARCH=$ISSM_ARCH \ + --with-debugging=no \ + --with-shared=0 COPTFLAGS=-O3 FOPTFLAGS=-O3 \ + --with-blas-lapack-dir=/opt/intel/mkl/9.1.023 \ + --with-mpi-lib=/usr/lib/libmpi.so \ + --with-mpi-include=/usr/include \ + --with-mpi-shared=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-plapack=yes \ + --FFLAGS=-I/usr/include \ + --with-cc=icc \ + --with-fc=ifort \ + --download-parmetis=yes + + echo "== Fix Plapack compilation manually (http://issm.jpl.nasa.gov/installation/compilationtroubleshooting/petsc31/) ==" + echo "== Then run STEP=2 ==" +fi +if [ $STEP -eq 2 ]; then + cd src + ./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-batch=1 \ + --ISSM_ARCH=$ISSM_ARCH \ + --with-debugging=no \ + --with-shared=0 COPTFLAGS=-O3 FOPTFLAGS=-O3 \ + --with-blas-lapack-dir=/opt/intel/mkl/9.1.023 \ + --with-mpi-lib=/usr/lib/libmpi.so \ + --with-mpi-include=/usr/include \ + --with-mpi-shared=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --with-plapack-dir=$PETSC_DIR/externalpackages/PLAPACKR32-hg/$ISSM_ARCH \ + --FFLAGS=-I/usr/include \ + --with-cc=icc \ + --with-fc=ifort \ + --download-parmetis=yes + echo "== Follow PETSc's instructions" +fi Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-cosmos.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-cosmos.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-cosmos.sh (revision 18231) @@ -0,0 +1,36 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.1-p7 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.1-p7.tar.gz +mv petsc-3.1-p7/* src/ +rm -rf petsc-3.1-p7 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-batch=1 \ + --ISSM_ARCH=$ISSM_ARCH \ + --with-debugging=no COPTFLAGS=-O3 FOPTFLAGS=-O3 \ + --with-blas-lapack-dir=/opt/intel/mkl/10.0.5.025/ \ + --with-mpi-dir=/opt/mpich/gm/intel10.1/ \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-plapack=yes \ + --FFLAGS=-I/usr/include \ + --with-mpi-shared=0 \ + --download-parmetis=yes + +#Compile petsc and install it +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-linux64-berg.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-linux64-berg.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-linux64-berg.sh (revision 18231) @@ -0,0 +1,45 @@ +#!/bin/bash + +#Get number of cpus on current platform +NUMCPUS=$1; + +#version of petsc? +#version='2.3.2-p3'; +version='3.1-p7' +#version='3.2-p3' + +#Some cleanup +rm -rf install petsc-$version src + +#Create src and install directories +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz' + +#Untar +tar -zxvf petsc-$version.tar.gz + +#Move petsc to install directory or src depending on the version +if [[ $version != "2.3.2-p3" ]] +then + mv petsc-$version/* src/ + rm -rf petsc-$version + cd src +else + mv petsc-$version/* install/ + rm -rf petsc-$version + cd install +fi + +#configure +../configure.sh + +#Compile petsc and install it +if [ -z $NUMCPUS ]; +then + make +else + make -j $NUMCPUS +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-macosx32-mathieu.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-macosx32-mathieu.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-macosx32-mathieu.sh (revision 18231) @@ -0,0 +1,39 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.1-p7 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.1-p7.tar.gz +mv petsc-3.1-p7/* src/ +rm -rf petsc-3.1-p7 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --PETSC_ARCH=macosx-gnu \ + --with-mpi-dir=$ISSM_DIR/externalpackages/mpich/install \ + --with-debugging=0 \ + --with-shared=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --download-plapack=yes \ + --FFLAGS="-I$ISSM_DIR/externalpackages/mpich/install/include -arch i386" \ + --COPTFLAGS="-march=opteron -O2 -arch i386" \ + --FOPTFLAGS="-march=opteron -O2 -arch i386" \ + --CXXOPTFLAGS="-march=opteron -O2 -arch i386" \ + --download-parmetis=yes + +#Compile petsc and install it +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-macosx32-ogive.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-macosx32-ogive.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-macosx32-ogive.sh (revision 18231) @@ -0,0 +1,40 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.1-p7 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.1-p7.tar.gz +mv petsc-3.1-p7/* src/ +rm -rf petsc-3.1-p7 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-mpi-dir=$ISSM_DIR/externalpackages/mpich/install \ + --PETSC_ARCH=macosx-gnu \ + --with-fc=/usr/local/bin/gfortran \ + --with-debugging=0 \ + --with-shared=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-plapack=yes \ + --download-parmetis=yes \ + --download-f-blas-lapack=yes \ + --COPTFLAGS="-march=opteron -O2 " \ + --FOPTFLAGS="-march=opteron -O2 " \ + --CXXOPTFLAGS="-march=opteron -O2 " \ + --FFLAGS="-I$ISSM_DIR/externalpackages/mpich/install/include -L$ISSM_DIR/externalpackages/mpich/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran " + +#Compile petsc and install it +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-pleiades.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-pleiades.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-pleiades.sh (revision 18231) @@ -0,0 +1,73 @@ +#!/bin/bash +set -eu +#Step 1: unzip and install +#Step 2: After Plapack implodes +STEP=0 + +if [ $STEP -eq 1 ]; then + #Some cleanup + rm -rf install petsc-3.1-p7 src + mkdir install src + + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz' + + #Untar and move petsc to install directory + tar -zxvf petsc-3.1-p7.tar.gz + mv petsc-3.1-p7/* install/ + rm -rf petsc-3.1-p7 + + #configure + cd src + ./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-batch=1 \ + --PETSC_ARCH="$ISSM_ARCH" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=no \ + --with-shared=0 \ + --with-blas-lapack-dir=/nasa/intel/mkl/10.0.011/ \ + --with-mpi-lib=/nasa/sgi/mpt/1.25/lib/libmpi.so \ + --with-mpi-include=/nasa/sgi/mpt/1.25/include \ + --known-mpi-shared=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-plapack=yes \ + --FFLAGS=-I/usr/include \ + --with-cc=icc \ + --with-fc=ifort \ + --COPTFLAGS=" -O3 -xS" \ + --FOPTFLAGS=" -O3 -xS" \ + --CXXOPTFLAGS=" -O3 -xS" \ + --with-pic=1 + echo "== Fix Plapack compilation manually (http://issm.jpl.nasa.gov/installation/compilationtroubleshooting/petsc31/) ==" + echo "== Then run STEP=2 ==" +fi +if [ $STEP -eq 2 ]; then + cd src + ./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-batch=1 \ + --PETSC_ARCH="$ISSM_ARCH" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=no \ + --with-shared=0 \ + --with-blas-lapack-dir=/nasa/intel/mkl/10.0.011/ \ + --with-mpi-lib=/nasa/sgi/mpt/1.25/lib/libmpi.so \ + --with-mpi-include=/nasa/sgi/mpt/1.25/include \ + --known-mpi-shared=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --with-plapack-dir=$ISSM_DIR/externalpackages/petsc/src/$ISSM_ARCH \ + --download-parmetis=yes \ + --FFLAGS=-I/usr/include \ + --with-cc=icc \ + --with-fc=ifort \ + --COPTFLAGS=" -O3 -xS" \ + --FOPTFLAGS=" -O3 -xS" \ + --CXXOPTFLAGS=" -O3 -xS" \ + --with-pic=1 + echo "== Follow PETSc's instructions" +fi Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-ubuntu64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-ubuntu64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-ubuntu64.sh (revision 18231) @@ -0,0 +1,40 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.1-p7 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.1-p7.tar.gz +mv petsc-3.1-p7/* src/ +rm -rf petsc-3.1-p7 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mpi-dir=$ISSM_DIR/externalpackages/mpich/install \ + --PETSC_ARCH=linux-gnu\ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --download-parmetis=yes \ + --FFLAGS=-I$ISSM_DIR/externalpackages/mpich/install/include \ + --download-plapack=yes \ + --COPTFLAGS="-O2" \ + --FOPTFLAGS="-O2" \ + --CXXOPTFLAGS="-O2" \ + --with-pic=1 + +#Compile petsc and install it +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-win7-parallel.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-win7-parallel.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-win7-parallel.sh (revision 18231) @@ -0,0 +1,35 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.1-p7 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.1-p7.tar.gz +mv petsc-3.1-p7/* src/ +rm -rf petsc-3.1-p7 + +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_ARCH=cygwin-intel \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --download-c-blas-lapack=yes \ + --with-cc='win32fe cl' \ + --with-fc=0 \ + --with-cxx='win32fe cl' \ + --with-clanguage=cxx \ + --with-mpi-include="/cygdrive/c/MPICH2/include" \ + --with-mpi-lib="/cygdrive/c/MPICH2/lib/mpi.lib" + + +#Compile petsc and install it +make +make install + +patch ../install/include/petscfix.h ../configs/3.1/win7/petscfix.h.patch Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-win7.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-win7.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.1-win7.sh (revision 18231) @@ -0,0 +1,57 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.1-p7 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.1-p7.tar.gz +mv petsc-3.1-p7/* src/ +rm -rf petsc-3.1-p7 + +export PETSC_DIR=`cygpath -u "$ISSM_DIR/externalpackages/petsc/src"` +export PREFIX_DIR=`cygpath -u "$ISSM_DIR/externalpackages/petsc/install"` + +#configure +cd src +./config/configure.py \ + --with-parallel-no \ + --prefix=$PREFIX_DIR \ + --PETSC_ARCH=cygwin-intel \ + --PETSC_DIR=$PETSC_DIR \ + --with-debugging=0 \ + --with-mpi=0 \ + --download-c-blas-lapack=yes \ + --with-cc='win32fe cl' \ + --with-fc=0 \ + --with-cxx='win32fe cl' \ + --with-clanguage=cxx + +#./config/configure.py \ +# --prefix="$ISSM_DIR/externalpackages/petsc/install" \ +# --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ +# --PETSC_ARCH=macosx-gnu \ +# --with-mpi-dir=$ISSM_DIR/externalpackages/mpich/install \ +# --with-debugging=0 \ +# --with-shared=0 \ +# --download-mumps=yes \ +# --download-scalapack=yes \ +# --download-blacs=yes \ +# --download-blas=yes \ +# --download-f-blas-lapack=yes \ +# --download-plapack=yes \ +# --FFLAGS="-I$ISSM_DIR/externalpackages/mpich/install/include -arch i386" \ +# --COPTFLAGS="-march=opteron -O2 -arch i386" \ +# --FOPTFLAGS="-march=opteron -O2 -arch i386" \ +# --CXXOPTFLAGS="-march=opteron -O2 -arch i386" \ +# --download-parmetis=yes + +#Compile petsc and install it +make +make install + +patch ../install/include/petscfix.h ../configs/3.1/win7/petscfix.h.patch Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.2-discover-intel13.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.2-discover-intel13.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.2-discover-intel13.sh (revision 18231) @@ -0,0 +1,39 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.2-p3 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.2-p3.tar.gz' 'petsc-3.2-p3.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.2-p3.tar.gz +mv petsc-3.2-p3/* src/ +rm -rf petsc-3.2-p3 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --PETSC_ARCH="$ISSM_ARCH" \ + --with-batch=1 \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --known-mpi-shared-libraries=1 \ + --with-mpi-dir=/usr/local/intel/mpi/4.0.3.008/lib64/ \ + --with-blas-lapack-dir=/usr/local/intel/Composer/composer_xe_2013.3.163/mkl/ \ + --with-scalapack-lib=/usr/local/intel/Composer/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_scalapack_lp64.a \ + --with-scalapack-include=/usr/local/intel/Composer/composer_xe_2013.3.163/mkl/include/ \ + --with-blacs-lib=/usr/local/intel/Composer/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a \ + --with-blacs-include=/usr/local/intel/Composer/composer_xe_2013.3.163/mkl/include/ \ + --download-mumps=yes \ + --download-scalapack=no \ + --download-blacs=no \ + --download-plapack=no \ + --download-parmetis=yes \ + --with-pic=1 + +echo "== Follow PETSc's instructions" Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.2-discover.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.2-discover.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.2-discover.sh (revision 18231) @@ -0,0 +1,39 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.2-p3 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.2-p3.tar.gz' 'petsc-3.2-p3.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.2-p3.tar.gz +mv petsc-3.2-p3/* src/ +rm -rf petsc-3.2-p3 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --PETSC_ARCH="$ISSM_ARCH" \ + --with-batch=1 \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --known-mpi-shared-libraries=1 \ + --with-mpi-dir=/usr/local/intel/mpi/4.0.3.008/lib64/ \ + --with-blas-lapack-dir=/usr/local/intel/mkl/10.1.2.024/lib/64/ \ + --with-scalapack-lib=/usr/local/intel/mkl/10.1.2.024/lib/64/libmkl_scalapack_lp64.a \ + --with-scalapack-include=/usr/local/intel/mkl/10.1.2.024/include/ \ + --with-blacs-lib=/usr/local/intel/mkl/10.1.2.024/lib/64/libmkl_blacs_intelmpi_lp64.a \ + --with-blacs-include=/usr/local/intel/mkl/10.1.2.024/include/ \ + --download-mumps=yes \ + --download-scalapack=no \ + --download-blacs=no \ + --download-plapack=no \ + --download-parmetis=yes \ + --with-pic=1 + +echo "== Follow PETSc's instructions" Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.2-greenplanet.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.2-greenplanet.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.2-greenplanet.sh (revision 18231) @@ -0,0 +1,35 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.2-p3 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.2-p3.tar.gz' 'petsc-3.2-p3.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.2-p3.tar.gz +mv petsc-3.2-p3/* src/ +rm -rf petsc-3.2-p3 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --PETSC_ARCH="$ISSM_ARCH" \ + --with-batch=1 \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --known-mpi-shared-libraries=1 \ + --with-mpi-dir=/sopt/mpi/openmpi-1.5.4_psm/intel/ \ + --with-blas-lapack-dir=/opt/intel/mkl/10.2.4.032/ \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-plapack=yes \ + --download-parmetis=yes \ + --with-pic=1 + +echo "== Follow PETSc's instructions" Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.2-hoffman2.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.2-hoffman2.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.2-hoffman2.sh (revision 18231) @@ -0,0 +1,35 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.2-p3 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.2-p3.tar.gz' 'petsc-3.2-p3.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.2-p3.tar.gz +mv petsc-3.2-p3/* src/ +rm -rf petsc-3.2-p3 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mpi=1 \ + --PETSC_ARCH=linux-gnu-amd64 \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --download-plapack=yes \ + --download-parmetis=yes \ + --with-pic=1 + +#Compile petsc and install it +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.2-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.2-linux64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.2-linux64.sh (revision 18231) @@ -0,0 +1,37 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.2-p3 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.2-p3.tar.gz' 'petsc-3.2-p3.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.2-p3.tar.gz +mv petsc-3.2-p3/* src/ +rm -rf petsc-3.2-p3 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ + --with-clanguage=C++ \ + --PETSC_ARCH=linux-gnu-amd64 \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --download-plapack=yes \ + --download-parmetis=yes \ + --with-pic=1 + +#Compile petsc and install it +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.2-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.2-macosx64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.2-macosx64.sh (revision 18231) @@ -0,0 +1,35 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.2-p3 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.2-p3.tar.gz' 'petsc-3.2-p3.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.2-p3.tar.gz +mv petsc-3.2-p3/* src/ +rm -rf petsc-3.2-p3 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --PETSC_ARCH="macosx-gnu" \ + --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-plapack=no \ + --download-parmetis=yes \ + --download-f-blas-lapack=yes + +#Compile petsc and install it +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.2-pleiades.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.2-pleiades.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.2-pleiades.sh (revision 18231) @@ -0,0 +1,88 @@ +#!/bin/bash +set -eu +#Step 1: unzip and install +#Step 2: After Plapack implodes +STEP=2 + +if [ $STEP -eq 1 ]; then + #Some cleanup + rm -rf install petsc-3.2-p3 src + mkdir install src + + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.2-p3.tar.gz' 'petsc-3.2-p3.tar.gz' + + #Untar and move petsc to install directory + tar -zxvf petsc-3.2-p3.tar.gz + mv petsc-3.2-p3/* src/ + rm -rf petsc-3.2-p3 + + #configure + cd src + ./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-batch=1 \ + --PETSC_ARCH="$ISSM_ARCH" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --with-blas-lapack-dir=/nasa/intel/mkl/10.0.011/ \ + --known-mpi-shared-libraries=1 \ + --with-mpi-lib=/nasa/sgi/mpt/1.25/lib/libmpi.so \ + --with-mpi-include=/nasa/sgi/mpt/1.25/include \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-plapack=yes \ + --FFLAGS=-I/usr/include \ + --with-cc=icc \ + --with-fc=ifort \ + --COPTFLAGS=" -O3 -xS" \ + --FOPTFLAGS=" -O3 -xS" \ + --CXXOPTFLAGS=" -O3 -xS" \ + --with-pic=1 + echo "== Fix Plapack compilation manually (http://issm.jpl.nasa.gov/documentation/faq/petsc32/) ==" + echo "== Then run STEP=2 ==" +fi +if [ $STEP -eq 2 ]; then + cd src + ./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-batch=1 \ + --PETSC_ARCH="$ISSM_ARCH" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --with-blas-lapack-dir=/nasa/intel/mkl/10.0.011/ \ + --with-mpi-lib=/nasa/sgi/mpt/1.25/lib/libmpi.so \ + --with-mpi-include=/nasa/sgi/mpt/1.25/include \ + --known-mpi-shared-libraries=1 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --with-plapack-dir=$ISSM_DIR/externalpackages/petsc/src/$ISSM_ARCH \ + --download-parmetis=yes \ + --FFLAGS=-I/usr/include \ + --with-cc=icc \ + --with-fc=ifort \ + --COPTFLAGS=" -O3 -xS" \ + --FOPTFLAGS=" -O3 -xS" \ + --CXXOPTFLAGS=" -O3 -xS" \ + --with-pic=1 + cat > src/script.queue << EOF +#PBS -S /bin/bash +#PBS -q debug +#PBS -l select=1:ncpus=1:model=har +#PBS -l walltime=200 +#PBS -W group_list=s1010 +#PBS -m e +. /usr/share/modules/init/bash +module load comp-intel/11.1.046 +module load mpi/mpt.1.25 +module load math/intel_mkl_64_10.0.011 +export PATH="$PATH:." +export MPI_GROUP_MAX=64 +mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py +EOF + echo "== Follow PETSc's instructions" +fi Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.2-ubuntu64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.2-ubuntu64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.2-ubuntu64.sh (revision 18231) @@ -0,0 +1,37 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.2-p3 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.2-p3.tar.gz' 'petsc-3.2-p3.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.2-p3.tar.gz +mv petsc-3.2-p3/* src/ +rm -rf petsc-3.2-p3 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mpi-dir=/usr/lib/mpich \ + --with-clanguage=C++ \ + --PETSC_ARCH=linux-gnu-amd64 \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --download-plapack=yes \ + --download-parmetis=yes \ + --with-pic=1 + +#Compile petsc and install it +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.3-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.3-linux64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.3-linux64.sh (revision 18231) @@ -0,0 +1,37 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.3-p6 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.3-p6.tar.gz' 'petsc-3.3-p6.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.3-p6.tar.gz +mv petsc-3.3-p6/* src/ +rm -rf petsc-3.3-p6 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mpi-dir=$ISSM_DIR/externalpackages/mpich/install \ + --PETSC_ARCH=linux-gnu-amd64 \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --download-plapack=yes \ + --download-parmetis=yes \ + --download-metis=yes \ + --with-pic=1 + +#Compile petsc and install it +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.3-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.3-macosx64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.3-macosx64.sh (revision 18231) @@ -0,0 +1,37 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.3-p6 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.3-p6.tar.gz' 'petsc-3.3-p6.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.3-p6.tar.gz +mv petsc-3.3-p6/* src/ +rm -rf petsc-3.3-p6 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mpi-dir=$ISSM_DIR/externalpackages/mpich/install \ + --PETSC_ARCH="macosx-gnu" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --download-plapack=yes \ + --download-parmetis=yes \ + --download-metis=yes \ + --with-debugging=yes + +#Compile petsc and install it +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.3-pleiades.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.3-pleiades.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.3-pleiades.sh (revision 18231) @@ -0,0 +1,61 @@ +#!/bin/bash + +#Some cleanup +rm -rf install petsc-3.3-p6 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.3-p6.tar.gz' 'petsc-3.3-p6.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.3-p6.tar.gz +mv petsc-3.3-p6/* src/ +rm -rf petsc-3.3-p6 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_ARCH="$ISSM_ARCH" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-batch=1 \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --known-mpi-shared-libraries=1 \ + --with-mpi=1 \ + --with-mpi-lib="/nasa/sgi/mpt/2.06rp16/lib/libmpi.so" \ + --with-mpi-include="/nasa/sgi/mpt/2.06rp16/include" \ + --with-blas-lapack-dir="/nasa/intel/Compiler/2013.1.117/composer_xe_2013.1.117/mkl/lib/intel64" \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-mumps=yes \ + --download-metis=yes \ + --download-parmetis=yes \ + --download-trilinos=yes \ + --download-euclid=yes \ + --download-hypre=yes \ + --COPTFLAGS="-lmpi -O3" \ + --FOPTFLAGS="-lmpi -O3" \ + --CXXOPTFLAGS="-lmpi -O3" + +#prepare script to reconfigure petsc +cat > script.queue << EOF +#PBS -S /bin/bash +#PBS -l select=1:ncpus=1:model=wes +#PBS -l walltime=200 +#PBS -W group_list=s1010 +#PBS -m e + +. /usr/share/modules/init/bash +module load comp-intel/2013.1.117 +module load mpi-sgi/mpt.2.06rp16 + +export PATH="$PATH:." +export MPI_GROUP_MAX=64 +mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py +EOF + +#print instructions +echo "== Now: cd src/ " +echo "== qsub -q devel script.queue " +echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.3-walgreen.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.3-walgreen.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.3-walgreen.sh (revision 18231) @@ -0,0 +1,36 @@ +#!/bin/bash + +#Some cleanup +rm -rf install petsc-3.3-p6 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.3-p6.tar.gz' 'petsc-3.3-p6.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.3-p6.tar.gz +mv petsc-3.3-p6/* src/ +rm -rf petsc-3.3-p6 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-mpi-dir=$ISSM_DIR/externalpackages/mpich/install \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --with-blas-lapack-dir=/opt/intel/mkl/10.0.1.014/ \ + --download-mumps=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --download-scalapack=yes \ + --download-parmetis=yes \ + --download-metis=yes \ + --download-superlu=yes \ + #--download-hypre=yes + +#Compile petsc and install it +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-acenet.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-acenet.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-acenet.sh (revision 18231) @@ -0,0 +1,33 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.4.3 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.4.3.tar.gz' 'petsc-3.4.3.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.4.3.tar.gz +mv petsc-3.4.3/* src/ +rm -rf petsc-3.4.3 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_ARCH="linux-gnu-amd64" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --known-mpi-shared-libraries=1 \ + --with-mpi-dir=$OPENMPI \ + --with-blas-lapack-dir=/usr/local/intel/composer_xe_2011_sp1.13.367/mkl/ \ + --download-scalapack=yes \ + --download-mumps=yes \ + --download-metis=yes \ + --download-parmetis=yes + +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-greenplanet.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-greenplanet.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-greenplanet.sh (revision 18231) @@ -0,0 +1,55 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.4.3 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.4.3.tar.gz' 'petsc-3.4.3.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.4.3.tar.gz +mv petsc-3.4.3/* src/ +rm -rf petsc-3.4.3 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_ARCH="$ISSM_ARCH" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-batch=1 \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --known-mpi-shared-libraries=1 \ + --with-mpi=1 \ + --with-mpi-dir=/sopt/mpi/openmpi-1.5.4_psm/intel/ \ + --with-blas-lapack-dir=/opt/intel/mkl/10.2.4.032/ \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-mumps=yes \ + --download-metis=yes \ + --download-parmetis=yes \ + --download-trilinos=yes \ + --download-euclid=yes \ + --download-hypre=yes \ + --COPTFLAGS="-lmpi -O3" \ + --FOPTFLAGS="-lmpi -O3" \ + --CXXOPTFLAGS="-lmpi -O3" + +#prepare script to reconfigure petsc +cat > script.queue << EOF +#PBS -S /bin/bash +#PBS -l nodes=1:ppn=1 +#PBS -q c6145 +#PBS -l walltime=10 + +cd $(echo $ISSM_DIR)/externalpackages/petsc/src/ +mpiexec -np 1 ./conftest-arch-linux2-c-opt +EOF + +#print instructions +echo "== Now: cd src/ " +echo "== qsub script.queue " +echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-hpc.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-hpc.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-hpc.sh (revision 18231) @@ -0,0 +1,39 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.4.3 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.4.3.tar.gz' 'petsc-3.4.3.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.4.3.tar.gz +mv petsc-3.4.3/* src/ +rm -rf petsc-3.4.3 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --known-mpi-shared-libraries=1 \ + --with-mpi=1 \ + --with-mpi-dir=/data/apps/mpi/openmpi-1.6.0/gcc-4.7.2// \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --download-mumps=yes \ + --download-metis=yes \ + --download-parmetis=yes \ + --COPTFLAGS="-O3" \ + --FOPTFLAGS="-O3" \ + --CXXOPTFLAGS="-O3" + +#Compile petsc and install it +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-linux64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-linux64.sh (revision 18231) @@ -0,0 +1,36 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.4.3 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.4.3.tar.gz' 'petsc-3.4.3.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.4.3.tar.gz +mv petsc-3.4.3/* src/ +rm -rf petsc-3.4.3 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ + --PETSC_ARCH=linux-gnu-amd64 \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --download-parmetis=yes \ + --download-metis=yes \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --with-pic=1 + +#Compile petsc and install it +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-macosx64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-macosx64.sh (revision 18231) @@ -0,0 +1,37 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.4.3 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.4.3.tar.gz' 'petsc-3.4.3.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.4.3.tar.gz +mv petsc-3.4.3/* src/ +rm -rf petsc-3.4.3 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ + --PETSC_ARCH="macosx-gnu" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --download-metis=yes \ + --download-parmetis=yes \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --with-debugging=yes + + +#Compile petsc and install it +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-pleiades-intel2012.0.032-mpt.2.06rp16 =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-pleiades-intel2012.0.032-mpt.2.06rp16 (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-pleiades-intel2012.0.032-mpt.2.06rp16 (revision 18231) @@ -0,0 +1,61 @@ +#!/bin/bash + +#Some cleanup +rm -rf install petsc-3.4.2 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.4.2.tar.gz' 'petsc-3.4.2.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.4.2.tar.gz +mv petsc-3.4.2/* src/ +rm -rf petsc-3.4.2 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_ARCH="$ISSM_ARCH" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-batch=1 \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --known-mpi-shared-libraries=1 \ + --with-mpi=1 \ + --with-mpi-lib="/nasa/sgi/mpt/2.06rp16/lib/libmpi.so" \ + --with-mpi-include="/nasa/sgi/mpt/2.06rp16/include" \ + --with-blas-lapack-dir="/nasa/intel/Compiler/2012.0.032/composer_xe_2011_sp1/mkl/lib/intel64" \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-mumps=yes \ + --download-metis=yes \ + --download-parmetis=yes \ + --download-trilinos=yes \ + --download-euclid=yes \ + --download-hypre=yes \ + --COPTFLAGS="-lmpi -O3" \ + --FOPTFLAGS="-lmpi -O3" \ + --CXXOPTFLAGS="-lmpi -O3" + +#prepare script to reconfigure petsc +cat > script.queue << EOF +#PBS -S /bin/bash +#PBS -l select=1:ncpus=1:model=wes +#PBS -l walltime=200 +#PBS -W group_list=s1010 +#PBS -m e + +. /usr/share/modules/init/bash +module load comp-intel/2012.0.032 +module load mpi-sgi/mpt.2.06rp16 + +export PATH="$PATH:." +export MPI_GROUP_MAX=64 +mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py +EOF + +#print instructions +echo "== Now: cd src/ " +echo "== qsub -q devel script.queue " +echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-pleiades-mpich2-gcc444.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-pleiades-mpich2-gcc444.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-pleiades-mpich2-gcc444.sh (revision 18231) @@ -0,0 +1,61 @@ +#!/bin/bash + +#Some cleanup +rm -rf install petsc-3.4.3 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.4.3.tar.gz' 'petsc-3.4.3.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.4.3.tar.gz +mv petsc-3.4.3/* src/ +rm -rf petsc-3.4.3 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_ARCH="$ISSM_ARCH" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-batch=1 \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --known-mpi-shared-libraries=1 \ + --with-mpi=1 \ + --with-mpi-lib="/nasa/mvapich2/1.4.1/gcc.sles11/lib/libmpich.a"\ + --with-mpi-include="/nasa/mvapich2/1.4.1/gcc.sles11/include"\ + --download-f-blas-lapack=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-mumps=yes \ + --download-metis=yes \ + --download-parmetis=yes \ + --download-trilinos=yes \ + --download-euclid=yes \ + --download-hypre=yes \ + --COPTFLAGS="-lmpich" \ + --FOPTFLAGS="-lmpich" \ + --CXXOPTFLAGS="-lmpich" + +#prepare script to reconfigure petsc +cat > script.queue << EOF +#PBS -S /bin/bash +#PBS -l select=1:ncpus=1:model=wes +#PBS -l walltime=200 +#PBS -W group_list=s1010 +#PBS -m e + +. /usr/share/modules/init/bash +module load mpi-mvapich2/1.4.1/gcc +module load gcc/4.4.4 + +export PATH="$PATH:." +export MPI_GROUP_MAX=64 +mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py +EOF + +#print instructions +echo "== Now: cd src/ " +echo "== qsub -q devel script.queue " +echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-pleiades-mpich2-gcc470.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-pleiades-mpich2-gcc470.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-pleiades-mpich2-gcc470.sh (revision 18231) @@ -0,0 +1,61 @@ +#!/bin/bash + +#Some cleanup +rm -rf install petsc-3.4.3 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.4.3.tar.gz' 'petsc-3.4.3.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.4.3.tar.gz +mv petsc-3.4.3/* src/ +rm -rf petsc-3.4.3 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_ARCH="$ISSM_ARCH" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-batch=1 \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --known-mpi-shared-libraries=1 \ + --with-mpi=1 \ + --with-mpi-lib="/nasa/mvapich2/1.6.sles11/gcc/lib/libmpich.a"\ + --with-mpi-include="/nasa/mvapich2/1.6.sles11/gcc/include" \ + --download-f-blas-lapack=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-mumps=yes \ + --download-metis=yes \ + --download-parmetis=yes \ + --download-trilinos=yes \ + --download-euclid=yes \ + --download-hypre=yes \ + --COPTFLAGS="-lmpich" \ + --FOPTFLAGS="-lmpich" \ + --CXXOPTFLAGS="-lmpich" + +#prepare script to reconfigure petsc +cat > script.queue << EOF +#PBS -S /bin/bash +#PBS -l select=1:ncpus=1:model=wes +#PBS -l walltime=200 +#PBS -W group_list=s1010 +#PBS -m e + +. /usr/share/modules/init/bash +module load mpi-mvapich2/1.6/gcc +module load gcc/4.7.0 + +export PATH="$PATH:." +export MPI_GROUP_MAX=64 +mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py +EOF + +#print instructions +echo "== Now: cd src/ " +echo "== qsub -q devel script.queue " +echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-pleiades-mpich2.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-pleiades-mpich2.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-pleiades-mpich2.sh (revision 18231) @@ -0,0 +1,68 @@ +#!/bin/bash + +#Some cleanup +rm -rf install petsc-3.4.2 src +mkdir install src + +export cc=gcc +alias cc='gcc' + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.4.2.tar.gz' 'petsc-3.4.2.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.4.2.tar.gz +mv petsc-3.4.2/* src/ +rm -rf petsc-3.4.2 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_ARCH="$ISSM_ARCH" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-batch=1 \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --with-mpi=1 \ + --with-mpi-lib="$ISSM_DIR/externalpackages/mpich/install/lib/libmpich.so"\ + --with-mpi-include="$ISSM_DIR/externalpackages/mpich/install/include" \ + --known-mpi-shared-libraries=1 \ + --download-f-blas-lapack=yes \ + --download-scalapack=yes \ + --download-metis=yes \ + --download-parmetis=yes \ + --download-blacs=yes \ + --download-mumps=yes \ + --download-trilinos=yes \ + --download-euclid=yes \ + --download-hypre=yes \ + --COPTFLAGS=" -O3 -march=corei7-avx" \ + --FOPTFLAGS=" -O3 -march=corei7-avx" \ + --CXXOPTFLAGS=" -O3 -march=corei7-avx" + +#--with-mpi-lib="/nasa/mvapich2/1.4.1/gcc.sles11/lib/libmpich.a" \ +# --with-mpi-include="/nasa/mvapich2/1.4.1/gcc.sles11/include" \ + + +#prepare script to reconfigure petsc +cat > script.queue << EOF +#PBS -S /bin/bash +#PBS -l select=1:ncpus=1:model=wes +#PBS -l walltime=200 +#PBS -W group_list=s1010 +#PBS -m e + +. /usr/share/modules/init/bash +module load mpi-mvapich2/1.6/gcc +module load gcc/4.7.0 + +export PATH="$PATH:." +export MPI_GROUP_MAX=64 +mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py +EOF + +#print instructions +echo "== Now: cd src/ " +echo "== qsub -q devel script.queue " +echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-pleiades.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-pleiades.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-pleiades.sh (revision 18231) @@ -0,0 +1,61 @@ +#!/bin/bash + +#Some cleanup +rm -rf install petsc-3.4.3 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.4.3.tar.gz' 'petsc-3.4.3.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.4.3.tar.gz +mv petsc-3.4.3/* src/ +rm -rf petsc-3.4.3 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_ARCH="$ISSM_ARCH" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-batch=1 \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --known-mpi-shared-libraries=1 \ + --with-mpi=1 \ + --with-mpi-lib="/nasa/sgi/mpt/2.06rp16/lib/libmpi.so" \ + --with-mpi-include="/nasa/sgi/mpt/2.06rp16/include" \ + --with-blas-lapack-dir="/nasa/intel/Compiler/2013.1.117/composer_xe_2013.1.117/mkl/lib/intel64" \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-mumps=yes \ + --download-metis=yes \ + --download-parmetis=yes \ + --download-trilinos=yes \ + --download-euclid=yes \ + --download-hypre=yes \ + --COPTFLAGS="-lmpi -O3" \ + --FOPTFLAGS="-lmpi -O3" \ + --CXXOPTFLAGS="-lmpi -O3" + +#prepare script to reconfigure petsc +cat > script.queue << EOF +#PBS -S /bin/bash +#PBS -l select=1:ncpus=1:model=wes +#PBS -l walltime=200 +#PBS -W group_list=s1010 +#PBS -m e + +. /usr/share/modules/init/bash +module load comp-intel/2013.1.117 +module load mpi-sgi/mpt.2.06rp16 + +export PATH="$PATH:." +export MPI_GROUP_MAX=64 +mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py +EOF + +#print instructions +echo "== Now: cd src/ " +echo "== qsub -q devel script.queue " +echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-pleiades2.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-pleiades2.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-3.4-pleiades2.sh (revision 18231) @@ -0,0 +1,61 @@ +#!/bin/bash + +#Some cleanup +rm -rf install petsc-3.4.3 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.4.3.tar.gz' 'petsc-3.4.3.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.4.3.tar.gz +mv petsc-3.4.3/* src/ +rm -rf petsc-3.4.3 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_ARCH="$ISSM_ARCH" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-batch=1 \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --known-mpi-shared-libraries=1 \ + --with-mpi=1 \ + --with-mpi-lib="/nasa/sgi/mpt/2.06rp16/lib/libmpi.so" \ + --with-mpi-include="/nasa/sgi/mpt/2.06rp16/include" \ + --with-blas-lapack-dir="/nasa/intel/Compiler/2013.1.117/composer_xe_2013.1.117/mkl/lib/intel64" \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-mumps=yes \ + --download-metis=yes \ + --download-parmetis=yes \ + --download-trilinos=yes \ + --download-euclid=yes \ + --download-hypre=yes \ + --COPTFLAGS="-lmpi -O3" \ + --FOPTFLAGS="-lmpi -O3" \ + --CXXOPTFLAGS="-lmpi -O3" + +#prepare script to reconfigure petsc +cat > script.queue << EOF +#PBS -S /bin/bash +#PBS -l select=1:ncpus=1:model=wes +#PBS -l walltime=200 +#PBS -W group_list=s1010 +#PBS -m e + +. /usr/share/modules/init/bash +module load comp-intel/2013.1.117 +module load mpi-sgi/mpt.2.06rp16 + +export PATH="$PATH:." +export MPI_GROUP_MAX=64 +mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py +EOF + +#print instructions +echo "== Now: cd src/ " +echo "== qsub -q devel script.queue " +echo "== Then run reconfigure script generated by PETSc and follow instructions" Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-dev-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-dev-linux64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-dev-linux64.sh (revision 18231) @@ -0,0 +1,59 @@ +#!/bin/bash + +STEP=2 + +if [ $STEP -eq 1 ]; then + # Used Mercurial to get code + rm -rf src + hg clone http://petsc.cs.iit.edu/petsc/petsc-dev src + cd src + hg clone http://petsc.cs.iit.edu/petsc/BuildSystem config/BuildSystem +fi + +# To update (via Mercurial): +# cd petsc-dev +# hg pull -u +# cd config/BuildSystem +# hg pull -u + +# configure script +# Note: +# Metis: -using metis from externalpackages did not work... +# -for now download new metis +# -rename metis in externalpackages to metis2 +# +# SuperLU: -If download-..-=yes does not work try downloading from +# --download-superlu=http://crd.lbl.gov/~xiaoye/SuperLU/superlu_4.3.tar.gz \ + + +if [ $STEP -eq 2 ]; then + rm -rf install + cd src + ./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \ + --with-clanguage=C++ \ + --PETSC_ARCH=linux-gnu-amd64 \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --download-parmetis=yes \ + --download-metis=yes \ + --download-trilinos=yes \ + --download-euclid=yes \ + --download-spooles=yes \ + --download-spai=yes \ + --download-superlu=http://crd.lbl.gov/~xiaoye/SuperLU/superlu_4.3.tar.gz \ + --download-hypre=yes \ + --download-c2html=yes +# --with-pic=1 + + #Compile petsc and install it + make + make install +fi Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-dev-pleiades.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-dev-pleiades.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/petsc/install-dev-pleiades.sh (revision 18231) @@ -0,0 +1,78 @@ +#!/bin/bash +#Step 0: download +#Step 1: install and write script +STEP=1 + +if [ $STEP -eq 0 ]; then + # Adapted from petsc 3.2. + # Used Mercurial to get code + rm -rf src + hg clone http://petsc.cs.iit.edu/petsc/petsc-dev src + cd src + hg clone http://petsc.cs.iit.edu/petsc/BuildSystem config/BuildSystem +fi + +# To update (via Mercurial): +# cd petsc-dev +# hg pull -u +# cd config/BuildSystem +# hg pull -u + +# configure script +# Note: using metis from externalpackages did not work... +# for now downloading new metis +# -then rename metis in externalpackages to metis2 +# +# --download-prometheus=yes \ +#--download-superlu=http://crd.lbl.gov/~xiaoye/SuperLU/superlu_4.3.tar.gz \ +# --download-plapack=yes \ + +if [ $STEP -eq 1 ]; then + + #configure + cd src + ./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --with-batch=1 \ + --PETSC_ARCH="$ISSM_ARCH" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared-libraries=1 \ + --with-blas-lapack-dir=/nasa/intel/mkl/10.0.011/ \ + --known-mpi-shared-libraries=1 \ + --with-mpi=1 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --download-parmetis=yes \ + --download-metis=yes \ + --download-trilinos=yes \ + --download-euclid=yes \ + --download-spai=yes \ + --download-superlu=http://crd.lbl.gov/~xiaoye/SuperLU/superlu_4.3.tar.gz \ + --download-hypre=yes \ + --with-cxx=/nasa/sgi/mpt/2.06a67/bin/mpicxx \ + --with-fc=/nasa/sgi/mpt/2.06a67/bin/mpif90 \ + --COPTFLAGS="-lmpi -O3" \ + --FOPTFLAGS="-lmpi -O3" \ + --CXXOPTFLAGS="-lmpi -O3" + cat > script.queue << EOF +#PBS -S /bin/bash +#PBS -l select=1:ncpus=1:model=wes +#PBS -l walltime=200 +#PBS -W group_list=s1010 +#PBS -m e +. /usr/share/modules/init/bash +module load comp-intel/2012.0.032 +module load mpi-sgi/mpt.2.06a67 +module load math/intel_mkl_64_10.0.011 +export PATH="$PATH:." +export MPI_GROUP_MAX=64 +mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py +EOF + echo "== Now: cd src/ " + echo "== qsub -q devel script.queue " + echo "== Then run reconfigure script generated by PETSc and follow instructions" +fi Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/polygonclipper/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/polygonclipper/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/polygonclipper/install.sh (revision 18231) @@ -0,0 +1,19 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/PolygonClipper.zip' 'PolygonClipper.zip' + +#install +mkdir install +cd install +cp ../PolygonClipper.zip . + +#uncompress +unzip PolygonClipper.zip + +#Make +mex gpc.c gpc_mexfile.c -O -output PolygonClip Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/proj.4/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/proj.4/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/proj.4/install.sh (revision 18231) @@ -0,0 +1,15 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install + +#Download trunk +svn checkout http://svn.osgeo.org/metacrs/proj/trunk/proj install + +#compile +cd install +./configure --prefix="$ISSM_DIR/externalpackages/proj.4/install" +make +make install +cd .. Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/pyclips/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/pyclips/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/pyclips/install.sh (revision 18231) @@ -0,0 +1,22 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install +rm -rf pyclips-1.0.7.348 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/pyclips-1.0.7.348.tar.gz' 'pyclips-1.0.7.348.tar.gz' + +#Untar +tar -zxvf pyclips-1.0.7.348.tar.gz + +#Move pyclips into install directory +mv pyclips/* install +rm -rf pyclips + +#install +cd install +python setup.py build +sudo python setup.py install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/pysvn/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/pysvn/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/pysvn/install.sh (revision 18231) @@ -0,0 +1,26 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf pysvn-1.7.6 +mkdir src + +export CC=/usr/local/gfortran/bin/gcc +export CXX=/usr/local/gfortran/bin/g++ +export FFLAGS=-ff2c + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/pysvn-1.7.6.tar.gz' 'pysvn-1.7.6.tar.gz' + +#Untar +tar -zxvf pysvn-1.7.6.tar.gz + +#Move pysvn into src directory +mv pysvn-1.7.6/* src +rm -rf pysvn-1.7.6 + +$install +cd src +python setup.py build +python setup.py install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/install-2.7.3-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/install-2.7.3-linux64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/install-2.7.3-linux64.sh (revision 18231) @@ -0,0 +1,33 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +rm -rf Python-2.7.3 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-2.7.3.tgz Python-2.7.3.tgz + +#Untar and move python into install directory +tar -zxvf Python-2.7.3.tgz +mv Python-2.7.3/* src +rm -rf Python-2.7.3 + +#Configure python +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/python/install" \ + --enable-shared + +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install + +cd ../install/include +cp python2.7/* ./ +cd ../lib +ln -s libpython2.7.so.1.0 libpython.so Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/install-2.7.3-macosx-lion.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/install-2.7.3-macosx-lion.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/install-2.7.3-macosx-lion.sh (revision 18231) @@ -0,0 +1,40 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +rm -rf Python-2.7.3 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-2.7.3.tgz Python-2.7.3.tgz + +#Untar and move python into install directory +tar -zxvf Python-2.7.3.tgz +mv Python-2.7.3/* src +rm -rf Python-2.7.3 + +#Configure and compile +cd src +./configure \ + --enable-framework="$ISSM_DIR/externalpackages/python/install/Library/Frameworks" +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install + +cd ../install + +#get rid of bin, because it's just a copy of +#Library/Frameworks/Python.framework/Versions/2.7/bin, and will not reflect +#new changes being made +rm -rf bin +ln -s Library/Frameworks/Python.framework/Headers include +ln -s Library/Frameworks/Python.framework/Versions/2.7/lib lib +ln -s Library/Frameworks/Python.framework/Versions/2.7/bin bin + +#Patch pyport.h: +cd include +patch pyport.h $ISSM_DIR/externalpackages/python/patches/pyport.h.patch Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/install-2.7.3-macosx-mlion.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/install-2.7.3-macosx-mlion.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/install-2.7.3-macosx-mlion.sh (revision 18231) @@ -0,0 +1,40 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +rm -rf Python-2.7.3 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-2.7.3.tgz Python-2.7.3.tgz + +#Untar and move python into install directory +tar -zxvf Python-2.7.3.tgz +mv Python-2.7.3/* src +rm -rf Python-2.7.3 + +#Configure and compile +cd src +./configure \ + --enable-framework="$ISSM_DIR/externalpackages/python/install/Library/Frameworks" +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install + +cd ../install + +#get rid of bin, because it's just a copy of +#Library/Frameworks/Python.framework/Versions/2.7/bin, and will not reflect +#new changes being made +rm -rf bin +ln -s Library/Frameworks/Python.framework/Headers include +ln -s Library/Frameworks/Python.framework/Versions/2.7/lib lib +ln -s Library/Frameworks/Python.framework/Versions/2.7/bin bin + +#Patch pyport.h: +cd include +patch pyport.h $ISSM_DIR/externalpackages/python/patches/pyport.h.patch Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/install-2.7.3-macosx-snowleopard.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/install-2.7.3-macosx-snowleopard.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/install-2.7.3-macosx-snowleopard.sh (revision 18231) @@ -0,0 +1,40 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +rm -rf Python-2.7.3 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-2.7.3.tgz Python-2.7.3.tgz + +#exports +export MACOSX_DEPLOYMENT_TARGET=10.6 + +#Untar and move python into install directory +tar -zxvf Python-2.7.3.tgz +mv Python-2.7.3/* src +rm -rf Python-2.7.3 + +#Configure doxygen +cd src +# --enable-framework needs to have the form "$SOME_PATH/Library/Frameworks" to avoid installing components in /Applications directory +# --prefix is recognized as $SOME_PATH as long as this form is taken, so it's not necessary to include +./configure --enable-framework="$ISSM_DIR/externalpackages/python/install/Library/Frameworks" + +#make +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install + +cd ../install +ln -s Library/Frameworks/Python.framework/Headers include +ln -s Library/Frameworks/Python.framework/Versions/2.7/lib lib + +#Patch pyport.h: +cd include +patch pyport.h $ISSM_DIR/externalpackages/python/patches/pyport.h.patch Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/install-3.2.2-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/install-3.2.2-linux64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/install-3.2.2-linux64.sh (revision 18231) @@ -0,0 +1,37 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +rm -rf Python-3.2.2 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-3.2.2.tgz Python-3.2.2.tgz + +#exports +export CC + +#Untar and move python into install directory +tar -zxvf Python-3.2.2.tgz +mv Python-3.2.2/* src +rm -rf Python-3.2.2 + +#Configure python +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/python/install" \ + --enable-shared + +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install + +cd ../install/bin +ln -s python3.2 python +cd ../ +ln -s Python.framework/Versions/3.2/include/python3.2m include +ln -s Python.framework/Versions/3.2/lib/ lib Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/install-3.2.2-macosx-lion.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/install-3.2.2-macosx-lion.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/install-3.2.2-macosx-lion.sh (revision 18231) @@ -0,0 +1,40 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +rm -rf Python-3.2.2 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-3.2.2.tgz Python-3.2.2.tgz + +#exports +export CC + +#Untar and move python into install directory +tar -zxvf Python-3.2.2.tgz +mv Python-3.2.2/* src +rm -rf Python-3.2.2 + +#Configure doxygen +cd src +./configure \ + --enable-framework="$ISSM_DIR/externalpackages/python/install/Library/Frameworks" + +#obsolete? +#./configure --prefix="$ISSM_DIR/externalpackages/python/install" --enable-framework="$ISSM_DIR/externalpackages/python/install" + +#make +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install + +cd install/bin +ln -s python3.2 python +cd ../ +ln -s Python.framework/Versions/3.2/include/python3.2m include +ln -s Python.framework/Versions/3.2/lib/ lib Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/install-3.2.2-macosx-snowleopard.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/install-3.2.2-macosx-snowleopard.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/install-3.2.2-macosx-snowleopard.sh (revision 18231) @@ -0,0 +1,41 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +rm -rf Python-3.2.2 +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-3.2.2.tgz Python-3.2.2.tgz + +#exports +export CC +export MACOSX_DEPLOYMENT_TARGET=10.6 + +#Untar and move python into install directory +tar -zxvf Python-3.2.2.tgz +mv Python-3.2.2/* src +rm -rf Python-3.2.2 + +#Configure doxygen +cd src +# --enable-framework needs to have the form "$SOME_PATH/Library/Frameworks" to avoid installing components in /Applications directory +# --prefix is recognized as $SOME_PATH as long as this form is taken, so it's not necessary to include +./configure \ + --enable-framework="$ISSM_DIR/externalpackages/python/install/Library/Frameworks" + +#make +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install +cd .. + +cd install/bin +ln -s python3.2 python +cd ../ +ln -s Python.framework/Versions/3.2/include/python3.2m include +ln -s Python.framework/Versions/3.2/lib/ lib Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/patches/pyport.h.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/patches/pyport.h.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/patches/pyport.h.patch (revision 18231) @@ -0,0 +1,22 @@ +680a681 +> #ifdef isalnum +682a684,685 +> #endif +> #ifdef isalpha +684a688,689 +> #endif +> #ifdef islower +686a692,693 +> #endif +> #ifdef isspace +688a696,697 +> #endif +> #ifdef isupper +690a700,701 +> #endif +> #ifdef tolower +692a704,705 +> #endif +> #ifdef toupper +695a709 +> #endif Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/patches/pyport.h.patch.bugreport =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/patches/pyport.h.patch.bugreport (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/python/patches/pyport.h.patch.bugreport (revision 18231) @@ -0,0 +1,1 @@ +http://bugs.python.org/issue10910 Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/qhull/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/qhull/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/qhull/install.sh (revision 18231) @@ -0,0 +1,23 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install qhull-2003.1 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/qhull-2003.1.tar.gz' 'qhull-2003.1.tar.gz' + +#Untar +tar -zxvf qhull-2003.1.tar.gz + +#Move qhull to src directory +rm -rf src/* +mv qhull-2003.1/* src/ +rm -rf qhull-2003.1 + +#Configure qhull +cd src +./configure --prefix="$ISSM_DIR/externalpackages/qhull/install" +make +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/rats/README =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/rats/README (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/rats/README (revision 18231) @@ -0,0 +1,3 @@ +Rought Auditing Tools for Software +Obtained code from https://www.fortify.com/ssa-elements/threat-intelligence/rats.html + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/rats/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/rats/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/rats/install.sh (revision 18231) @@ -0,0 +1,21 @@ +#!/bin/bash +set -eu + +#Erase install +rm -rf install src rats-2.3 + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/rats-2.3.tar.gz' 'rats-2.3.tar.gz' + +#install directory +mkdir src +tar -zxvf rats-2.3.tar.gz +mv rats-2.3/* src +rm -rf rats-2.3 + +#compile +cd src +./configure --prefix=$ISSM_DIR/externalpackages/rats/install +make +make install +cd .. Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/readline/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/readline/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/readline/install.sh (revision 18231) @@ -0,0 +1,21 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf readline-6.2.2 +mkdir src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/readline-6.2.2.tar.gz' 'readline-6.2.2.tar.gz' + +#Untar +tar -zxvf readline-6.2.2.tar.gz + +#Move readline into src directory +mv readline-6.2.2/* src +rm -rf readline-6.2.2 + +#install +cd src +python setup.py install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/rose/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/rose/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/rose/install.sh (revision 18231) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf source build install +mkdir install source build + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/rose-0.9.5a-13219.tar.gz' 'rose-0.9.5a-13219.tar.gz' + +#Untar +tar -zxvf rose-0.9.5a-13219.tar.gz + +#Move rose into install directory +mv rose-0.9.5a-13219/* source +rm -rf rose-0.9.5a-13219 + +#Configure +cd build +../source/configure \ + --prefix=$ISSM_DIR/externalpackages/rose/install \ + --with-boost=$ISSM_DIR/externalpackages/boost/install\ + --srcdir=$ISSM_DIR/externalpackages/rose/source + +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/satstress/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/satstress/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/satstress/install.sh (revision 18231) @@ -0,0 +1,20 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install SatStress-0.1.2 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/SatStress-0.1.2.tar.gz' 'SatStress-0.1.2.tar.gz' + +#Untar +tar -zxvf SatStress-0.1.2.tar.gz + +#Move SatStress into install directory +mv SatStress-0.1.2/* install +rm -rf SatStress-0.1.2 + +#Compile SatStress +cd install +make test Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scipy/README =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scipy/README (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scipy/README (revision 18231) @@ -0,0 +1,9 @@ +For OSX 10.7 (Lion), the instructions here can be followed: +http://www.scipy.org/Installing_SciPy/Mac_OS_X + +For OSX 10.6 (Snow Leopard), the scipy folks recommend gcc and g++ version 4.0. +However, ISSM needs the gfortran version recommended in $ISSM_DIR/externalpackages/gfortran. +On the webpage listed above, make sure the "export CC" and "export CXX" commands point to the +binaries associated with this gfortran version (likely in /usr/local/gfortran/bin by default). +Once this gfortran is installed, the install script in this directory for Snow Leopard should +work. Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scipy/install-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scipy/install-linux64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scipy/install-linux64.sh (revision 18231) @@ -0,0 +1,27 @@ +#!/bin/bash +set -eu + +export CC="gcc -fPIC" +export CXX="g++ -fPIC" +export F77="gfortran -fPIC" +export FC="gfortran -fPIC" +export FFLAGS=-ff2c + +#clean up +rm -rf scipy +#download scipy +export GIT_SSL_NO_VERIFY=true +git clone https://github.com/scipy/scipy.git + +#install scipy +cd scipy +export BLAS_SRC=$ISSM_DIR/externalpackages/blas/install/lib +export BLAS=$ISSM_DIR/externalpackages/blas/install/lib +export LAPACK_SRC=$ISSM_DIR/externalpackages/lapack/install/lib +export LAPACK=$ISSM_DIR/externalpackages/lapack/install/lib + +python setup.py build +python setup.py install +cd .. +python -c "import scipy; print 'Installed SciPy', scipy.__version__" +#python -c "import scipy; scipy.test()" Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scipy/install-macosx-lion.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scipy/install-macosx-lion.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scipy/install-macosx-lion.sh (revision 18231) @@ -0,0 +1,23 @@ +#!/bin/bash +set -eu + +export CC=gcc +export CXX=g++ +export FFLAGS=-ff2c + +#download scipy +git clone https://github.com/scipy/scipy.git + +#install scipy +cd scipy +export BLAS_SRC=$ISSM_DIR/externalpackages/blas/install/lib +export BLAS=$ISSM_DIR/externalpackages/blas/install/lib +export LAPACK_SRC=$ISSM_DIR/externalpackages/lapack/install/lib +export LAPACK=$ISSM_DIR/externalpackages/lapack/install/lib + +#install scipy +python setup.py build +python setup.py install +cd .. +python -c "import scipy; print 'Installed SciPy', scipy.__version__" +#python -c "import scipy; scipy.test()" Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scipy/install-macosx-mlion.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scipy/install-macosx-mlion.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scipy/install-macosx-mlion.sh (revision 18231) @@ -0,0 +1,23 @@ +#!/bin/bash +set -eu + +export CC=gcc +export CXX=g++ +export FFLAGS=-ff2c + +#download scipy +git clone https://github.com/scipy/scipy.git + +#install scipy +cd scipy +export BLAS_SRC=$ISSM_DIR/externalpackages/blas/install/lib +export BLAS=$ISSM_DIR/externalpackages/blas/install/lib +export LAPACK_SRC=$ISSM_DIR/externalpackages/lapack/install/lib +export LAPACK=$ISSM_DIR/externalpackages/lapack/install/lib + +#install scipy +python setup.py build +python setup.py install +cd .. +python -c "import scipy; print 'Installed SciPy', scipy.__version__" +#python -c "import scipy; scipy.test()" Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scipy/install-macosx-snowleopard.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scipy/install-macosx-snowleopard.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scipy/install-macosx-snowleopard.sh (revision 18231) @@ -0,0 +1,17 @@ +#!/bin/bash +set -eu + +# On OSX 10.6, fgortran gets installed in /usr/local/gfortran +export CC="/usr/local/gfortran/bin/gcc" +export CXX="/usr/local/gfortran/bin/g++" + +#download scipy +git clone https://github.com/scipy/scipy.git + +#install scipy +cd scipy +python setup.py build +python setup.py install +cd .. +python -c "import scipy; print 'Installed SciPy', scipy.__version__" +#python -c "import scipy; scipy.test()" Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/Makefile.inc =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/Makefile.inc (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/Makefile.inc (revision 18231) @@ -0,0 +1,26 @@ +EXE = +LIB = .a +OBJ = .o +MEX = .mexa64 + +MAKE = make +AR = ar +ARFLAGS = -ruv +CAT = cat +CCS = gcc +CCP = mpicc +CCD = mpicc +CCM = ${MATLAB_DIR}/bin/mex +#CFLAGS = -m64 -O3 -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Du_int32_t=uint32_t -Du_int64_t=uint64_t -DCOMMON_TIMING_OLD -DMATLAB -fPIC -I${MATLAB_DIR}/extern/include +CFLAGS = -m64 -O3 -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Du_int32_t=uint32_t -Du_int64_t=uint64_t -DCOMMON_TIMING_OLD -fPIC +#LDFLAGS = -lz -lm -lrt -L${MATLAB_DIR}/bin/glnxa64 -lmex -lmat +#LDFLAGS = -lz -lm -lrt -Wl,-rpath-link,${MATLAB_DIR}/bin/glnxa64 -L${MATLAB_DIR}/bin/glnxa64 -lmex -lmat +LDFLAGS = -lz -lm -lrt +MFLAGS = -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Du_int32_t=uint32_t -Du_int64_t=uint64_t -DCOMMON_TIMING_OLD -DNOFILEIO -DMATLAB -I${MATLAB_DIR}/extern/include -largeArrayDims +CP = cp +LEX = flex +LN = ln +MKDIR = mkdir +MV = mv +RANLIB = ranlib +YACC = yacc Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/gmap.m =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/gmap.m (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/gmap.m (revision 18231) @@ -0,0 +1,66 @@ +% +% function to call the gmap module of the scotch partitioner. +% +% [maptab]=gmap(adj_mat,vlist,vwgt,ewgt,atype,apar,... +% options) +% +% where the required input is: +% adj_mat (double [sparse nv x nv], vertex adjacency matrix) +% vlist (double [nv], vertex labels or []) +% vwgt (double [nv], vertex weights (integers) or []) +% ewgt (double [sparse nv x nv], edge weights (integers) or []) +% atype (character, architecture type) +% 'cmplt' complete graph +% 'cmpltw' weighted complete graph +% 'hcub' binary hypercube +% 'leaf' tree-leaf architecture +% 'mesh2d' bidimensional array +% 'mesh3d' tridimensional array +% 'torus2d' bidimensional array with wraparound edges +% 'torus3d' tridimensional array with wraparound edges +% apars (double, architecture params (corresponding to atype)) +% [size] cmplt +% [size load0 load1 ...] cmpltw +% [dim] hcub +% [height cluster weight] leaf +% [dimX dimY] mesh2d +% [dimX dimY dimZ] mesh3d +% [dimX dimY] torus2d +% [dimX dimY dimZ] torus3d +% +% the required output is: +% maptab (double [nv x 2], vertex labels and partitions) +% +% the optional input is: +% options (character, options to gmap) +% " -h : Display this help" +% " -m : Set mapping strategy (see user's manual)" +% " -s : Force unity weights on :" +% " e : edges" +% " v : vertices" +% " -V : Print program version and copyright" +% " -v : Set verbose mode to :" +% " m : mapping information" +% " s : strategy information" +% " t : timing information" +% "" +% "See default strategy with option '-vs'" +% +function [maptab]=gmap(adj_mat,vlist,vwgt,ewgt,atype,apars,... + varargin) + +if ~nargin + help gmap + return +end + +% gmap_mex uses static variables, so clear those out before every run +clear gmap_mex + +[maptab]=gmap_mex(adj_mat,vlist,vwgt,ewgt,atype,apars,... + varargin{:}); + +% doesn't hurt to clear out after every run, too +clear gmap_mex + +end Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/gmap_mex.c =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/gmap_mex.c (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/gmap_mex.c (revision 18231) @@ -0,0 +1,286 @@ + +#define THISFUNCTION "Gmap" + +/* Gmap structures and prototypes */ + +#ifdef MATLAB + #include "mat.h" + #include "mex.h" + #include "matrix.h" + + #define printf mexPrintf + #define fprintf(file,...) (file == stdout || file == stderr ? mexPrintf(__VA_ARGS__) : fprintf(file,__VA_ARGS__)) + #define malloc mxMalloc + #define calloc mxCalloc + #define realloc mxRealloc + #define free mxFree + #define exit(status) mexErrMsgTxt("exit=" #status) +#endif + +void GmapUsage( void ); + + +int +gmapx ( + int (**pmaptabi)[2], + int argcm, + char *argvm[], + int nvi, + int ne2i, + int *ir, + int *jc, + int *vli, + int *vwi, + int *ewi, + char archtyp[], + int nai, + int *api); + +/******************************/ +/* */ +/* This is the main function. */ +/* */ +/******************************/ + +void mexFunction( int nlhs, + mxArray *plhs[], + int nrhs, + const mxArray *prhs[] ) +{ + int argcm; + char **argvm=NULL; + int nvert =0,nedge2=0,napar =0; + mwIndex *ir=NULL,*jc=NULL; + int *adjir=NULL,*adjjc=NULL; + double *vld=NULL,*vwd=NULL,*ewd=NULL,*apd=NULL; + int *vli=NULL,*vwi=NULL,*ewi=NULL,*api=NULL; + char *archtyp=NULL; + int (*maptabi)[2]=NULL; + double* maptabd=NULL; + int i,j,k,imi=0,imo=0,isi=0,ierr; + + /* Check for proper number of arguments */ + + if (nrhs == 0 && nlhs == 0) { + GmapUsage(); + return; + } + else if (nrhs < 6 || nlhs > 1) { + GmapUsage(); + mexErrMsgTxt(" "); + } + +/* load matlab argument list and convert to integer (note that converting here + and in the x-layer is inefficient, but it makes the x-layer more general) */ + + argvm = (char **) calloc(nrhs,sizeof(char *)); + + if (!(mxIsNumeric(prhs[imi]) && + (mxGetM(prhs[imi]) == 1 && mxGetN(prhs[imi]) == 1))) { + argvm[isi] = (char *) calloc(4+1,sizeof(char)); + strcpy(argvm[isi],"gmap"); + mexPrintf("%s -- Using \"%s\" entry point.\n", + THISFUNCTION,argvm[isi]); + isi++; + } + else { + argvm[isi] = (char *) calloc(5+1,sizeof(char)); + strcpy(argvm[isi],"gpart"); + mexPrintf("%s -- Using \"%s\" entry point.\n", + THISFUNCTION,argvm[isi]); + isi++; + + argvm[isi] = (char *) calloc(17,sizeof(char)); + sprintf(argvm[isi],"%d",(int)mxGetScalar(prhs[imi])); + mexPrintf("%s -- Number of parts is %s.\n", + THISFUNCTION,argvm[isi]); + isi++; + imi++; + } + + if (!mxIsNumeric(prhs[imi]) || (!mxIsEmpty(prhs[imi]) && !mxIsSparse(prhs[imi]))) { + mexPrintf("%s -- Adjacency matrix must be numeric and sparse.\n",THISFUNCTION); + mexErrMsgTxt(" "); + } + else { + nvert =mxGetM(prhs[imi]); + nedge2=mxGetNzmax(prhs[imi]); + if (mxGetNzmax(prhs[imi])) { + ir =mxGetIr(prhs[imi]); + adjir = (int *) malloc(mxGetNzmax(prhs[imi])*sizeof(int)); + for (i=0; i= 5) && + (strncmp (argvm[0] + strlen (argvm[0]) - 5, "gpart", 5) == 0))) { + if (!mxIsChar(prhs[imi])) { + mexPrintf("%s -- Architecture type must be character.\n",THISFUNCTION); + mexErrMsgTxt(" "); + } + else { + if (mxGetM(prhs[imi])*mxGetN(prhs[imi])) { + archtyp = (char *) calloc(mxGetM(prhs[imi])*mxGetN(prhs[imi])+1,sizeof(char)); + mxGetString(prhs[imi],archtyp,mxGetM(prhs[imi])*mxGetN(prhs[imi])+1); + } + mexPrintf("%s -- Architecture type is \"%s\".\n", + THISFUNCTION,archtyp); + } + imi++; + + if (!mxIsNumeric(prhs[imi])) { + mexPrintf("%s -- Architecture parameter vector must be numeric.\n",THISFUNCTION); + mexErrMsgTxt(" "); + } + else { + napar =mxGetM(prhs[imi])*mxGetN(prhs[imi]); + if (mxGetM(prhs[imi])*mxGetN(prhs[imi])) { + apd=mxGetPr(prhs[imi]); + api = (int *) malloc(mxGetM(prhs[imi])*mxGetN(prhs[imi])*sizeof(int)); + for (i=0; i=0; i--) + free(argvm[i]); + if (api) free(api); + if (archtyp) free(archtyp); + if (ewi) free(ewi); + if (vwi) free(vwi); + if (vli) free(vli); + if (adjjc) free(adjjc); + if (adjir) free(adjir); + + return; +} + +void GmapUsage( void ) +{ + + mexPrintf("\n"); + mexPrintf("Usage: [maptab]=Gmap_mex(adjmat,vertlb,vertwt,edgewt,archtyp,archpar,\n"); + mexPrintf(" Scotch-specific parameters);\n"); + mexPrintf("\n"); + + return; +} + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/gmapx.c =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/gmapx.c (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/gmapx.c (revision 18231) @@ -0,0 +1,385 @@ +/* Copyright 2004,2007,2008 ENSEIRB, INRIA & CNRS +** +** This file is part of the Scotch software package for static mapping, +** graph partitioning and sparse matrix ordering. +** +** This software is governed by the CeCILL-C license under French law +** and abiding by the rules of distribution of free software. You can +** use, modify and/or redistribute the software under the terms of the +** CeCILL-C license as circulated by CEA, CNRS and INRIA at the following +** URL: "http://www.cecill.info". +** +** As a counterpart to the access to the source code and rights to copy, +** modify and redistribute granted by the license, users are provided +** only with a limited warranty and the software's author, the holder of +** the economic rights, and the successive licensors have only limited +** liability. +** +** In this respect, the user's attention is drawn to the risks associated +** with loading, using, modifying and/or developing or reproducing the +** software by the user in light of its specific status of free software, +** that may mean that it is complicated to manipulate, and that also +** therefore means that it is reserved for developers and experienced +** professionals having in-depth computer knowledge. Users are therefore +** encouraged to load and test the software's suitability as regards +** their requirements in conditions enabling the security of their +** systems and/or data to be ensured and, more generally, to use and +** operate it in the same conditions as regards security. +** +** The fact that you are presently reading this means that you have had +** knowledge of the CeCILL-C license and that you accept its terms. +*/ +/************************************************************/ +/** **/ +/** NAME : gmap.c **/ +/** **/ +/** AUTHOR : Francois PELLEGRINI **/ +/** **/ +/** FUNCTION : Part of a graph mapping software. **/ +/** This module contains the main function. **/ +/** **/ +/** DATES : # Version 0.0 : from : 05 jan 1993 **/ +/** to 12 may 1993 **/ +/** # Version 1.1 : from : 15 oct 1993 **/ +/** to 15 oct 1993 **/ +/** # Version 1.3 : from : 06 apr 1994 **/ +/** to 18 may 1994 **/ +/** # Version 2.0 : from : 06 jun 1994 **/ +/** to 17 nov 1994 **/ +/** # Version 2.1 : from : 07 apr 1995 **/ +/** to 18 jun 1995 **/ +/** # Version 3.0 : from : 01 jul 1995 **/ +/** to 02 oct 1995 **/ +/** # Version 3.1 : from : 07 nov 1995 **/ +/** to 25 apr 1996 **/ +/** # Version 3.2 : from : 24 sep 1996 **/ +/** to 26 may 1998 **/ +/** # Version 3.3 : from : 19 oct 1998 **/ +/** to : 30 mar 1999 **/ +/** # Version 3.4 : from : 03 feb 2000 **/ +/** to : 03 feb 2000 **/ +/** # Version 4.0 : from : 16 jan 2004 **/ +/** to : 27 dec 2004 **/ +/** # Version 5.0 : from : 23 dec 2007 **/ +/** to : 18 jun 2008 **/ +/** **/ +/************************************************************/ + +/* +** The defines and includes. +*/ + +#define GMAP + +#include "module.h" +#include "common.h" +#include "scotch.h" +#include "gmap.h" + +/* +** The static variables. +*/ + +static int C_partNbr = 2; /* Default number of parts */ +static int C_paraNum = 0; /* Number of parameters */ +static int C_paraNbr = 0; /* No parameters for mapping */ +static int C_fileNum = 0; /* Number of file in arg list */ +static int C_fileNbr = 4; /* Number of files for mapping */ +static File C_fileTab[C_FILENBR] = { /* File array */ + { "-", NULL, "r" }, + { "-", NULL, "r" }, + { "-", NULL, "w" }, + { "-", NULL, "w" } }; + +static const char * C_usageList[] = { /* Usage */ + "gmap [ [ [ []]]] ", + "gpart [] [ [ []]] ", + " -h : Display this help", + " -m : Set mapping strategy (see user's manual)", + " -s : Force unity weights on :", + " e : edges", + " v : vertices", + " -V : Print program version and copyright", + " -v : Set verbose mode to :", + " m : mapping information", + " s : strategy information", + " t : timing information", + "", + "See default strategy with option '-vs'", + NULL }; + +/******************************/ +/* */ +/* This is the main function. */ +/* */ +/******************************/ + +int +gmapx ( + int (**pmaptabi)[2], + int argcm, + char *argvm[], + int nvi, + int ne2i, + int *ir, + int *jc, + int *vli, + int *vwi, + int *ewi, + char archtyp[], + int nai, + int *api) +{ + SCOTCH_Graph grafdat; /* Source graph */ + SCOTCH_Num grafflag; /* Source graph properties */ + SCOTCH_Arch archdat; /* Target architecture */ + SCOTCH_Strat stradat; /* Mapping strategy */ + SCOTCH_Mapping mapdat; /* Mapping data */ + Clock runtime[2]; /* Timing variables */ + SCOTCH_Num nvert =0; + SCOTCH_Num nedge2=0; + SCOTCH_Num* adjir =NULL; + SCOTCH_Num* adjjc =NULL; + SCOTCH_Num* vertlab=NULL; + SCOTCH_Num* vertwgt=NULL; + SCOTCH_Num* edgewgt=NULL; + SCOTCH_Num napar =0; + SCOTCH_Num* archpar=NULL; + SCOTCH_Num (*maptab)[2]=NULL; + int (*maptabi)[2]=NULL; + int flagval; + int i,j,k; + +/* reset static variables from previous runs (jes, 4/27/10) */ + + C_partNbr = 2; /* Default number of parts */ + C_paraNum = 0; /* Number of parameters */ + C_paraNbr = 0; /* No parameters for mapping */ + C_fileNum = 0; /* Number of file in arg list */ + C_fileNbr = 4; /* Number of files for mapping */ + for (i=0; i= 5) && (strncmp (argvm[0] + i - 5, "gpart", 5) == 0)) { + flagval |= C_FLAGPART; + C_paraNbr = 1; /* One more parameter */ + C_fileNbr = 3; /* One less file to provide */ + errorProg ("gpart"); + } + else + errorProg ("gmap"); + + intRandResetStatic (); + intRandInit (); + + if ((argcm >= 2) && (argvm[1][0] == '?')) { /* If need for help */ + usagePrint (stdout, C_usageList); + return (0); + } + + grafflag = 0; /* Use vertex and edge weights */ + SCOTCH_stratInit (&stradat); /* Set default mapping strategy */ + + for (i = 0; i < C_FILENBR; i ++) /* Set default stream pointers */ + C_fileTab[i].pntr = (C_fileTab[i].mode[0] == 'r') ? stdin : stdout; + for (i = 1; i < argcm; i ++) { /* Loop for all option codes */ + if ((argvm[i][0] != '-') || (argvm[i][1] == '\0') || (argvm[i][1] == '.')) { /* If found a file name */ + if (C_paraNum < C_paraNbr) { /* If number of parameters not reached */ + if ((C_partNbr = atoi (argvm[i])) < 1) /* Get the number of parts */ + errorPrint ("main: invalid number of parts (\"%s\")", argvm[i]); + C_paraNum ++; + continue; /* Process the other parameters */ + } + if (C_fileNum < C_fileNbr) /* A file name has been given */ + C_fileTab[C_fileNum ++].name = argvm[i]; + else + errorPrint ("main: too many file names given"); + } + else { /* If found an option name */ + switch (argvm[i][1]) { + case 'H' : /* Give the usage message */ + case 'h' : + usagePrint (stdout, C_usageList); + return (0); + case 'M' : + case 'm' : + SCOTCH_stratExit (&stradat); + SCOTCH_stratInit (&stradat); + SCOTCH_stratGraphMap (&stradat, &argvm[i][2]); + break; + case 'S' : + case 's' : /* Source graph parameters */ + for (j = 2; argvm[i][j] != '\0'; j ++) { + switch (argvm[i][j]) { + case 'E' : + case 'e' : + grafflag |= 2; /* Do not load edge weights */ + break; + case 'V' : + case 'v' : + grafflag |= 1; /* Do not load vertex weights */ + break; + default : + errorPrint ("main: invalid source graph option (\"%c\")", argvm[i][j]); + } + } + break; + case 'V' : + fprintf (stderr, "gmap/gpart, version %s - F. Pellegrini\n", SCOTCH_VERSION); + fprintf (stderr, "Copyright 2004,2007,2008 ENSEIRB, INRIA & CNRS, France\n"); + fprintf (stderr, "This software is libre/free software under CeCILL-C -- see the user's manual for more information\n"); + return (0); + case 'v' : /* Output control info */ + for (j = 2; argvm[i][j] != '\0'; j ++) { + switch (argvm[i][j]) { + case 'M' : + case 'm' : + flagval |= C_FLAGVERBMAP; + break; + case 'S' : + case 's' : + flagval |= C_FLAGVERBSTR; + break; + case 'T' : + case 't' : + flagval |= C_FLAGVERBTIM; + break; + default : + errorPrint ("main: unprocessed parameter \"%c\" in \"%s\"", argvm[i][j], argvm[i]); + } + } + break; + default : + errorPrint ("main: unprocessed option (\"%s\")", argvm[i]); + } + } + } + if ((flagval & C_FLAGPART) != 0) { /* If program run as the partitioner */ + C_fileTab[3].name = C_fileTab[2].name; /* Put provided file names at their right place */ + C_fileTab[2].name = C_fileTab[1].name; + C_fileTab[1].name = "-"; + } + + fileBlockOpen (C_fileTab, C_FILENBR); /* Open all files */ + + clockInit (&runtime[0]); + clockStart (&runtime[0]); + + SCOTCH_graphInit (&grafdat); /* Create graph structure */ + SCOTCH_graphLoad (&grafdat, C_filepntrsrcinp, -1, grafflag, nvert, nedge2, adjir, adjjc, vertlab, vertwgt, edgewgt); /* Read source graph */ + + SCOTCH_archInit (&archdat); /* Create architecture structure */ + if ((flagval & C_FLAGPART) != 0) /* If program run as the partitioner */ + SCOTCH_archCmplt (&archdat, C_partNbr); /* Create a complete graph of proper size */ + else + SCOTCH_archLoad (&archdat, C_filepntrtgtinp, archtyp, napar, archpar); /* Read target architecture */ + + clockStop (&runtime[0]); /* Get input time */ + clockInit (&runtime[1]); + clockStart (&runtime[1]); + + SCOTCH_graphMapInit (&grafdat, &mapdat, &archdat, NULL); + SCOTCH_graphMapCompute (&grafdat, &mapdat, &stradat); /* Perform mapping */ + + clockStop (&runtime[1]); /* Get computation time */ + clockStart (&runtime[0]); + + SCOTCH_graphMapSave (&nvert, &maptab, &grafdat, &mapdat, C_filepntrmapout); /* Write mapping */ + +/* convert output arguments from scotch data types */ + + if (maptab) { + *pmaptabi = (int (*)[2]) malloc(nvert*2*sizeof(int)); + maptabi = *pmaptabi; + for (j=0; j<2; j++) + for (i=0; i : Set mapping strategy (see user's manual)" +% " -s : Force unity weights on :" +% " e : edges" +% " v : vertices" +% " -V : Print program version and copyright" +% " -v : Set verbose mode to :" +% " m : mapping information" +% " s : strategy information" +% " t : timing information" +% "" +% "See default strategy with option '-vs'" +% +function [maptab]=gpart(npart,adj_mat,vlist,vwgt,ewgt,... + varargin) + +if ~nargin + help gpart + return +end + +% gmap_mex uses static variables, so clear those out before every run +clear gmap_mex + +[maptab]=gmap_mex(npart,adj_mat,vlist,vwgt,ewgt,... + varargin{:}); + +% doesn't hurt to clear out after every run, too +clear gmap_mex + +end Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/install.sh (revision 18231) @@ -0,0 +1,57 @@ +#!/bin/bash +set -eu + +# Some cleanup +rm -rf scotch_5.1 +rm -rf src +rm -rf install + +# Create src and install directories +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/scotch_5.1.6.tar.gz' 'scotch_5.1.6.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/docs/ptscotch_user5.1.pdf' 'ptscotch_user5.1.pdf' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/docs/scotch_user5.1.pdf' 'scotch_user5.1.pdf' + +# Untar +tar -xvzf scotch_5.1.6.tar.gz + +# Apply patches (all at once, since many) +# (written by diff -rc old_src new_src > scotch.patch) +patch -p0 < scotch.patch + +# Move scotch to src directory +mv scotch_5.1/* src +rm -rf scotch_5.1 + +# Build scotch +cp -p Makefile.inc src/src +cp -p gmap_mex.c src/src/scotch +cp -p gmapx.c src/src/scotch +cd src/src +# For stand-alone scotch modules: +make scotch +make clean +# For no-file-io scotch modules: +make nfioscotch +# Clean up +make clean +cd ../.. + +# Populate install directory +cp -pr src/grf install +cp -pr src/tgt install +cp -pr src/doc install +cp -pr src/man install +mkdir install/include +cp -p src/src/libscotch/module.h install/include/scotch_module.h +cp -p src/src/libscotch/common.h install/include/scotch_common.h +cp -p src/include/scotch.h install/include/ +cp -p src/src/scotch/gmap.h install/include/scotch_gmap.h +mkdir install/lib +mv src/lib/* install/lib +mkdir install/bin +mv src/bin/* install/bin +#cp -p gmap.m install/bin +#cp -p gpart.m install/bin Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/mex/Gmap.c =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/mex/Gmap.c (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/mex/Gmap.c (revision 18231) @@ -0,0 +1,278 @@ + +#define THISFUNCTION "Gmap" + +/* Gmap structures and prototypes */ + +#include "mat.h" +#include "mex.h" +#include "matrix.h" + +void GmapUsage( void ); + + +int +Gmapx ( + int (**pmaptabi)[2], + int argcm, + char *argvm[], + int nvi, + int ne2i, + int *ir, + int *jc, + int *vli, + int *vwi, + int *ewi, + char archtyp[], + int nai, + int *api); + +/******************************/ +/* */ +/* This is the main function. */ +/* */ +/******************************/ + +void mexFunction( int nlhs, + mxArray *plhs[], + int nrhs, + const mxArray *prhs[] ) +{ + int argcm; + char **argvm=NULL; + int nvert =0,nedge2=0,napar =0; + mwIndex *ir=NULL,*jc=NULL; + int *adjir=NULL,*adjjc=NULL; + double *vld=NULL,*vwd=NULL,*ewd=NULL,*apd=NULL; + int *vli=NULL,*vwi=NULL,*ewi=NULL,*api=NULL; + char *archtyp=NULL; + int (*maptabi)[2]=NULL; + double* maptabd=NULL; + int i,j,k,imi=0,imo=0,isi=0,ierr; + + /* Check for proper number of arguments */ + + if (nrhs == 0 && nlhs == 0) { + GmapUsage(); + return; + } + else if (nrhs < 6 || nlhs > 1) { + GmapUsage(); + mexErrMsgTxt(" "); + } + +/* load matlab argument list and convert to integer (note that converting here + and in the x-layer is inefficient, but it makes the x-layer more general) */ + + argvm = (char **) calloc(nrhs,sizeof(char *)); + + if (!(mxIsNumeric(prhs[imi]) && + (mxGetM(prhs[imi]) == 1 && mxGetN(prhs[imi]) == 1))) { + argvm[isi] = (char *) calloc(4+1,sizeof(char)); + strcpy(argvm[isi],"Gmap"); + mexPrintf("%s -- Using \"%s\" entry point.\n", + THISFUNCTION,argvm[isi]); + isi++; + } + else { + argvm[isi] = (char *) calloc(5+1,sizeof(char)); + strcpy(argvm[isi],"Gpart"); + mexPrintf("%s -- Using \"%s\" entry point.\n", + THISFUNCTION,argvm[isi]); + isi++; + + argvm[isi] = (char *) calloc(17,sizeof(char)); + sprintf(argvm[isi],"%d",(int)mxGetScalar(prhs[imi])); + mexPrintf("%s -- Number of parts is %s.\n", + THISFUNCTION,argvm[isi]); + isi++; + imi++; + } + + if (!mxIsNumeric(prhs[imi]) || (!mxIsEmpty(prhs[imi]) && !mxIsSparse(prhs[imi]))) { + mexPrintf("%s -- Adjacency matrix must be numeric and sparse.\n",THISFUNCTION); + mexErrMsgTxt(" "); + } + else { + nvert =mxGetM(prhs[imi]); + nedge2=mxGetNzmax(prhs[imi]); + if (mxGetNzmax(prhs[imi])) { + ir =mxGetIr(prhs[imi]); + adjir = (int *) malloc(mxGetNzmax(prhs[imi])*sizeof(int)); + for (i=0; i= 5) && + (strncmp (argvm[0] + strlen (argvm[0]) - 5, "Gpart", 5) == 0))) { + if (!mxIsChar(prhs[imi])) { + mexPrintf("%s -- Architecture type must be character.\n",THISFUNCTION); + mexErrMsgTxt(" "); + } + else { + if (mxGetM(prhs[imi])*mxGetN(prhs[imi])) { + archtyp = (char *) calloc(mxGetM(prhs[imi])*mxGetN(prhs[imi])+1,sizeof(char)); + mxGetString(prhs[imi],archtyp,mxGetM(prhs[imi])*mxGetN(prhs[imi])+1); + } + mexPrintf("%s -- Architecture type is \"%s\".\n", + THISFUNCTION,archtyp); + } + imi++; + + if (!mxIsNumeric(prhs[imi])) { + mexPrintf("%s -- Architecture parameter vector must be numeric.\n",THISFUNCTION); + mexErrMsgTxt(" "); + } + else { + napar =mxGetM(prhs[imi])*mxGetN(prhs[imi]); + if (mxGetM(prhs[imi])*mxGetN(prhs[imi])) { + apd=mxGetPr(prhs[imi]); + api = (int *) malloc(mxGetM(prhs[imi])*mxGetN(prhs[imi])*sizeof(int)); + for (i=0; i=0; i--) + free(argvm[i]); + free(argvm); + } + + return; +} + +void GmapUsage( void ) +{ + + mexPrintf("\n"); + mexPrintf("Usage: [maptab]=Gmap(adjmat,vertlb,vertwt,edgewt,archtyp,archpar,\n"); + mexPrintf(" Scotch-specific parameters);\n"); + mexPrintf("\n"); + + return; +} + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/mex/Gmapx.c =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/mex/Gmapx.c (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/mex/Gmapx.c (revision 18231) @@ -0,0 +1,385 @@ +/* Copyright 2004,2007,2008 ENSEIRB, INRIA & CNRS +** +** This file is part of the Scotch software package for static mapping, +** graph partitioning and sparse matrix ordering. +** +** This software is governed by the CeCILL-C license under French law +** and abiding by the rules of distribution of free software. You can +** use, modify and/or redistribute the software under the terms of the +** CeCILL-C license as circulated by CEA, CNRS and INRIA at the following +** URL: "http://www.cecill.info". +** +** As a counterpart to the access to the source code and rights to copy, +** modify and redistribute granted by the license, users are provided +** only with a limited warranty and the software's author, the holder of +** the economic rights, and the successive licensors have only limited +** liability. +** +** In this respect, the user's attention is drawn to the risks associated +** with loading, using, modifying and/or developing or reproducing the +** software by the user in light of its specific status of free software, +** that may mean that it is complicated to manipulate, and that also +** therefore means that it is reserved for developers and experienced +** professionals having in-depth computer knowledge. Users are therefore +** encouraged to load and test the software's suitability as regards +** their requirements in conditions enabling the security of their +** systems and/or data to be ensured and, more generally, to use and +** operate it in the same conditions as regards security. +** +** The fact that you are presently reading this means that you have had +** knowledge of the CeCILL-C license and that you accept its terms. +*/ +/************************************************************/ +/** **/ +/** NAME : gmap.c **/ +/** **/ +/** AUTHOR : Francois PELLEGRINI **/ +/** **/ +/** FUNCTION : Part of a graph mapping software. **/ +/** This module contains the main function. **/ +/** **/ +/** DATES : # Version 0.0 : from : 05 jan 1993 **/ +/** to 12 may 1993 **/ +/** # Version 1.1 : from : 15 oct 1993 **/ +/** to 15 oct 1993 **/ +/** # Version 1.3 : from : 06 apr 1994 **/ +/** to 18 may 1994 **/ +/** # Version 2.0 : from : 06 jun 1994 **/ +/** to 17 nov 1994 **/ +/** # Version 2.1 : from : 07 apr 1995 **/ +/** to 18 jun 1995 **/ +/** # Version 3.0 : from : 01 jul 1995 **/ +/** to 02 oct 1995 **/ +/** # Version 3.1 : from : 07 nov 1995 **/ +/** to 25 apr 1996 **/ +/** # Version 3.2 : from : 24 sep 1996 **/ +/** to 26 may 1998 **/ +/** # Version 3.3 : from : 19 oct 1998 **/ +/** to : 30 mar 1999 **/ +/** # Version 3.4 : from : 03 feb 2000 **/ +/** to : 03 feb 2000 **/ +/** # Version 4.0 : from : 16 jan 2004 **/ +/** to : 27 dec 2004 **/ +/** # Version 5.0 : from : 23 dec 2007 **/ +/** to : 18 jun 2008 **/ +/** **/ +/************************************************************/ + +/* +** The defines and includes. +*/ + +#define GMAP + +#include "module.h" +#include "common.h" +#include "scotch.h" +#include "gmap.h" + +/* +** The static variables. +*/ + +static int C_partNbr = 2; /* Default number of parts */ +static int C_paraNum = 0; /* Number of parameters */ +static int C_paraNbr = 0; /* No parameters for mapping */ +static int C_fileNum = 0; /* Number of file in arg list */ +static int C_fileNbr = 4; /* Number of files for mapping */ +static File C_fileTab[C_FILENBR] = { /* File array */ + { "-", NULL, "r" }, + { "-", NULL, "r" }, + { "-", NULL, "w" }, + { "-", NULL, "w" } }; + +static const char * C_usageList[] = { /* Usage */ + "gmap [ [ [ []]]] ", + "gpart [] [ [ []]] ", + " -h : Display this help", + " -m : Set mapping strategy (see user's manual)", + " -s : Force unity weights on :", + " e : edges", + " v : vertices", + " -V : Print program version and copyright", + " -v : Set verbose mode to :", + " m : mapping information", + " s : strategy information", + " t : timing information", + "", + "See default strategy with option '-vs'", + NULL }; + +/******************************/ +/* */ +/* This is the main function. */ +/* */ +/******************************/ + +int +Gmapx ( + int (**pmaptabi)[2], + int argcm, + char *argvm[], + int nvi, + int ne2i, + int *ir, + int *jc, + int *vli, + int *vwi, + int *ewi, + char archtyp[], + int nai, + int *api) +{ + SCOTCH_Graph grafdat; /* Source graph */ + SCOTCH_Num grafflag; /* Source graph properties */ + SCOTCH_Arch archdat; /* Target architecture */ + SCOTCH_Strat stradat; /* Mapping strategy */ + SCOTCH_Mapping mapdat; /* Mapping data */ + Clock runtime[2]; /* Timing variables */ + SCOTCH_Num nvert =0; + SCOTCH_Num nedge2=0; + SCOTCH_Num* adjir =NULL; + SCOTCH_Num* adjjc =NULL; + SCOTCH_Num* vertlab=NULL; + SCOTCH_Num* vertwgt=NULL; + SCOTCH_Num* edgewgt=NULL; + SCOTCH_Num napar =0; + SCOTCH_Num* archpar=NULL; + SCOTCH_Num (*maptab)[2]=NULL; + int (*maptabi)[2]=NULL; + int flagval; + int i,j,k; + +/* reset static variables from previous runs (jes, 4/27/10) */ + + C_partNbr = 2; /* Default number of parts */ + C_paraNum = 0; /* Number of parameters */ + C_paraNbr = 0; /* No parameters for mapping */ + C_fileNum = 0; /* Number of file in arg list */ + C_fileNbr = 4; /* Number of files for mapping */ + for (i=0; i= 5) && (strncmp (argvm[0] + i - 5, "Gpart", 5) == 0)) { + flagval |= C_FLAGPART; + C_paraNbr = 1; /* One more parameter */ + C_fileNbr = 3; /* One less file to provide */ + errorProg ("Gpart"); + } + else + errorProg ("Gmap"); + + intRandResetStatic (); + intRandInit (); + + if ((argcm >= 2) && (argvm[1][0] == '?')) { /* If need for help */ + usagePrint (stdout, C_usageList); + return (0); + } + + grafflag = 0; /* Use vertex and edge weights */ + SCOTCH_stratInit (&stradat); /* Set default mapping strategy */ + + for (i = 0; i < C_FILENBR; i ++) /* Set default stream pointers */ + C_fileTab[i].pntr = (C_fileTab[i].mode[0] == 'r') ? stdin : stdout; + for (i = 1; i < argcm; i ++) { /* Loop for all option codes */ + if ((argvm[i][0] != '-') || (argvm[i][1] == '\0') || (argvm[i][1] == '.')) { /* If found a file name */ + if (C_paraNum < C_paraNbr) { /* If number of parameters not reached */ + if ((C_partNbr = atoi (argvm[i])) < 1) /* Get the number of parts */ + errorPrint ("main: invalid number of parts (\"%s\")", argvm[i]); + C_paraNum ++; + continue; /* Process the other parameters */ + } + if (C_fileNum < C_fileNbr) /* A file name has been given */ + C_fileTab[C_fileNum ++].name = argvm[i]; + else + errorPrint ("main: too many file names given"); + } + else { /* If found an option name */ + switch (argvm[i][1]) { + case 'H' : /* Give the usage message */ + case 'h' : + usagePrint (stdout, C_usageList); + return (0); + case 'M' : + case 'm' : + SCOTCH_stratExit (&stradat); + SCOTCH_stratInit (&stradat); + SCOTCH_stratGraphMap (&stradat, &argvm[i][2]); + break; + case 'S' : + case 's' : /* Source graph parameters */ + for (j = 2; argvm[i][j] != '\0'; j ++) { + switch (argvm[i][j]) { + case 'E' : + case 'e' : + grafflag |= 2; /* Do not load edge weights */ + break; + case 'V' : + case 'v' : + grafflag |= 1; /* Do not load vertex weights */ + break; + default : + errorPrint ("main: invalid source graph option (\"%c\")", argvm[i][j]); + } + } + break; + case 'V' : + fprintf (stderr, "Gmap/Gpart, version %s - F. Pellegrini\n", SCOTCH_VERSION); + fprintf (stderr, "Copyright 2004,2007,2008 ENSEIRB, INRIA & CNRS, France\n"); + fprintf (stderr, "This software is libre/free software under CeCILL-C -- see the user's manual for more information\n"); + return (0); + case 'v' : /* Output control info */ + for (j = 2; argvm[i][j] != '\0'; j ++) { + switch (argvm[i][j]) { + case 'M' : + case 'm' : + flagval |= C_FLAGVERBMAP; + break; + case 'S' : + case 's' : + flagval |= C_FLAGVERBSTR; + break; + case 'T' : + case 't' : + flagval |= C_FLAGVERBTIM; + break; + default : + errorPrint ("main: unprocessed parameter \"%c\" in \"%s\"", argvm[i][j], argvm[i]); + } + } + break; + default : + errorPrint ("main: unprocessed option (\"%s\")", argvm[i]); + } + } + } + if ((flagval & C_FLAGPART) != 0) { /* If program run as the partitioner */ + C_fileTab[3].name = C_fileTab[2].name; /* Put provided file names at their right place */ + C_fileTab[2].name = C_fileTab[1].name; + C_fileTab[1].name = "-"; + } + + fileBlockOpen (C_fileTab, C_FILENBR); /* Open all files */ + + clockInit (&runtime[0]); + clockStart (&runtime[0]); + + SCOTCH_graphInit (&grafdat); /* Create graph structure */ + SCOTCH_graphLoad (&grafdat, C_filepntrsrcinp, -1, grafflag, nvert, nedge2, adjir, adjjc, vertlab, vertwgt, edgewgt); /* Read source graph */ + + SCOTCH_archInit (&archdat); /* Create architecture structure */ + if ((flagval & C_FLAGPART) != 0) /* If program run as the partitioner */ + SCOTCH_archCmplt (&archdat, C_partNbr); /* Create a complete graph of proper size */ + else + SCOTCH_archLoad (&archdat, C_filepntrtgtinp, archtyp, napar, archpar); /* Read target architecture */ + + clockStop (&runtime[0]); /* Get input time */ + clockInit (&runtime[1]); + clockStart (&runtime[1]); + + SCOTCH_graphMapInit (&grafdat, &mapdat, &archdat, NULL); + SCOTCH_graphMapCompute (&grafdat, &mapdat, &stradat); /* Perform mapping */ + + clockStop (&runtime[1]); /* Get computation time */ + clockStart (&runtime[0]); + + SCOTCH_graphMapSave (&nvert, &maptab, &grafdat, &mapdat, C_filepntrmapout); /* Write mapping */ + +/* convert output arguments from scotch data types */ + + if (maptab) { + *pmaptabi = (int (*)[2]) malloc(nvert*2*sizeof(int)); + maptabi = *pmaptabi; + for (j=0; j<2; j++) + for (i=0; i +#include /* strcasecmp */ +#include /* clock,time,difftime */ +#include "mex.h" + + +/* Input Arguments */ + +#define IR_IN prhs[0] +#define JC_IN prhs[1] +#define PR_IN prhs[2] +#define M_IN prhs[3] +#define N_IN prhs[4] + +/* Output Arguments */ + +#define A_OUT plhs[0] + + +void VectorToSparseUsage( void ); + + +void mexFunction( int nlhs, + mxArray *plhs[], + int nrhs, + const mxArray *prhs[] ) +{ + int min,nin; + mwIndex *ir =NULL,*jc =NULL; + double *ird=NULL,*jcd=NULL,*pr=NULL,*prd=NULL; + int i,mrow; + + /* Check for proper number of arguments */ + + if (nrhs == 0 && nlhs == 0) { + VectorToSparseUsage(); + return; + } + else if (nrhs < 2 || nlhs != 1) { + VectorToSparseUsage(); + mexErrMsgTxt(" "); + } + + /* Create matrices for the return arguments */ + + if (!mxIsNumeric(IR_IN) || !mxIsNumeric(JC_IN)) { + mexPrintf("%s -- Input matrices IR and JC must be numeric.\n",THISFUNCTION); + mexErrMsgTxt(" "); + } + + mrow = 0; + ird = mxGetPr(IR_IN); + for (i=0; i mrow) + mrow=(int)ird[i]+1; + + if (nrhs >= 4 && mxIsNumeric(M_IN) && !mxIsEmpty(M_IN)) + min = mxGetScalar(M_IN); + else { + min = mrow; + } + + if (mrow > min) { + mexPrintf("%s -- Number of rows specified by M (%d) and IR (%d) is inconsistent.\n", + THISFUNCTION,min,mrow); + mexErrMsgTxt(" "); + } + + if (nrhs >= 5 && mxIsNumeric(N_IN) && !mxIsEmpty(N_IN)) + nin = mxGetScalar(N_IN); + else + nin = mxGetM(JC_IN)*mxGetN(JC_IN)-1; + + if (mxGetM(JC_IN)*mxGetN(JC_IN)-1 != nin) { + mexPrintf("%s -- Number of columns specified by N (%d) and JC (%d) is inconsistent.\n", + THISFUNCTION,nin,mxGetM(JC_IN)*mxGetN(JC_IN)-1); + mexErrMsgTxt(" "); + } + + A_OUT = mxCreateSparse(min, nin, mxGetM(IR_IN)*mxGetN(IR_IN), mxREAL); + if (mxGetM(IR_IN)*mxGetN(IR_IN)) { + ird = mxGetPr(IR_IN); + ir = mxGetIr(A_OUT); + for (i=0; i= 3 && mxIsNumeric(PR_IN) && !mxIsEmpty(PR_IN)) { + if (mxGetM(PR_IN)*mxGetN(PR_IN) != mxGetM(IR_IN)*mxGetN(IR_IN)) { + mexPrintf("%s -- Number of terms specified by IR (%d) and PR (%d) is inconsistent.\n", + THISFUNCTION,mxGetM(IR_IN)*mxGetN(IR_IN),mxGetM(PR_IN)*mxGetN(PR_IN)); + mexErrMsgTxt(" "); + } + + if (mxGetM(PR_IN)*mxGetN(PR_IN)) { + prd = mxGetPr(PR_IN); + pr = mxGetPr(A_OUT); + for (i=0; iarchLoad != NULL) { /* If class has loading function */ ++ #ifndef NOFILEIO + if (class->archLoad (&archptr->data, stream) != 0) { /* Load class data */ ++ #else /* NOFILEIO */ ++ if (class->archLoad (&archptr->data, stream, napar, archpar) != 0) { /* Load class data */ ++ #endif /* NOFILEIO */ + errorPrint ("archLoad: cannot load architecture data"); + memset (archptr, 0, sizeof (Arch)); /* Initialize architecture body */ + return (1); +diff -crB scotch_5.1/src/libscotch/arch_cmplt.c src/src/libscotch/arch_cmplt.c +*** scotch_5.1/src/libscotch/arch_cmplt.c 2008-05-22 06:44:41.000000000 -0700 +--- src/src/libscotch/arch_cmplt.c 2013-05-06 14:14:11.000000000 -0700 +*************** +*** 90,99 **** + int + archCmpltArchLoad ( + ArchCmplt * restrict const archptr, +! FILE * restrict const stream) + { + long numnbr; + + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchCmplt) > sizeof (ArchDummy)) || + (sizeof (ArchCmpltDom) > sizeof (ArchDomDummy))) { +--- 90,109 ---- + int + archCmpltArchLoad ( + ArchCmplt * restrict const archptr, +! FILE * restrict const stream +! #ifdef NOFILEIO +! , +! const Anum napar, +! const Anum * archpar +! #endif /* NOFILEIO */ +! ) + { + long numnbr; + ++ #ifdef NOFILEIO ++ // printf("archCmpltArchLoad - napar=%d,archpar=%p\n",napar,archpar); ++ #endif /* NOFILEIO */ ++ + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchCmplt) > sizeof (ArchDummy)) || + (sizeof (ArchCmpltDom) > sizeof (ArchDomDummy))) { +*************** +*** 102,109 **** +--- 112,124 ---- + } + #endif /* SCOTCH_DEBUG_ARCH1 */ + ++ #ifndef NOFILEIO + if ((fscanf (stream, "%ld", &numnbr) != 1) || + (numnbr < 1)) { ++ #else /* NOFILEIO */ ++ if ((napar < 1) || ++ ((numnbr=(long)archpar[0]) < 1)) { ++ #endif /* NOFILEIO */ + errorPrint ("archCmpltArchLoad: bad input"); + return (1); + } +diff -crB scotch_5.1/src/libscotch/arch_cmplt.h src/src/libscotch/arch_cmplt.h +*** scotch_5.1/src/libscotch/arch_cmplt.h 2008-05-22 06:44:41.000000000 -0700 +--- src/src/libscotch/arch_cmplt.h 2013-05-06 14:14:11.000000000 -0700 +*************** +*** 87,93 **** +--- 87,97 ---- + #define static + #endif + ++ #ifndef NOFILEIO + int archCmpltArchLoad (ArchCmplt * restrict const, FILE * restrict const); ++ #else /* NOFILEIO */ ++ int archCmpltArchLoad (ArchCmplt * restrict const, FILE * restrict const, const Anum, const Anum *); ++ #endif /* NOFILEIO */ + int archCmpltArchSave (const ArchCmplt * const, FILE * restrict const); + #define archCmpltArchFree NULL + ArchDomNum archCmpltDomNum (const ArchCmplt * const, const ArchCmpltDom * const); +diff -crB scotch_5.1/src/libscotch/arch_cmpltw.c src/src/libscotch/arch_cmpltw.c +*** scotch_5.1/src/libscotch/arch_cmpltw.c 2008-08-27 14:22:22.000000000 -0700 +--- src/src/libscotch/arch_cmpltw.c 2013-05-06 14:14:12.000000000 -0700 +*************** +*** 200,211 **** + int + archCmpltwArchLoad ( + ArchCmpltw * restrict const archptr, +! FILE * restrict const stream) + { + long vertnbr; + Gnum velosum; + Anum vertnum; + + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchCmpltw) > sizeof (ArchDummy)) || + (sizeof (ArchCmpltwDom) > sizeof (ArchDomDummy))) { +--- 200,221 ---- + int + archCmpltwArchLoad ( + ArchCmpltw * restrict const archptr, +! FILE * restrict const stream +! #ifdef NOFILEIO +! , +! const Anum napar, +! const Anum * archpar +! #endif /* NOFILEIO */ +! ) + { + long vertnbr; + Gnum velosum; + Anum vertnum; + ++ #ifdef NOFILEIO ++ // printf("archCmpltwArchLoad - napar=%d,archpar=%p\n",napar,archpar); ++ #endif /* NOFILEIO */ ++ + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchCmpltw) > sizeof (ArchDummy)) || + (sizeof (ArchCmpltwDom) > sizeof (ArchDomDummy))) { +*************** +*** 214,221 **** +--- 224,236 ---- + } + #endif /* SCOTCH_DEBUG_ARCH1 */ + ++ #ifndef NOFILEIO + if ((fscanf (stream, "%ld", &vertnbr) != 1) || + (vertnbr < 1)) { ++ #else /* NOFILEIO */ ++ if ((napar < 1) || ++ ((vertnbr=(long)archpar[0]) < 1)) { ++ #endif /* NOFILEIO */ + errorPrint ("archCmpltwArchLoad: bad input (1)"); + return (1); + } +*************** +*** 230,237 **** +--- 245,257 ---- + long veloval; + Gnum velotmp; + ++ #ifndef NOFILEIO + if ((fscanf (stream, "%ld", &veloval) != 1) || + (veloval < 1)) { ++ #else /* NOFILEIO */ ++ if ((napar < 1+(vertnum+1)) || ++ ((veloval=(long)archpar[1+(vertnum+1)]) < 1)) { ++ #endif /* NOFILEIO */ + errorPrint ("archCmpltwArchLoad: bad input (2)"); + return (1); + } +diff -crB scotch_5.1/src/libscotch/arch_cmpltw.h src/src/libscotch/arch_cmpltw.h +*** scotch_5.1/src/libscotch/arch_cmpltw.h 2008-05-22 06:44:41.000000000 -0700 +--- src/src/libscotch/arch_cmpltw.h 2013-05-06 14:14:12.000000000 -0700 +*************** +*** 86,92 **** +--- 86,96 ---- + #endif + + int archCmpltwArchBuild (ArchCmpltw * restrict const archptr, const Gnum, const Gnum * restrict const); ++ #ifndef NOFILEIO + int archCmpltwArchLoad (ArchCmpltw * restrict const, FILE * restrict const); ++ #else /* NOFILEIO */ ++ int archCmpltwArchLoad (ArchCmpltw * restrict const, FILE * restrict const, const Anum, const Anum *); ++ #endif /* NOFILEIO */ + int archCmpltwArchSave (const ArchCmpltw * const, FILE * restrict const); + int archCmpltwArchFree (ArchCmpltw * restrict const); + ArchDomNum archCmpltwDomNum (const ArchCmpltw * const, const ArchCmpltwDom * const); +diff -crB scotch_5.1/src/libscotch/arch_deco.c src/src/libscotch/arch_deco.c +*** scotch_5.1/src/libscotch/arch_deco.c 2008-09-28 06:35:27.000000000 -0700 +--- src/src/libscotch/arch_deco.c 2013-05-06 14:14:12.000000000 -0700 +*************** +*** 211,217 **** + int + archDecoArchLoad ( + ArchDeco * restrict const archptr, +! FILE * restrict const stream) + { + INT decotype; /* Type of decomposition */ + INT termdomnbr; /* Number of terminal domains (ie processors) */ +--- 211,223 ---- + int + archDecoArchLoad ( + ArchDeco * restrict const archptr, +! FILE * restrict const stream +! #ifdef NOFILEIO +! , +! const Anum napar, +! const Anum * archpar +! #endif /* NOFILEIO */ +! ) + { + INT decotype; /* Type of decomposition */ + INT termdomnbr; /* Number of terminal domains (ie processors) */ +*************** +*** 220,225 **** +--- 226,237 ---- + Anum * restrict termdisttab; /* Table of terminal-to-terminal distances */ + INT i, j; + ++ #ifdef NOFILEIO ++ // printf("archDecoArchLoad - napar=%d,archpar=%p\n",napar,archpar); ++ errorPrint ("archDecoArchLoad - not yet converted to matlab matrices"); ++ return (1); ++ #endif /* NOFILEIO */ ++ + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchDeco) > sizeof (ArchDummy)) || + (sizeof (ArchDecoDom) > sizeof (ArchDomDummy))) { +diff -crB scotch_5.1/src/libscotch/arch_deco.h src/src/libscotch/arch_deco.h +*** scotch_5.1/src/libscotch/arch_deco.h 2008-09-27 07:49:46.000000000 -0700 +--- src/src/libscotch/arch_deco.h 2013-05-06 14:14:13.000000000 -0700 +*************** +*** 113,119 **** +--- 113,123 ---- + #endif + + int archDecoArchBuild (ArchDeco * const, const Anum, const Anum, const ArchDecoTermVert * const, const Anum * const); ++ #ifndef NOFILEIO + int archDecoArchLoad (ArchDeco * const, FILE * restrict const); ++ #else /* NOFILEIO */ ++ int archDecoArchLoad (ArchDeco * const, FILE * restrict const, const Anum, const Anum *); ++ #endif /* NOFILEIO */ + int archDecoArchSave (const ArchDeco * const, FILE * restrict const); + int archDecoArchFree (ArchDeco * const); + Anum archDecoArchSize (ArchDeco * const, const Anum); +diff -crB scotch_5.1/src/libscotch/arch.h src/src/libscotch/arch.h +*** scotch_5.1/src/libscotch/arch.h 2009-04-28 08:11:27.000000000 -0700 +--- src/src/libscotch/arch.h 2013-05-06 14:14:13.000000000 -0700 +*************** +*** 175,181 **** +--- 175,185 ---- + int archInit (Arch * restrict const); + int archExit (Arch * restrict const); + int archFree (Arch * restrict const); ++ #ifndef NOFILEIO + int archLoad (Arch * restrict const, FILE * const); ++ #else /* NOFILEIO */ ++ int archLoad (Arch * restrict const, FILE * const, const char *, const Anum, const Anum *); ++ #endif /* NOFILEIO */ + int archSave (const Arch * const, FILE * const); + char * archName (const Arch * const); + const ArchClass * archClass (const char * const); +diff -crB scotch_5.1/src/libscotch/arch_hcub.c src/src/libscotch/arch_hcub.c +*** scotch_5.1/src/libscotch/arch_hcub.c 2008-05-22 06:44:41.000000000 -0700 +--- src/src/libscotch/arch_hcub.c 2013-05-06 14:14:13.000000000 -0700 +*************** +*** 88,95 **** + int + archHcubArchLoad ( + ArchHcub * restrict const archptr, +! FILE * restrict const stream) + { + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchHcub) > sizeof (ArchDummy)) || + (sizeof (ArchHcubDom) > sizeof (ArchDomDummy))) { +--- 88,105 ---- + int + archHcubArchLoad ( + ArchHcub * restrict const archptr, +! FILE * restrict const stream +! #ifdef NOFILEIO +! , +! const Anum napar, +! const Anum * archpar +! #endif /* NOFILEIO */ +! ) + { ++ #ifdef NOFILEIO ++ // printf("archHcubArchLoad - napar=%d,archpar=%p\n",napar,archpar); ++ #endif /* NOFILEIO */ ++ + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchHcub) > sizeof (ArchDummy)) || + (sizeof (ArchHcubDom) > sizeof (ArchDomDummy))) { +*************** +*** 98,105 **** +--- 108,120 ---- + } + #endif /* SCOTCH_DEBUG_ARCH1 */ + ++ #ifndef NOFILEIO + if ((intLoad (stream, &archptr->dimmax) != 1) || + (archptr->dimmax < 1) || ++ #else /* NOFILEIO */ ++ if ((napar < 1) || ++ ((archptr->dimmax=archpar[0]) < 1) || ++ #endif /* NOFILEIO */ + (archptr->dimmax > (sizeof (archptr->dimmax) << 3))) { + errorPrint ("archHcubArchLoad: bad input"); + return (1); +diff -crB scotch_5.1/src/libscotch/arch_hcub.h src/src/libscotch/arch_hcub.h +*** scotch_5.1/src/libscotch/arch_hcub.h 2008-05-22 06:44:41.000000000 -0700 +--- src/src/libscotch/arch_hcub.h 2013-05-06 14:14:14.000000000 -0700 +*************** +*** 85,91 **** +--- 85,95 ---- + #define static + #endif + ++ #ifndef NOFILEIO + int archHcubArchLoad (ArchHcub * restrict const, FILE * restrict const); ++ #else /* NOFILEIO */ ++ int archHcubArchLoad (ArchHcub * restrict const, FILE * restrict const, const Anum, const Anum *); ++ #endif /* NOFILEIO */ + int archHcubArchSave (const ArchHcub * const, FILE * restrict const); + #define archHcubArchFree NULL + ArchDomNum archHcubDomNum (const ArchHcub * const, const ArchHcubDom * const); +diff -crB scotch_5.1/src/libscotch/arch_mesh.c src/src/libscotch/arch_mesh.c +*** scotch_5.1/src/libscotch/arch_mesh.c 2008-05-22 06:44:41.000000000 -0700 +--- src/src/libscotch/arch_mesh.c 2013-05-06 14:14:14.000000000 -0700 +*************** +*** 96,103 **** + int + archMesh2ArchLoad ( + ArchMesh2 * restrict const archptr, +! FILE * restrict const stream) +! { + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchMesh2) > sizeof (ArchDummy)) || + (sizeof (ArchMesh2Dom) > sizeof (ArchDomDummy))) { +--- 96,113 ---- + int + archMesh2ArchLoad ( + ArchMesh2 * restrict const archptr, +! FILE * restrict const stream +! #ifdef NOFILEIO +! , +! const Anum napar, +! const Anum * archpar +! #endif /* NOFILEIO */ +! ) +! { +! #ifdef NOFILEIO +! // printf("archMesh2ArchLoad - napar=%d,archpar=%p\n",napar,archpar); +! #endif /* NOFILEIO */ +! + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchMesh2) > sizeof (ArchDummy)) || + (sizeof (ArchMesh2Dom) > sizeof (ArchDomDummy))) { +*************** +*** 106,114 **** +--- 116,130 ---- + } + #endif /* SCOTCH_DEBUG_ARCH1 */ + ++ #ifndef NOFILEIO + if ((intLoad (stream, &archptr->c[0]) != 1) || + (intLoad (stream, &archptr->c[1]) != 1) || + (archptr->c[0] < 1) || (archptr->c[1] < 1)) { ++ #else /* NOFILEIO */ ++ if ((napar < 2) || ++ ((archptr->c[0]=archpar[0]) < 1) || ++ ((archptr->c[1]=archpar[1]) < 1)) { ++ #endif /* NOFILEIO */ + errorPrint ("archMesh2ArchLoad: bad input"); + return (1); + } +*************** +*** 421,428 **** + int + archMesh3ArchLoad ( + ArchMesh3 * restrict const archptr, +! FILE * restrict const stream) +! { + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchMesh3) > sizeof (ArchDummy)) || + (sizeof (ArchMesh3Dom) > sizeof (ArchDomDummy))) { +--- 437,454 ---- + int + archMesh3ArchLoad ( + ArchMesh3 * restrict const archptr, +! FILE * restrict const stream +! #ifdef NOFILEIO +! , +! const Anum napar, +! const Anum * archpar +! #endif /* NOFILEIO */ +! ) +! { +! #ifdef NOFILEIO +! // printf("archMesh3ArchLoad - napar=%d,archpar=%p\n",napar,archpar); +! #endif /* NOFILEIO */ +! + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchMesh3) > sizeof (ArchDummy)) || + (sizeof (ArchMesh3Dom) > sizeof (ArchDomDummy))) { +*************** +*** 431,440 **** +--- 457,473 ---- + } + #endif /* SCOTCH_DEBUG_ARCH1 */ + ++ #ifndef NOFILEIO + if ((intLoad (stream, &archptr->c[0]) != 1) || + (intLoad (stream, &archptr->c[1]) != 1) || + (intLoad (stream, &archptr->c[2]) != 1) || + (archptr->c[0] < 1) || (archptr->c[1] < 1) || (archptr->c[2] < 1)) { ++ #else /* NOFILEIO */ ++ if ((napar < 3) || ++ ((archptr->c[0]=archpar[0]) < 1) || ++ ((archptr->c[1]=archpar[1]) < 1) || ++ ((archptr->c[2]=archpar[2]) < 1)) { ++ #endif /* NOFILEIO */ + errorPrint ("archMesh3ArchLoad: bad input"); + return (1); + } +diff -crB scotch_5.1/src/libscotch/arch_mesh.h src/src/libscotch/arch_mesh.h +*** scotch_5.1/src/libscotch/arch_mesh.h 2008-05-22 06:44:41.000000000 -0700 +--- src/src/libscotch/arch_mesh.h 2013-05-06 14:14:14.000000000 -0700 +*************** +*** 96,102 **** +--- 96,106 ---- + #define static + #endif + ++ #ifndef NOFILEIO + int archMesh2ArchLoad (ArchMesh2 * restrict const, FILE * restrict const); ++ #else /* NOFILEIO */ ++ int archMesh2ArchLoad (ArchMesh2 * restrict const, FILE * restrict const, const Anum, const Anum *); ++ #endif /* NOFILEIO */ + int archMesh2ArchSave (const ArchMesh2 * const, FILE * restrict const); + #define archMesh2ArchFree NULL + ArchDomNum archMesh2DomNum (const ArchMesh2 * const, const ArchMesh2Dom * const); +*************** +*** 114,120 **** +--- 118,128 ---- + int archMesh2DomMpiType (const ArchMesh2 * const, MPI_Datatype * const); + #endif /* SCOTCH_PTSCOTCH */ + ++ #ifndef NOFILEIO + int archMesh3ArchLoad (ArchMesh3 * restrict const, FILE * restrict const); ++ #else /* NOFILEIO */ ++ int archMesh3ArchLoad (ArchMesh3 * restrict const, FILE * restrict const, const Anum, const Anum *); ++ #endif /* NOFILEIO */ + int archMesh3ArchSave (const ArchMesh3 * const, FILE * restrict const); + #define archMesh3ArchFree NULL + ArchDomNum archMesh3DomNum (const ArchMesh3 * const, const ArchMesh3Dom * const); +diff -crB scotch_5.1/src/libscotch/arch_tleaf.c src/src/libscotch/arch_tleaf.c +*** scotch_5.1/src/libscotch/arch_tleaf.c 2008-05-22 06:44:41.000000000 -0700 +--- src/src/libscotch/arch_tleaf.c 2013-05-06 14:14:14.000000000 -0700 +*************** +*** 92,99 **** + int + archTleafArchLoad ( + ArchTleaf * restrict const archptr, +! FILE * restrict const stream) + { + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchTleaf) > sizeof (ArchDummy)) || + (sizeof (ArchTleafDom) > sizeof (ArchDomDummy))) { +--- 92,109 ---- + int + archTleafArchLoad ( + ArchTleaf * restrict const archptr, +! FILE * restrict const stream +! #ifdef NOFILEIO +! , +! const Anum napar, +! const Anum * archpar +! #endif /* NOFILEIO */ +! ) + { ++ #ifdef NOFILEIO ++ // printf("archTleafArchLoad - napar=%d,archpar=%p\n",napar,archpar); ++ #endif /* NOFILEIO */ ++ + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchTleaf) > sizeof (ArchDummy)) || + (sizeof (ArchTleafDom) > sizeof (ArchDomDummy))) { +*************** +*** 102,107 **** +--- 112,118 ---- + } + #endif /* SCOTCH_DEBUG_ARCH1 */ + ++ #ifndef NOFILEIO + if ((intLoad (stream, &archptr->leafdep) != 1) || + (intLoad (stream, &archptr->clusdep) != 1) || + (intLoad (stream, &archptr->linkval) != 1) || +*************** +*** 109,114 **** +--- 120,132 ---- + (archptr->clusdep < 0) || + (archptr->clusdep > archptr->leafdep) || + (archptr->linkval < 1)) { ++ #else /* NOFILEIO */ ++ if ((napar < 3) || ++ ((archptr->leafdep=archpar[0]) < 1) || ++ ((archptr->clusdep=archpar[1]) < 0) || ++ ( archptr->clusdep > archptr->leafdep) || ++ ((archptr->linkval=archpar[2]) < 1)) { ++ #endif /* NOFILEIO */ + errorPrint ("archTleafArchLoad: bad input"); + return (1); + } +diff -crB scotch_5.1/src/libscotch/arch_tleaf.h src/src/libscotch/arch_tleaf.h +*** scotch_5.1/src/libscotch/arch_tleaf.h 2008-05-22 06:44:41.000000000 -0700 +--- src/src/libscotch/arch_tleaf.h 2013-05-06 14:14:15.000000000 -0700 +*************** +*** 89,95 **** +--- 89,99 ---- + #define static + #endif + ++ #ifndef NOFILEIO + int archTleafArchLoad (ArchTleaf * restrict const, FILE * restrict const); ++ #else /* NOFILEIO */ ++ int archTleafArchLoad (ArchTleaf * restrict const, FILE * restrict const, const Anum, const Anum *); ++ #endif /* NOFILEIO */ + int archTleafArchSave (const ArchTleaf * const, FILE * restrict const); + #define archTleafArchFree NULL + ArchDomNum archTleafDomNum (const ArchTleaf * const, const ArchTleafDom * const); +diff -crB scotch_5.1/src/libscotch/arch_torus.c src/src/libscotch/arch_torus.c +*** scotch_5.1/src/libscotch/arch_torus.c 2008-05-22 06:44:41.000000000 -0700 +--- src/src/libscotch/arch_torus.c 2013-05-06 14:14:15.000000000 -0700 +*************** +*** 90,97 **** + int + archTorus2ArchLoad ( + ArchTorus2 * restrict const archptr, +! FILE * restrict const stream) +! { + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchTorus2) > sizeof (ArchDummy)) || + (sizeof (ArchTorus2Dom) > sizeof (ArchDomDummy))) { +--- 90,107 ---- + int + archTorus2ArchLoad ( + ArchTorus2 * restrict const archptr, +! FILE * restrict const stream +! #ifdef NOFILEIO +! , +! const Anum napar, +! const Anum * archpar +! #endif /* NOFILEIO */ +! ) +! { +! #ifdef NOFILEIO +! // printf("archTorus2ArchLoad - napar=%d,archpar=%p\n",napar,archpar); +! #endif /* NOFILEIO */ +! + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchTorus2) > sizeof (ArchDummy)) || + (sizeof (ArchTorus2Dom) > sizeof (ArchDomDummy))) { +*************** +*** 100,108 **** +--- 110,124 ---- + } + #endif /* SCOTCH_DEBUG_ARCH1 */ + ++ #ifndef NOFILEIO + if ((intLoad (stream, &archptr->c[0]) != 1) || + (intLoad (stream, &archptr->c[1]) != 1) || + (archptr->c[0] < 1) || (archptr->c[1] < 1)) { ++ #else /* NOFILEIO */ ++ if ((napar < 2) || ++ ((archptr->c[0]=archpar[0]) < 1) || ++ ((archptr->c[1]=archpar[1]) < 1)) { ++ #endif /* NOFILEIO */ + errorPrint ("archTorus2ArchLoad: bad input"); + return (1); + } +*************** +*** 363,370 **** + int + archTorus3ArchLoad ( + ArchTorus3 * restrict const archptr, +! FILE * restrict const stream) +! { + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchTorus3) > sizeof (ArchDummy)) || + (sizeof (ArchTorus3Dom) > sizeof (ArchDomDummy))) { +--- 379,396 ---- + int + archTorus3ArchLoad ( + ArchTorus3 * restrict const archptr, +! FILE * restrict const stream +! #ifdef NOFILEIO +! , +! const Anum napar, +! const Anum * archpar +! #endif /* NOFILEIO */ +! ) +! { +! #ifdef NOFILEIO +! // printf("archTorus3ArchLoad - napar=%d,archpar=%p\n",napar,archpar); +! #endif /* NOFILEIO */ +! + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchTorus3) > sizeof (ArchDummy)) || + (sizeof (ArchTorus3Dom) > sizeof (ArchDomDummy))) { +*************** +*** 373,382 **** +--- 399,415 ---- + } + #endif /* SCOTCH_DEBUG_ARCH1 */ + ++ #ifndef NOFILEIO + if ((intLoad (stream, &archptr->c[0]) != 1) || + (intLoad (stream, &archptr->c[1]) != 1) || + (intLoad (stream, &archptr->c[2]) != 1) || + (archptr->c[0] < 1) || (archptr->c[1] < 1) || (archptr->c[2] < 1)) { ++ #else /* NOFILEIO */ ++ if ((napar < 3) || ++ ((archptr->c[0]=archpar[0]) < 1) || ++ ((archptr->c[1]=archpar[1]) < 1) || ++ ((archptr->c[2]=archpar[2]) < 1)) { ++ #endif /* NOFILEIO */ + errorPrint ("archTorus3ArchLoad: bad input"); + return (1); + } +diff -crB scotch_5.1/src/libscotch/arch_torus.h src/src/libscotch/arch_torus.h +*** scotch_5.1/src/libscotch/arch_torus.h 2008-05-22 06:44:41.000000000 -0700 +--- src/src/libscotch/arch_torus.h 2013-05-06 14:14:15.000000000 -0700 +*************** +*** 96,102 **** +--- 96,106 ---- + #define static + #endif + ++ #ifndef NOFILEIO + int archTorus2ArchLoad (ArchTorus2 * restrict const, FILE * restrict const); ++ #else /* NOFILEIO */ ++ int archTorus2ArchLoad (ArchTorus2 * restrict const, FILE * restrict const, const Anum, const Anum *); ++ #endif /* NOFILEIO */ + int archTorus2ArchSave (const ArchTorus2 * const, FILE * restrict const); + #define archTorus2ArchFree NULL + ArchDomNum archTorus2DomNum (const ArchTorus2 * const, const ArchTorus2Dom * const); +*************** +*** 114,120 **** +--- 118,128 ---- + int archTorus2DomMpiType (const ArchTorus2 * const, MPI_Datatype * const); + #endif /* SCOTCH_PTSCOTCH */ + ++ #ifndef NOFILEIO + int archTorus3ArchLoad (ArchTorus3 * restrict const, FILE * restrict const); ++ #else /* NOFILEIO */ ++ int archTorus3ArchLoad (ArchTorus3 * restrict const, FILE * restrict const, const Anum, const Anum *); ++ #endif /* NOFILEIO */ + int archTorus3ArchSave (const ArchTorus3 * const, FILE * restrict const); + #define archTorus3ArchFree NULL + ArchDomNum archTorus3DomNum (const ArchTorus3 * const, const ArchTorus3Dom * const); +diff -crB scotch_5.1/src/libscotch/common.c src/src/libscotch/common.c +*** scotch_5.1/src/libscotch/common.c 2008-05-22 06:44:41.000000000 -0700 +--- src/src/libscotch/common.c 2013-05-06 14:14:15.000000000 -0700 +*************** +*** 100,106 **** +--- 100,112 ---- + { + const char ** cptr; + ++ #ifndef MATLAB + fprintf (stream, "Usage is:\n"); + for (cptr = data; *cptr != NULL; cptr ++) + fprintf (stream, " %s\n", *cptr); ++ #else /* MATLAB */ ++ mexPrintf ("Usage is:\n"); ++ for (cptr = data; *cptr != NULL; cptr ++) ++ mexPrintf (" %s\n", *cptr); ++ #endif /* MATLAB */ + } +diff -crB scotch_5.1/src/libscotch/common.h src/src/libscotch/common.h +*** scotch_5.1/src/libscotch/common.h 2009-02-06 14:20:55.000000000 -0800 +--- src/src/libscotch/common.h 2013-05-09 11:49:35.317220518 -0700 +*************** +*** 1,3 **** +--- 1,5 ---- ++ #ifndef _SCOTCH_COMMON_H_ ++ #define _SCOTCH_COMMON_H_ + /* Copyright 2004,2007-2009 ENSEIRB, INRIA & CNRS + ** + ** This file is part of the Scotch software package for static mapping, +*************** +*** 79,84 **** +--- 81,87 ---- + #include + #endif /* COMMON_TIMING_OLD */ + #include ++ #include + + #ifdef SCOTCH_PTSCOTCH + #include +*************** +*** 106,113 **** + #define memCpy(dst,src,siz) memcpy((dst),(src),(siz)) + #define memMov(dst,src,siz) memmove((dst),(src),(siz)) + +- #define MIN(x,y) (((x) < (y)) ? (x) : (y)) +- #define MAX(x,y) (((x) < (y)) ? (y) : (x)) + #define ABS(x) MAX ((x), -(x)) + #define SIGN(x) (((x) < 0) ? -1 : 1) + +--- 109,114 ---- +*************** +*** 171,179 **** + /** The file structure. **/ + + typedef struct File_ { +! char * name; /*+ File name +*/ + FILE * pntr; /*+ File pointer +*/ +! char * mode; /*+ Opening mode +*/ + } File; + + /* +--- 172,180 ---- + /** The file structure. **/ + + typedef struct File_ { +! const char * name; /*+ File name +*/ + FILE * pntr; /*+ File pointer +*/ +! const char * mode; /*+ Opening mode +*/ + } File; + + /* +*************** +*** 190,216 **** + size_t memMax (); + #endif /* COMMON_MEMORY_TRACE */ + +- void usagePrint (FILE * const, const char (* [])); + +- int fileBlockOpen (File * const, const int); + int fileBlockOpenDist (File * const, const int, const int, const int, const int); +- void fileBlockClose (File * const, const int); + FILE * fileCompress (FILE * const, const int); + int fileCompressType (const char * const); + FILE * fileUncompress (FILE * const, const int); + int fileUncompressType (const char * const); + int fileNameDistExpand (char ** const, const int, const int, const int); + + void errorProg (const char * const); + void errorPrint (const char * const, ...); + void errorPrintW (const char * const, ...); + + int intLoad (FILE * const, INT * const); + int intSave (FILE * const, const INT); + void intAscn (INT * const, const INT, const INT); + void intPerm (INT * const, const INT); + void intRandReset (void); +- void intRandInit (void); + INT intRandVal (INT); + void intSort1asc1 (void * const, const INT); + void intSort2asc1 (void * const, const INT); +--- 191,227 ---- + size_t memMax (); + #endif /* COMMON_MEMORY_TRACE */ + + + int fileBlockOpenDist (File * const, const int, const int, const int, const int); + FILE * fileCompress (FILE * const, const int); + int fileCompressType (const char * const); + FILE * fileUncompress (FILE * const, const int); + int fileUncompressType (const char * const); + int fileNameDistExpand (char ** const, const int, const int, const int); + ++ #ifdef __cplusplus ++ extern "C" { ++ #endif /* __cplusplus */ ++ + void errorProg (const char * const); + void errorPrint (const char * const, ...); + void errorPrintW (const char * const, ...); ++ double clockGet (void); ++ void usagePrint (FILE * const, const char (* [])); ++ void intRandInit (void); ++ int fileBlockOpen (File * const, const int); ++ void fileBlockClose (File * const, const int); ++ void intRandResetStatic (void); ++ ++ #ifdef __cplusplus ++ } ++ #endif /* __cplusplus */ + + int intLoad (FILE * const, INT * const); + int intSave (FILE * const, const INT); + void intAscn (INT * const, const INT, const INT); + void intPerm (INT * const, const INT); + void intRandReset (void); + INT intRandVal (INT); + void intSort1asc1 (void * const, const INT); + void intSort2asc1 (void * const, const INT); +*************** +*** 221,227 **** + void clockStart (Clock * const); + void clockStop (Clock * const); + double clockVal (Clock * const); +- double clockGet (void); + + /* + ** Macro definitions. +--- 232,237 ---- +*************** +*** 249,251 **** +--- 259,263 ---- + void nl##__ pl \ + { nu pc; } \ + void nu pl ++ ++ #endif //#ifndef _SCOTCH_COMMON_H_ +diff -crB scotch_5.1/src/libscotch/common_integer.c src/src/libscotch/common_integer.c +*** scotch_5.1/src/libscotch/common_integer.c 2009-01-21 01:32:32.000000000 -0800 +--- src/src/libscotch/common_integer.c 2013-05-06 14:14:16.000000000 -0700 +*************** +*** 191,196 **** +--- 191,209 ---- + static volatile int intrandflag = 0; /*+ Flag set if generator already initialized +*/ + static unsigned int intrandseed = 1; /*+ Random seed +*/ + ++ void ++ intRandResetStatic (void) ++ { ++ #ifdef MATLAB ++ // printf("intRandResetStatic begin - intrandflag=%d,intrandseed=%d\n",intrandflag,intrandseed); ++ #endif /* MATLAB */ ++ intrandflag = 0; /*+ Flag set if generator already initialized +*/ ++ intrandseed = 1; /*+ Random seed +*/ ++ #ifdef MATLAB ++ // printf("intRandResetStatic end - intrandflag=%d,intrandseed=%d\n",intrandflag,intrandseed); ++ #endif /* MATLAB */ ++ } ++ + /* This routine initializes the pseudo-random + ** generator if necessary. In order for multi-sequential + ** programs to have exactly the same behavior on any +*************** +*** 205,210 **** +--- 218,226 ---- + void + intRandInit (void) + { ++ #ifdef MATLAB ++ // printf("intRandInit begin - intrandflag=%d,intrandseed=%d\n",intrandflag,intrandseed); ++ #endif /* MATLAB */ + if (intrandflag == 0) { /* If generator not yet initialized */ + #if ! ((defined COMMON_DEBUG) || (defined COMMON_RANDOM_FIXED_SEED) || (defined SCOTCH_DETERMINISTIC)) + intrandseed = time (NULL); /* Set random seed if needed */ +*************** +*** 216,221 **** +--- 232,240 ---- + #endif /* COMMON_RANDOM_RAND */ + intrandflag = 1; /* Generator has been initialized */ + } ++ #ifdef MATLAB ++ // printf("intRandInit end - intrandflag=%d,intrandseed=%d\n",intrandflag,intrandseed); ++ #endif /* MATLAB */ + } + + /* This routine reinitializes the pseudo-random +*************** +*** 228,233 **** +--- 247,255 ---- + void + intRandReset (void) + { ++ #ifdef MATLAB ++ // printf("intRandReset begin - intrandflag=%d,intrandseed=%d\n",intrandflag,intrandseed); ++ #endif /* MATLAB */ + if (intrandflag != 0) { /* Keep seed computed during first initialization */ + #ifdef COMMON_RANDOM_RAND + srand (intrandseed); +*************** +*** 237,242 **** +--- 259,267 ---- + } + else + intRandInit (); ++ #ifdef MATLAB ++ // printf("intRandReset end - intrandflag=%d,intrandseed=%d\n",intrandflag,intrandseed); ++ #endif /* MATLAB */ + } + + /*********************/ +diff -crB scotch_5.1/src/libscotch/common_memory.c src/src/libscotch/common_memory.c +*** scotch_5.1/src/libscotch/common_memory.c 2009-01-03 02:16:11.000000000 -0800 +--- src/src/libscotch/common_memory.c 2013-05-06 14:14:16.000000000 -0700 +*************** +*** 87,93 **** +--- 87,95 ---- + size_t newadd; + byte * newptr; + ++ printf("memAllocRecord begin -- memorysiz=%d,memorymax=%d\n",memorysiz,memorymax); + #if (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) ++ printf("memAllocRecord begin -- muteflag=%d,mutelocdat=%p\n",muteflag,mutelocdat); + if (muteflag != 0) { /* Unsafe code with respect to race conditions but should work as first allocs are sequential */ + muteflag = 0; + pthread_mutex_init (&mutelocdat, NULL); /* Initialize local mutex */ +*************** +*** 109,116 **** +--- 111,120 ---- + + #if (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) + pthread_mutex_unlock (&mutelocdat); /* Unlock local mutex */ ++ printf("memAllocRecord end -- muteflag=%d,mutelocdat=%p\n",muteflag,mutelocdat); + #endif /* (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) */ + ++ printf("memAllocRecord end -- memorysiz=%d,memorymax=%d\n",memorysiz,memorymax); + return ((void *) newptr); /* Return skewed pointer or NULL */ + } + +*************** +*** 124,133 **** +--- 128,139 ---- + size_t oldsiz; + size_t newadd; + ++ printf("memReallocRecord begin -- memorysiz=%d,memorymax=%d\n",memorysiz,memorymax); + tmpptr = ((byte *) oldptr) - COMMON_MEMORY_SKEW; + oldsiz = *((size_t *) tmpptr); + + #if (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) ++ printf("memReallocRecord begin -- muteflag=%d,mutelocdat=%p\n",muteflag,mutelocdat); + pthread_mutex_lock (&mutelocdat); /* Lock local mutex */ + #endif /* (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) */ + +*************** +*** 145,152 **** +--- 151,160 ---- + + #if (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) + pthread_mutex_unlock (&mutelocdat); /* Unlock local mutex */ ++ printf("memReallocRecord end -- muteflag=%d,mutelocdat=%p\n",muteflag,mutelocdat); + #endif /* (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) */ + ++ printf("memReallocRecord end -- memorysiz=%d,memorymax=%d\n",memorysiz,memorymax); + return ((void *) newptr); /* Return skewed pointer or NULL */ + } + +*************** +*** 157,166 **** +--- 165,176 ---- + byte * tmpptr; + size_t oldsiz; + ++ printf("memFreeRecord begin -- memorysiz=%d,memorymax=%d\n",memorysiz,memorymax); + tmpptr = ((byte *) oldptr) - COMMON_MEMORY_SKEW; + oldsiz = *((size_t *) tmpptr); + + #if (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) ++ printf("memFreeRecord begin -- muteflag=%d,mutelocdat=%p\n",muteflag,mutelocdat); + pthread_mutex_lock (&mutelocdat); /* Lock local mutex */ + #endif /* (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) */ + +*************** +*** 169,175 **** +--- 179,187 ---- + + #if (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) + pthread_mutex_unlock (&mutelocdat); /* Unlock local mutex */ ++ printf("memFreeRecord end -- muteflag=%d,mutelocdat=%p\n",muteflag,mutelocdat); + #endif /* (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) */ ++ printf("memFreeRecord end -- memorysiz=%d,memorymax=%d\n",memorysiz,memorymax); + } + + size_t +*************** +*** 177,183 **** +--- 189,197 ---- + { + size_t curmax; + ++ printf("memMax begin -- memorysiz=%d,memorymax=%d\n",memorysiz,memorymax); + #if (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) ++ printf("memMax begin -- muteflag=%d,mutelocdat=%p\n",muteflag,mutelocdat); + pthread_mutex_lock (&mutelocdat); /* Lock local mutex */ + #endif /* (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) */ + +*************** +*** 185,192 **** +--- 199,208 ---- + + #if (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) + pthread_mutex_unlock (&mutelocdat); /* Unlock local mutex */ ++ printf("memMax end -- muteflag=%d,mutelocdat=%p\n",muteflag,mutelocdat); + #endif /* (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) */ + ++ printf("memMax end -- memorysiz=%d,memorymax=%d\n",memorysiz,memorymax); + return (curmax); + } + #endif /* COMMON_MEMORY_TRACE */ +diff -crB scotch_5.1/src/libscotch/dummysizes.c src/src/libscotch/dummysizes.c +*** scotch_5.1/src/libscotch/dummysizes.c 2009-05-09 16:08:02.000000000 -0700 +--- src/src/libscotch/dummysizes.c 2013-05-06 14:14:16.000000000 -0700 +*************** +*** 267,271 **** +--- 267,273 ---- + } + #endif /* SCOTCH_DEBUG_MAIN1 */ + ++ #ifndef MATLAB + exit (0); ++ #endif /* MATLAB */ + } +diff -crB scotch_5.1/src/libscotch/graph.c src/src/libscotch/graph.c +*** scotch_5.1/src/libscotch/graph.c 2008-05-22 06:44:42.000000000 -0700 +--- src/src/libscotch/graph.c 2013-05-06 14:14:17.000000000 -0700 +*************** +*** 135,141 **** + if ((grafptr->velotax != NULL) && /* Free graph tables */ + ((grafptr->flagval & GRAPHVERTGROUP) == 0)) + memFree (grafptr->velotax + grafptr->baseval); +! if (grafptr->vlbltax != NULL) + memFree (grafptr->vlbltax + grafptr->baseval); + if ((grafptr->edlotax != NULL) && + ((grafptr->flagval & GRAPHEDGEGROUP) == 0)) +--- 135,144 ---- + if ((grafptr->velotax != NULL) && /* Free graph tables */ + ((grafptr->flagval & GRAPHVERTGROUP) == 0)) + memFree (grafptr->velotax + grafptr->baseval); +! /* vlbltax must also check GRAPHVERTGROUP (jes, 12/11/09) */ +! // if (grafptr->vlbltax != NULL) +! if ((grafptr->vlbltax != NULL) && +! ((grafptr->flagval & GRAPHVERTGROUP) == 0)) + memFree (grafptr->vlbltax + grafptr->baseval); + if ((grafptr->edlotax != NULL) && + ((grafptr->flagval & GRAPHEDGEGROUP) == 0)) +diff -crB scotch_5.1/src/libscotch/graph.h src/src/libscotch/graph.h +*** scotch_5.1/src/libscotch/graph.h 2008-06-01 02:49:11.000000000 -0700 +--- src/src/libscotch/graph.h 2013-05-06 14:14:17.000000000 -0700 +*************** +*** 159,165 **** +--- 159,169 ---- + int graphInit (Graph * const); + void graphExit (Graph * const); + void graphFree (Graph * const); ++ #ifndef NOFILEIO + int graphLoad (Graph * const, FILE * const, const Gnum, const GraphFlag); ++ #else /* NOFILEIO */ ++ int graphLoad (Graph * const, FILE * const, const Gnum, const GraphFlag, const Gnum, const Gnum, const Gnum*, const Gnum*, const Gnum*, const Gnum*, const Gnum*); ++ #endif /* NOFILEIO */ + int graphLoad2 (const Gnum, const Gnum, const Gnum * const, const Gnum * const, Gnum * restrict const, const Gnum, const Gnum * const); + int graphSave (const Graph * const, FILE * const); + Gnum graphBase (Graph * const, const Gnum); +diff -crB scotch_5.1/src/libscotch/graph_io.c src/src/libscotch/graph_io.c +*** scotch_5.1/src/libscotch/graph_io.c 2008-05-22 06:44:42.000000000 -0700 +--- src/src/libscotch/graph_io.c 2013-05-06 14:14:17.000000000 -0700 +*************** +*** 86,92 **** + Graph * restrict const grafptr, /* Graph structure to fill */ + FILE * const stream, /* Stream from which to read graph data */ + const Gnum baseval, /* Base value (-1 means keep file base) */ +! const GraphFlag flagval) /* Graph loading flags */ + { + Gnum edgenum; /* Number of edges really allocated */ + Gnum edgennd; +--- 86,103 ---- + Graph * restrict const grafptr, /* Graph structure to fill */ + FILE * const stream, /* Stream from which to read graph data */ + const Gnum baseval, /* Base value (-1 means keep file base) */ +! const GraphFlag flagval /* Graph loading flags */ +! #ifdef NOFILEIO +! , +! const Gnum nvert, +! const Gnum nedge2, +! const Gnum* adjir, +! const Gnum* adjjc, +! const Gnum* vertlab, +! const Gnum* vertwgt, +! const Gnum* edgewgt +! #endif /* NOFILEIO */ +! ) + { + Gnum edgenum; /* Number of edges really allocated */ + Gnum edgennd; +*************** +*** 104,120 **** +--- 115,141 ---- + char proptab[4]; + Gnum vertnum; + ++ #ifdef NOFILEIO ++ // printf("graphLoad - stream=%p; nvert=%d,nedge2=%d\n",stream,nvert,nedge2); ++ // printf("graphLoad - adjir=%p,adjjc=%p,vertlab=%p,vertwgt=%p,edgewgt=%p\n", ++ // adjir,adjjc,vertlab,vertwgt,edgewgt); ++ #endif /* NOFILEIO */ + memSet (grafptr, 0, sizeof (Graph)); + ++ #ifndef NOFILEIO + if (intLoad (stream, &versval) != 1) { /* Read version number */ + errorPrint ("graphLoad: bad input (1)"); + return (1); + } ++ #else /* NOFILEIO */ ++ versval=0; ++ #endif /* NOFILEIO */ + if (versval != 0) { /* If version not zero */ + errorPrint ("graphLoad: old-style graph format no longer supported"); + return (1); + } + ++ #ifndef NOFILEIO + if ((intLoad (stream, &grafptr->vertnbr) != 1) || /* Read rest of header */ + (intLoad (stream, &grafptr->edgenbr) != 1) || + (intLoad (stream, &baseadj) != 1) || +*************** +*** 124,129 **** +--- 145,159 ---- + errorPrint ("graphLoad: bad input (2)"); + return (1); + } ++ #else /* NOFILEIO */ ++ grafptr->vertnbr=nvert; ++ grafptr->edgenbr=nedge2; ++ baseadj=1; ++ propval=0; ++ if (vertlab) propval+=100; ++ if (edgewgt) propval+= 10; ++ if (vertwgt) propval+= 1; ++ #endif /* NOFILEIO */ + sprintf (proptab, "%3.3d", (int) propval); /* Compute file properties */ + proptab[0] -= '0'; /* Vertex labels flag */ + proptab[1] -= '0'; /* Edge weights flag */ +*************** +*** 140,145 **** +--- 170,179 ---- + } + if (proptab[0] != 0) /* If vertex labels, no base adjust */ + baseadj = 0; ++ #ifdef NOFILEIO ++ // printf("graphLoad - baseadj=%d,baseval=%d,grafptr->baseval=%d\n", ++ // baseadj,baseval,grafptr->baseval); ++ #endif /* NOFILEIO */ + + velonbr = ((proptab[2] != 0) && ((flagval & GRAPHIONOLOADVERT) == 0)) ? grafptr->vertnbr : 0; + vlblnbr = (proptab[0] != 0) ? grafptr->vertnbr : 0; +*************** +*** 178,188 **** +--- 212,226 ---- + if (grafptr->vlbltax != NULL) { /* If must read label */ + Gnum vlblval; /* Value where to read vertex label */ + ++ #ifndef NOFILEIO + if (intLoad (stream, &vlblval) != 1) { /* Read label data */ + errorPrint ("graphLoad: bad input (3)"); + graphFree (grafptr); + return (1); + } ++ #else /* NOFILEIO */ ++ vlblval=vertlab[vertnum-grafptr->baseval]; ++ #endif /* NOFILEIO */ + grafptr->vlbltax[vertnum] = vlblval; + if (grafptr->vlbltax[vertnum] > vlblmax) /* Get maximum vertex label */ + vlblmax = grafptr->vlbltax[vertnum]; +*************** +*** 190,209 **** +--- 228,257 ---- + if (proptab[2] != 0) { /* If must read vertex load */ + Gnum veloval; /* Value where to read vertex load */ + ++ #ifndef NOFILEIO + if (intLoad (stream, &veloval) != 1) { /* Read vertex load data */ + errorPrint ("graphLoad: bad input (4)"); + graphFree (grafptr); + return (1); + } ++ #else /* NOFILEIO */ ++ veloval=vertwgt[vertnum-grafptr->baseval]; ++ #endif /* NOFILEIO */ + if (grafptr->velotax != NULL) + velosum += + grafptr->velotax[vertnum] = veloval; + } ++ #ifndef NOFILEIO + if (intLoad (stream, °rval) != 1) { /* Read vertex degree */ + errorPrint ("graphLoad: bad input (5)"); + graphFree (grafptr); + return (1); + } ++ #else /* NOFILEIO */ ++ // printf("old degrval=%d; new degrval=%d\n", ++ // degrval,adjjc[vertnum-grafptr->baseval+1]-adjjc[vertnum-grafptr->baseval]); ++ degrval=adjjc[vertnum-grafptr->baseval+1]-adjjc[vertnum-grafptr->baseval]; ++ #endif /* NOFILEIO */ + if (degrmax < degrval) /* Set maximum degree */ + degrmax = degrval; + +*************** +*** 219,238 **** +--- 267,301 ---- + if (proptab[1] != 0) { /* If must read edge load */ + Gnum edloval; /* Value where to read edge load */ + ++ #ifndef NOFILEIO + if (intLoad (stream, &edloval) != 1) { /* Read edge load data */ + errorPrint ("graphLoad: bad input (6)"); + graphFree (grafptr); + return (1); + } ++ #else /* NOFILEIO */ ++ edloval=edgewgt[edgenum-grafptr->baseval]; ++ #endif /* NOFILEIO */ + if (grafptr->edlotax != NULL) + edlosum += + grafptr->edlotax[edgenum] = (Gnum) edloval; + } ++ #ifndef NOFILEIO + if (intLoad (stream, &edgeval) != 1) { /* Read edge data */ + errorPrint ("graphLoad: bad input (7)"); + graphFree (grafptr); + return (1); + } ++ #else /* NOFILEIO */ ++ // printf("edgenum=%d: old edgeval=%d; new edgeval[%d]=%d\n", ++ // edgenum,edgeval,edgenum-grafptr->baseval,adjir[edgenum-grafptr->baseval]+1); ++ /* if vertex labels are supplied, they must be referenced (jes, 1/05/10) */ ++ // edgeval=adjir[edgenum-grafptr->baseval]+1; ++ if (vertlab) ++ edgeval=vertlab[adjir[edgenum-grafptr->baseval] ]; ++ else ++ edgeval= adjir[edgenum-grafptr->baseval]+1; ++ #endif /* NOFILEIO */ + grafptr->edgetax[edgenum] = edgeval + baseadj; + } + } +*************** +*** 279,284 **** +--- 342,351 ---- + Gnum vertnum; /* Number of current vertex */ + Gnum * restrict indxtab; /* Vertex label/number index table */ + ++ #ifdef NOFILEIO ++ printf("graphLoad2 - baseval=%d,vertnnd=%d,vlblmax=%d\n", ++ baseval,vertnnd,vlblmax); ++ #endif /* NOFILEIO */ + if ((indxtab = (Gnum *) memAlloc ((vlblmax + 1) * sizeof (Gnum))) == NULL) { + errorPrint ("graphLoad2: out of memory"); + return (1); +*************** +*** 286,291 **** +--- 353,362 ---- + + memSet (indxtab, ~0, (vlblmax + 1) * sizeof (Gnum)); /* Assume labels not used */ + for (vertnum = baseval; vertnum < vertnnd; vertnum ++) { ++ #ifdef NOFILEIO ++ // printf("graphLoad2 - vertnum=%d; vlbltax=%d,indxtab=%d\n", ++ // vertnum,vlbltax[vertnum],indxtab[vlbltax[vertnum]]); ++ #endif /* NOFILEIO */ + if (indxtab[vlbltax[vertnum]] != ~0) { /* If vertex label already used */ + errorPrint ("graphLoad2: duplicate vertex label"); + memFree (indxtab); +*************** +*** 294,299 **** +--- 365,374 ---- + indxtab[vlbltax[vertnum]] = vertnum; /* Set vertex number index */ + } + for (vertnum = baseval; vertnum < vertnnd; vertnum ++) { ++ #ifdef NOFILEIO ++ // printf("graphLoad2 - vertnum=%d; vlbltax=%d,indxtab=%d\n", ++ // vertnum,vlbltax[vertnum],indxtab[vlbltax[vertnum]]); ++ #endif /* NOFILEIO */ + Gnum edgenum; /* Number of current edge */ + + for (edgenum = verttax[vertnum]; edgenum < vendtax[vertnum]; edgenum ++) { +*************** +*** 307,313 **** +--- 382,396 ---- + memFree (indxtab); + return (1); + } ++ #ifdef NOFILEIO ++ // printf("graphLoad2 - edgenum=%d; old edgetax=%d,", ++ // edgenum,edgetax[edgenum]); ++ #endif /* NOFILEIO */ + edgetax[edgenum] = indxtab[edgetax[edgenum]]; /* Replace label by number */ ++ #ifdef NOFILEIO ++ // printf("new edgetax=%d\n", ++ // edgetax[edgenum]); ++ #endif /* NOFILEIO */ + } + } + +diff -crB scotch_5.1/src/libscotch/graph_io_scot.c src/src/libscotch/graph_io_scot.c +*** scotch_5.1/src/libscotch/graph_io_scot.c 2008-05-22 06:44:42.000000000 -0700 +--- src/src/libscotch/graph_io_scot.c 2013-05-06 14:14:17.000000000 -0700 +*************** +*** 89,95 **** +--- 89,99 ---- + int o; + + if (filesrcptr != NULL) { ++ #ifndef NOFILEIO + if (graphLoad (grafptr, filesrcptr, -1, 0) != 0) ++ #else /* NOFILEIO */ ++ if (graphLoad (grafptr, filesrcptr, -1, 0, 0, 0, NULL, NULL, NULL, NULL, NULL) != 0) ++ #endif /* NOFILEIO */ + return (1); + } + +diff -crB scotch_5.1/src/libscotch/library_arch.c src/src/libscotch/library_arch.c +*** scotch_5.1/src/libscotch/library_arch.c 2008-05-22 06:44:42.000000000 -0700 +--- src/src/libscotch/library_arch.c 2013-05-06 14:14:17.000000000 -0700 +*************** +*** 120,128 **** + int + SCOTCH_archLoad ( + SCOTCH_Arch * const archptr, +! FILE * const stream) + { + return (archLoad ((Arch *) archptr, stream)); + } + + /*+ This routine saves the given opaque +--- 120,139 ---- + int + SCOTCH_archLoad ( + SCOTCH_Arch * const archptr, +! FILE * const stream +! #ifdef NOFILEIO +! , +! const char * archtyp, +! const SCOTCH_Num napar, +! const SCOTCH_Num * archpar +! #endif /* NOFILEIO */ +! ) + { ++ #ifndef NOFILEIO + return (archLoad ((Arch *) archptr, stream)); ++ #else /* NOFILEIO */ ++ return (archLoad ((Arch *) archptr, stream, archtyp, napar, archpar)); ++ #endif /* NOFILEIO */ + } + + /*+ This routine saves the given opaque +diff -crB scotch_5.1/src/libscotch/library_arch_f.c src/src/libscotch/library_arch_f.c +*** scotch_5.1/src/libscotch/library_arch_f.c 2008-05-22 06:44:42.000000000 -0700 +--- src/src/libscotch/library_arch_f.c 2013-05-06 14:14:18.000000000 -0700 +*************** +*** 121,127 **** +--- 121,131 ---- + } + setbuf (stream, NULL); /* Do not buffer on input */ + ++ #ifndef NOFILEIO + o = SCOTCH_archLoad (archptr, stream); ++ #else /* NOFILEIO */ ++ o = SCOTCH_archLoad (archptr, stream, "", 0, NULL); ++ #endif /* NOFILEIO */ + + fclose (stream); /* This closes filenum too */ + +diff -crB scotch_5.1/src/libscotch/library_error_exit.c src/src/libscotch/library_error_exit.c +*** scotch_5.1/src/libscotch/library_error_exit.c 2009-01-20 00:36:33.000000000 -0800 +--- src/src/libscotch/library_error_exit.c 2013-05-06 14:14:18.000000000 -0700 +*************** +*** 114,119 **** +--- 114,120 ---- + int proclocnum; + #endif /* SCOTCH_PTSCOTCH */ + ++ #ifndef MATLAB + fprintf (stderr, "%s", _SCOTCHerrorProgName); + #ifdef SCOTCH_PTSCOTCH + if ((MPI_Initialized (&proclocnum) == MPI_SUCCESS) && +*************** +*** 131,136 **** +--- 132,155 ---- + fprintf (stderr, "\n"); + fflush (stderr); /* In case it has been set to buffered mode */ + ++ #else /* MATLAB */ ++ mexPrintf ("%s", _SCOTCHerrorProgName); ++ #ifdef SCOTCH_PTSCOTCH ++ if ((MPI_Initialized (&proclocnum) == MPI_SUCCESS) && ++ (proclocnum != 0) && ++ (MPI_Comm_rank (MPI_COMM_WORLD, &proclocnum) == MPI_SUCCESS)) ++ mexPrintf ("(%d): ", proclocnum); ++ #else /* SCOTCH_PTSCOTCH */ ++ if (_SCOTCHerrorProgName[0] != '\0') ++ mexPrintf (": "); ++ #endif /* SCOTCH_PTSCOTCH */ ++ mexPrintf ("ERROR: "); ++ va_start (errlist, errstr); ++ mexPrintf (errstr, errlist); /* Print arguments */ ++ va_end (errlist); ++ mexPrintf ("\n"); ++ #endif /* MATLAB */ ++ + #ifdef SCOTCH_ERROR_SLEEP + sleep (SCOTCH_ERROR_SLEEP); /* Wait for messages to be propagated */ + #endif /* SCOTCH_ERROR_SLEEP */ +*************** +*** 155,160 **** +--- 174,180 ---- + int proclocnum; + #endif /* SCOTCH_PTSCOTCH */ + ++ #ifndef MATLAB + fprintf (stderr, "%s", _SCOTCHerrorProgName); + #ifdef SCOTCH_PTSCOTCH + if ((MPI_Initialized (&proclocnum) == MPI_SUCCESS) && +*************** +*** 171,174 **** +--- 191,212 ---- + va_end (errlist); + fprintf (stderr, "\n"); + fflush (stderr); /* In case it has been set to buffered mode */ ++ ++ #else /* MATLAB */ ++ mexPrintf ("%s", _SCOTCHerrorProgName); ++ #ifdef SCOTCH_PTSCOTCH ++ if ((MPI_Initialized (&proclocnum) == MPI_SUCCESS) && ++ (proclocnum != 0) && ++ (MPI_Comm_rank (MPI_COMM_WORLD, &proclocnum) == MPI_SUCCESS)) ++ mexPrintf ("(%d): ", proclocnum); ++ #else /* SCOTCH_PTSCOTCH */ ++ if (_SCOTCHerrorProgName[0] != '\0') ++ mexPrintf (": "); ++ #endif /* SCOTCH_PTSCOTCH */ ++ mexPrintf ("WARNING: "); ++ va_start (errlist, errstr); ++ mexPrintf (errstr, errlist); /* Print arguments */ ++ va_end (errlist); ++ mexPrintf ("\n"); ++ #endif /* MATLAB */ + } +diff -crB scotch_5.1/src/libscotch/library_graph.c src/src/libscotch/library_graph.c +*** scotch_5.1/src/libscotch/library_graph.c 2008-05-22 07:28:12.000000000 -0700 +--- src/src/libscotch/library_graph.c 2013-05-06 14:14:18.000000000 -0700 +*************** +*** 137,143 **** + SCOTCH_Graph * const grafptr, + FILE * const stream, + const SCOTCH_Num baseval, +! const SCOTCH_Num flagval) + { + GraphFlag srcgrafflag; /* Graph flags */ + +--- 137,154 ---- + SCOTCH_Graph * const grafptr, + FILE * const stream, + const SCOTCH_Num baseval, +! const SCOTCH_Num flagval +! #ifdef NOFILEIO +! , +! const SCOTCH_Num nvert, +! const SCOTCH_Num nedge2, +! const SCOTCH_Num* adjir, +! const SCOTCH_Num* adjjc, +! const SCOTCH_Num* vertlab, +! const SCOTCH_Num* vertwgt, +! const SCOTCH_Num* edgewgt +! #endif /* NOFILEIO */ +! ) + { + GraphFlag srcgrafflag; /* Graph flags */ + +*************** +*** 153,159 **** +--- 164,174 ---- + srcgrafflag = (((flagval & 1) != 0) ? GRAPHIONOLOADVERT : 0) + + (((flagval & 2) != 0) ? GRAPHIONOLOADEDGE : 0); + ++ #ifndef NOFILEIO + return (graphLoad ((Graph * const) grafptr, stream, (Gnum) baseval, srcgrafflag)); ++ #else /* NOFILEIO */ ++ return (graphLoad ((Graph * const) grafptr, stream, (Gnum) baseval, srcgrafflag, (const Gnum) nvert, (const Gnum) nedge2, (const Gnum *) adjir, (const Gnum *) adjjc, (const Gnum *) vertlab, (const Gnum *) vertwgt, (const Gnum *) edgewgt)); ++ #endif /* NOFILEIO */ + } + + /*+ This routine saves the contents of the given +diff -crB scotch_5.1/src/libscotch/library_graph_f.c src/src/libscotch/library_graph_f.c +*** scotch_5.1/src/libscotch/library_graph_f.c 2008-05-22 06:44:43.000000000 -0700 +--- src/src/libscotch/library_graph_f.c 2013-05-06 14:14:18.000000000 -0700 +*************** +*** 136,142 **** +--- 136,146 ---- + } + setbuf (stream, NULL); /* Do not buffer on input */ + ++ #ifndef NOFILEIO + o = SCOTCH_graphLoad (grafptr, stream, *baseptr, *flagptr); ++ #else /* NOFILEIO */ ++ o = SCOTCH_graphLoad (grafptr, stream, *baseptr, *flagptr, 0, 0, NULL, NULL, NULL, NULL, NULL); ++ #endif /* NOFILEIO */ + + fclose (stream); /* This closes filenum too */ + +diff -crB scotch_5.1/src/libscotch/library_graph_map.c src/src/libscotch/library_graph_map.c +*** scotch_5.1/src/libscotch/library_graph_map.c 2008-09-28 04:04:05.000000000 -0700 +--- src/src/libscotch/library_graph_map.c 2013-05-06 14:14:19.000000000 -0700 +*************** +*** 182,192 **** +--- 182,200 ---- + + int + SCOTCH_graphMapSave ( ++ #ifdef NOFILEIO ++ Gnum *pnvert, ++ Gnum (**pmaptab)[2], ++ #endif /* NOFILEIO */ + const SCOTCH_Graph * const grafptr, /*+ Graph to order +*/ + const SCOTCH_Mapping * const mappptr, /*+ Mapping to save +*/ + FILE * const stream) /*+ Output stream +*/ + { ++ #ifndef NOFILEIO + return (mapSave (&((LibMapping *) mappptr)->m, ((Graph *) grafptr)->vlbltax, stream)); ++ #else /* NOFILEIO */ ++ return (mapSave (pnvert, pmaptab, &((LibMapping *) mappptr)->m, ((Graph *) grafptr)->vlbltax, stream)); ++ #endif /* NOFILEIO */ + } + + /*+ This routine computes a mapping +diff -crB scotch_5.1/src/libscotch/library_graph_map_f.c src/src/libscotch/library_graph_map_f.c +*** scotch_5.1/src/libscotch/library_graph_map_f.c 2008-06-28 03:44:26.000000000 -0700 +--- src/src/libscotch/library_graph_map_f.c 2013-05-06 14:14:19.000000000 -0700 +*************** +*** 183,189 **** +--- 183,193 ---- + return; + } + ++ #ifndef NOFILEIO + o = SCOTCH_graphMapSave (grafptr, mapptr, stream); ++ #else /* NOFILEIO */ ++ o = SCOTCH_graphMapSave (NULL, NULL, grafptr, mapptr, stream); ++ #endif /* NOFILEIO */ + + fclose (stream); /* This closes filenum too */ + +diff -crB scotch_5.1/src/libscotch/library.h src/src/libscotch/library.h +*** scotch_5.1/src/libscotch/library.h 2009-05-09 16:08:03.000000000 -0700 +--- src/src/libscotch/library.h 2013-05-06 14:14:19.000000000 -0700 +*************** +*** 1,3 **** +--- 1,5 ---- ++ #ifndef _SCOTCH_H_ ++ #define _SCOTCH_H_ + /* Copyright 2004,2007-2009 ENSEIRB, INRIA & CNRS + ** + ** This file is part of the Scotch software package for static mapping, +*************** +*** 134,140 **** +--- 136,146 ---- + + int SCOTCH_archInit (SCOTCH_Arch * const); + void SCOTCH_archExit (SCOTCH_Arch * const); ++ #ifndef NOFILEIO + int SCOTCH_archLoad (SCOTCH_Arch * const, FILE * const); ++ #else /* NOFILEIO */ ++ int SCOTCH_archLoad (SCOTCH_Arch * const, FILE * const, const char *, const SCOTCH_Num, const SCOTCH_Num *); ++ #endif /* NOFILEIO */ + int SCOTCH_archSave (const SCOTCH_Arch * const, FILE * const); + int SCOTCH_archBuild (SCOTCH_Arch * const, const SCOTCH_Graph * const, const SCOTCH_Num, const SCOTCH_Num * const, const SCOTCH_Strat * const); + int SCOTCH_archCmplt (SCOTCH_Arch * const, const SCOTCH_Num); +*************** +*** 191,197 **** +--- 197,207 ---- + int SCOTCH_graphInit (SCOTCH_Graph * const); + void SCOTCH_graphExit (SCOTCH_Graph * const); + void SCOTCH_graphFree (SCOTCH_Graph * const); ++ #ifndef NOFILEIO + int SCOTCH_graphLoad (SCOTCH_Graph * const, FILE * const, const SCOTCH_Num, const SCOTCH_Num); ++ #else /* NOFILEIO */ ++ int SCOTCH_graphLoad (SCOTCH_Graph * const, FILE * const, const SCOTCH_Num, const SCOTCH_Num, const SCOTCH_Num, const SCOTCH_Num, const SCOTCH_Num *, const SCOTCH_Num *, const SCOTCH_Num *, const SCOTCH_Num *, const SCOTCH_Num *); ++ #endif /* NOFILEIO */ + int SCOTCH_graphSave (const SCOTCH_Graph * const, FILE * const); + int SCOTCH_graphBuild (SCOTCH_Graph * const, const SCOTCH_Num, const SCOTCH_Num, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num, const SCOTCH_Num * const, const SCOTCH_Num * const); + SCOTCH_Num SCOTCH_graphBase (SCOTCH_Graph * const, const SCOTCH_Num baseval); +*************** +*** 210,216 **** +--- 220,230 ---- + int SCOTCH_graphMapInit (const SCOTCH_Graph * const, SCOTCH_Mapping * const, const SCOTCH_Arch * const, SCOTCH_Num * const); + void SCOTCH_graphMapExit (const SCOTCH_Graph * const, SCOTCH_Mapping * const); + int SCOTCH_graphMapLoad (const SCOTCH_Graph * const, const SCOTCH_Mapping * const, FILE * const); ++ #ifndef NOFILEIO + int SCOTCH_graphMapSave (const SCOTCH_Graph * const, const SCOTCH_Mapping * const, FILE * const); ++ #else /* NOFILEIO */ ++ int SCOTCH_graphMapSave (SCOTCH_Num *, SCOTCH_Num (**)[2], const SCOTCH_Graph * const, const SCOTCH_Mapping * const, FILE * const); ++ #endif /* NOFILEIO */ + int SCOTCH_graphMapView (const SCOTCH_Graph * const, const SCOTCH_Mapping * const, FILE * const); + int SCOTCH_graphMapCompute (const SCOTCH_Graph * const, SCOTCH_Mapping * const, const SCOTCH_Strat * const); + int SCOTCH_graphMap (const SCOTCH_Graph * const, const SCOTCH_Arch * const, const SCOTCH_Strat * const, SCOTCH_Num * const); +*************** +*** 278,280 **** +--- 292,296 ---- + #ifdef __cplusplus + } + #endif /* __cplusplus */ ++ ++ #endif //#ifndef _SCOTCH_H_ +diff -crB scotch_5.1/src/libscotch/Makefile src/src/libscotch/Makefile +*** scotch_5.1/src/libscotch/Makefile 2009-05-09 16:08:04.000000000 -0700 +--- src/src/libscotch/Makefile 2013-05-06 14:14:19.000000000 -0700 +*************** +*** 49,55 **** + ## Project rules. + ## + +! .PHONY : ptscotch scotch ptinstall install clean realclean + + scotch : clean + $(MAKE) CC="$(CCS)" CCD="$(CCS)" SCOTCHLIB=scotch \ +--- 49,55 ---- + ## Project rules. + ## + +! .PHONY : ptscotch scotch nfioscotch mexscotch ptinstall install nfioinstall mexinstall clean realclean + + scotch : clean + $(MAKE) CC="$(CCS)" CCD="$(CCS)" SCOTCHLIB=scotch \ +*************** +*** 68,73 **** +--- 68,93 ---- + libptscotcherr$(LIB) \ + libptscotcherrexit$(LIB) + ++ nfioscotch : clean ++ $(MAKE) CFLAGS="$(CFLAGS)" CC="$(CCS)" CCD="$(CCS)" LDFLAGS="$(LDFLAGS)" SCOTCHLIB=scotch \ ++ dummysizes$(EXE) ++ $(MAKE) CFLAGS="$(CFLAGS) -DNOFILEIO" CC="$(CCS)" CCD="$(CCS)" SCOTCHLIB=nfioscotch \ ++ scotch.h \ ++ scotchf.h \ ++ libnfioscotch$(LIB) \ ++ libnfioscotcherr$(LIB) \ ++ libnfioscotcherrexit$(LIB) ++ ++ mexscotch : clean ++ $(MAKE) CFLAGS="$(CFLAGS)" CC="$(CCS)" CCD="$(CCS)" LDFLAGS="$(LDFLAGS)" SCOTCHLIB=scotch \ ++ dummysizes$(EXE) ++ $(MAKE) CFLAGS="$(CFLAGS) -DNOFILEIO -DMATLAB -I${MATLAB_DIR}/extern/include" CC="$(CCS)" CCD="$(CCS)" LDFLAGS="$(LDFLAGS) -Wl,-rpath-link,${MATLAB_DIR}/bin/glnxa64 -L${MATLAB_DIR}/bin/glnxa64 -lmex -lmat" SCOTCHLIB=mexscotch \ ++ scotch.h \ ++ scotchf.h \ ++ libmexscotch$(LIB) \ ++ libmexscotcherr$(LIB) \ ++ libmexscotcherrexit$(LIB) ++ + install : + -$(CP) scotch.h scotchf.h $(includedir) + -$(CP) libscotch$(LIB) libscotcherr*$(LIB) $(libdir) +*************** +*** 77,82 **** +--- 97,110 ---- + -$(CP) scotchf.h $(includedir)/ptscotchf.h + -$(CP) libptscotch*$(LIB) $(libdir) + ++ nfioinstall : ++ -$(CP) scotch.h scotchf.h $(includedir) ++ -$(CP) libnfioscotch$(LIB) libnfioscotcherr*$(LIB) $(libdir) ++ ++ mexinstall : ++ -$(CP) scotch.h scotchf.h $(includedir) ++ -$(CP) libmexscotch$(LIB) libmexscotcherr*$(LIB) $(libdir) ++ + clean : + -$(RM) *~ *$(OBJ) lib*$(LIB) common2* parser_yy.c parser_ly.h parser_ll.c *scotch.h *scotchf.h y.output dummysizes$(EXE) + +*************** +*** 2452,2457 **** +--- 2480,2807 ---- + $(AR) $(ARFLAGS) lib$(SCOTCHLIB)$(LIB) $(?) + -$(RANLIB) lib$(SCOTCHLIB)$(LIB) + ++ libnfioscotch$(LIB) : arch$(OBJ) \ ++ arch_build$(OBJ) \ ++ arch_cmplt$(OBJ) \ ++ arch_cmpltw$(OBJ) \ ++ arch_deco$(OBJ) \ ++ arch_hcub$(OBJ) \ ++ arch_mesh$(OBJ) \ ++ arch_tleaf$(OBJ) \ ++ arch_torus$(OBJ) \ ++ arch_vcmplt$(OBJ) \ ++ arch_vhcub$(OBJ) \ ++ bgraph$(OBJ) \ ++ bgraph_bipart_bd$(OBJ) \ ++ bgraph_bipart_df$(OBJ) \ ++ bgraph_bipart_ex$(OBJ) \ ++ bgraph_bipart_fm$(OBJ) \ ++ bgraph_bipart_gg$(OBJ) \ ++ bgraph_bipart_gp$(OBJ) \ ++ bgraph_bipart_ml$(OBJ) \ ++ bgraph_bipart_st$(OBJ) \ ++ bgraph_bipart_zr$(OBJ) \ ++ bgraph_check$(OBJ) \ ++ bgraph_store$(OBJ) \ ++ common$(OBJ) \ ++ common_file$(OBJ) \ ++ common_file_compress$(OBJ) \ ++ common_file_uncompress$(OBJ) \ ++ common_integer$(OBJ) \ ++ common_memory$(OBJ) \ ++ common_stub$(OBJ) \ ++ gain$(OBJ) \ ++ geom$(OBJ) \ ++ graph$(OBJ) \ ++ graph_base$(OBJ) \ ++ graph_check$(OBJ) \ ++ graph_coarsen$(OBJ) \ ++ graph_induce$(OBJ) \ ++ graph_io$(OBJ) \ ++ graph_io_chac$(OBJ) \ ++ graph_io_habo$(OBJ) \ ++ graph_io_mmkt$(OBJ) \ ++ graph_io_scot$(OBJ) \ ++ graph_list$(OBJ) \ ++ hall_order_hd$(OBJ) \ ++ hall_order_hf$(OBJ) \ ++ hall_order_hx$(OBJ) \ ++ hgraph$(OBJ) \ ++ hgraph_check$(OBJ) \ ++ hgraph_induce$(OBJ) \ ++ hgraph_order_bl$(OBJ) \ ++ hgraph_order_cp$(OBJ) \ ++ hgraph_order_gp$(OBJ) \ ++ hgraph_order_hd$(OBJ) \ ++ hgraph_order_hf$(OBJ) \ ++ hgraph_order_hx$(OBJ) \ ++ hgraph_order_nd$(OBJ) \ ++ hgraph_order_si$(OBJ) \ ++ hgraph_order_st$(OBJ) \ ++ hmesh$(OBJ) \ ++ hmesh_check$(OBJ) \ ++ hmesh_hgraph$(OBJ) \ ++ hmesh_induce$(OBJ) \ ++ hmesh_mesh$(OBJ) \ ++ hmesh_order_bl$(OBJ) \ ++ hmesh_order_cp$(OBJ) \ ++ hmesh_order_gr$(OBJ) \ ++ hmesh_order_gp$(OBJ) \ ++ hmesh_order_hd$(OBJ) \ ++ hmesh_order_hf$(OBJ) \ ++ hmesh_order_hx$(OBJ) \ ++ hmesh_order_nd$(OBJ) \ ++ hmesh_order_si$(OBJ) \ ++ hmesh_order_st$(OBJ) \ ++ kgraph$(OBJ) \ ++ kgraph_map_rb$(OBJ) \ ++ kgraph_map_rb_map$(OBJ) \ ++ kgraph_map_rb_part$(OBJ) \ ++ kgraph_map_st$(OBJ) \ ++ library_arch$(OBJ) \ ++ library_arch_f$(OBJ) \ ++ library_arch_build$(OBJ) \ ++ library_arch_build_f$(OBJ) \ ++ library_arch_cmpltw$(OBJ) \ ++ library_arch_cmpltw_f$(OBJ) \ ++ library_geom$(OBJ) \ ++ library_geom_f$(OBJ) \ ++ library_graph$(OBJ) \ ++ library_graph_f$(OBJ) \ ++ library_graph_base$(OBJ) \ ++ library_graph_base_f$(OBJ) \ ++ library_graph_check$(OBJ) \ ++ library_graph_check_f$(OBJ) \ ++ library_graph_io_chac$(OBJ) \ ++ library_graph_io_chac_f$(OBJ) \ ++ library_graph_io_habo$(OBJ) \ ++ library_graph_io_habo_f$(OBJ) \ ++ library_graph_io_mmkt$(OBJ) \ ++ library_graph_io_mmkt_f$(OBJ) \ ++ library_graph_io_scot$(OBJ) \ ++ library_graph_io_scot_f$(OBJ) \ ++ library_graph_map$(OBJ) \ ++ library_graph_map_f$(OBJ) \ ++ library_graph_map_view$(OBJ) \ ++ library_graph_map_view_f$(OBJ) \ ++ library_graph_order$(OBJ) \ ++ library_graph_order_f$(OBJ) \ ++ library_mesh$(OBJ) \ ++ library_mesh_f$(OBJ) \ ++ library_mesh_graph$(OBJ) \ ++ library_mesh_graph_f$(OBJ) \ ++ library_mesh_io_habo$(OBJ) \ ++ library_mesh_io_habo_f$(OBJ) \ ++ library_mesh_io_scot$(OBJ) \ ++ library_mesh_io_scot_f$(OBJ) \ ++ library_mesh_order$(OBJ) \ ++ library_mesh_order_f$(OBJ) \ ++ library_parser$(OBJ) \ ++ library_parser_f$(OBJ) \ ++ library_random$(OBJ) \ ++ library_random_f$(OBJ) \ ++ mapping$(OBJ) \ ++ mapping_io$(OBJ) \ ++ mesh$(OBJ) \ ++ mesh_check$(OBJ) \ ++ mesh_coarsen$(OBJ) \ ++ mesh_graph$(OBJ) \ ++ mesh_induce_sepa$(OBJ) \ ++ mesh_io$(OBJ) \ ++ mesh_io_habo$(OBJ) \ ++ mesh_io_scot$(OBJ) \ ++ order$(OBJ) \ ++ order_check$(OBJ) \ ++ order_io$(OBJ) \ ++ parser$(OBJ) \ ++ parser_ll$(OBJ) \ ++ parser_yy$(OBJ) \ ++ vgraph$(OBJ) \ ++ vgraph_check$(OBJ) \ ++ vgraph_separate_bd$(OBJ) \ ++ vgraph_separate_es$(OBJ) \ ++ vgraph_separate_fm$(OBJ) \ ++ vgraph_separate_gg$(OBJ) \ ++ vgraph_separate_gp$(OBJ) \ ++ vgraph_separate_ml$(OBJ) \ ++ vgraph_separate_st$(OBJ) \ ++ vgraph_separate_th$(OBJ) \ ++ vgraph_separate_vw$(OBJ) \ ++ vgraph_separate_zr$(OBJ) \ ++ vgraph_store$(OBJ) \ ++ vmesh$(OBJ) \ ++ vmesh_check$(OBJ) \ ++ vmesh_separate_fm$(OBJ) \ ++ vmesh_separate_gg$(OBJ) \ ++ vmesh_separate_gr$(OBJ) \ ++ vmesh_separate_ml$(OBJ) \ ++ vmesh_separate_zr$(OBJ) \ ++ vmesh_separate_st$(OBJ) \ ++ vmesh_store$(OBJ) ++ $(AR) $(ARFLAGS) lib$(SCOTCHLIB)$(LIB) $(?) ++ -$(RANLIB) lib$(SCOTCHLIB)$(LIB) ++ ++ libmexscotch$(LIB) : arch$(OBJ) \ ++ arch_build$(OBJ) \ ++ arch_cmplt$(OBJ) \ ++ arch_cmpltw$(OBJ) \ ++ arch_deco$(OBJ) \ ++ arch_hcub$(OBJ) \ ++ arch_mesh$(OBJ) \ ++ arch_tleaf$(OBJ) \ ++ arch_torus$(OBJ) \ ++ arch_vcmplt$(OBJ) \ ++ arch_vhcub$(OBJ) \ ++ bgraph$(OBJ) \ ++ bgraph_bipart_bd$(OBJ) \ ++ bgraph_bipart_df$(OBJ) \ ++ bgraph_bipart_ex$(OBJ) \ ++ bgraph_bipart_fm$(OBJ) \ ++ bgraph_bipart_gg$(OBJ) \ ++ bgraph_bipart_gp$(OBJ) \ ++ bgraph_bipart_ml$(OBJ) \ ++ bgraph_bipart_st$(OBJ) \ ++ bgraph_bipart_zr$(OBJ) \ ++ bgraph_check$(OBJ) \ ++ bgraph_store$(OBJ) \ ++ common$(OBJ) \ ++ common_file$(OBJ) \ ++ common_file_compress$(OBJ) \ ++ common_file_uncompress$(OBJ) \ ++ common_integer$(OBJ) \ ++ common_memory$(OBJ) \ ++ common_stub$(OBJ) \ ++ gain$(OBJ) \ ++ geom$(OBJ) \ ++ graph$(OBJ) \ ++ graph_base$(OBJ) \ ++ graph_check$(OBJ) \ ++ graph_coarsen$(OBJ) \ ++ graph_induce$(OBJ) \ ++ graph_io$(OBJ) \ ++ graph_io_chac$(OBJ) \ ++ graph_io_habo$(OBJ) \ ++ graph_io_mmkt$(OBJ) \ ++ graph_io_scot$(OBJ) \ ++ graph_list$(OBJ) \ ++ hall_order_hd$(OBJ) \ ++ hall_order_hf$(OBJ) \ ++ hall_order_hx$(OBJ) \ ++ hgraph$(OBJ) \ ++ hgraph_check$(OBJ) \ ++ hgraph_induce$(OBJ) \ ++ hgraph_order_bl$(OBJ) \ ++ hgraph_order_cp$(OBJ) \ ++ hgraph_order_gp$(OBJ) \ ++ hgraph_order_hd$(OBJ) \ ++ hgraph_order_hf$(OBJ) \ ++ hgraph_order_hx$(OBJ) \ ++ hgraph_order_nd$(OBJ) \ ++ hgraph_order_si$(OBJ) \ ++ hgraph_order_st$(OBJ) \ ++ hmesh$(OBJ) \ ++ hmesh_check$(OBJ) \ ++ hmesh_hgraph$(OBJ) \ ++ hmesh_induce$(OBJ) \ ++ hmesh_mesh$(OBJ) \ ++ hmesh_order_bl$(OBJ) \ ++ hmesh_order_cp$(OBJ) \ ++ hmesh_order_gr$(OBJ) \ ++ hmesh_order_gp$(OBJ) \ ++ hmesh_order_hd$(OBJ) \ ++ hmesh_order_hf$(OBJ) \ ++ hmesh_order_hx$(OBJ) \ ++ hmesh_order_nd$(OBJ) \ ++ hmesh_order_si$(OBJ) \ ++ hmesh_order_st$(OBJ) \ ++ kgraph$(OBJ) \ ++ kgraph_map_rb$(OBJ) \ ++ kgraph_map_rb_map$(OBJ) \ ++ kgraph_map_rb_part$(OBJ) \ ++ kgraph_map_st$(OBJ) \ ++ library_arch$(OBJ) \ ++ library_arch_f$(OBJ) \ ++ library_arch_build$(OBJ) \ ++ library_arch_build_f$(OBJ) \ ++ library_arch_cmpltw$(OBJ) \ ++ library_arch_cmpltw_f$(OBJ) \ ++ library_geom$(OBJ) \ ++ library_geom_f$(OBJ) \ ++ library_graph$(OBJ) \ ++ library_graph_f$(OBJ) \ ++ library_graph_base$(OBJ) \ ++ library_graph_base_f$(OBJ) \ ++ library_graph_check$(OBJ) \ ++ library_graph_check_f$(OBJ) \ ++ library_graph_io_chac$(OBJ) \ ++ library_graph_io_chac_f$(OBJ) \ ++ library_graph_io_habo$(OBJ) \ ++ library_graph_io_habo_f$(OBJ) \ ++ library_graph_io_mmkt$(OBJ) \ ++ library_graph_io_mmkt_f$(OBJ) \ ++ library_graph_io_scot$(OBJ) \ ++ library_graph_io_scot_f$(OBJ) \ ++ library_graph_map$(OBJ) \ ++ library_graph_map_f$(OBJ) \ ++ library_graph_map_view$(OBJ) \ ++ library_graph_map_view_f$(OBJ) \ ++ library_graph_order$(OBJ) \ ++ library_graph_order_f$(OBJ) \ ++ library_mesh$(OBJ) \ ++ library_mesh_f$(OBJ) \ ++ library_mesh_graph$(OBJ) \ ++ library_mesh_graph_f$(OBJ) \ ++ library_mesh_io_habo$(OBJ) \ ++ library_mesh_io_habo_f$(OBJ) \ ++ library_mesh_io_scot$(OBJ) \ ++ library_mesh_io_scot_f$(OBJ) \ ++ library_mesh_order$(OBJ) \ ++ library_mesh_order_f$(OBJ) \ ++ library_parser$(OBJ) \ ++ library_parser_f$(OBJ) \ ++ library_random$(OBJ) \ ++ library_random_f$(OBJ) \ ++ mapping$(OBJ) \ ++ mapping_io$(OBJ) \ ++ mesh$(OBJ) \ ++ mesh_check$(OBJ) \ ++ mesh_coarsen$(OBJ) \ ++ mesh_graph$(OBJ) \ ++ mesh_induce_sepa$(OBJ) \ ++ mesh_io$(OBJ) \ ++ mesh_io_habo$(OBJ) \ ++ mesh_io_scot$(OBJ) \ ++ order$(OBJ) \ ++ order_check$(OBJ) \ ++ order_io$(OBJ) \ ++ parser$(OBJ) \ ++ parser_ll$(OBJ) \ ++ parser_yy$(OBJ) \ ++ vgraph$(OBJ) \ ++ vgraph_check$(OBJ) \ ++ vgraph_separate_bd$(OBJ) \ ++ vgraph_separate_es$(OBJ) \ ++ vgraph_separate_fm$(OBJ) \ ++ vgraph_separate_gg$(OBJ) \ ++ vgraph_separate_gp$(OBJ) \ ++ vgraph_separate_ml$(OBJ) \ ++ vgraph_separate_st$(OBJ) \ ++ vgraph_separate_th$(OBJ) \ ++ vgraph_separate_vw$(OBJ) \ ++ vgraph_separate_zr$(OBJ) \ ++ vgraph_store$(OBJ) \ ++ vmesh$(OBJ) \ ++ vmesh_check$(OBJ) \ ++ vmesh_separate_fm$(OBJ) \ ++ vmesh_separate_gg$(OBJ) \ ++ vmesh_separate_gr$(OBJ) \ ++ vmesh_separate_ml$(OBJ) \ ++ vmesh_separate_zr$(OBJ) \ ++ vmesh_separate_st$(OBJ) \ ++ vmesh_store$(OBJ) ++ $(AR) $(ARFLAGS) lib$(SCOTCHLIB)$(LIB) $(?) ++ -$(RANLIB) lib$(SCOTCHLIB)$(LIB) ++ + libptscotcherr$(LIB) : library_error$(OBJ) + $(AR) $(ARFLAGS) $(@) $(?) + -$(RANLIB) $(@) +*************** +*** 2467,2469 **** +--- 2817,2835 ---- + libscotcherrexit$(LIB) : library_error_exit$(OBJ) + $(AR) $(ARFLAGS) $(@) $(?) + -$(RANLIB) $(@) ++ ++ libnfioscotcherr$(LIB) : library_error$(OBJ) ++ $(AR) $(ARFLAGS) $(@) $(?) ++ -$(RANLIB) $(@) ++ ++ libnfioscotcherrexit$(LIB) : library_error_exit$(OBJ) ++ $(AR) $(ARFLAGS) $(@) $(?) ++ -$(RANLIB) $(@) ++ ++ libmexscotcherr$(LIB) : library_error$(OBJ) ++ $(AR) $(ARFLAGS) $(@) $(?) ++ -$(RANLIB) $(@) ++ ++ libmexscotcherrexit$(LIB) : library_error_exit$(OBJ) ++ $(AR) $(ARFLAGS) $(@) $(?) ++ -$(RANLIB) $(@) +diff -crB scotch_5.1/src/libscotch/mapping.h src/src/libscotch/mapping.h +*** scotch_5.1/src/libscotch/mapping.h 2008-10-27 08:27:47.000000000 -0700 +--- src/src/libscotch/mapping.h 2013-05-06 14:14:20.000000000 -0700 +*************** +*** 106,112 **** +--- 106,116 ---- + int mapInit2 (Mapping * restrict const, const Gnum, const Gnum, const Arch * restrict const, const ArchDom * restrict const); + void mapExit (Mapping * const); + int mapLoad (Mapping * restrict const, const Gnum * restrict const, FILE * restrict const); ++ #ifndef NOFILEIO + int mapSave (const Mapping * restrict const, const Gnum * restrict const, FILE * restrict const); ++ #else /* NOFILEIO */ ++ int mapSave (Gnum *, Gnum (**)[2], const Mapping * restrict const, const Gnum * restrict const, FILE * restrict const); ++ #endif /* NOFILEIO */ + int mapView (const Mapping * restrict const, const Graph * restrict const, FILE * const); + + #undef static +diff -crB scotch_5.1/src/libscotch/mapping_io.c src/src/libscotch/mapping_io.c +*** scotch_5.1/src/libscotch/mapping_io.c 2008-05-22 06:44:43.000000000 -0700 +--- src/src/libscotch/mapping_io.c 2013-05-06 14:14:20.000000000 -0700 +*************** +*** 199,204 **** +--- 199,208 ---- + + int + mapSave ( ++ #ifdef NOFILEIO ++ Gnum *pnvert, ++ Gnum (**pmaptab)[2], ++ #endif /* NOFILEIO */ + const Mapping * restrict const mappptr, + const Gnum * restrict const vlbltab, + FILE * restrict const stream) +*************** +*** 206,226 **** + const Gnum * restrict vlbltax; + Gnum vertnum; + + vlbltax = (vlbltab != NULL) ? (vlbltab - mappptr->baseval) : NULL; + + if (fprintf (stream, "%ld\n", (long) mappptr->vertnbr) == EOF) { + errorPrint ("mapSave: bad output (1)"); + return (1); + } + + for (vertnum = mappptr->baseval; vertnum < (mappptr->vertnbr + mappptr->baseval); vertnum ++) { + if (fprintf (stream, "%ld\t%ld\n", +! (long) ((vlbltax != NULL) ? vlbltax[vertnum] : vertnum), + (long) archDomNum (&mappptr->archdat, &mappptr->domntab[mappptr->parttax[vertnum]])) == EOF) { + errorPrint ("mapSave: bad output (2)"); + return (1); + } + } + + return (0); + } +--- 210,258 ---- + const Gnum * restrict vlbltax; + Gnum vertnum; + ++ #ifdef NOFILEIO ++ // printf("mapSave - stream=%p\n",stream); ++ #endif /* NOFILEIO */ + vlbltax = (vlbltab != NULL) ? (vlbltab - mappptr->baseval) : NULL; + ++ #ifndef NOFILEIO + if (fprintf (stream, "%ld\n", (long) mappptr->vertnbr) == EOF) { + errorPrint ("mapSave: bad output (1)"); + return (1); + } ++ #else /* NOFILEIO */ ++ if (pnvert) { ++ *pnvert=mappptr->vertnbr; ++ // printf("mapSave - nvert=%d\n",*pnvert); ++ } ++ if (pmaptab) { ++ *pmaptab = (Gnum (*)[2]) malloc(mappptr->vertnbr*2*sizeof(Gnum)); ++ // printf("mapSave - maptab=%p\n",*pmaptab); ++ } ++ #endif /* NOFILEIO */ + ++ #ifndef NOFILEIO + for (vertnum = mappptr->baseval; vertnum < (mappptr->vertnbr + mappptr->baseval); vertnum ++) { + if (fprintf (stream, "%ld\t%ld\n", +! /* not sure why, but need to offset vlbltax in other direction (jes, 12/11/09) */ +! // (long) ((vlbltax != NULL) ? vlbltax[vertnum] : vertnum), +! (long) ((vlbltax != NULL) ? vlbltax[vertnum+mappptr->baseval] : vertnum), + (long) archDomNum (&mappptr->archdat, &mappptr->domntab[mappptr->parttax[vertnum]])) == EOF) { + errorPrint ("mapSave: bad output (2)"); + return (1); + } + } ++ #else /* NOFILEIO */ ++ if (pmaptab && *pmaptab) ++ for (vertnum = mappptr->baseval; vertnum < (mappptr->vertnbr + mappptr->baseval); vertnum ++) { ++ /* not sure why, but need to offset vlbltax in other direction (jes, 12/11/09) */ ++ // (*pmaptab)[vertnum-mappptr->baseval][0]=((vlbltax != NULL) ? vlbltax[vertnum] : vertnum); ++ (*pmaptab)[vertnum-mappptr->baseval][0]=((vlbltax != NULL) ? vlbltax[vertnum+mappptr->baseval] : vertnum); ++ (*pmaptab)[vertnum-mappptr->baseval][1]=archDomNum (&mappptr->archdat, &mappptr->domntab[mappptr->parttax[vertnum]]); ++ // printf("mapSave - vertnum=%d; vlbltax=%d,archDomNum=%d\n", ++ // vertnum,((vlbltax != NULL) ? vlbltax[vertnum+mappptr->baseval] : -1),archDomNum (&mappptr->archdat, &mappptr->domntab[mappptr->parttax[vertnum]])); ++ } ++ #endif /* NOFILEIO */ + + return (0); + } +diff -crB scotch_5.1/src/libscotch/mesh_io_scot.c src/src/libscotch/mesh_io_scot.c +*** scotch_5.1/src/libscotch/mesh_io_scot.c 2008-05-22 06:44:43.000000000 -0700 +--- src/src/libscotch/mesh_io_scot.c 2013-05-06 14:14:20.000000000 -0700 +*************** +*** 85,91 **** +--- 85,95 ---- + int o; + + if (filesrcptr != NULL) { ++ #ifndef NOFILEIO + if (graphLoad (meshptr, filesrcptr, -1, 0) != 0) ++ #else /* NOFILEIO */ ++ if (graphLoad (meshptr, filesrcptr, -1, 0, 0, 0, NULL, NULL, NULL, NULL, NULL) != 0) ++ #endif /* NOFILEIO */ + return (1); + } + +diff -crB scotch_5.1/src/libscotch/module.h src/src/libscotch/module.h +*** scotch_5.1/src/libscotch/module.h 2009-04-26 23:07:14.000000000 -0700 +--- src/src/libscotch/module.h 2013-05-06 14:14:20.000000000 -0700 +*************** +*** 1,3 **** +--- 1,5 ---- ++ #ifndef _SCOTCH_MODULE_H_ ++ #define _SCOTCH_MODULE_H_ + /* Copyright 2004,2007-2009 ENSEIRB, INRIA & CNRS + ** + ** This file is part of the Scotch software package for static mapping, +*************** +*** 55,60 **** +--- 57,65 ---- + + #define MODULE_H + ++ /*Don't forget stdint.h:*/ ++ #include "stdint.h" ++ + /* + ** Collective communication handling. + */ +*************** +*** 156,161 **** +--- 161,167 ---- + #define intSave _SCOTCHintSave + #define intAscn _SCOTCHintAscn + #define intPerm _SCOTCHintPerm ++ #define intRandResetStatic _SCOTCHintRandResetStatic + #define intRandReset _SCOTCHintRandReset + #define intRandInit _SCOTCHintRandInit + /* #define intRandVal _SCOTCHintRandVal Already a macro */ +*************** +*** 681,683 **** +--- 687,691 ---- + #define vmeshStoreSave _SCOTCHvmeshStoreSave + #define vmeshStoreUpdt _SCOTCHvmeshStoreUpdt + #endif /* SCOTCH_RENAME */ ++ ++ #endif //#ifndef _SCOTCH_MODULE_H_ +diff -crB scotch_5.1/src/libscotch/parser_ll.l src/src/libscotch/parser_ll.l +*** scotch_5.1/src/libscotch/parser_ll.l 2008-05-22 06:44:43.000000000 -0700 +--- src/src/libscotch/parser_ll.l 2013-05-06 14:14:21.000000000 -0700 +*************** +*** 192,197 **** +--- 192,214 ---- + stratParserInit ( + const char * const string) /*+ Strategy string to parse +*/ + { ++ /* reset static variables from previous runs (jes, 4/29/10) */ ++ yy_current_buffer = 0; ++ yy_hold_char = (char) 0; ++ yy_n_chars=0; /* number of characters read into yy_ch_buf */ ++ yy_c_buf_p = (char *) 0; ++ yy_init = 1; /* whether we need to initialize */ ++ yy_start = 0; /* start state number */ ++ yy_did_buffer_switch_on_eof=0; ++ yy_last_accepting_state=0; ++ yy_last_accepting_cpos = (char *) 0; ++ stratparserstringptr = (char *) 0; /* Pointer to the string to parse */ ++ #if YY_STACK_USED ++ yy_start_stack_ptr = 0; ++ yy_start_stack_depth = 0; ++ yy_start_stack = 0; ++ #endif ++ + #ifdef FLEX_SCANNER + yyrestart (yyin); /* (Re-)initialize the parser */ + #endif /* FLEX_SCANNER */ +diff -crB scotch_5.1/src/libscotch/parser_yy.y src/src/libscotch/parser_yy.y +*** scotch_5.1/src/libscotch/parser_yy.y 2008-10-22 15:12:48.000000000 -0700 +--- src/src/libscotch/parser_yy.y 2013-05-06 14:14:21.000000000 -0700 +*************** +*** 774,779 **** +--- 774,780 ---- + stratParserInit (string); /* Initialize the lexical parser */ + parserstrattab = strattab; /* Point to the parsing tables */ + parserstratcurr = NULL; /* Clear up the temporary strategy pointer */ ++ parserparamcurr = NULL; /* reset the last static (jes, 4/29/10) */ + + if (stratParserParse2 () != 0) { /* Parse the strategy string */ + if (parserstratcurr != NULL) +diff -crB scotch_5.1/src/libscotch/vgraph_separate_vw.c src/src/libscotch/vgraph_separate_vw.c +*** scotch_5.1/src/libscotch/vgraph_separate_vw.c 2008-05-22 06:44:43.000000000 -0700 +--- src/src/libscotch/vgraph_separate_vw.c 2013-05-06 14:14:21.000000000 -0700 +*************** +*** 83,88 **** +--- 83,89 ---- + FILE * restrict fileptr; + Gnum vertnum; /* Vertex number */ + ++ printf("vgraphSeparateVw begin -- vgraphseparatevwfilenum=%d\n",vgraphseparatevwfilenum); + sprintf (nametab, "vgraphseparatevw_output_%08d.map", vgraphseparatevwfilenum ++); + if ((fileptr = fopen (nametab, "w+")) == NULL) { + errorPrint ("vgraphSeparateVw: cannot open partition file"); +*************** +*** 102,106 **** +--- 103,108 ---- + } + } + ++ printf("vgraphSeparateVw end -- vgraphseparatevwfilenum=%d\n",vgraphseparatevwfilenum); + return (0); + } +diff -crB scotch_5.1/src/Makefile src/src/Makefile +*** scotch_5.1/src/Makefile 2008-09-15 05:50:51.000000000 -0700 +--- src/src/Makefile 2013-05-06 14:14:21.000000000 -0700 +*************** +*** 97,102 **** +--- 97,109 ---- + (cd scotch ; $(MAKE) VERSION=\"$(VERSION)\" ptscotch && $(MAKE) ptinstall) + (cd libscotchmetis ; $(MAKE) ptscotch && $(MAKE) ptinstall) + ++ nfioscotch : required ++ (cd libscotch ; $(MAKE) VERSION=\"$(VERSION)\" nfioscotch && $(MAKE) nfioinstall) ++ ++ mexscotch : required ++ (cd libscotch ; $(MAKE) VERSION=\"$(VERSION)\" mexscotch && $(MAKE) mexinstall) ++ (cd scotch ; $(MAKE) VERSION=\"$(VERSION)\" mexscotch && $(MAKE) mexinstall) ++ + install : required $(bindir) $(includedir) $(libdir) $(mandir)/man1 + -$(CP) -f ../bin/[agm]*$(EXE) $(bindir) + -$(CP) -f ../include/*scotch*.h $(includedir) +Only in src/src: Makefile.inc +diff -crB scotch_5.1/src/scotch/gmap.h src/src/scotch/gmap.h +*** scotch_5.1/src/scotch/gmap.h 2008-06-18 11:05:17.000000000 -0700 +--- src/src/scotch/gmap.h 2013-05-06 14:14:22.000000000 -0700 +*************** +*** 1,3 **** +--- 1,5 ---- ++ #ifndef _SCOTCH_GMAP_H_ ++ #define _SCOTCH_GMAP_H_ + /* Copyright 2004,2007,2008 ENSEIRB, INRIA & CNRS + ** + ** This file is part of the Scotch software package for static mapping, +*************** +*** 87,89 **** +--- 89,93 ---- + #define C_FLAGVERBSTR 0x0002 /* Verbose flags */ + #define C_FLAGVERBTIM 0x0004 + #define C_FLAGVERBMAP 0x0008 ++ ++ #endif //#ifndef _SCOTCH_GMAP_H_ +Only in src/src/scotch: gmap_mex.c +Only in src/src/scotch: gmapx.c +diff -crB scotch_5.1/src/scotch/Makefile src/src/scotch/Makefile +*** scotch_5.1/src/scotch/Makefile 2009-04-27 02:19:43.000000000 -0700 +--- src/src/scotch/Makefile 2013-05-06 14:14:22.000000000 -0700 +*************** +*** 49,59 **** + %$(EXE) : %.c + $(CC) $(CFLAGS) -I$(includedir) -I../libscotch -DSCOTCH_VERSION=\"$(VERSION)\" $(<) -o $(@) -L$(libdir) -l$(SCOTCHLIB) -l$(SCOTCHLIB)errexit $(LDFLAGS) + + ## + ## Project rules. + ## + +! .PHONY : ptscotch scotch ptinstall install clean realclean + + scotch : clean + $(MAKE) CC="$(CCS)" SCOTCHLIB=scotch \ +--- 49,62 ---- + %$(EXE) : %.c + $(CC) $(CFLAGS) -I$(includedir) -I../libscotch -DSCOTCH_VERSION=\"$(VERSION)\" $(<) -o $(@) -L$(libdir) -l$(SCOTCHLIB) -l$(SCOTCHLIB)errexit $(LDFLAGS) + ++ %$(MEX) : %.c ++ $(CCM) $(MFLAGS) -I$(includedir) -I../libscotch -DSCOTCH_VERSION=\"$(VERSION)\" $(<) -o $(@) -L$(libdir) -l$(SCOTCHLIB) -l$(SCOTCHLIB)errexit $(LDFLAGS) ++ + ## + ## Project rules. + ## + +! .PHONY : ptscotch scotch mexscotch ptinstall install mexinstall clean realclean + + scotch : clean + $(MAKE) CC="$(CCS)" SCOTCHLIB=scotch \ +*************** +*** 94,99 **** +--- 97,108 ---- + dgscat$(EXE) \ + dgtst$(EXE) + ++ mexscotch : clean ++ $(MAKE) CFLAGS="$(CFLAGS) -DNOFILEIO -DMATLAB -I${MATLAB_DIR}/extern/include" CC="$(CCS)" CCD="$(CCS)" LDFLAGS="$(LDFLAGS) -Wl,-rpath-link,${MATLAB_DIR}/bin/glnxa64 -L${MATLAB_DIR}/bin/glnxa64 -lmex -lmat" SCOTCHLIB=mexscotch \ ++ gmapx$(OBJ) ++ $(MAKE) CFLAGS="$(CFLAGS) -DNOFILEIO -DMATLAB -I${MATLAB_DIR}/extern/include" CC="$(CCS)" LDFLAGS="$(LDFLAGS) -Wl,-rpath-link,${MATLAB_DIR}/bin/glnxa64 -L${MATLAB_DIR}/bin/glnxa64 -lmex -lmat gmapx$(OBJ)" SCOTCHLIB=mexscotch \ ++ gmap_mex$(MEX) ++ + install : + -$(CP) acpl$(EXE) amk_ccc$(EXE) amk_fft2$(EXE) amk_grf$(EXE) amk_hy$(EXE) amk_m2$(EXE) amk_p2$(EXE) atst$(EXE) gbase$(EXE) gcv$(EXE) gmap$(EXE) gmk_hy$(EXE) gmk_m2$(EXE) gmk_m3$(EXE) gmk_msh$(EXE) gmk_ub2$(EXE) gmtst$(EXE) gord$(EXE) gotst$(EXE) gout$(EXE) *gtst$(EXE) gscat$(EXE) mcv$(EXE) mmk_m2$(EXE) mmk_m3$(EXE) mord$(EXE) mtst$(EXE) $(bindir) + -$(RM) $(bindir)/gpart$(EXE) +*************** +*** 104,111 **** +--- 113,126 ---- + -$(RM) $(bindir)/dgpart$(EXE) + -$(LN) $(bindir)/dgmap$(EXE) $(bindir)/dgpart$(EXE) + ++ mexinstall : ++ -$(CP) gmap_mex$(MEX) $(bindir) ++ -$(RM) $(bindir)/gpart_mex$(MEX) ++ -$(LN) $(bindir)/gmap_mex$(MEX) $(bindir)/gpart_mex$(MEX) ++ + clean : + -$(RM) *~ *$(OBJ) acpl$(EXE) amk_ccc$(EXE) amk_fft2$(EXE) amk_grf$(EXE) amk_hy$(EXE) amk_m2$(EXE) amk_p2$(EXE) atst$(EXE) gbase$(EXE) gcv$(EXE) *gmap$(EXE) gmk_hy$(EXE) gmk_m2$(EXE) gmk_m3$(EXE) gmk_msh$(EXE) gmk_ub2$(EXE) gmtst$(EXE) *gord$(EXE) gotst$(EXE) gout$(EXE) *gpart$(EXE) *gscat$(EXE) *gtst$(EXE) mcv$(EXE) mmk_m2$(EXE) mmk_m3$(EXE) mord$(EXE) mtst$(EXE) ++ -$(RM) gmap_mex$(MEX) + + realclean : clean + +*************** +*** 365,367 **** +--- 380,403 ---- + $(libdir)/libscotch$(LIB) \ + $(libdir)/libscotcherrexit$(LIB) \ + mtst.h ++ ++ gmapx$(OBJ) : gmapx.c \ ++ ../libscotch/module.h \ ++ ../libscotch/common.h \ ++ $(includedir)/scotch.h \ ++ $(libdir)/libmexscotch$(LIB) \ ++ $(libdir)/libmexscotcherrexit$(LIB) \ ++ gmap.h ++ ++ gmap_mex$(MEX) : gmap_mex.c \ ++ ../libscotch/module.h \ ++ ../libscotch/common.h \ ++ $(includedir)/scotch.h \ ++ $(libdir)/libmexscotch$(LIB) \ ++ $(libdir)/libmexscotcherrexit$(LIB) \ ++ gmap.h ++ ++ gpart_mex$(MEX) : gmap_mex$(MEX) ++ -$(RM) gpart_mex$(MEX) ++ -$(LN) gmap_mex$(MEX) gpart_mex$(MEX) ++ Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/scotch_README.txt =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/scotch_README.txt (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/scotch_README.txt (revision 18231) @@ -0,0 +1,296 @@ +8/06/09: + +following INSTALL.txt: +- GNU Make 3.81, lex, yacc all present + + +[jschierm@astrid src]$ diff Makefile_old.inc Makefile.inc + +- started with Makefile.inc.i686_sun_solaris5 +- changed CCS from cc to gcc +- removed SCOTCH_PTHREAD, since MPICH2 1.0.2p1 is prior to 1.0.7 +- added -std=c99 to CFLAGS for "restrict" attribute (based on various internet pages) +- added -DCOMMON_TIMING_OLD to CFLAGS for undeclared CLOCK_REALTIME (based on common2.c) +- added MEX, CCM, and MFLAGS for Matlab mex modules (as well as Matlab libraries and -largeArrayDims) +- removed -DCOMMON_PTHREAD from CFLAGS and MFLAGS to eliminate fatal exception at pthread_exit in gmap_mex.c +- removed -DCOMMON_FILE_COMPRESS_GZ from CFLAGS and MFLAGS since gzip not used +- added -Wl,-rpath-link,/usr/local/pkgs/matlab-7.6/bin/glnxa64 to LDFLAGS to eliminate missing libhdf5.so.0 in Matlab directories (based on Cielo make) + +3a4 +> MEX = .mexa64 +12,13c13,16 +< CFLAGS = -m64 -O3 -std=c99 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Du_int32_t=uint32_t -Du_int64_t=uint64_t -DINTSIZE64 -Dintptr_t="long int" -DCOMMON_TIMING_OLD +< LDFLAGS = -lz -lm -lrt +--- +> CCM = mex +> CFLAGS = -m64 -O3 -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Du_int32_t=uint32_t -Du_int64_t=uint64_t -DCOMMON_TIMING_OLD -DMATLAB -fPIC -I/usr/local/pkgs/matlab-7.6/extern/include +> LDFLAGS = -lz -lm -lrt -Wl,-rpath-link,/usr/local/pkgs/matlab-7.6/bin/glnxa64 -L/usr/local/pkgs/matlab-7.6/bin/glnxa64 -lmex -lmat +> MFLAGS = -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Du_int32_t=uint32_t -Du_int64_t=uint64_t -DCOMMON_TIMING_OLD -DMATLAB -I/usr/local/pkgs/matlab-7.6/extern/include -largeArrayDims + + +[jschierm@astrid libscotch]$ diff common_old.c common.c + +- redirect usagePrint to within Matlab +102a103 +> #ifndef MATLAB +105a107,111 +> #else /* MATLAB */ +> mexPrintf ("Usage is:\n"); +> for (cptr = data; *cptr != NULL; cptr ++) +> mexPrintf (" %s\n", *cptr); +> #endif /* MATLAB */ + + +[jschierm@astrid libscotch]$ diff common_old.h common.h + +- fix undeclared type intptr_t +68a69 +> #include /* added for intptr_t */ + +- for running as a matlab mex function +- add macro for fprintf to capture missing output +- fix exits to exit within Matlab +90a92,105 +> #ifdef MATLAB +> #include "mat.h" +> #include "mex.h" +> #include "matrix.h" +> +> #define printf mexPrintf +> #define fprintf(file,...) (file == stdout || file == stderr ? mexPrintf(__VA_ARGS__) : fprintf(file,__VA_ARGS__)) +> #define malloc mxMalloc +> #define calloc mxCalloc +> #define realloc mxRealloc +> #define free mxFree +> #define exit(status) mexErrMsgTxt("exit=" #status) +> #endif +> + + +[jschierm@astrid libscotch]$ diff dummysizes_old.c dummysizes.c + +- dummysizes must run by itself during compilation and exit cleanly +269a270 +> #ifndef MATLAB +270a272 +> #endif /* MATLAB */ + + +[jschierm@astrid libscotch]$ diff library_error_exit_old.c library_error_exit.c + +- redirect errorPrint and errorPrintW to within Matlab +116a117 +> #ifndef MATLAB +133a135,152 +> #else /* MATLAB */ +> mexPrintf ("%s", _SCOTCHerrorProgName); +> #ifdef SCOTCH_PTSCOTCH +> if ((MPI_Initialized (&proclocnum) == MPI_SUCCESS) && +> (proclocnum != 0) && +> (MPI_Comm_rank (MPI_COMM_WORLD, &proclocnum) == MPI_SUCCESS)) +> mexPrintf ("(%d): ", proclocnum); +> #else /* SCOTCH_PTSCOTCH */ +> if (_SCOTCHerrorProgName[0] != '\0') +> mexPrintf (": "); +> #endif /* SCOTCH_PTSCOTCH */ +> mexPrintf ("ERROR: "); +> va_start (errlist, errstr); +> mexPrintf (errstr, errlist); /* Print arguments */ +> va_end (errlist); +> mexPrintf ("\n"); +> #endif /* MATLAB */ +> +157a177 +> #ifndef MATLAB +173a194,211 +> +> #else /* MATLAB */ +> mexPrintf ("%s", _SCOTCHerrorProgName); +> #ifdef SCOTCH_PTSCOTCH +> if ((MPI_Initialized (&proclocnum) == MPI_SUCCESS) && +> (proclocnum != 0) && +> (MPI_Comm_rank (MPI_COMM_WORLD, &proclocnum) == MPI_SUCCESS)) +> mexPrintf ("(%d): ", proclocnum); +> #else /* SCOTCH_PTSCOTCH */ +> if (_SCOTCHerrorProgName[0] != '\0') +> mexPrintf (": "); +> #endif /* SCOTCH_PTSCOTCH */ +> mexPrintf ("WARNING: "); +> va_start (errlist, errstr); +> mexPrintf (errstr, errlist); /* Print arguments */ +> va_end (errlist); +> mexPrintf ("\n"); +> #endif /* MATLAB */ + + +[jschierm@astrid scotch]$ diff Makefile_old Makefile +- add MEX rule +- add gmap_mex into scotch, clean, and install rules +- add gmap_mex object +51a52,54 +> %$(MEX) : %.c +> $(CCM) $(MFLAGS) -I$(includedir) -I../libscotch -DSCOTCH_VERSION=\"$(VERSION)\" $(<) -o $(@) -L$(libdir) -l$(SCOTCHLIB) -l$(SCOTCHLIB)errexit $(LDFLAGS) +> +70a74 +> gmap_mex$(MEX) \ +98c102 +< -$(CP) acpl$(EXE) amk_ccc$(EXE) amk_fft2$(EXE) amk_grf$(EXE) amk_hy$(EXE) amk_m2$(EXE) amk_p2$(EXE) atst$(EXE) gbase$(EXE) gcv$(EXE) gmap$(EXE) gmk_hy$(EXE) gmk_m2$(EXE) gmk_m3$(EXE) gmk_msh$(EXE) gmk_ub2$(EXE) gmtst$(EXE) gord$(EXE) gotst$(EXE) gout$(EXE) *gtst$(EXE) gscat$(EXE) mcv$(EXE) mmk_m2$(EXE) mmk_m3$(EXE) mord$(EXE) mtst$(EXE) $(bindir) +--- +> -$(CP) acpl$(EXE) amk_ccc$(EXE) amk_fft2$(EXE) amk_grf$(EXE) amk_hy$(EXE) amk_m2$(EXE) amk_p2$(EXE) atst$(EXE) gbase$(EXE) gcv$(EXE) gmap$(EXE) gmap_mex$(MEX) gmk_hy$(EXE) gmk_m2$(EXE) gmk_m3$(EXE) gmk_msh$(EXE) gmk_ub2$(EXE) gmtst$(EXE) gord$(EXE) gotst$(EXE) gout$(EXE) *gtst$(EXE) gscat$(EXE) mcv$(EXE) mmk_m2$(EXE) mmk_m3$(EXE) mord$(EXE) mtst$(EXE) $(bindir) +108c112 +< -$(RM) *~ *$(OBJ) acpl$(EXE) amk_ccc$(EXE) amk_fft2$(EXE) amk_grf$(EXE) amk_hy$(EXE) amk_m2$(EXE) amk_p2$(EXE) atst$(EXE) gbase$(EXE) gcv$(EXE) *gmap$(EXE) gmk_hy$(EXE) gmk_m2$(EXE) gmk_m3$(EXE) gmk_msh$(EXE) gmk_ub2$(EXE) gmtst$(EXE) *gord$(EXE) gotst$(EXE) gout$(EXE) *gpart$(EXE) *gscat$(EXE) *gtst$(EXE) mcv$(EXE) mmk_m2$(EXE) mmk_m3$(EXE) mord$(EXE) mtst$(EXE) +--- +> -$(RM) *~ *$(OBJ) acpl$(EXE) amk_ccc$(EXE) amk_fft2$(EXE) amk_grf$(EXE) amk_hy$(EXE) amk_m2$(EXE) amk_p2$(EXE) atst$(EXE) gbase$(EXE) gcv$(EXE) *gmap$(EXE) gmap_mex$(MEX) gmk_hy$(EXE) gmk_m2$(EXE) gmk_m3$(EXE) gmk_msh$(EXE) gmk_ub2$(EXE) gmtst$(EXE) *gord$(EXE) gotst$(EXE) gout$(EXE) *gpart$(EXE) *gscat$(EXE) *gtst$(EXE) mcv$(EXE) mmk_m2$(EXE) mmk_m3$(EXE) mord$(EXE) mtst$(EXE) +239a244,251 +> gmap_mex$(MEX) : gmap_mex.c \ +> ../libscotch/module.h \ +> ../libscotch/common.h \ +> $(includedir)/scotch.h \ +> $(libdir)/libscotch$(LIB) \ +> $(libdir)/libscotcherrexit$(LIB) \ +> gmap.h +> + + +[jschierm@astrid scotch]$ diff gmap.c gmap_mex.c +- convert gmap to gmap_mex mex function with variable argument list +117,120c117,120 +< int +< main ( +< int argc, +< char * argv[]) +--- +> void mexFunction( int nlhs, +> mxArray *plhs[], +> int nrhs, +> const mxArray *prhs[] ) +121a122,123 +> int argcm; +> char argvm[21][257]; +130a133,152 +> /* check static variables from previous runs */ +> +> if (C_paraNum > 0 || C_fileNum > 0) +> mexErrMsgTxt("gmap_mex still in memory -- clear gmap_mex and try again.\n"); +> +> /* load matlab argument list */ +> +> argcm=nrhs+1; +> mexPrintf("argcm=%d\n",argcm); +> strcpy(argvm[0],"gmap"); +> for (i=0; i if (!mxIsChar(prhs[i])) { +> mexPrintf("%s -- prhs[%d] must be character.\n","gmap",i); +> mexErrMsgTxt(" "); +> } +> else +> mxGetString(prhs[i],argvm[i+1],256); +> for (i=0; i mexPrintf("argvm[%d]=%s\n",i,argvm[i]); +> +132,133c154,155 +< i = strlen (argv[0]); +< if ((i >= 5) && (strncmp (argv[0] + i - 5, "gpart", 5) == 0)) { +--- +> i = strlen (argvm[0]); +> if ((i >= 5) && (strncmp (argvm[0] + i - 5, "gpart", 5) == 0)) { +144c166 +< if ((argc >= 2) && (argv[1][0] == '?')) { /* If need for help */ +--- +> if ((argcm >= 2) && (argvm[1][0] == '?')) { /* If need for help */ +151a174,175 +> printf("point 0: C_FILENBR=%d, C_fileNbr=%d, C_paraNbr=%d\n", +> C_FILENBR,C_fileNbr,C_paraNbr); +154,155c178,183 +< for (i = 1; i < argc; i ++) { /* Loop for all option codes */ +< if ((argv[i][0] != '-') || (argv[i][1] == '\0') || (argv[i][1] == '.')) { /* If found a file name */ +--- +> for (i = 1; i < argcm; i ++) { /* Loop for all option codes */ +> printf("point 1: i=%d; C_fileNbr=%d, C_fileNum=%d, C_paraNbr=%d, C_paraNum=%d\n", +> i,C_fileNbr,C_fileNum,C_paraNbr,C_paraNum); +> if ((argvm[i][0] != '-') || (argvm[i][1] == '\0') || (argvm[i][1] == '.')) { /* If found a file name */ +> printf("point 2: i=%d; C_fileNbr=%d, C_fileNum=%d, C_paraNbr=%d, C_paraNum=%d\n", +> i,C_fileNbr,C_fileNum,C_paraNbr,C_paraNum); +157,158c185,186 +< if ((C_partNbr = atoi (argv[i])) < 1) /* Get the number of parts */ +< errorPrint ("main: invalid number of parts (\"%s\")", argv[i]); +--- +> if ((C_partNbr = atoi (argvm[i])) < 1) /* Get the number of parts */ +> errorPrint ("main: invalid number of parts (\"%s\")", argvm[i]); +161a190,191 +> printf("point 3: i=%d; C_fileNbr=%d, C_fileNum=%d, C_paraNbr=%d, C_paraNum=%d\n", +> i,C_fileNbr,C_fileNum,C_paraNbr,C_paraNum); +163c193 +< C_fileTab[C_fileNum ++].name = argv[i]; +--- +> C_fileTab[C_fileNum ++].name = argvm[i]; +165a196,197 +> printf("point 4: i=%d; C_fileNbr=%d, C_fileNum=%d, C_paraNbr=%d, C_paraNum=%d\n", +> i,C_fileNbr,C_fileNum,C_paraNbr,C_paraNum); +168c200 +< switch (argv[i][1]) { +--- +> switch (argvm[i][1]) { +177c209 +< SCOTCH_stratGraphMap (&stradat, &argv[i][2]); +--- +> SCOTCH_stratGraphMap (&stradat, &argvm[i][2]); +181,182c213,214 +< for (j = 2; argv[i][j] != '\0'; j ++) { +< switch (argv[i][j]) { +--- +> for (j = 2; argvm[i][j] != '\0'; j ++) { +> switch (argvm[i][j]) { +192c224 +< errorPrint ("main: invalid source graph option (\"%c\")", argv[i][j]); +--- +> errorPrint ("main: invalid source graph option (\"%c\")", argvm[i][j]); +202,203c234,235 +< for (j = 2; argv[i][j] != '\0'; j ++) { +< switch (argv[i][j]) { +--- +> for (j = 2; argvm[i][j] != '\0'; j ++) { +> switch (argvm[i][j]) { +217c249 +< errorPrint ("main: unprocessed parameter \"%c\" in \"%s\"", argv[i][j], argv[i]); +--- +> errorPrint ("main: unprocessed parameter \"%c\" in \"%s\"", argvm[i][j], argvm[i]); +222c254 +< errorPrint ("main: unprocessed option (\"%s\")", argv[i]); +--- +> errorPrint ("main: unprocessed option (\"%s\")", argvm[i]); +225a258 +> printf("point 5\n"); +230a264 +> printf("point 6\n"); +232a267 +> printf("point 7\n"); +235a271 +> printf("point 8\n"); +239a276 +> printf("point 9\n"); +244a282 +> printf("point 10\n"); +251a290 +> printf("point 11\n"); +256a296 +> printf("point 12\n"); +264a305 +> printf("point 13\n"); +271a313 +> printf("point 14\n"); +273a316 +> printf("point 15\n"); +276a320 +> printf("point 16\n"); +277a322 +> printf("point 16a\n"); +278a324 +> printf("point 16b\n"); +279a326 +> printf("point 16c\n"); +280a328 +> printf("point 17\n"); +284a333 +> printf("point 18\n"); + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/scotch_jes_notes.txt =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/scotch_jes_notes.txt (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/scotch/scotch_jes_notes.txt (revision 18231) @@ -0,0 +1,308 @@ +8/06/09: + +following INSTALL.txt: +- GNU Make 3.81, lex, yacc all present +- started with Makefile.inc.i686_sun_solaris5 +- changed CCS from cc to gcc +- removed SCOTCH_PTHREAD, since MPICH2 1.0.2p1 is prior to 1.0.7 + +graph.h:110: error: expected :, ,, ;, ) or __attribute__ before vnumtab +(and so on for "restrict" attribute in graph.h,geom.h,mesh.h,arch.h,mapping.h,order.h) +- added -std=c99 to CFLAGS (based on various internet pages) + +bgraph_bipart_gg.c:267: error: intptr_t undeclared +- according to various internet pages, should be included in c99 standard +- defined in /usr/include/stdint.h (also referenced in inttypes.h), so why not included? +- added -DINTSIZE64 to CFLAGS, still didn't work (based on INSTALL.txt) +- added -Dintptr_t="long int" (based on /usr/include/stdint.h) + +common2.c:764: error: storage size of tp isn't known +common2.c:766: error: CLOCK_REALTIME undeclared +- added -DCOMMON_TIMING_OLD to CFLAGS (based on source code) + +8/13/09: + +for running as a matlab mex function: +[jschierm@astrid libscotch]$ diff common_old.h common.h +90a91,102 +> #ifdef MATLAB +> #include "mat.h" +> #include "mex.h" +> #include "matrix.h" +> +> #define printf mexPrintf +> #define malloc mxMalloc +> #define calloc mxCalloc +> #define realloc mxRealloc +> #define free mxFree +> #endif +> + +[jschierm@astrid src]$ diff Makefile_old.inc Makefile.inc +12,13c12,13 +< CFLAGS = -m64 -O3 -std=c99 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Du_int32_t=uint32_t -Du_int64_t=uint64_t -DINTSIZE64 -Dintptr_t="long int" -DCOMMON_TIMING_OLD +< LDFLAGS = -lz -lm -lrt +--- +> CFLAGS = -m64 -O3 -std=c99 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Du_int32_t=uint32_t -Du_int64_t=uint64_t -DINTSIZE64 -Dintptr_t="long int" -DCOMMON_TIMING_OLD -DMATLAB -fPIC -I/usr/local/pkgs/matlab-7.6/extern/include +> LDFLAGS = -lz -lm -lrt -L/usr/local/pkgs/matlab-7.6/bin/glnxa64 -lmat -lmex + +8/19/09: + +- still having problems with intptr_t: +gcc: int: No such file or directory +In file included from ../libscotch/common.h:81, + from gmap_mex.c:75: +/usr/include/unistd.h:238: error: two or more data types in declaration specifiers +- removed -DINTSIZE64 and -Dintptr_t="long int" from CFLAGS above +[jschierm@astrid libscotch]$ diff common_old.h common.h +68a69 +> #include /* added for intptr_t */ + +8/20/09: + +- must fix exits to exit within Matlab: +[jschierm@astrid libscotch]$ diff common_old.h common.h +68a69 +> #include /* added for intptr_t */ +90a92,104 +> #ifdef MATLAB +> #include "mat.h" +> #include "mex.h" +> #include "matrix.h" +> +> #define printf mexPrintf +> #define malloc mxMalloc +> #define calloc mxCalloc +> #define realloc mxRealloc +> #define free mxFree +> #define exit(status) mexErrMsgTxt("exit=" #status) +> #endif +> + +- however, dummysizes must run by itself during compilation and exit cleanly: +[jschierm@astrid libscotch]$ diff dummysizes_old.c dummysizes.c +269a270 +> #ifndef MATLAB +270a272 +> #endif /* MATLAB */ + +- redirect errorPrint and errorPrintW to within Matlab: +[jschierm@astrid libscotch]$ diff library_error_exit_old.c +library_error_exit.c +116a117 +> #ifndef MATLAB +133a135,152 +> #else /* MATLAB */ +> mexPrintf ("%s", _SCOTCHerrorProgName); +> #ifdef SCOTCH_PTSCOTCH +> if ((MPI_Initialized (&proclocnum) == MPI_SUCCESS) && +> (proclocnum != 0) && +> (MPI_Comm_rank (MPI_COMM_WORLD, &proclocnum) == MPI_SUCCESS)) +> mexPrintf ("(%d): ", proclocnum); +> #else /* SCOTCH_PTSCOTCH */ +> if (_SCOTCHerrorProgName[0] != '\0') +> mexPrintf (": "); +> #endif /* SCOTCH_PTSCOTCH */ +> mexPrintf ("ERROR: "); +> va_start (errlist, errstr); +> mexPrintf (errstr, errlist); /* Print arguments */ +> va_end (errlist); +> mexPrintf ("\n"); +> #endif /* MATLAB */ +> +157a177 +> #ifndef MATLAB +173a194,211 +> +> #else /* MATLAB */ +> mexPrintf ("%s", _SCOTCHerrorProgName); +> #ifdef SCOTCH_PTSCOTCH +> if ((MPI_Initialized (&proclocnum) == MPI_SUCCESS) && +> (proclocnum != 0) && +> (MPI_Comm_rank (MPI_COMM_WORLD, &proclocnum) == MPI_SUCCESS)) +> mexPrintf ("(%d): ", proclocnum); +> #else /* SCOTCH_PTSCOTCH */ +> if (_SCOTCHerrorProgName[0] != '\0') +> mexPrintf (": "); +> #endif /* SCOTCH_PTSCOTCH */ +> mexPrintf ("WARNING: "); +> va_start (errlist, errstr); +> mexPrintf (errstr, errlist); /* Print arguments */ +> va_end (errlist); +> mexPrintf ("\n"); +> #endif /* MATLAB */ + +- redirect usagePrint to within Matlab: +[jschierm@astrid libscotch]$ diff common_old.c common.c +102a103 +> #ifndef MATLAB +105a107,111 +> #else /* MATLAB */ +> mexPrintf ("Usage is:\n"); +> for (cptr = data; *cptr != NULL; cptr ++) +> mexPrintf (" %s\n", *cptr); +> #endif /* MATLAB */ + +8/21/09: + +- removed -DCOMMON_PTHREAD from CFLAGS and MFLAGS to eliminate fatal exception at pthread_exit in gmap_mex.c +- removed -DCOMMON_FILE_COMPRESS_GZ from CFLAGS and MFLAGS because unused + +8/25/09: + +added macro for fprintf to capture missing output: +[jschierm@astrid libscotch]$ diff common_old.h common.h +68a69 +> #include /* added for intptr_t */ +90a92,105 +> #ifdef MATLAB +> #include "mat.h" +> #include "mex.h" +> #include "matrix.h" +> +> #define printf mexPrintf +> #define fprintf(file,...) (file == stdout || file == stderr ? mexPrintf(__VA_ARGS__) : fprintf(file,__VA_ARGS__)) +> #define malloc mxMalloc +> #define calloc mxCalloc +> #define realloc mxRealloc +> #define free mxFree +> #define exit(status) mexErrMsgTxt("exit=" #status) +> #endif +> + +11/12/09: + +- added -Wl,-rpath-link,/usr/local/pkgs/matlab-7.6/bin/glnxa64 to LDFLAGS to eliminate missing libhdf5.so.0 in Matlab directories (based on Cielo make, but why did this not occur before?) + +11/18/09: + +- changed the following files to allow adjir,adjjc,vertlab,vertwgt,edgewgt rather than graph file + +libscotch/library.h +- argument list for SCOTCH_graphLoad +libscotch/library_graph.c +- SCOTCH_graphLoad changes and call to graphLoad +libscotch/graph.h +- argument list for graphLoad +libscotch/graph_io.c +- graphLoad changes +libscotch/graph_io_scot.c +- miscellaneous call to graphLoad +libscotch/mesh_io_scot.c +- miscellaneous call to graphLoad +libscotch/library_graph_f.c +- miscellaneous call to SCOTCH_graphLoad +scotch/gmap_mex.c +- input/processing of Matlab arguments and call to SCOTCH_graphLoad + +11/30/09: + +- changed the following files to allow nvert,maptab rather than map file + +libscotch/library.h +- argument list for SCOTCH_graphMapSave +libscotch/library_graph_map.c +- SCOTCH_graphMapSave changes and call to mapSave +libscotch/mapping.h +- argument list for mapSave +libscotch/mapping_io.c +- mapSave changes +libscotch/library_graph_map_f.c +- miscellaneous call to SCOTCH_graphMapSave +scotch/gmap_mex.c +- call to SCOTCH_graphMapSave and processing/output of Matlab arguments + +12/08/09: + +- changed the following files to allow archtyp,napar,archpar rather than target file + +libscotch/library.h +- argument list for SCOTCH_archLoad +libscotch/library_arch.c +- SCOTCH_archLoad changes and call to archLoad +libscotch/arch.h +- argument list for archLoad +libscotch/arch.c +- archLoad changes and call to class->archLoad +libscotch/arch_cmplt.h +libscotch/arch_cmpltw.h +libscotch/arch_deco.h +libscotch/arch_hcub.h +libscotch/arch_mesh.h +libscotch/arch_tleaf.h +libscotch/arch_torus.h +- argument lists for arch*ArchLoad +libscotch/arch_cmplt.c +libscotch/arch_cmpltw.c +libscotch/arch_deco.c +libscotch/arch_hcub.c +libscotch/arch_mesh.c +libscotch/arch_tleaf.c +libscotch/arch_torus.c +- arch*ArchLoad changes +libscotch/library_arch_f.c +- miscellaneous call to SCOTCH_archLoad +scotch/gmap_mex.c +- input/processing of Matlab arguments and call to SCOTCH_archLoad + +12/11/09: + +- fixed a couple bugs + +libscotch/graph.c -- caused crash when trying to free vertex labels +138c138,141 +< if (grafptr->vlbltax != NULL) +--- +> /* vlbltax must also check GRAPHVERTGROUP (jes, 12/11/09) */ +> // if (grafptr->vlbltax != NULL) +> if ((grafptr->vlbltax != NULL) && +> ((grafptr->flagval & GRAPHVERTGROUP) == 0)) + +libscotch/mapping_io.c -- caused first vertex label to be uninitialized +> /* not sure why, but need to offset vlbltax in other direction (jes, 12/11/09 +> // (long) ((vlbltax != NULL) ? vlbltax[vertnum] : vertnum), +> (long) ((vlbltax != NULL) ? vlbltax[vertnum+mappptr->baseva + +1/05/10: + +libscotch/graph_io.c -- if vertex labels are supplied, they must be referenced +263c265,268 +< edgeval=adjir[edgenum-grafptr->baseval]+1; +--- +> if (vertlab) +> edgeval=vertlab[adjir[edgenum-grafptr->baseval] ]; +> else +> edgeval= adjir[edgenum-grafptr->baseval]+1; + +2/08/10: + +- modified all source code changes to use the MATLAB compiler conditional, so that both mex and stand-alone modules could be built simultaneously + +2/10/10: + +- added mexscotch target to makefiles to separate mex from stand-alone modules +- removed Matlab-specific switches from CFLAGS and LDFLAGS and added them to mexscotch target + +3/03/10: + +- separated dummysizes within mexscotch target in libscotch/Makefile so that it is built without the matlab flag, includes, and libraries (matlab 7.8 would fail even though matlab 7.6 was okay). + +4/26/10: + +- separated gmap_mex.c driver into gmap_mex.c matlab-layer (independent of scotch) and gmapx.c x-layer (independent of matlab). + +4/29/10: + +- made changes to gmapx.c, parser_yy.y/stratParserParse, and parser_ll.l/stratParserInit to reset static variables from previous runs. +- inserted print statements into common_integer.c/intRand*, common_memory.c/mem*, and vgraph_separate_vw.c/vgraphSeparateVw to monitor static variables in case those have to be reset. + +5/03/10: + +- implemented gpart functionality in gmap_mex.c, gmapx.c, and new gpart.m. +- implemented common_integer.c/intRandResetStatic to reset static variables from previous runs. + +6/16/10: + +- renamed scotch x-layer and separated it from rest of build. +- set up scotch to build both stand-alone and mex libraries. + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/shapelib/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/shapelib/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/shapelib/install.sh (revision 18231) @@ -0,0 +1,56 @@ +#!/bin/bash +set -eu + +# Some cleanup +rm -rf shapelib-1.2.10 +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/shapelib-1.2.10.tar.gz' 'shapelib-1.2.10.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/shape_eg_data.zip' 'shape_eg_data.zip' +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/docs/shapefile.pdf' 'shapefile.pdf' + +# Untar +tar -xvzf shapelib-1.2.10.tar.gz +unzip shape_eg_data.zip -d shapelib-1.2.10/eg_data + +# Move shapelib to src directory +mv shapelib-1.2.10/* src +rm -rf shapelib-1.2.10 + +# Apply patches (all at once) +# (written by diff -rc old_src new_src > shapelib.patch) +patch -p0 < shapelib.patch + +# Build shapelib and run self-tests +cd src +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make test + +# Clean up objects (but not library or executable) +#make clean +cd .. + +# Populate install directory +cp -p src/README install +cp -p src/*.html install +mkdir install/include +cp -p src/shapefil.h install/include +mkdir install/lib +mv src/libshape.a install/lib/libshape.a +mkdir install/exec +mv src/shpcreate install/exec +mv src/shpadd install/exec +mv src/shpdump install/exec +mv src/shprewind install/exec +mv src/dbfcreate install/exec +mv src/dbfadd install/exec +mv src/dbfdump install/exec +mv src/shputils install/exec +mv src/shptest install/exec Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/shapelib/shapelib.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/shapelib/shapelib.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/shapelib/shapelib.patch (revision 18231) @@ -0,0 +1,139 @@ +diff -rc src/Makefile src_new/Makefile +*** src/Makefile 2003-04-07 06:03:22.000000000 -0700 +--- src_new/Makefile 2011-10-19 11:58:13.993411828 -0700 +*************** +*** 1,20 **** + + #LINKOPT = /usr/local/lib/libdbmalloc.a +! CFLAGS = -g + + default: all + +! all: shpcreate shpadd shpdump shprewind dbfcreate dbfadd dbfdump shptest + + shpopen.o: shpopen.c shapefil.h + $(CC) $(CFLAGS) -c shpopen.c + +- shptree.o: shptree.c shapefil.h +- $(CC) $(CFLAGS) -c shptree.c +- + dbfopen.o: dbfopen.c shapefil.h + $(CC) $(CFLAGS) -c dbfopen.c + + shpcreate: shpcreate.c shpopen.o + $(CC) $(CFLAGS) shpcreate.c shpopen.o $(LINKOPT) -o shpcreate + +--- 1,24 ---- + + #LINKOPT = /usr/local/lib/libdbmalloc.a +! CC = gcc +! #CFLAGS = -g +! CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g +! AR = /usr/bin/ar rcv +! RANLIB = /usr/bin/ranlib + + default: all + +! all: libshape.a shpcreate shpadd shpdump shprewind dbfcreate dbfadd dbfdump shputils shptest + + shpopen.o: shpopen.c shapefil.h + $(CC) $(CFLAGS) -c shpopen.c + + dbfopen.o: dbfopen.c shapefil.h + $(CC) $(CFLAGS) -c dbfopen.c + ++ libshape.a: shpopen.o dbfopen.o ++ ${AR} libshape.a shpopen.o dbfopen.o ; ${RANLIB} libshape.a ++ + shpcreate: shpcreate.c shpopen.o + $(CC) $(CFLAGS) shpcreate.c shpopen.o $(LINKOPT) -o shpcreate + +*************** +*** 36,58 **** + dbfdump: dbfdump.c dbfopen.o + $(CC) $(CFLAGS) dbfdump.c dbfopen.o $(LINKOPT) -o dbfdump + + shptest: shptest.c shpopen.o + $(CC) $(CFLAGS) shptest.c shpopen.o $(LINKOPT) -o shptest + +! shputils: shputils.c shpopen.o dbfopen.o +! $(CC) $(CFLAGS) shputils.c shpopen.o dbfopen.o $(LINKOPT) -o shputils + + shptreedump: shptreedump.c shptree.o shpopen.o + $(CC) $(CFLAGS) shptreedump.c shptree.o shpopen.o $(LINKOPT) \ + -o shptreedump + + clean: +! rm -f *.o dbfdump dbfcreate dbfadd shpdump shpcreate shpadd shputils + rm -f shptreedump + rm -rf *.lo *.la .libs +- rm -f shptest + +! test: test2 test3 + + # + # Note this stream only works if example data is accessable. +--- 40,64 ---- + dbfdump: dbfdump.c dbfopen.o + $(CC) $(CFLAGS) dbfdump.c dbfopen.o $(LINKOPT) -o dbfdump + ++ shputils: shputils.c shpopen.o dbfopen.o ++ $(CC) $(CFLAGS) shputils.c shpopen.o dbfopen.o $(LINKOPT) -o shputils ++ + shptest: shptest.c shpopen.o + $(CC) $(CFLAGS) shptest.c shpopen.o $(LINKOPT) -o shptest + +! shptree.o: shptree.c shapefil.h +! $(CC) $(CFLAGS) -c shptree.c + + shptreedump: shptreedump.c shptree.o shpopen.o + $(CC) $(CFLAGS) shptreedump.c shptree.o shpopen.o $(LINKOPT) \ + -o shptreedump + + clean: +! rm -f *.o *.a shpcreate shpadd shpdump shprewind dbfcreate dbfadd dbfdump shputils shptest + rm -f shptreedump + rm -rf *.lo *.la .libs + +! test: test1 test2 test3 + + # + # Note this stream only works if example data is accessable. +diff -rc src/shputils.c src_new/shputils.c +*** src/shputils.c 2003-04-07 06:03:22.000000000 -0700 +--- src_new/shputils.c 2011-10-14 14:52:32.179022813 -0700 +*************** +*** 274,280 **** + if (factor == 0) + { + if (infactor ==0) +! { puts("ERROR: Input unit must be defined before output unit"); exit(); } + factor=infactor/outfactor; + } + printf("Output file coordinate values will be factored by %lg\n",factor); +--- 274,280 ---- + if (factor == 0) + { + if (infactor ==0) +! { puts("ERROR: Input unit must be defined before output unit"); exit( 1 ); } + factor=infactor/outfactor; + } + printf("Output file coordinate values will be factored by %lg\n",factor); +diff -rc src/stream1.sh src_new/stream1.sh +*** src/stream1.sh 2003-04-07 06:03:22.000000000 -0700 +--- src_new/stream1.sh 2011-10-19 11:45:08.192964291 -0700 +*************** +*** 1,6 **** + #!/bin/sh + +! EG_DATA=/u/www/projects/shapelib/eg_data + + echo ------------------------------------------------------------------------- + echo Test 1: dump anno.shp +--- 1,6 ---- + #!/bin/sh + +! EG_DATA=./eg_data + + echo ------------------------------------------------------------------------- + echo Test 1: dump anno.shp Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/shell2junit/README =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/shell2junit/README (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/shell2junit/README (revision 18231) @@ -0,0 +1,9 @@ +http://code.google.com/p/shell2junit/ + +Shell2junit + +Shell2junit is a simple utility which facilitates to generate junit reports for batch processes executed in shell scripts. + +The reports can be easily parsed in Hudson and other CI software in order to monitor and generate trends and alerts. + +This page teaches how to do it in Hudson. Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/shell2junit/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/shell2junit/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/shell2junit/install.sh (revision 18231) @@ -0,0 +1,9 @@ +#!/bin/bash +set -eu + + +#Some cleanup +rm -rf install +mkdir install + +cp patch/sh2ju.sh install/ Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/shell2junit/install.sh.old =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/shell2junit/install.sh.old (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/shell2junit/install.sh.old (revision 18231) @@ -0,0 +1,20 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +rm -rf shell2junit +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/shell2junit-1.0.0.zip' 'shell2junit-1.0.0.zip' + +#Untar +unzip shell2junit-1.0.0.zip + +#Move shell2junit into install directory +mv shell2junit/* src +rm -rf shell2junit + +#Copy executable: +cp src/sh2ju.sh install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/shell2junit/patch/sh2ju.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/shell2junit/patch/sh2ju.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/shell2junit/patch/sh2ju.sh (revision 18231) @@ -0,0 +1,131 @@ +#!/bin/sh +### Copyright 2010 Manuel Carrasco Moñino. (manolo at apache.org) +### +### Licensed under the Apache License, Version 2.0. +### You may obtain a copy of it at +### http://www.apache.org/licenses/LICENSE-2.0 + +### +### A library for shell scripts which creates reports in jUnit format. +### These reports can be used in Hudson, or any other CI. +### +### Usage: +### - Include this file in your shell script +### - Use juLog to call your command any time you want to produce a new report +### Usage: juLog command arguments +### options: +### -name="TestName" : the test name which will be shown in the junit report +### -error="RegExp" : a regexp which sets the test as failure when the output matches it +### -ierror="RegExp" : same as -error but case insensitive +### - Junit reports are left in the folder 'result' under the directory where the script is executed. +### - Configure hudson to parse junit files from the generated folder +### + +asserts=00; errors=0; total=0; content="" + +# create output folder +juDIR=`pwd`/results +mkdir -p $juDIR || exit + +# The name of the suite is calculated based in your script name +suite=`basename $0 | sed -e 's/.sh$//' | tr "." "_"` + +# A wrapper for the eval method witch allows catching seg-faults and use tee +errfile=/tmp/evErr.$$.log +eVal() { + eval "$1" + echo $? | tr -d "\n" >$errfile +} + +# Method to clean old tests +juLogClean() { + echo "+++ Removing old junit reports from: $juDIR " + rm -f $juDIR/TEST-* +} + +# Execute a command and record its results +juLog() { + + # parse arguments + ya=""; icase=""; testname=""; + while [ -z "$ya" ]; do + case "$1" in + -name=*) name=$asserts-`echo "$1" | sed -e 's/-name=//'`; shift;; + -ierror=*) ereg=`echo "$1" | sed -e 's/-ierror=//'`; icase="-i"; shift;; + -error=*) ereg=`echo "$1" | sed -e 's/-error=//'`; shift;; + -test=*) testname=`echo "$1" | sed -e 's/-test=//'`; shift;; + *) ya=1;; + esac + done + + # use first arg as name if it was not given + if [ -z "$name" ]; then + name="$asserts-$1" + shift + fi + + # calculate command to eval + [ -z "$1" ] && return + cmd="$1"; shift + while [ -n "$1" ] + do + cmd="$cmd \"$1\"" + shift + done + + # eval the command sending output to a file + outf=/var/tmp/ju$$.txt + >$outf + echo "" | tee -a $outf + echo "+++ Running case: $testname " | tee -a $outf + echo "+++ working dir: "`pwd` | tee -a $outf + #echo "+++ command: $cmd" | tee -a $outf + ini=`date +%s` + eVal "$cmd" 2>&1 | tee -a $outf + evErr=`cat $errfile` + rm -f $errfile + end=`date +%s` + echo "+++ exit code: $evErr" | tee -a $outf + + # set the appropriate error, based in the exit code and the regex + [ $evErr != 0 ] && err=1 || err=0 + out=`cat $outf | sed -e 's/^\([^+]\)/| \1/g'` + if [ $err = 0 -a -n "$ereg" ]; then + H=`echo "$out" | egrep $icase "$ereg"` + [ -n "$H" ] && err=1 + fi + echo "+++ error: $err" | tee -a $outf + rm -f $outf + + # calculate vars + asserts=`expr $asserts + 1` + asserts=`printf "%.2d" $asserts` + errors=`expr $errors + $err` + time=`expr $end - $ini` + total=`expr $total + $time` + + # write the junit xml report + ## failure tag + [ $err = 0 ] && failure="" || failure=" + + " + ## testcase tag + content="$content + + $failure + + + + + " + ## testsuite block + cat <$juDIR/TEST-$suite.xml + + $content + +EOF + +} + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/slepc/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/slepc/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/slepc/install.sh (revision 18231) @@ -0,0 +1,25 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install slepc-2.3.2 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/slepc-2.3.2.tgz' 'slepc-2.3.2.tgz' + +#Untar +tar -zxvf slepc-2.3.2.tgz + +#Move slepc to install directory +mv slepc-2.3.2/* install/ +rm -rf slepc-2.3.2 + +#Make slepc +cd install +./config/configure.py +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/snowpack/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/snowpack/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/snowpack/install.sh (revision 18231) @@ -0,0 +1,56 @@ +#!/bin/bash +#SNOWPACK install package: this package is not distributed by ISSM. Please request access to the code by +#contacting Mathias Bavay () or logging onto http://models.slf.ch/ and registering. Once you have a tarball +#of the code, please use this script to install. + +#we assume you have a Snowpack-*-src.tar.gz tarball +set -eu + +#Do some inquiry about the names of the tar balls: +source_tar=`ls Snowpack-*-src.tar.gz` +source_version=`echo $source_tar | sed 's/Snowpack-//g' | sed 's/-src.tar.gz//g'` + +if [[ $source_tar == "" ]]; then + echo "Could not identify a tar ball for the source code, name should be Snowpack-*-src.tar.gz" + exit 1 +fi +if [[ $source_version == "" ]]; then + echo "Could not identify a tar ball version for the source code" + exit 1 +fi + +#Some cleanup +rm -rf src install Snowpack-$source_version + +#First deal with source code +tar -zxvf $source_tar +mv Snowpack-$source_version/usr src +rm -rf Snowpack-$source_version + +#Build library +cd src && rm -rf CMakeCache.txt +cmake -DCMAKE_INSTALL_PREFIX:PATH=$ISSM_DIR/externalpackages/snowpack/install \ + -DMETEOIO_INCLUDE_DIR:PATH=$ISSM_DIR/externalpackages/meteoio/install/include \ + -DMETEOIO_LIBRARY:PATH=$ISSM_DIR/externalpackages/meteoio/install/lib/libmeteoio.dylib\ + . + #-DCMAKE_VERBOSE_MAKEFILE=true \ + +#Compile +if [ $# -eq 0 ]; then + make all install +else + make -j $1 all install +fi + +#Build binary: +cd applications/snowpack +cmake -DCMAKE_MODULE_PATH:PATH=/Users/larour/issm-uci/trunk-jpl/externalpackages/snowpack/src/tools/cmake/ -DMETEOIO_INCLUDE_DIR:PATH=$ISSM_DIR/externalpackages/meteoio/install/include . + +#Compile +if [ $# -eq 0 ]; then + make all install +else + make -j $1 all install +fi + + Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/sqlite/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/sqlite/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/sqlite/install.sh (revision 18231) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf sqlite-autoconf-3071300 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/sqlite-autoconf-3071300.tar.gz' 'sqlite-autoconf-3071300.tar.gz' + +#Untar +tar -zxvf sqlite-autoconf-3071300.tar.gz + +#Move sqlite-autoconf into src directory +mv sqlite-autoconf-3071300/* src +rm -rf sqlite-autoconf-3071300 + +#Configure sqlite-autoconf +cd src +./configure --prefix="$ISSM_DIR/externalpackages/sqlite/install" + +#Compile and install sqlite-autoconf +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/starcluster/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/starcluster/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/starcluster/install.sh (revision 18231) @@ -0,0 +1,7 @@ +#/bin/bash + +git clone git://github.com/jtriley/StarCluster.git + +cd StarCluster +python distribute_setup.py +python setup.py install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/svn/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/svn/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/svn/install.sh (revision 18231) @@ -0,0 +1,33 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf subversion-1.6.18 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/subversion-1.6.18.tar.gz' 'subversion-1.6.18.tar.gz' + +#Untar +tar -zxvf subversion-1.6.18.tar.gz + +#Move subversion into src directory +mv subversion-1.6.18/* src +rm -rf subversion-1.6.18 + +#Configure subversion +cd src +./configure --prefix="$ISSM_DIR/externalpackages/svn/install" \ + --with-swig="$ISSM_DIR/externalpackages/swig/install" \ + PYTHON2="$ISSM_DIR/externalpackages/python/install/bin/python" \ + --with-sqlite="$ISSM_DIR/externalpackages/sqlite/install" + +#Compile and install subversion +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/swig/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/swig/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/swig/install.sh (revision 18231) @@ -0,0 +1,37 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install +rm -rf swig-2.0.4 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/swig-2.0.4.tar.gz' 'swig-2.0.4.tar.gz' + +#Untar and move python into install directory +tar -zxvf swig-2.0.4.tar.gz +mv swig-2.0.4/* install +rm -rf swig-2.0.4 + +#Copy pcre prototype in include directory +cd install +#cp $ISSM_DIR/externalpackages/pcre/install/pcre.h ./Source/Include/ +#cp $ISSM_DIR/externalpackages/pcre/install/.libs/* ./Source/Include/ +export CFLAGS="-I$ISSM_DIR/externalpackages/pcre/install" +export LDFLAGS="-L$ISSM_DIR/externalpackages/pcre/install/.libs/" +export LIBS="-lpcre" +#Configure swig +./configure \ + --prefix="$ISSM_DIR/externalpackages/swig/install" \ + --with-pcre-prefix="$ISSM_DIR/externalpackages/pcre/install" \ + --with-pcre-exec-prefix="$ISSM_DIR/externalpackages/pcre/install" \ + --with-python="$ISSM_DIR/externalpackages/python/install/bin/python" + +#Compile and install gdal +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/tao/install-2.0.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/tao/install-2.0.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/tao/install-2.0.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu +#http://www.mcs.anl.gov/research/projects/tao/download/index.html + +#Compatible with PETSc 3.2 + +#Some cleanup +rm -rf install tao-2.0-p3 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/tao-2.0-p3.tar.gz' 'tao-2.0-p3.tar.gz' + +#Untar +tar -zxvf tao-2.0-p3.tar.gz + +#move into place +mv tao-2.0-p3/* install/ +rm -rf tao-2.0-p3 +cd install +export TAO_DIR="$ISSM_DIR/externalpackages/tao/install/" + +#petsc needs to be compiled with --with-clanguage=C++ +make Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/tao/install-2.1.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/tao/install-2.1.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/tao/install-2.1.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu +#http://www.mcs.anl.gov/research/projects/tao/download/index.html + +#compatible with PETSc 3.3 + +#Some cleanup +rm -rf install tao-2.1-p0 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/tao-2.1-p0.tar.gz' 'tao-2.1-p0.tar.gz' + +#Untar +tar -zxvf tao-2.1-p0.tar.gz + +#move into place +mv tao-2.1-p0/* install/ +rm -rf tao-2.1-p0 +cd install +export TAO_DIR="$ISSM_DIR/externalpackages/tao/install/" + +#petsc needs to be compiled with --with-clanguage=C++ +make Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/tao/install-2.2.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/tao/install-2.2.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/tao/install-2.2.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu +#http://www.mcs.anl.gov/research/projects/tao/download/tao-2.2.2.tar.gz + +#compatible with PETSc 3.4 + +#Some cleanup +rm -rf install tao-2.2.2 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/tao-2.2.2.tar.gz' 'tao-2.2.2.tar.gz' + +#Untar +tar -zxvf tao-2.2.2.tar.gz + +#move into place +mv tao-2.2.2/* install/ +rm -rf tao-2.2.2 + +#compile +cd install +export TAO_DIR="$ISSM_DIR/externalpackages/tao/install/" +make Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/tcl/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/tcl/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/tcl/install.sh (revision 18231) @@ -0,0 +1,49 @@ +#!/bin/bash +set -eu + +sudochoice=0; + +#Some cleanup +rm -rf src +rm -rf install +rm -rf tcl8.5.11 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/tcl8.5.11.tar.gz' 'tcl8.5.11.tar.gz' + +#Untar +tar -zxvf tcl8.5.11.tar.gz + +#Move tcl into src directory +mv tcl8.5.11/* src +rm -rf tcl8.5.11 + +#Configure tcl +ver="8.4.12" + +cd src/unix + +#User mode: +if [[ $sudochoice == "0" ]]; +then + ./configure --prefix=$ISSM_DIR/externalpackages/tcl/install + if [ $# -eq 0 ]; then + make + else + make -j $1 + fi + make install +fi + +#sudo mode: +if [[ $sudochoice == "1" ]]; +then + sudo ./configure + if [ $# -eq 0 ]; then + sudo make + else + sudo make -j $1 + fi + sudo make install +fi Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/tclx/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/tclx/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/tclx/install.sh (revision 18231) @@ -0,0 +1,32 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf tclx8.4 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/tclx8.4.tar.gz' 'tclx8.4.tar.gz' + +#Untar +tar -zxvf tclx8.4.tar.gz + +#Move tclx into src directory +mv tclx8.4/* src +rm -rf tclx8.4 + +#Configure tclx +cd src +./configure --prefix="$ISSM_DIR/externalpackages/tclx/install" \ + --exec-prefix="$ISSM_DIR/externalpackages/tclx/install" \ + --with-tcl=$ISSM_DIR/externalpackages/tcl/install/Library/Frameworks/Tcl.framework + +#Compile and install tclx +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/tex2im/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/tex2im/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/tex2im/install.sh (revision 18231) @@ -0,0 +1,16 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/tex2im-1.8.tar.gz' 'tex2im-1.8.tar.gz' + +#Untar +tar -zxvf tex2im-1.8.tar.gz + +#Move tex2im into src directory +mv tex2im-1.8/tex2im install/ +rm -rf tex2im-1.8 Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/tk/install.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/tk/install.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/tk/install.sh (revision 18231) @@ -0,0 +1,46 @@ +#!/bin/bash +set -eu + +sudochoice=0; + +#Some cleanup +rm -rf src +rm -rf install +rm -rf tk8.5.12 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/tk8.5.12-src.tar.gz' 'tk8.5.12.tar.gz' + +#Untar +tar -zxvf tk8.5.12.tar.gz + +#Move tk into src directory +mv tk8.5.12/* src +rm -rf tk8.5.12 + +cd src/unix + +#User mode: +if [[ $sudochoice == "0" ]]; +then + ./configure --prefix=$ISSM_DIR/externalpackages/tk/install + if [ $# -eq 0 ]; then + make + else + make -j $1 + fi + make install +fi + +#sudo mode: +if [[ $sudochoice == "1" ]]; +then + sudo ./configure + if [ $# -eq 0 ]; then + sudo make + else + sudo make -j $1 + fi + sudo make install +fi Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/altix64/configure.make =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/altix64/configure.make (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/altix64/configure.make (revision 18231) @@ -0,0 +1,4 @@ +CC=gcc +CSWITCHES = $(CFLAGS) -DNO_TIMER -DLINUX -fPIC +OBJ_EXT=o +LIB_EXT=a Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/android/configure.make =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/android/configure.make (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/android/configure.make (revision 18231) @@ -0,0 +1,18 @@ +# This makefile configures build process to cross-compile to the android platform. +# The binary tools referenced below are specifically configured to target armeabi-v7a. +# Furthermore, the compilers (which are simply wrappers around GNU GCC) are set to +# produce binaries that are EABI compliant. +# +# Note that the AAPCS standard defines 'EABI' as a moniker used to specify +# a _family_ of similar but distinct ABIs. Android follows the little-endian +# ARM GNU/Linux ABI as documented in the following document: +# +# http://www.codesourcery.com/gnu_toolchains/arm/arm_gnu_linux_abi.pdf + +CC=${host_triplet}-gcc +AR=${host_triplet}-ar +RANLIB=${host_triplet}-ranlib +CSWITCHES = $(CFLAGS) -DNO_TIMER +TRILIBDEFS = -DTRILIBRARY +OBJ_EXT=o +LIB_EXT=a Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/linux64/configure.make =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/linux64/configure.make (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/linux64/configure.make (revision 18231) @@ -0,0 +1,4 @@ +CC=gcc +CSWITCHES = $(CFLAGS) -DNO_TIMER -DLINUX -fPIC +OBJ_EXT=o +LIB_EXT=a Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/macosx32/configure.make =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/macosx32/configure.make (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/macosx32/configure.make (revision 18231) @@ -0,0 +1,5 @@ +CC=gcc -arch i386 +CSWITCHES = $(CFLAGS) -DNO_TIMER -fPIC +TRILIBDEFS = -DTRILIBRARY +OBJ_EXT=o +LIB_EXT=a Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/macosx64/configure.make =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/macosx64/configure.make (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/macosx64/configure.make (revision 18231) @@ -0,0 +1,5 @@ +CC=gcc -arch x86_64 +CSWITCHES = $(CFLAGS) -DNO_TIMER -fPIC +TRILIBDEFS = -DTRILIBRARY +OBJ_EXT=o +LIB_EXT=a Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/pleiades/configure.make =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/pleiades/configure.make (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/pleiades/configure.make (revision 18231) @@ -0,0 +1,4 @@ +CC=gcc +CSWITCHES = $(CFLAGS) -DNO_TIMER -DLINUX -fPIC +OBJ_EXT=o +LIB_EXT=a Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/win32/configure.make =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/win32/configure.make (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/win32/configure.make (revision 18231) @@ -0,0 +1,4 @@ +CC=icl +CSWITCHES = $(CFLAGS) -DNO_TIMER -DWIN32 +OBJ_EXT=obj +LIB_EXT=a Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/win7/configure.make =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/win7/configure.make (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/win7/configure.make (revision 18231) @@ -0,0 +1,4 @@ +CC=cl +CSWITCHES = $(CFLAGS) -DNO_TIMER +OBJ_EXT=obj +LIB_EXT=lib Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/win7/makefile =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/win7/makefile (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/configs/win7/makefile (revision 18231) @@ -0,0 +1,21 @@ +#Adaptation of Triangle makefile to compile only the triangle.c file, +#into a standalone library that can then be used to compile mex modules + +include ./configure.make + +AR = ar + +TRILIBDEFS = -DTRILIBRARY + +all: triangle.$(LIB_EXT) + +OBJECTS=triangle.$(OBJ_EXT) + +triangle.$(LIB_EXT): $(OBJECTS) + lib -out:triangle.$(LIB_EXT) $(OBJECTS) + +triangle.$(OBJ_EXT): triangle.c triangle.h + $(CC) $(CSWITCHES) $(TRILIBDEFS) -c triangle.c + +clean: + rm -rf *.$(LIB_EXT) *.$(OBJ_EXT) *.LIB *.LST *.$(OBJ_EXT)bj *.BAK Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-altix64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-altix64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-altix64.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install triangle +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip' + +#Untar +cd install +cp ../triangle.zip ./ +unzip triangle.zip + +#copy new makefile +cp ../configs/altix64/configure.make ./ +cp ../makefile ./ + +#Compile triangle +make + +#Patch triangle.h +patch triangle.h ../triangle.h.patch Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-android.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-android.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-android.sh (revision 18231) @@ -0,0 +1,26 @@ +#!/bin/bash +set -eu + +source $ANDROID_DIR/android_aux.sh + +#Some cleanup +rm -rf install triangle +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip' + +#Untar +cd install +cp ../triangle.zip ./ +unzip triangle.zip + +#copy new makefile +cp ../configs/android/configure.make ./ +cp ../makefile ./ + +#Compile triangle +make + +#Patch triangle.h +patch triangle.h ../triangle.h.patch Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-discover.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-discover.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-discover.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install triangle +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip' + +#Untar +cd install +cp ../triangle.zip ./ +unzip triangle.zip + +#copy new makefile +cp ../configs/pleiades/configure.make ./ +cp ../makefile ./ + +#Compile triangle +make + +#Patch triangle.h +patch triangle.h ../triangle.h.patch Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-linux64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-linux64.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install triangle +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip' + +#Untar +cd install +cp ../triangle.zip ./ +unzip triangle.zip + +#copy new makefile +cp ../configs/linux64/configure.make ./ +cp ../makefile ./ + +#Compile triangle +make + +#Patch triangle.h +patch triangle.h ../triangle.h.patch Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-macosx32.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-macosx32.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-macosx32.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install triangle +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip' + +#Untar +cd install +cp ../triangle.zip ./ +unzip triangle.zip + +#copy new makefile +cp ../configs/macosx32/configure.make ./ +cp ../makefile ./ + +#Compile triangle +make + +#Patch triangle.h +patch triangle.h ../triangle.h.patch Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-macosx64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-macosx64.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install triangle +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip' + +#Untar +cd install +cp ../triangle.zip ./ +unzip triangle.zip + +#copy new makefile +cp ../configs/macosx64/configure.make ./ +cp ../makefile ./ + +#Compile triangle +make + +#Patch triangle.h +patch triangle.h ../triangle.h.patch Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-pleiades.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-pleiades.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-pleiades.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install triangle +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip' + +#Untar +cd install +cp ../triangle.zip ./ +unzip triangle.zip + +#copy new makefile +cp ../configs/pleiades/configure.make ./ +cp ../makefile ./ + +#Compile triangle +make + +#Patch triangle.h +patch triangle.h ../triangle.h.patch Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-win32.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-win32.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-win32.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install triangle +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip' + +#Untar +cd install +cp ../triangle.zip ./ +unzip triangle.zip + +#copy new makefile +cp ../configs/win32/configure.make ./ +cp ../makefile ./ + +#Compile triangle +make + +#Patch triangle.h +patch triangle.h ../triangle.h.patch Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-win7.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-win7.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/install-win7.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install triangle +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip' + +#Untar +cd install +cp ../triangle.zip ./ +unzip triangle.zip + +#copy new makefile +cp ../configs/win7/configure.make ./ +cp ../configs/win7/makefile ./ + +#Compile triangle +make + +#Patch triangle.h +patch triangle.h ../triangle.h.patch Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/makefile =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/makefile (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/makefile (revision 18231) @@ -0,0 +1,32 @@ +#Adaptation of Triangle makefile to compile only the triangle.c file, +#into a standalone library that can then be used to compile mex modules + +include ./configure.make + +ifeq "$(origin CC)" "undefined" + CC = cc +endif + +ifeq "$(origin AR)" "undefined" + AR = ar +endif + +ifeq "$(origin RANLIB)" "undefined" + RANLIB = ranlib +endif + +TRILIBDEFS = -DTRILIBRARY + +all: triangle.$(LIB_EXT) + +OBJECTS=triangle.$(OBJ_EXT) + +triangle.$(LIB_EXT): $(OBJECTS) + $(AR) cr triangle.$(LIB_EXT) $(OBJECTS) + $(RANLIB) triangle.$(LIB_EXT) + +triangle.$(OBJ_EXT): triangle.c triangle.h + $(CC) $(CSWITCHES) $(TRILIBDEFS) -c triangle.c + +clean: + rm -rf *.$(LIB_EXT) *.$(OBJ_EXT) *.LIB *.LST *.$(OBJ_EXT)bj *.BAK Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/triangle.h.patch =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/triangle.h.patch (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/triangle/triangle.h.patch (revision 18231) @@ -0,0 +1,12 @@ +250a251,257 +> /*Patch for ISSM*/ +> #ifndef REAL +> typedef double REAL; +> typedef void VOID; +> #endif +> /*End patch*/ +> +283c290 +< void triangulate(char *, struct triangulateio *, struct triangulateio *, +--- +> extern "C" void triangulate(char *, struct triangulateio *, struct triangulateio *, Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/valgrind/install-altix64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/valgrind/install-altix64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/valgrind/install-altix64.sh (revision 18231) @@ -0,0 +1,28 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install valgrind-3.8.1 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.8.1.tar.bz2' 'valgrind-3.8.1.tar.bz2' + +#Untar +tar -jxvf valgrind-3.8.1.tar.bz2 + +#Move valgrind into install directory +mv valgrind-3.8.1/* install +rm -rf valgrind-3.8.1 + +#configure +cd install +./configure --prefix="$ISSM_DIR/externalpackages/valgrind/install" + +#Compile valgrind +make -j 4 +make install + +#final thing: if mpi is compiled in, soft link its target to a simpler name +cd lib +ln -s valgrind/libmpi* ./libmpidebug.so Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/valgrind/install-linux64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/valgrind/install-linux64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/valgrind/install-linux64.sh (revision 18231) @@ -0,0 +1,28 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install valgrind-3.8.1 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.8.1.tar.bz2' 'valgrind-3.8.1.tar.bz2' + +#Untar +tar -jxvf valgrind-3.8.1.tar.bz2 + +#Move valgrind into install directory +mv valgrind-3.8.1/* install +rm -rf valgrind-3.8.1 + +#configure +cd install +./configure --prefix="$ISSM_DIR/externalpackages/valgrind/install" + +#Compile valgrind +make -j 4 +make install + +#final thing: if mpi is compiled in, soft link its target to a simpler name +cd lib +ln -s valgrind/libmpiwrap-* ./libmpidebug.so Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/valgrind/install-macosx32.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/valgrind/install-macosx32.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/valgrind/install-macosx32.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install valgrind-3.8.1 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.8.1.tar.bz2' 'valgrind-3.8.1.tar.bz2' + +#Untar +tar -jxvf valgrind-3.8.1.tar.bz2 + +#Move valgrind into install directory +mv valgrind-3.8.1/* install +rm -rf valgrind-3.8.1 + +#configure +cd install +./configure --prefix="$ISSM_DIR/externalpackages/valgrind/install" --enable-only32bit + +#Compile valgrind +make -j 4 +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/valgrind/install-macosx64.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/valgrind/install-macosx64.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/valgrind/install-macosx64.sh (revision 18231) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install valgrind-3.8.1 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.8.1.tar.bz2' 'valgrind-3.8.1.tar.bz2' + +#Untar +tar -jxvf valgrind-3.8.1.tar.bz2 + +#Move valgrind into install directory +mv valgrind-3.8.1/* install +rm -rf valgrind-3.8.1 + +#configure +cd install +./configure --prefix="$ISSM_DIR/externalpackages/valgrind/install" --enable-only64bit + +#Compile valgrind +make -j 8 +make install Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/valgrind/install-win32.sh =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/valgrind/install-win32.sh (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/valgrind/install-win32.sh (revision 18231) @@ -0,0 +1,28 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install valgrind-3.8.1 +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.8.1.tar.bz2' 'valgrind-3.8.1.tar.bz2' + +#Untar +tar -jxvf valgrind-3.8.1.tar.bz2 + +#Move valgrind into install directory +mv valgrind-3.8.1/* install +rm -rf valgrind-3.8.1 + +#configure +cd install +./configure --prefix="$ISSM_DIR/externalpackages/valgrind/install" + +#Compile valgrind +make -j 4 +make install + +#final thing: if mpi is compiled in, soft link its target to a simpler name +cd lib +ln -s valgrind/libmpi* ./libmpidebug.so Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/valgrind/issm.supp =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/valgrind/issm.supp (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/valgrind/issm.supp (revision 18231) @@ -0,0 +1,213 @@ +# This holds the errors to be suppressed from valgrind report for ISSM. +# See: http://valgrind.org/docs/manual/manual-core.html#manual-core.suppress +# +# to add errors: +# 1. in m/classes/clusters/generic.m, +# add: --gen-suppressions=all +# 2. in the errlog, copy and paste the suppression log +# in this file. + +#OS specific errors{{{ +#http://stackoverflow.com/questions/14474691/wifstream-with-imbue-locale-produces-valgrind-errors (larsen) +{ + + Memcheck:Addr8 + fun:wcscmp + fun:_ZNSt10moneypunctIwLb1EED1Ev + fun:_ZNSt10moneypunctIwLb1EED0Ev +} +{ + + Memcheck:Addr8 + fun:wcscmp + fun:_ZNSt10moneypunctIwLb0EED1Ev + fun:_ZNSt10moneypunctIwLb0EED0Ev + fun:_ZNSt6locale5_ImplD1Ev + fun:_ZNSt6localeD1Ev + fun:__cxa_finalize + obj:/u/astrid-r1b/morlighe/issmjpl/cron/trunk-jpl/externalpackages/boost/install/lib/libboost_filesystem.so.1.49.0 + obj:/u/astrid-r1b/morlighe/issmjpl/cron/trunk-jpl/externalpackages/boost/install/lib/libboost_filesystem.so.1.49.0 + fun:__run_exit_handlers + fun:exit + fun:(below main) +} +{ + + Memcheck:Leak + fun:_Znwm + fun:_ZNSs4_Rep9_S_createEmmRKSaIcE + fun:_ZNSs12_S_constructIPKcEEPcT_S3_RKSaIcESt20forward_iterator_tag + fun:_ZNSsC1EPKcRKSaIcE +} +#}}} +#PETSc {{{ +{ + + Memcheck:User + fun:PMPI_Get_count + fun:maybe_complete + fun:PMPI_Waitany + fun:MatStashScatterGetMesg_Private + fun:MatAssemblyEnd_MPIAIJ + fun:MatAssemblyEnd +} +{ + + Memcheck:User + fun:PMPI_Get_count + fun:maybe_complete + fun:PMPI_Waitany + fun:VecStashScatterGetMesg_Private + fun:VecAssemblyEnd_MPI + fun:VecAssemblyEnd + fun:_ZN8PetscVec8AssembleEv +} +{ + + Memcheck:User + fun:PMPI_Get_count + fun:PMPI_Recv + fun:_Z14VecToMPISerialPPdP6_p_Veci + fun:_ZN8PetscVec11ToMPISerialEv +} +{ + + Memcheck:User + fun:PMPI_Get_count + fun:maybe_complete + fun:PMPI_Waitany + fun:VecScatterCreate_PtoS + fun:VecScatterCreate + fun:MatSetUpMultiply_MPIAIJ + fun:MatAssemblyEnd_MPIAIJ + fun:MatAssemblyEnd +} +{ + + Memcheck:Leak + fun:malloc + fun:mumps_397.3148 + fun:__mumps_static_mapping_MOD_mumps_369 + fun:dmumps_537_ + fun:dmumps_26_ + fun:dmumps_ + fun:dmumps_f77_ + fun:dmumps_c + fun:MatLUFactorSymbolic_AIJMUMPS + fun:MatLUFactorSymbolic + fun:PCSetUp_LU + fun:PCSetUp +} +{ + + Memcheck:User + fun:PMPI_Get_count + fun:PMPI_Recv + fun:mpi_recv + fun:dmumps_664_ +} +{ + + Memcheck:User + fun:PMPI_Get_count + fun:maybe_complete + fun:PMPI_Waitany + fun:mpi_waitany + fun:dmumps_664_ +} +{ + + Memcheck:User + fun:PMPI_Get_count + fun:PMPI_Recv + fun:mpi_recv + fun:dmumps_282_ +} +{ + + Memcheck:User + fun:PMPI_Get_count + fun:PMPI_Recv + fun:mpi_recv + fun:dmumps_255_ +} +{ + + Memcheck:User + fun:PMPI_Get_count + fun:maybe_complete + fun:PMPI_Wait + fun:PMPI_WAIT + fun:dmumps_255_ +} +{ + + Memcheck:User + fun:PMPI_Get_count + fun:PMPI_Recv + fun:mpi_recv + fun:dmumps_638_ +} +{ + + Memcheck:User + fun:PMPI_Get_count + fun:PMPI_Recv + fun:mpi_recv + fun:dmumps_640.3488 +} +{ + + Memcheck:User + fun:PMPI_Get_count + fun:MPI_GET_COUNT + fun:dmumps_638_ +} +{ + + Memcheck:User + fun:check_mem_is_defined_untyped + fun:PMPI_Pack + fun:PMPI_PACK + fun:__dmumps_comm_buffer_MOD_dmumps_62 +} +{ + + Memcheck:User + fun:check_mem_is_defined_untyped + fun:PMPI_Pack + fun:PMPI_PACK + fun:__dmumps_comm_buffer_MOD_dmumps_62 +} +{ + + Memcheck:User + fun:check_mem_is_defined_untyped + fun:PMPI_Isend + fun:libparmetis__gkMPI_Isend + fun:libparmetis__CommInterfaceData + fun:libparmetis__CompactGraph + fun:libparmetis__MultilevelOrder + fun:ParMETIS_V32_NodeND + fun:ParMETIS_V3_NodeND + fun:mumps_parmetis_ +} +{ + + Memcheck:User + fun:check_mem_is_defined_untyped + fun:PMPI_Bcast + fun:MPI_BCAST + fun:__dmumps_parallel_analysis_MOD_dmumps_718 + fun:__dmumps_parallel_analysis_MOD_dmumps_717 + fun:__dmumps_parallel_analysis_MOD_dmumps_715 +} +{ + + Memcheck:Leak + fun:malloc + fun:__dmumps_parallel_analysis_MOD_dmumps_775 + fun:__dmumps_parallel_analysis_MOD_dmumps_720 + fun:__dmumps_parallel_analysis_MOD_dmumps_715 +} +#}}} Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/vim/addons/README =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/vim/addons/README (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/vim/addons/README (revision 18231) @@ -0,0 +1,5 @@ +To use ISSM's settings for vim: + +1. Add the settings from vimrc to your .vimrc file + +2. Add softlinks from vim to your .vim directory Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/vim/addons/vim/autoload/Align.vim =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/vim/addons/vim/autoload/Align.vim (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/vim/addons/vim/autoload/Align.vim (revision 18231) @@ -0,0 +1,1029 @@ +" Align: tool to align multiple fields based on one or more separators +" Author: Charles E. Campbell, Jr. +" Date: Mar 03, 2009 +" Version: 35 +" GetLatestVimScripts: 294 1 :AutoInstall: Align.vim +" GetLatestVimScripts: 1066 1 :AutoInstall: cecutil.vim +" Copyright: Copyright (C) 1999-2007 Charles E. Campbell, Jr. {{{1 +" Permission is hereby granted to use and distribute this code, +" with or without modifications, provided that this copyright +" notice is copied with it. Like anything else that's free, +" Align.vim is provided *as is* and comes with no warranty +" of any kind, either expressed or implied. By using this +" plugin, you agree that in no event will the copyright +" holder be liable for any damages resulting from the use +" of this software. +" +" Romans 1:16,17a : For I am not ashamed of the gospel of Christ, for it is {{{1 +" the power of God for salvation for everyone who believes; for the Jew first, +" and also for the Greek. For in it is revealed God's righteousness from +" faith to faith. + +" --------------------------------------------------------------------- +" Load Once: {{{1 +if exists("g:loaded_Align") || &cp + finish +endif +let g:loaded_Align = "v35" +if v:version < 700 + echohl WarningMsg + echo "***warning*** this version of Align needs vim 7.0" + echohl Normal + finish +endif +let s:keepcpo= &cpo +set cpo&vim +"DechoTabOn + +" --------------------------------------------------------------------- +" Debugging Support: {{{1 +"if !exists("g:loaded_Decho") | runtime plugin/Decho.vim | endif + +" --------------------------------------------------------------------- +" Options: {{{1 +if !exists("g:Align_xstrlen") + if &enc == "latin1" || $LANG == "en_US.UTF-8" || !has("multi_byte") + let g:Align_xstrlen= 0 + else + let g:Align_xstrlen= 1 + endif +endif + +" --------------------------------------------------------------------- +" Align#AlignCtrl: enter alignment patterns here {{{1 +" +" Styles = all alignment-break patterns are equivalent +" C cycle through alignment-break pattern(s) +" l left-justified alignment +" r right-justified alignment +" c center alignment +" - skip separator, treat as part of field +" : treat rest of line as field +" + repeat previous [lrc] style +" < left justify separators +" > right justify separators +" | center separators +" +" Builds = s:AlignPat s:AlignCtrl s:AlignPatQty +" C s:AlignPat s:AlignCtrl s:AlignPatQty +" p s:AlignPrePad +" P s:AlignPostPad +" w s:AlignLeadKeep +" W s:AlignLeadKeep +" I s:AlignLeadKeep +" l s:AlignStyle +" r s:AlignStyle +" - s:AlignStyle +" + s:AlignStyle +" : s:AlignStyle +" c s:AlignStyle +" g s:AlignGPat +" v s:AlignVPat +" < s:AlignSep +" > s:AlignSep +" | s:AlignSep +fun! Align#AlignCtrl(...) + +" call Dfunc("AlignCtrl(...) a:0=".a:0) + + " save options that will be changed + let keep_search = @/ + let keep_ic = &ic + + " turn ignorecase off + set noic + + " clear visual mode so that old visual-mode selections don't + " get applied to new invocations of Align(). + if v:version < 602 + if !exists("s:Align_gavemsg") + let s:Align_gavemsg= 1 + echomsg "Align needs at least Vim version 6.2 to clear visual-mode selection" + endif + elseif exists("s:dovisclear") +" call Decho("clearing visual mode a:0=".a:0." a:1<".a:1.">") + let clearvmode= visualmode(1) + endif + + " set up a list akin to an argument list + if a:0 > 0 + let A= s:QArgSplitter(a:1) + else + let A=[0] + endif + + if A[0] > 0 + let style = A[1] + + " Check for bad separator patterns (zero-length matches) + " (but zero-length patterns for g/v is ok) + if style !~# '[gv]' + let ipat= 2 + while ipat <= A[0] + if "" =~ A[ipat] + echoerr "AlignCtrl: separator<".A[ipat]."> matches zero-length string" + let &ic= keep_ic +" call Dret("AlignCtrl") + return + endif + let ipat= ipat + 1 + endwhile + endif + endif + +" call Decho("AlignCtrl() A[0]=".A[0]) + if !exists("s:AlignStyle") + let s:AlignStyle= "l" + endif + if !exists("s:AlignPrePad") + let s:AlignPrePad= 0 + endif + if !exists("s:AlignPostPad") + let s:AlignPostPad= 0 + endif + if !exists("s:AlignLeadKeep") + let s:AlignLeadKeep= 'w' + endif + + if A[0] == 0 + " ---------------------- + " List current selection + " ---------------------- + if !exists("s:AlignPatQty") + let s:AlignPatQty= 0 + endif + echo "AlignCtrl<".s:AlignCtrl."> qty=".s:AlignPatQty." AlignStyle<".s:AlignStyle."> Padding<".s:AlignPrePad."|".s:AlignPostPad."> LeadingWS=".s:AlignLeadKeep." AlignSep=".s:AlignSep +" call Decho("AlignCtrl<".s:AlignCtrl."> qty=".s:AlignPatQty." AlignStyle<".s:AlignStyle."> Padding<".s:AlignPrePad."|".s:AlignPostPad."> LeadingWS=".s:AlignLeadKeep." AlignSep=".s:AlignSep) + if exists("s:AlignGPat") && !exists("s:AlignVPat") + echo "AlignGPat<".s:AlignGPat.">" + elseif !exists("s:AlignGPat") && exists("s:AlignVPat") + echo "AlignVPat<".s:AlignVPat.">" + elseif exists("s:AlignGPat") && exists("s:AlignVPat") + echo "AlignGPat<".s:AlignGPat."> AlignVPat<".s:AlignVPat.">" + endif + let ipat= 1 + while ipat <= s:AlignPatQty + echo "Pat".ipat."<".s:AlignPat_{ipat}.">" +" call Decho("Pat".ipat."<".s:AlignPat_{ipat}.">") + let ipat= ipat + 1 + endwhile + + else + " ---------------------------------- + " Process alignment control settings + " ---------------------------------- +" call Decho("process the alignctrl settings") +" call Decho("style<".style.">") + + if style ==? "default" + " Default: preserve initial leading whitespace, left-justified, + " alignment on '=', one space padding on both sides + if exists("s:AlignCtrlStackQty") + " clear AlignCtrl stack + while s:AlignCtrlStackQty > 0 + call Align#AlignPop() + endwhile + unlet s:AlignCtrlStackQty + endif + " Set AlignCtrl to its default value + call Align#AlignCtrl("Ilp1P1=<",'=') + call Align#AlignCtrl("g") + call Align#AlignCtrl("v") + let s:dovisclear = 1 + let &ic = keep_ic + let @/ = keep_search +" call Dret("AlignCtrl") + return + endif + + if style =~# 'm' + " map support: Do an AlignPush now and the next call to Align() + " will do an AlignPop at exit +" call Decho("style case m: do AlignPush") + call Align#AlignPush() + let s:DoAlignPop= 1 + endif + + " = : record a list of alignment patterns that are equivalent + if style =~# "=" +" call Decho("style case =: record list of equiv alignment patterns") + let s:AlignCtrl = '=' + if A[0] >= 2 + let s:AlignPatQty= 1 + let s:AlignPat_1 = A[2] + let ipat = 3 + while ipat <= A[0] + let s:AlignPat_1 = s:AlignPat_1.'\|'.A[ipat] + let ipat = ipat + 1 + endwhile + let s:AlignPat_1= '\('.s:AlignPat_1.'\)' +" call Decho("AlignCtrl<".s:AlignCtrl."> AlignPat<".s:AlignPat_1.">") + endif + + "c : cycle through alignment pattern(s) + elseif style =~# 'C' +" call Decho("style case C: cycle through alignment pattern(s)") + let s:AlignCtrl = 'C' + if A[0] >= 2 + let s:AlignPatQty= A[0] - 1 + let ipat = 1 + while ipat < A[0] + let s:AlignPat_{ipat}= A[ipat+1] +" call Decho("AlignCtrl<".s:AlignCtrl."> AlignQty=".s:AlignPatQty." AlignPat_".ipat."<".s:AlignPat_{ipat}.">") + let ipat= ipat + 1 + endwhile + endif + endif + + if style =~# 'p' + let s:AlignPrePad= substitute(style,'^.*p\(\d\+\).*$','\1','') +" call Decho("style case p".s:AlignPrePad.": pre-separator padding") + if s:AlignPrePad == "" + echoerr "AlignCtrl: 'p' needs to be followed by a numeric argument' + let @/ = keep_search + let &ic= keep_ic +" call Dret("AlignCtrl") + return + endif + endif + + if style =~# 'P' + let s:AlignPostPad= substitute(style,'^.*P\(\d\+\).*$','\1','') +" call Decho("style case P".s:AlignPostPad.": post-separator padding") + if s:AlignPostPad == "" + echoerr "AlignCtrl: 'P' needs to be followed by a numeric argument' + let @/ = keep_search + let &ic= keep_ic +" call Dret("AlignCtrl") + return + endif + endif + + if style =~# 'w' +" call Decho("style case w: ignore leading whitespace") + let s:AlignLeadKeep= 'w' + elseif style =~# 'W' +" call Decho("style case w: keep leading whitespace") + let s:AlignLeadKeep= 'W' + elseif style =~# 'I' +" call Decho("style case w: retain initial leading whitespace") + let s:AlignLeadKeep= 'I' + endif + + if style =~# 'g' + " first list item is a "g" selector pattern +" call Decho("style case g: global selector pattern") + if A[0] < 2 + if exists("s:AlignGPat") + unlet s:AlignGPat +" call Decho("unlet s:AlignGPat") + endif + else + let s:AlignGPat= A[2] +" call Decho("s:AlignGPat<".s:AlignGPat.">") + endif + elseif style =~# 'v' + " first list item is a "v" selector pattern +" call Decho("style case v: global selector anti-pattern") + if A[0] < 2 + if exists("s:AlignVPat") + unlet s:AlignVPat +" call Decho("unlet s:AlignVPat") + endif + else + let s:AlignVPat= A[2] +" call Decho("s:AlignVPat<".s:AlignVPat.">") + endif + endif + + "[-lrc+:] : set up s:AlignStyle + if style =~# '[-lrc+:]' +" call Decho("style case [-lrc+:]: field justification") + let s:AlignStyle= substitute(style,'[^-lrc:+]','','g') +" call Decho("AlignStyle<".s:AlignStyle.">") + endif + + "[<>|] : set up s:AlignSep + if style =~# '[<>|]' +" call Decho("style case [-lrc+:]: separator justification") + let s:AlignSep= substitute(style,'[^<>|]','','g') +" call Decho("AlignSep ".s:AlignSep) + endif + endif + + " sanity + if !exists("s:AlignCtrl") + let s:AlignCtrl= '=' + endif + + " restore search and options + let @/ = keep_search + let &ic= keep_ic + +" call Dret("AlignCtrl ".s:AlignCtrl.'p'.s:AlignPrePad.'P'.s:AlignPostPad.s:AlignLeadKeep.s:AlignStyle) + return s:AlignCtrl.'p'.s:AlignPrePad.'P'.s:AlignPostPad.s:AlignLeadKeep.s:AlignStyle +endfun + +" --------------------------------------------------------------------- +" s:MakeSpace: returns a string with spacecnt blanks {{{1 +fun! s:MakeSpace(spacecnt) +" call Dfunc("MakeSpace(spacecnt=".a:spacecnt.")") + let str = "" + let spacecnt = a:spacecnt + while spacecnt > 0 + let str = str . " " + let spacecnt = spacecnt - 1 + endwhile +" call Dret("MakeSpace <".str.">") + return str +endfun + +" --------------------------------------------------------------------- +" Align#Align: align selected text based on alignment pattern(s) {{{1 +fun! Align#Align(hasctrl,...) range +" call Dfunc("Align#Align(hasctrl=".a:hasctrl.",...) a:0=".a:0) + + " sanity checks + if string(a:hasctrl) != "0" && string(a:hasctrl) != "1" + echohl Error|echo 'usage: Align#Align(hasctrl<'.a:hasctrl.'> (should be 0 or 1),"separator(s)" (you have '.a:0.') )'|echohl None +" call Dret("Align#Align") + return + endif + if exists("s:AlignStyle") && s:AlignStyle == ":" + echohl Error |echo '(Align#Align) your AlignStyle is ":", which implies "do-no-alignment"!'|echohl None +" call Dret("Align#Align") + return + endif + + " set up a list akin to an argument list + if a:0 > 0 + let A= s:QArgSplitter(a:1) + else + let A=[0] + endif + + " if :Align! was used, then the first argument is (should be!) an AlignCtrl string + " Note that any alignment control set this way will be temporary. + let hasctrl= a:hasctrl +" call Decho("hasctrl=".hasctrl) + if a:hasctrl && A[0] >= 1 +" call Decho("Align! : using A[1]<".A[1]."> for AlignCtrl") + if A[1] =~ '[gv]' + let hasctrl= hasctrl + 1 + call Align#AlignCtrl('m') + call Align#AlignCtrl(A[1],A[2]) +" call Decho("Align! : also using A[2]<".A[2]."> for AlignCtrl") + elseif A[1] !~ 'm' + call Align#AlignCtrl(A[1]."m") + else + call Align#AlignCtrl(A[1]) + endif + endif + + " Check for bad separator patterns (zero-length matches) + let ipat= 1 + hasctrl + while ipat <= A[0] + if "" =~ A[ipat] + echoerr "Align: separator<".A[ipat]."> matches zero-length string" +" call Dret("Align#Align") + return + endif + let ipat= ipat + 1 + endwhile + + " record current search pattern for subsequent restoration + let keep_search= @/ + let keep_ic = &ic + let keep_report= &report + set noic report=10000 + + if A[0] > hasctrl + " Align will accept a list of separator regexps +" call Decho("A[0]=".A[0].": accepting list of separator regexp") + + if s:AlignCtrl =~# "=" + "= : consider all separators to be equivalent +" call Decho("AlignCtrl: record list of equivalent alignment patterns") + let s:AlignCtrl = '=' + let s:AlignPat_1 = A[1 + hasctrl] + let s:AlignPatQty= 1 + let ipat = 2 + hasctrl + while ipat <= A[0] + let s:AlignPat_1 = s:AlignPat_1.'\|'.A[ipat] + let ipat = ipat + 1 + endwhile + let s:AlignPat_1= '\('.s:AlignPat_1.'\)' +" call Decho("AlignCtrl<".s:AlignCtrl."> AlignPat<".s:AlignPat_1.">") + + elseif s:AlignCtrl =~# 'C' + "c : cycle through alignment pattern(s) +" call Decho("AlignCtrl: cycle through alignment pattern(s)") + let s:AlignCtrl = 'C' + let s:AlignPatQty= A[0] - hasctrl + let ipat = 1 + while ipat <= s:AlignPatQty + let s:AlignPat_{ipat}= A[(ipat + hasctrl)] +" call Decho("AlignCtrl<".s:AlignCtrl."> AlignQty=".s:AlignPatQty." AlignPat_".ipat."<".s:AlignPat_{ipat}.">") + let ipat= ipat + 1 + endwhile + endif + endif + + " Initialize so that begline + " is greater than the line's string length -> ragged right. + " Have to be careful about visualmode() -- it returns the last visual + " mode used whether or not it was used currently. + let begcol = virtcol("'<")-1 + let endcol = virtcol("'>")-1 + if begcol > endcol + let begcol = virtcol("'>")-1 + let endcol = virtcol("'<")-1 + endif +" call Decho("begcol=".begcol." endcol=".endcol) + let begline = a:firstline + let endline = a:lastline + if begline > endline + let begline = a:lastline + let endline = a:firstline + endif +" call Decho("begline=".begline." endline=".endline) + let fieldcnt = 0 + if (begline == line("'>") && endline == line("'<")) || (begline == line("'<") && endline == line("'>")) + let vmode= visualmode() +" call Decho("vmode=".vmode) + if vmode == "\" + if exists("g:Align_xstrlen") && g:Align_xstrlen + let ragged = ( col("'>") > s:Strlen(getline("'>")) || col("'<") > s:Strlen(getline("'<")) ) + else + let ragged = ( col("'>") > strlen(getline("'>")) || col("'<") > strlen(getline("'<")) ) + endif + else + let ragged= 1 + endif + else + let ragged= 1 + endif + if ragged + let begcol= 0 + endif +" call Decho("lines[".begline.",".endline."] col[".begcol.",".endcol."] ragged=".ragged." AlignCtrl<".s:AlignCtrl.">") + + " Keep user options + let etkeep = &l:et + let pastekeep= &l:paste + setlocal et paste + + " convert selected range of lines to use spaces instead of tabs + " but if first line's initial white spaces are to be retained + " then use 'em + if begcol <= 0 && s:AlignLeadKeep == 'I' + " retain first leading whitespace for all subsequent lines + let bgntxt= substitute(getline(begline),'^\(\s*\).\{-}$','\1','') +" call Decho("retaining 1st leading whitespace: bgntxt<".bgntxt.">") + set noet + endif + exe begline.",".endline."ret" + + " Execute two passes + " First pass: collect alignment data (max field sizes) + " Second pass: perform alignment + let pass= 1 + while pass <= 2 +" call Decho(" ") +" call Decho("---- Pass ".pass.": ----") + + let line= begline + while line <= endline + " Process each line + let txt = getline(line) +" call Decho(" ") +" call Decho("Pass".pass.": Line ".line." <".txt.">") + + " AlignGPat support: allows a selector pattern (akin to g/selector/cmd ) + if exists("s:AlignGPat") +" call Decho("Pass".pass.": AlignGPat<".s:AlignGPat.">") + if match(txt,s:AlignGPat) == -1 +" call Decho("Pass".pass.": skipping") + let line= line + 1 + continue + endif + endif + + " AlignVPat support: allows a selector pattern (akin to v/selector/cmd ) + if exists("s:AlignVPat") +" call Decho("Pass".pass.": AlignVPat<".s:AlignVPat.">") + if match(txt,s:AlignVPat) != -1 +" call Decho("Pass".pass.": skipping") + let line= line + 1 + continue + endif + endif + + " Always skip blank lines + if match(txt,'^\s*$') != -1 +" call Decho("Pass".pass.": skipping") + let line= line + 1 + continue + endif + + " Extract visual-block selected text (init bgntxt, endtxt) + if exists("g:Align_xstrlen") && g:Align_xstrlen + let txtlen= s:Strlen(txt) + else + let txtlen= strlen(txt) + endif + if begcol > 0 + " Record text to left of selected area + let bgntxt= strpart(txt,0,begcol) +" call Decho("Pass".pass.": record text to left: bgntxt<".bgntxt.">") + elseif s:AlignLeadKeep == 'W' + let bgntxt= substitute(txt,'^\(\s*\).\{-}$','\1','') +" call Decho("Pass".pass.": retaining all leading ws: bgntxt<".bgntxt.">") + elseif s:AlignLeadKeep == 'w' || !exists("bgntxt") + " No beginning text + let bgntxt= "" +" call Decho("Pass".pass.": no beginning text") + endif + if ragged + let endtxt= "" + else + " Elide any text lying outside selected columnar region + let endtxt= strpart(txt,endcol+1,txtlen-endcol) + let txt = strpart(txt,begcol,endcol-begcol+1) + endif +" call Decho(" ") +" call Decho("Pass".pass.": bgntxt<".bgntxt.">") +" call Decho("Pass".pass.": txt<". txt .">") +" call Decho("Pass".pass.": endtxt<".endtxt.">") + if !exists("s:AlignPat_{1}") + echohl Error|echo "no separators specified!"|echohl None +" call Dret("Align#Align") + return + endif + + " Initialize for both passes + let seppat = s:AlignPat_{1} + let ifield = 1 + let ipat = 1 + let bgnfield = 0 + let endfield = 0 + let alignstyle = s:AlignStyle + let doend = 1 + let newtxt = "" + let alignprepad = s:AlignPrePad + let alignpostpad= s:AlignPostPad + let alignsep = s:AlignSep + let alignophold = " " + let alignop = "l" +" call Decho("Pass".pass.": initial alignstyle<".alignstyle."> seppat<".seppat.">") + + " Process each field on the line + while doend > 0 + + " C-style: cycle through pattern(s) + if s:AlignCtrl == 'C' && doend == 1 + let seppat = s:AlignPat_{ipat} +" call Decho("Pass".pass.": processing field: AlignCtrl=".s:AlignCtrl." ipat=".ipat." seppat<".seppat.">") + let ipat = ipat + 1 + if ipat > s:AlignPatQty + let ipat = 1 + endif + endif + + " cyclic alignment/justification operator handling + let alignophold = alignop + let alignop = strpart(alignstyle,0,1) + if alignop == '+' || doend == 2 + let alignop= alignophold + else + let alignstyle = strpart(alignstyle,1).strpart(alignstyle,0,1) + let alignopnxt = strpart(alignstyle,0,1) + if alignop == ':' + let seppat = '$' + let doend = 2 +" call Decho("Pass".pass.": alignop<:> case: setting seppat<$> doend==2") + endif + endif + + " cylic separator alignment specification handling + let alignsepop= strpart(alignsep,0,1) + let alignsep = strpart(alignsep,1).alignsepop + + " mark end-of-field and the subsequent end-of-separator. + " Extend field if alignop is '-' + let endfield = match(txt,seppat,bgnfield) + let sepfield = matchend(txt,seppat,bgnfield) + let skipfield= sepfield +" call Decho("Pass".pass.": endfield=match(txt<".txt.">,seppat<".seppat.">,bgnfield=".bgnfield.")=".endfield) + while alignop == '-' && endfield != -1 + let endfield = match(txt,seppat,skipfield) + let sepfield = matchend(txt,seppat,skipfield) + let skipfield = sepfield + let alignop = strpart(alignstyle,0,1) + let alignstyle= strpart(alignstyle,1).strpart(alignstyle,0,1) +" call Decho("Pass".pass.": extend field: endfield<".strpart(txt,bgnfield,endfield-bgnfield)."> alignop<".alignop."> alignstyle<".alignstyle.">") + endwhile + let seplen= sepfield - endfield +" call Decho("Pass".pass.": seplen=[sepfield=".sepfield."] - [endfield=".endfield."]=".seplen) + + if endfield != -1 + if pass == 1 + " --------------------------------------------------------------------- + " Pass 1: Update FieldSize to max +" call Decho("Pass".pass.": before lead/trail remove: field<".strpart(txt,bgnfield,endfield-bgnfield).">") + let field = substitute(strpart(txt,bgnfield,endfield-bgnfield),'^\s*\(.\{-}\)\s*$','\1','') + if s:AlignLeadKeep == 'W' + let field = bgntxt.field + let bgntxt= "" + endif + if exists("g:Align_xstrlen") && g:Align_xstrlen + let fieldlen = s:Strlen(field) + else + let fieldlen = strlen(field) + endif + let sFieldSize = "FieldSize_".ifield + if !exists(sFieldSize) + let FieldSize_{ifield}= fieldlen +" call Decho("Pass".pass.": set FieldSize_{".ifield."}=".FieldSize_{ifield}." <".field.">") + elseif fieldlen > FieldSize_{ifield} + let FieldSize_{ifield}= fieldlen +" call Decho("Pass".pass.": oset FieldSize_{".ifield."}=".FieldSize_{ifield}." <".field.">") + endif + let sSepSize= "SepSize_".ifield + if !exists(sSepSize) + let SepSize_{ifield}= seplen +" call Decho(" set SepSize_{".ifield."}=".SepSize_{ifield}." <".field.">") + elseif seplen > SepSize_{ifield} + let SepSize_{ifield}= seplen +" call Decho("Pass".pass.": oset SepSize_{".ifield."}=".SepSize_{ifield}." <".field.">") + endif + + else + " --------------------------------------------------------------------- + " Pass 2: Perform Alignment + let prepad = strpart(alignprepad,0,1) + let postpad = strpart(alignpostpad,0,1) + let alignprepad = strpart(alignprepad,1).strpart(alignprepad,0,1) + let alignpostpad = strpart(alignpostpad,1).strpart(alignpostpad,0,1) + let field = substitute(strpart(txt,bgnfield,endfield-bgnfield),'^\s*\(.\{-}\)\s*$','\1','') + if s:AlignLeadKeep == 'W' + let field = bgntxt.field + let bgntxt= "" + endif + if doend == 2 + let prepad = 0 + let postpad= 0 + endif + if exists("g:Align_xstrlen") && g:Align_xstrlen + let fieldlen = s:Strlen(field) + else + let fieldlen = strlen(field) + endif + let sep = s:MakeSpace(prepad).strpart(txt,endfield,sepfield-endfield).s:MakeSpace(postpad) + if seplen < SepSize_{ifield} + if alignsepop == "<" + " left-justify separators + let sep = sep.s:MakeSpace(SepSize_{ifield}-seplen) + elseif alignsepop == ">" + " right-justify separators + let sep = s:MakeSpace(SepSize_{ifield}-seplen).sep + else + " center-justify separators + let sepleft = (SepSize_{ifield} - seplen)/2 + let sepright = SepSize_{ifield} - seplen - sepleft + let sep = s:MakeSpace(sepleft).sep.s:MakeSpace(sepright) + endif + endif + let spaces = FieldSize_{ifield} - fieldlen +" call Decho("Pass".pass.": Field #".ifield."<".field."> spaces=".spaces." be[".bgnfield.",".endfield."] pad=".prepad.','.postpad." FS_".ifield."<".FieldSize_{ifield}."> sep<".sep."> ragged=".ragged." doend=".doend." alignop<".alignop.">") + + " Perform alignment according to alignment style justification + if spaces > 0 + if alignop == 'c' + " center the field + let spaceleft = spaces/2 + let spaceright= FieldSize_{ifield} - spaceleft - fieldlen + let newtxt = newtxt.s:MakeSpace(spaceleft).field.s:MakeSpace(spaceright).sep + elseif alignop == 'r' + " right justify the field + let newtxt= newtxt.s:MakeSpace(spaces).field.sep + elseif ragged && doend == 2 + " left justify rightmost field (no trailing blanks needed) + let newtxt= newtxt.field + else + " left justfiy the field + let newtxt= newtxt.field.s:MakeSpace(spaces).sep + endif + elseif ragged && doend == 2 + " field at maximum field size and no trailing blanks needed + let newtxt= newtxt.field + else + " field is at maximum field size already + let newtxt= newtxt.field.sep + endif +" call Decho("Pass".pass.": newtxt<".newtxt.">") + endif " pass 1/2 + + " bgnfield indexes to end of separator at right of current field + " Update field counter + let bgnfield= sepfield + let ifield = ifield + 1 + if doend == 2 + let doend= 0 + endif + " handle end-of-text as end-of-field + elseif doend == 1 + let seppat = '$' + let doend = 2 + else + let doend = 0 + endif " endfield != -1 + endwhile " doend loop (as well as regularly separated fields) + + if pass == 2 + " Write altered line to buffer +" call Decho("Pass".pass.": bgntxt<".bgntxt."> line=".line) +" call Decho("Pass".pass.": newtxt<".newtxt.">") +" call Decho("Pass".pass.": endtxt<".endtxt.">") + call setline(line,bgntxt.newtxt.endtxt) + endif + + let line = line + 1 + endwhile " line loop + + let pass= pass + 1 + endwhile " pass loop +" call Decho("end of two pass loop") + + " Restore user options + let &l:et = etkeep + let &l:paste = pastekeep + + if exists("s:DoAlignPop") + " AlignCtrl Map support + call Align#AlignPop() + unlet s:DoAlignPop + endif + + " restore current search pattern + let @/ = keep_search + let &ic = keep_ic + let &report = keep_report + +" call Dret("Align#Align") + return +endfun + +" --------------------------------------------------------------------- +" Align#AlignPush: this command/function pushes an alignment control string onto a stack {{{1 +fun! Align#AlignPush() +" call Dfunc("AlignPush()") + + " initialize the stack + if !exists("s:AlignCtrlStackQty") + let s:AlignCtrlStackQty= 1 + else + let s:AlignCtrlStackQty= s:AlignCtrlStackQty + 1 + endif + + " construct an AlignCtrlStack entry + if !exists("s:AlignSep") + let s:AlignSep= '' + endif + let s:AlignCtrlStack_{s:AlignCtrlStackQty}= s:AlignCtrl.'p'.s:AlignPrePad.'P'.s:AlignPostPad.s:AlignLeadKeep.s:AlignStyle.s:AlignSep +" call Decho("AlignPush: AlignCtrlStack_".s:AlignCtrlStackQty."<".s:AlignCtrlStack_{s:AlignCtrlStackQty}.">") + + " push [GV] patterns onto their own stack + if exists("s:AlignGPat") + let s:AlignGPat_{s:AlignCtrlStackQty}= s:AlignGPat + else + let s:AlignGPat_{s:AlignCtrlStackQty}= "" + endif + if exists("s:AlignVPat") + let s:AlignVPat_{s:AlignCtrlStackQty}= s:AlignVPat + else + let s:AlignVPat_{s:AlignCtrlStackQty}= "" + endif + +" call Dret("AlignPush") +endfun + +" --------------------------------------------------------------------- +" Align#AlignPop: this command/function pops an alignment pattern from a stack {{{1 +" and into the AlignCtrl variables. +fun! Align#AlignPop() +" call Dfunc("Align#AlignPop()") + + " sanity checks + if !exists("s:AlignCtrlStackQty") + echoerr "AlignPush needs to be used prior to AlignPop" +" call Dret("Align#AlignPop <> : AlignPush needs to have been called first") + return "" + endif + if s:AlignCtrlStackQty <= 0 + unlet s:AlignCtrlStackQty + echoerr "AlignPush needs to be used prior to AlignPop" +" call Dret("Align#AlignPop <> : AlignPop needs to have been called first") + return "" + endif + + " pop top of AlignCtrlStack and pass value to AlignCtrl + let retval=s:AlignCtrlStack_{s:AlignCtrlStackQty} + unlet s:AlignCtrlStack_{s:AlignCtrlStackQty} + call Align#AlignCtrl(retval) + + " pop G pattern stack + if s:AlignGPat_{s:AlignCtrlStackQty} != "" + call Align#AlignCtrl('g',s:AlignGPat_{s:AlignCtrlStackQty}) + else + call Align#AlignCtrl('g') + endif + unlet s:AlignGPat_{s:AlignCtrlStackQty} + + " pop V pattern stack + if s:AlignVPat_{s:AlignCtrlStackQty} != "" + call Align#AlignCtrl('v',s:AlignVPat_{s:AlignCtrlStackQty}) + else + call Align#AlignCtrl('v') + endif + + unlet s:AlignVPat_{s:AlignCtrlStackQty} + let s:AlignCtrlStackQty= s:AlignCtrlStackQty - 1 + +" call Dret("Align#AlignPop <".retval."> : AlignCtrlStackQty=".s:AlignCtrlStackQty) + return retval +endfun + +" --------------------------------------------------------------------- +" Align#AlignReplaceQuotedSpaces: {{{1 +fun! Align#AlignReplaceQuotedSpaces() +" call Dfunc("AlignReplaceQuotedSpaces()") + + let l:line = getline(line(".")) + if exists("g:Align_xstrlen") && g:Align_xstrlen + let l:linelen = s:Strlen(l:line) + else + let l:linelen = strlen(l:line) + endif + let l:startingPos = 0 + let l:startQuotePos = 0 + let l:endQuotePos = 0 + let l:spacePos = 0 + let l:quoteRe = '\\\@, is needed. {{{1 +" However, doesn't split at all, so this function returns a list +" of arguments which has been: +" * split at whitespace +" * unless inside "..."s. One may escape characters with a backslash inside double quotes. +" along with a leading length-of-list. +" +" Examples: %Align "\"" will align on "s +" %Align " " will align on spaces +" +" The resulting list: qarglist[0] corresponds to a:0 +" qarglist[i] corresponds to a:{i} +fun! s:QArgSplitter(qarg) +" call Dfunc("s:QArgSplitter(qarg<".a:qarg.">)") + + if a:qarg =~ '".*"' + " handle "..." args, which may include whitespace + let qarglist = [] + let args = a:qarg +" call Decho("handle quoted arguments: args<".args.">") + while args != "" + let iarg = 0 + let arglen = strlen(args) +" call Decho("args[".iarg."]<".args[iarg]."> arglen=".arglen) + " find index to first not-escaped '"' + while args[iarg] != '"' && iarg < arglen + if args[iarg] == '\' + let args= strpart(args,1) + endif + let iarg= iarg + 1 + endwhile +" call Decho("args<".args."> iarg=".iarg." arglen=".arglen) + + if iarg > 0 + " handle left of quote or remaining section +" call Decho("handle left of quote or remaining section") + if args[iarg] == '"' + let qarglist= qarglist + split(strpart(args,0,iarg-1)) + else + let qarglist= qarglist + split(strpart(args,0,iarg)) + endif + let args = strpart(args,iarg) + let arglen = strlen(args) + + elseif iarg < arglen && args[0] == '"' + " handle "quoted" section +" call Decho("handle quoted section") + let iarg= 1 + while args[iarg] != '"' && iarg < arglen + if args[iarg] == '\' + let args= strpart(args,1) + endif + let iarg= iarg + 1 + endwhile +" call Decho("args<".args."> iarg=".iarg." arglen=".arglen) + if args[iarg] == '"' + call add(qarglist,strpart(args,1,iarg-1)) + let args= strpart(args,iarg+1) + else + let qarglist = qarglist + split(args) + let args = "" + endif + endif +" call Decho("qarglist".string(qarglist)." iarg=".iarg." args<".args.">") + endwhile + + else + " split at all whitespace + let qarglist= split(a:qarg) + endif + + let qarglistlen= len(qarglist) + let qarglist = insert(qarglist,qarglistlen) +" call Dret("s:QArgSplitter ".string(qarglist)) + return qarglist +endfun + +" --------------------------------------------------------------------- +" s:Strlen: this function returns the length of a string, even if its {{{1 +" using two-byte etc characters. +" Currently, its only used if g:Align_xstrlen is set to a +" nonzero value. Solution from Nicolai Weibull, vim docs +" (:help strlen()), Tony Mechelynck, and my own invention. +fun! s:Strlen(x) +" call Dfunc("s:Strlen(x<".a:x.">") + if g:Align_xstrlen == 1 + " number of codepoints (Latin a + combining circumflex is two codepoints) + " (comment from TM, solution from NW) + let ret= strlen(substitute(a:x,'.','c','g')) + + elseif g:Align_xstrlen == 2 + " number of spacing codepoints (Latin a + combining circumflex is one spacing + " codepoint; a hard tab is one; wide and narrow CJK are one each; etc.) + " (comment from TM, solution from TM) + let ret=strlen(substitute(a:x, '.\Z', 'x', 'g')) + + elseif g:Align_xstrlen == 3 + " virtual length (counting, for instance, tabs as anything between 1 and + " 'tabstop', wide CJK as 2 rather than 1, Arabic alif as zero when immediately + " preceded by lam, one otherwise, etc.) + " (comment from TM, solution from me) + let modkeep= &l:mod + exe "norm! o\" + call setline(line("."),a:x) + let ret= virtcol("$") - 1 + d + let &l:mod= modkeep + + else + " at least give a decent default + ret= strlen(a:x) + endif +" call Dret("s:Strlen ".ret) + return ret +endfun + +" --------------------------------------------------------------------- +" Set up default values: {{{1 +"call Decho("-- Begin AlignCtrl Initialization --") +call Align#AlignCtrl("default") +"call Decho("-- End AlignCtrl Initialization --") + +" --------------------------------------------------------------------- +" Restore: {{{1 +let &cpo= s:keepcpo +unlet s:keepcpo +" vim: ts=4 fdm=marker Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/vim/addons/vim/autoload/AlignMaps.vim =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/vim/addons/vim/autoload/AlignMaps.vim (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/vim/addons/vim/autoload/AlignMaps.vim (revision 18231) @@ -0,0 +1,330 @@ +" AlignMaps.vim : support functions for AlignMaps +" Author: Charles E. Campbell, Jr. +" Date: Mar 03, 2009 +" Version: 41 +" --------------------------------------------------------------------- +" Load Once: {{{1 +if &cp || exists("g:loaded_AlignMaps") + finish +endif +let g:loaded_AlignMaps= "v41" +let s:keepcpo = &cpo +set cpo&vim + +" ===================================================================== +" Functions: {{{1 + +" --------------------------------------------------------------------- +" AlignMaps#WrapperStart: {{{2 +fun! AlignMaps#WrapperStart(vis) range +" call Dfunc("AlignMaps#WrapperStart(vis=".a:vis.")") + + if a:vis + norm! ' + endif + + if line("'y") == 0 || line("'z") == 0 || !exists("s:alignmaps_wrapcnt") || s:alignmaps_wrapcnt <= 0 +" call Decho("wrapper initialization") + let s:alignmaps_wrapcnt = 1 + let s:alignmaps_keepgd = &gdefault + let s:alignmaps_keepsearch = @/ + let s:alignmaps_keepch = &ch + let s:alignmaps_keepmy = SaveMark("'y") + let s:alignmaps_keepmz = SaveMark("'z") + let s:alignmaps_posn = SaveWinPosn(0) + " set up fencepost blank lines + put ='' + norm! mz'a + put! ='' + ky + let s:alignmaps_zline = line("'z") + exe "'y,'zs/@/\177/ge" + else +" call Decho("embedded wrapper") + let s:alignmaps_wrapcnt = s:alignmaps_wrapcnt + 1 + norm! 'yjma'zk + endif + + " change some settings to align-standard values + set nogd + set ch=2 + AlignPush + norm! 'zk +" call Dret("AlignMaps#WrapperStart : alignmaps_wrapcnt=".s:alignmaps_wrapcnt." my=".line("'y")." mz=".line("'z")) +endfun + +" --------------------------------------------------------------------- +" AlignMaps#WrapperEnd: {{{2 +fun! AlignMaps#WrapperEnd() range +" call Dfunc("AlignMaps#WrapperEnd() alignmaps_wrapcnt=".s:alignmaps_wrapcnt." my=".line("'y")." mz=".line("'z")) + + " remove trailing white space introduced by whatever in the modification zone + 'y,'zs/ \+$//e + + " restore AlignCtrl settings + AlignPop + + let s:alignmaps_wrapcnt= s:alignmaps_wrapcnt - 1 + if s:alignmaps_wrapcnt <= 0 + " initial wrapper ending + exe "'y,'zs/\177/@/ge" + + " if the 'z line hasn't moved, then go ahead and restore window position + let zstationary= s:alignmaps_zline == line("'z") + + " remove fencepost blank lines. + " restore 'a + norm! 'yjmakdd'zdd + + " restore original 'y, 'z, and window positioning + call RestoreMark(s:alignmaps_keepmy) + call RestoreMark(s:alignmaps_keepmz) + if zstationary > 0 + call RestoreWinPosn(s:alignmaps_posn) +" call Decho("restored window positioning") + endif + + " restoration of options + let &gd= s:alignmaps_keepgd + let &ch= s:alignmaps_keepch + let @/ = s:alignmaps_keepsearch + + " remove script variables + unlet s:alignmaps_keepch + unlet s:alignmaps_keepsearch + unlet s:alignmaps_keepmy + unlet s:alignmaps_keepmz + unlet s:alignmaps_keepgd + unlet s:alignmaps_posn + endif + +" call Dret("AlignMaps#WrapperEnd : alignmaps_wrapcnt=".s:alignmaps_wrapcnt." my=".line("'y")." mz=".line("'z")) +endfun + +" --------------------------------------------------------------------- +" AlignMaps#StdAlign: some semi-standard align calls {{{2 +fun! AlignMaps#StdAlign(mode) range +" call Dfunc("AlignMaps#StdAlign(mode=".a:mode.")") + if a:mode == 1 + " align on @ +" call Decho("align on @") + AlignCtrl mIp1P1=l @ + 'a,.Align + elseif a:mode == 2 + " align on @, retaining all initial white space on each line +" call Decho("align on @, retaining all initial white space on each line") + AlignCtrl mWp1P1=l @ + 'a,.Align + elseif a:mode == 3 + " like mode 2, but ignore /* */-style comments +" call Decho("like mode 2, but ignore /* */-style comments") + AlignCtrl v ^\s*/[/*] + AlignCtrl mWp1P1=l @ + 'a,.Align + else + echoerr "(AlignMaps) AlignMaps#StdAlign doesn't support mode#".a:mode + endif +" call Dret("AlignMaps#StdAlign") +endfun + +" --------------------------------------------------------------------- +" AlignMaps#CharJoiner: joins lines which end in the given character (spaces {{{2 +" at end are ignored) +fun! AlignMaps#CharJoiner(chr) +" call Dfunc("AlignMaps#CharJoiner(chr=".a:chr.")") + let aline = line("'a") + let rep = line(".") - aline + while rep > 0 + norm! 'a + while match(getline(aline),a:chr . "\s*$") != -1 && rep >= 0 + " while = at end-of-line, delete it and join with next + norm! 'a$ + j! + let rep = rep - 1 + endwhile + " update rep(eat) count + let rep = rep - 1 + if rep <= 0 + " terminate loop if at end-of-block + break + endif + " prepare for next line + norm! jma + let aline = line("'a") + endwhile +" call Dret("AlignMaps#CharJoiner") +endfun + +" --------------------------------------------------------------------- +" AlignMaps#Equals: supports \t= and \T= {{{2 +fun! AlignMaps#Equals() range +" call Dfunc("AlignMaps#Equals()") + 'a,'zs/\s\+\([*/+\-%|&\~^]\==\)/ \1/e + 'a,'zs@ \+\([*/+\-%|&\~^]\)=@\1=@ge + 'a,'zs/==/\="\\"/ge + 'a,'zs/\([!<>:]\)=/\=submatch(1)."\"/ge + norm g'zk + AlignCtrl mIp1P1=l = + AlignCtrl g = + 'a,'z-1Align + 'a,'z-1s@\([*/+\-%|&\~^!=]\)\( \+\)=@\2\1=@ge + 'a,'z-1s/\( \+\);/;\1/ge + if &ft == "c" || &ft == "cpp" +" call Decho("exception for ".&ft) + 'a,'z-1v/^\s*\/[*/]/s/\/[*/]/@&@/e + 'a,'z-1v/^\s*\/[*/]/s/\*\//@&/e + if exists("g:mapleader") + exe "norm 'zk" + call AlignMaps#StdAlign(1) + else + exe "norm 'zk" + call AlignMaps#StdAlign(1) + endif + 'y,'zs/^\(\s*\) @/\1/e + endif + 'a,'z-1s/\%x0f/=/ge + 'y,'zs/ @//eg +" call Dret("AlignMaps#Equals") +endfun + +" --------------------------------------------------------------------- +" AlignMaps#Afnc: useful for splitting one-line function beginnings {{{2 +" into one line per argument format +fun! AlignMaps#Afnc() +" call Dfunc("AlignMaps#Afnc()") + + " keep display quiet + let chkeep = &ch + let gdkeep = &gd + let vekeep = &ve + set ch=2 nogd ve= + + " will use marks y,z ; save current values + let mykeep = SaveMark("'y") + let mzkeep = SaveMark("'z") + + " Find beginning of function -- be careful to skip over comments + let cmmntid = synIDtrans(hlID("Comment")) + let stringid = synIDtrans(hlID("String")) + exe "norm! ]]" + while search(")","bW") != 0 +" call Decho("line=".line(".")." col=".col(".")) + let parenid= synIDtrans(synID(line("."),col("."),1)) + if parenid != cmmntid && parenid != stringid + break + endif + endwhile + norm! %my + s/(\s*\(\S\)/(\r \1/e + exe "norm! `y%" + s/)\s*\(\/[*/]\)/)\r\1/e + exe "norm! `y%mz" + 'y,'zs/\s\+$//e + 'y,'zs/^\s\+//e + 'y+1,'zs/^/ / + + " insert newline after every comma only one parenthesis deep + sil! exe "norm! `y\h" + let parens = 1 + let cmmnt = 0 + let cmmntline= -1 + while parens >= 1 +" call Decho("parens=".parens." @a=".@a) + exe 'norm! ma "ay`a ' + if @a == "(" + let parens= parens + 1 + elseif @a == ")" + let parens= parens - 1 + + " comment bypass: /* ... */ or //... + elseif cmmnt == 0 && @a == '/' + let cmmnt= 1 + elseif cmmnt == 1 + if @a == '/' + let cmmnt = 2 " //... + let cmmntline= line(".") + elseif @a == '*' + let cmmnt= 3 " /*... + else + let cmmnt= 0 + endif + elseif cmmnt == 2 && line(".") != cmmntline + let cmmnt = 0 + let cmmntline= -1 + elseif cmmnt == 3 && @a == '*' + let cmmnt= 4 + elseif cmmnt == 4 + if @a == '/' + let cmmnt= 0 " ...*/ + elseif @a != '*' + let cmmnt= 3 + endif + + elseif @a == "," && parens == 1 && cmmnt == 0 + exe "norm! i\\" + endif + endwhile + norm! `y%mz% + sil! 'y,'zg/^\s*$/d + + " perform substitutes to mark fields for Align + sil! 'y+1,'zv/^\//s/^\s\+\(\S\)/ \1/e + sil! 'y+1,'zv/^\//s/\(\S\)\s\+/\1 /eg + sil! 'y+1,'zv/^\//s/\* \+/*/ge + sil! 'y+1,'zv/^\//s/\w\zs\s*\*/ */ge + " func + " ws <- declaration -> <-ptr -> <-var-> <-[array][] -> <-glop-> <-end-> + sil! 'y+1,'zv/^\//s/^\s*\(\(\K\k*\s*\)\+\)\s\+\([(*]*\)\s*\(\K\k*\)\s*\(\(\[.\{-}]\)*\)\s*\(.\{-}\)\=\s*\([,)]\)\s*$/ \1@#\3@\4\5@\7\8/e + sil! 'y+1,'z+1g/^\s*\/[*/]/norm! kJ + sil! 'y+1,'z+1s%/[*/]%@&@%ge + sil! 'y+1,'z+1s%*/%@&%ge + AlignCtrl mIp0P0=l @ + sil! 'y+1,'zAlign + sil! 'y,'zs%@\(/[*/]\)@%\t\1 %e + sil! 'y,'zs%@\*/% */%e + sil! 'y,'zs/@\([,)]\)/\1/ + sil! 'y,'zs/@/ / + AlignCtrl mIlrp0P0= # @ + sil! 'y+1,'zAlign + sil! 'y+1,'zs/#/ / + sil! 'y+1,'zs/@// + sil! 'y+1,'zs/\(\s\+\)\([,)]\)/\2\1/e + + " Restore + call RestoreMark(mykeep) + call RestoreMark(mzkeep) + let &ch= chkeep + let &gd= gdkeep + let &ve= vekeep + +" call Dret("AlignMaps#Afnc") +endfun + +" --------------------------------------------------------------------- +" AlignMaps#FixMultiDec: converts a type arg,arg,arg; line to multiple lines {{{2 +fun! AlignMaps#FixMultiDec() +" call Dfunc("AlignMaps#FixMultiDec()") + + " save register x + let xkeep = @x + let curline = getline(".") +" call Decho("curline<".curline.">") + + " Get the type. I'm assuming one type per line (ie. int x; double y; on one line will not be handled properly) + let @x=substitute(curline,'^\(\s*[a-zA-Z_ \t][a-zA-Z0-9_ \t]*\)\s\+[(*]*\h.*$','\1','') +" call Decho("@x<".@x.">") + + " transform line + exe 's/,/;\r'.@x.' /ge' + + "restore register x + let @x= xkeep + +" call Dret("AlignMaps#FixMultiDec : my=".line("'y")." mz=".line("'z")) +endfun + +" --------------------------------------------------------------------- +" Restore: {{{1 +let &cpo= s:keepcpo +unlet s:keepcpo +" vim: ts=4 fdm=marker Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/vim/addons/vim/colors/issm_black.vim =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/vim/addons/vim/colors/issm_black.vim (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/vim/addons/vim/colors/issm_black.vim (revision 18231) @@ -0,0 +1,86 @@ +" issm_black color scheme +" table http://www.calmar.ws/vim/256-xterm-24bit-rgb-color-chart.html + +"Set up coloring +hi clear +if exists("syntax_on") + syntax reset +endif +syntax on +let colors_name = "issm_black" + +"preferred colors: +" 0 : black +" 9 : red +" 15 : white +" 69 : blue +" 87 : cyan +" 129 : dark purple +" 202 : orange +" 214 : light orange +" 227 : yellow +" 234 : very dark gray +" 241 : dark gray +" 244 : gray +" 255 : light gray + +" forground background style (reverse,bold,..) +" General colors +hi Normal ctermfg=NONE ctermbg=NONE cterm=NONE +hi NonText ctermfg=129 ctermbg=NONE cterm=NONE +hi Cursor ctermfg=NONE ctermbg=NONE cterm=reverse +hi LineNr ctermfg=15 ctermbg=241 cterm=NONE +hi VertSplit ctermfg=241 ctermbg=241 cterm=NONE +hi StatusLine ctermfg=241 ctermbg=87 cterm=NONE +hi StatusLineNC ctermfg=87 ctermbg=241 cterm=NONE +hi Folded ctermfg=141 ctermbg=236 cterm=NONE +hi Title ctermfg=NONE ctermbg=NONE cterm=NONE +hi Visual ctermfg=NONE ctermbg=NONE cterm=reverse +hi SpecialKey ctermfg=NONE ctermbg=NONE cterm=NONE +hi WildMenu ctermfg=0 ctermbg=227 cterm=NONE +hi PmenuSbar ctermfg=0 ctermbg=129 cterm=NONE +hi Error ctermfg=15 ctermbg=129 cterm=NONE +hi ErrorMsg ctermfg=15 ctermbg=129 cterm=NONE +hi WarningMsg ctermfg=15 ctermbg=129 cterm=NONE + +" Message displayed in lower left, such as --INSERT-- +hi ModeMsg ctermfg=0 ctermbg=87 cterm=BOLD +if version >= 700 " Vim 7.x specific colors + hi CursorLine ctermfg=NONE ctermbg=NONE cterm=BOLD + hi CursorColumn ctermfg=NONE ctermbg=NONE cterm=BOLD + hi MatchParen ctermfg=87 ctermbg=241 cterm=reverse "matching parenthesis + hi Pmenu ctermfg=0 ctermbg=15 cterm=NONE "auto completion panel + hi PmenuSel ctermfg=255 ctermbg=241 cterm=NONE + hi Search ctermfg=0 ctermbg=220 cterm=NONE +endif + +" Syntax highlighting +hi Comment ctermfg=244 ctermbg=NONE cterm=NONE +hi String ctermfg=120 ctermbg=NONE cterm=NONE +hi Number ctermfg=201 ctermbg=NONE cterm=NONE +hi Keyword ctermfg=9 ctermbg=NONE cterm=NONE " matlab function +hi PreProc ctermfg=9 ctermbg=NONE cterm=NONE " def undef include +hi Conditional ctermfg=220 ctermbg=NONE cterm=NONE " if else end +hi Todo ctermfg=214 ctermbg=NONE cterm=NONE +hi Constant ctermfg=196 ctermbg=NONE cterm=NONE +hi Identifier ctermfg=9 ctermbg=NONE cterm=NONE +hi Function ctermfg=69 ctermbg=NONE cterm=NONE "functions 69 = pastel blue +hi Type ctermfg=87 ctermbg=NONE cterm=NONE "cterm matlab global +hi Statement ctermfg=69 ctermbg=NONE cterm=NONE "cd ls sed mv +hi Special ctermfg=202 ctermbg=NONE cterm=NONE " matlab '...' +hi Delimiter ctermfg=NONE ctermbg=NONE cterm=NONE " [ ] +hi Operator ctermfg=202 ctermbg=NONE cterm=NONE " == & +hi Directory ctermfg=87 ctermbg=NONE cterm=NONE " == & + +"Specific for diff +hi DiffAdd cterm=none ctermfg=0 ctermbg=119 +hi DiffChange cterm=none ctermfg=0 ctermbg=228 +hi DiffText cterm=none ctermfg=0 ctermbg=178 +hi DiffDelete cterm=none ctermfg=0 ctermbg=197 +hi diffLine cterm=bold ctermfg=241 +hi diffOldLine cterm=none ctermfg=241 +hi diffOldFile cterm=none ctermfg=241 +hi diffNewFile cterm=none ctermfg=241 +hi diffAdded cterm=none +hi diffRemoved cterm=none ctermfg=9 +hi diffChanged cterm=none ctermfg=69 Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/vim/addons/vim/colors/issm_white.vim =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/vim/addons/vim/colors/issm_white.vim (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/vim/addons/vim/colors/issm_white.vim (revision 18231) @@ -0,0 +1,86 @@ +" issm_white scheme +" table http://www.calmar.ws/vim/256-xterm-24bit-rgb-color-chart.html + +"Set up coloring +hi clear +if exists("syntax_on") + syntax reset +endif +syntax on +let colors_name = "issm_black" + +"preferred colors: +" 0 : black +" 9 : red +" 15 : white +" 20 : blue +" 33 : cyan +" 129 : dark purple +" 202 : orange +" 204 : light orange +" 227 : yellow +" 234 : very dark gray +" 241 : dark gray +" 244 : gray +" 255 : light gray + +" forground background style (reverse,bold,..) +" General colors +hi Normal ctermfg=NONE ctermbg=NONE cterm=NONE +hi NonText ctermfg=129 ctermbg=NONE cterm=NONE +hi Cursor ctermfg=NONE ctermbg=NONE cterm=reverse +hi LineNr ctermfg=15 ctermbg=241 cterm=NONE +hi VertSplit ctermfg=241 ctermbg=241 cterm=NONE +hi StatusLine ctermfg=241 ctermbg=33 cterm=NONE +hi StatusLineNC ctermfg=33 ctermbg=241 cterm=NONE +hi Folded ctermfg=93 ctermbg=254 cterm=NONE +hi Title ctermfg=NONE ctermbg=NONE cterm=NONE +hi Visual ctermfg=NONE ctermbg=NONE cterm=reverse +hi SpecialKey ctermfg=NONE ctermbg=NONE cterm=NONE +hi WildMenu ctermfg=0 ctermbg=227 cterm=NONE +hi PmenuSbar ctermfg=0 ctermbg=129 cterm=NONE +hi Error ctermfg=15 ctermbg=129 cterm=NONE +hi ErrorMsg ctermfg=15 ctermbg=129 cterm=NONE +hi WarningMsg ctermfg=15 ctermbg=129 cterm=NONE + +" Message displayed in lower left, such as --INSERT-- +hi ModeMsg ctermfg=0 ctermbg=33 cterm=BOLD +if version >= 700 " Vim 7.x specific colors + hi CursorLine ctermfg=NONE ctermbg=NONE cterm=BOLD + hi CursorColumn ctermfg=NONE ctermbg=NONE cterm=BOLD + hi MatchParen ctermfg=33 ctermbg=241 cterm=reverse "matching parenthesis + hi Pmenu ctermfg=0 ctermbg=15 cterm=NONE "auto completion panel + hi PmenuSel ctermfg=255 ctermbg=241 cterm=NONE + hi Search ctermfg=0 ctermbg=220 cterm=NONE +endif + +" Syntax highlighting +hi Comment ctermfg=241 ctermbg=NONE cterm=NONE +hi String ctermfg=28 ctermbg=NONE cterm=NONE +hi Number ctermfg=201 ctermbg=NONE cterm=NONE +hi Keyword ctermfg=9 ctermbg=NONE cterm=NONE " matlab function +hi PreProc ctermfg=9 ctermbg=NONE cterm=NONE " def undef include +hi Conditional ctermfg=220 ctermbg=NONE cterm=NONE " if else end +hi Todo ctermfg=204 ctermbg=NONE cterm=NONE +hi Constant ctermfg=196 ctermbg=NONE cterm=NONE +hi Identifier ctermfg=9 ctermbg=NONE cterm=NONE +hi Function ctermfg=20 ctermbg=NONE cterm=NONE "functions 20 = pastel blue +hi Type ctermfg=33 ctermbg=NONE cterm=NONE "cterm matlab global +hi Statement ctermfg=20 ctermbg=NONE cterm=NONE "cd ls sed mv +hi Special ctermfg=202 ctermbg=NONE cterm=NONE " matlab '...' +hi Delimiter ctermfg=NONE ctermbg=NONE cterm=NONE " [ ] +hi Operator ctermfg=202 ctermbg=NONE cterm=NONE " == & +hi Directory ctermfg=33 ctermbg=NONE cterm=NONE " == & + +"Specific for diff +hi DiffAdd cterm=none ctermfg=0 ctermbg=119 +hi DiffChange cterm=none ctermfg=0 ctermbg=228 +hi DiffText cterm=none ctermfg=0 ctermbg=178 +hi DiffDelete cterm=none ctermfg=0 ctermbg=197 +hi diffLine cterm=bold ctermfg=241 +hi diffOldLine cterm=none ctermfg=241 +hi diffOldFile cterm=none ctermfg=241 +hi diffNewFile cterm=none ctermfg=241 +hi diffAdded cterm=none +hi diffRemoved cterm=none ctermfg=9 +hi diffChanged cterm=none ctermfg=20 Index: /issm/branches/trunk-jpl-ad2-integrated/externalpackages/vim/addons/vim/doc/Align.txt =================================================================== --- /issm/branches/trunk-jpl-ad2-integrated/externalpackages/vim/addons/vim/doc/Align.txt (revision 18231) +++ /issm/branches/trunk-jpl-ad2-integrated/externalpackages/vim/addons/vim/doc/Align.txt (revision 18231) @@ -0,0 +1,1469 @@ +*align.txt* The Alignment Tool Mar 04, 2009 + +Author: Charles E. Campbell, Jr. + (remove NOSPAM from Campbell's email first) +Copyright: (c) 2004-2008 by Charles E. Campbell, Jr. *Align-copyright* + The VIM LICENSE applies to Align.vim, AlignMaps.vim, and Align.txt + (see |copyright|) except use "Align and AlignMaps" instead of "Vim" + NO WARRANTY, EXPRESS OR IMPLIED. USE AT-YOUR-OWN-RISK. + +============================================================================== +1. Contents *align* *align-contents* {{{1 + + 1. Contents.................: |align-contents| + 2. Alignment Manual.........: |align-manual| + 3. Alignment Usage..........: |align-usage| + Alignment Concepts.......: |align-concepts| + Alignment Commands.......: |align-commands| + Alignment Control........: |align-control| + Separators.............: |alignctrl-separators| + Initial Whitespace.....: |alignctrl-w| |alignctrl-W| |alignctrl-I| + Justification..........: |alignctrl-l| |alignctrl-r| |alignctrl-c| + Justification Control..: |alignctrl--| |alignctrl-+| |alignctrl-:| + Cyclic/Sequential......: |alignctrl-=| |alignctrl-C| + Separator Justification: |alignctrl-<| |alignctrl->| |alignctrl-|| + Line (de)Selection.....: |alignctrl-g| |alignctrl-v| + Temporary Settings.....: |alignctrl-m| + Padding................: |alignctrl-p| |alignctrl-P| + Current Options........: |alignctrl-settings| |alignctrl-| + Alignment................: |align-align| + 4. Alignment Maps...........: |align-maps| + \a,....................: |alignmap-a,| + \a?....................: |alignmap-a?| + \a<....................: |alignmap-a<| + \abox..................: |alignmap-abox| + \acom..................: |alignmap-acom| + \anum..................: |alignmap-anum| + \ascom.................: |alignmap-ascom| + \adec..................: |alignmap-adec| + \adef..................: |alignmap-adef| + \afnc..................: |alignmap-afnc| + \adcom.................: |alignmap-adcom| + \aocom.................: |alignmap-aocom| + \tsp...................: |alignmap-tsp| + \tsq...................: |alignmap-tsq| + \tt....................: |alignmap-tt| + \t=....................: |alignmap-t=| + \T=....................: |alignmap-T=| + \Htd...................: |alignmap-Htd| + 5. Alignment Tool History...: |align-history| + +============================================================================== +2. Align Manual *alignman* *alignmanual* *align-manual* {{{1 + + Align comes as a vimball; simply typing > + vim Align.vba.gz + :so % +< should put its components where they belong. The components are: > + .vim/plugin/AlignPlugin.vim + .vim/plugin/AlignMapsPlugin.vim + .vim/plugin/cecutil.vim + .vim/autoload/Align.vim + .vim/autoload/AlignMaps.vim + .vim/doc/Align.txt +< To see a user's guide, see |align-userguide| + To see examples, see |alignctrl| and |alignmaps| +> +/=============+=========+=====================================================\ +|| \ Default/ || +|| Commands \ Value/ Explanation || +|| | | || +++==============+====+=======================================================++ +|| AlignCtrl | | =Clrc-+:pPIWw [..list-of-separator-patterns..] || +|| | +-------------------------------------------------------+| +|| | | may be called as a command or as a function: || +|| | | :AlignCtrl =lp0P0W & \\ || +|| | | :call Align#AlignCtrl('=lp0P0W','&','\\') || +|| | | || +|| | +-------------------------------------------------------++ +|| 1st arg | = | = all separator patterns are equivalent and are || +|| | | simultaneously active. Patterns are |regexp|. || +|| | | C cycle through separator patterns. Patterns are || +|| | | |regexp| and are active sequentially. || +|| | | || +|| | < | < left justify separator Separators are justified, || +|| | | > right justify separator too. Separator styles || +|| | | | center separator are cyclic. || +|| | | || +|| | l | l left justify Justification styles are always || +|| | | r right justify cyclic (ie. lrc would mean left j., || +|| | | c center then right j., then center, repeat. || +|| | | - skip this separator || +|| | | + re-use last justification method || +|| | | : treat rest of text as a field || +|| | | || +|| | p1 | p### pad separator on left by # blanks || +|| | P1 | P### pad separator on right by # blanks || +|| | | || +|| | I | I preserve and apply first line's leading white || +|| | | space to all lines || +|| | | W preserve leading white space on every line, even || +|| | | if it varies from line to line || +|| | | w don't preserve leading white space || +|| | | || +|| | | g second argument is a selection pattern -- only || +|| | | align on lines that have a match (inspired by || +|| | | :g/selection pattern/command) || +|| | | v second argument is a selection pattern -- only || +|| | | align on lines that _don't_ have a match (inspired || +|| | | by :v/selection pattern/command) || +|| | | || +|| | | m Map support: AlignCtrl will immediately do an || +|| | | AlignPush() and the next call to Align() will do || +|| | | an AlignPop at the end. This feature allows maps || +|| | | to preserve user settings. || +|| | | || +|| | | default || +|| | | AlignCtrl default || +|| | | will clear the AlignCtrl || +|| | | stack & set the default: AlignCtrl "Ilp1P1=" '=' || +|| | | || +|| +----+-------------------------------------------------------+| +|| More args | More arguments are interpreted as describing separators || +|| +------------------------------------------------------------+| +|| No args | AlignCtrl will display its current settings || +||==============+============================================================+| +||[range]Align | [..list-of-separators..] || +||[range]Align! | [AlignCtrl settings] [..list-of-separators..] || +|| +------------------------------------------------------------+| +|| | Aligns text over the given range. The range may be || +|| | selected via visual mode (v, V, or ctrl-v) or via || +|| | the command line. The Align operation may be invoked || +|| | as a command or as a function; as a function, the first || +|| | argument is 0=separators only, 1=AlignCtrl option string || +|| | followed by a list of separators. || +|| | :[range]Align || +|| | :[range]Align [list of separators] || +|| | :[range]call Align#Align(0) || +|| | :[range]call Align#Align(0,"list","of","separators",...) || +\=============================================================================/ + +============================================================================== +3. Alignment Usage *alignusage* *align-usage* *align-userguide* {{{1 + + +ALIGNMENT CONCEPTS *align-concept* *align-concepts* {{{2 + + The typical text to be aligned is considered to be: + + * composed of two or more fields + * separated by one or more separator pattern(s): + * two or more lines +> + ws field ws separator ws field ws separator ... + ws field ws separator ws field ws separator ... +< + where "ws" stands for "white space" such as blanks and/or tabs, + and "fields" are arbitrary text. For example, consider > + + x= y= z= 3; + xx= yy= zz= 4; + zzz= yyy= zzz= 5; + a= b= c= 3; +< + Assume that it is desired to line up all the "=" signs; these, + then, are the separators. The fields are composed of all the + alphameric text. Assuming they lie on lines 1-4, one may align + those "=" signs with: > + :AlignCtrl l + :1,4Align = +< The result is: > + x = y = z = 3; + xx = yy = zz = 4; + zzz = yyy = zzz = 5; + a = b = c = 3; + +< Note how each "=" sign is surrounded by a single space; the + default padding is p1P1 (p1 means one space before the separator, + and P1 means one space after it). If you wish to change the + padding, say to no padding, use (see |alignctrl-p|) > + :AlignCtrl lp0P0 + +< Next, note how each field is left justified; that's what the "l" + (a small letter "ell") does. If right-justification of the fields + had been desired, an "r" could've been used: > + :AlignCtrl r +< yielding > + x = y = z = 3; + xx = yy = zz = 4; + zzz = yyy = zzz = 5; + a = b = c = 3; +< There are many more options available for field justification: see + |alignctrl-c| and |alignctrl--|. + + Separators, although commonly only one character long, are actually + specified by regular expressions (see |regexp|), and one may left + justify, right justify, or center them, too (see |alignctrl-<|). + + Assume that for some reason a left-right-left-right-... justification + sequence was wished. This wish is simply achieved with > + :AlignCtrl lr + :1,4Align = +< because the justification commands are considered to be "cylic"; ie. + lr is the same as lrlrlrlrlrlrlr... + + There's a lot more discussed under |alignctrl|; hopefully the examples + there will help, too. + + +ALIGNMENT COMMANDS *align-command* *align-commands* {{{2 + + The script includes two primary commands and two + minor commands: + + AlignCtrl : this command/function sets up alignment options + which persist until changed for later Align calls. + It controls such things as: how to specify field + separators, initial white space, padding about + separators, left/right/center justification, etc. > + ex. AlignCtrl wp0P1 + Interpretation: during subsequent alignment + operations, preserve each line's initial + whitespace. Use no padding before separators + but provide one padding space after separators. +< + Align : this command/function operates on the range given it to + align text based on one or more separator patterns. The + patterns may be provided via AlignCtrl or via Align + itself. > + + ex. :%Align , + Interpretation: align all commas over the entire + file. +< The :Align! format permits alignment control commands + to precede the alignment patterns. > + ex. :%Align! p2P2 = +< This will align all "=" in the file with two padding + spaces on both sides of each "=" sign. + + NOTE ON USING PATTERNS WITH ALIGN:~ + Align and AlignCtrl use || to obtain their + input patterns and they use an internal function to + split arguments at whitespace unless inside "..."s. + One may escape characters inside a double-quote string + by preceding such characters with a backslash. + + AlignPush : this command/function pushes the current AlignCtrl + state onto an internal stack. > + ex. :AlignPush + Interpretation: save the current AlignCtrl + settings, whatever they may be. They'll + also remain as the current settings until + AlignCtrl is used to change them. +< + AlignPop : this command/function pops the current AlignCtrl + state from an internal stack. > + ex. :AlignPop + Interpretation: presumably AlignPush was + used (at least once) previously; this command + restores the AlignCtrl settings when AlignPush + was last used. +< Also see |alignctrl-m| for a way to automatically do + an AlignPop after an Align (primarily this is for maps). + +ALIGNMENT OPTIONS *align-option* *align-options* {{{2 + *align-utf8* *align-utf* *align-codepoint* *align-strlen* *align-multibyte* + + For those of you who are using 2-byte (or more) characters such as are + available with utf-8, Align now provides a special option which you + may choose based upon your needs: + + Use Built-in strlen() ~ +> + let g:Align_xstrlen= 0 + +< This is the fastest method, but it doesn't handle multibyte characters + well. It is the default for: + + enc=latin1 + vim compiled without multi-byte support + $LANG is en_US.UTF-8 (assuming USA english) + + Number of codepoints (Latin a + combining circumflex is two codepoints)~ +> + let g:Align_xstrlen= 1 (default) +< + Number of spacing codepoints (Latin a + combining circumflex is one~ + spacing codepoint; a hard tab is one; wide and narrow CJK are one~ + each; etc.)~ +> + let g:Align_xstrlen= 2 +< + Virtual length (counting, for instance, tabs as anything between 1 and~ + 'tabstop', wide CJK as 2 rather than 1, Arabic alif as zero when~ + immediately preceded by lam, one otherwise, etc.)~ +> + let g:Align_xstrlen= 3 +< + By putting one of these settings into your <.vimrc>, Align will use an + internal (interpreted) function to determine a string's length instead + of the Vim's built-in |strlen()| function. Since the function is + interpreted, Align will run a bit slower but will handle such strings + correctly. The last setting (g:Align_xstrlen= 3) probably will run + the slowest but be the most accurate. (thanks to Tony Mechelynck for + these) + + +ALIGNMENT CONTROL *alignctrl* *align-control* {{{2 + + This command doesn't do the alignment operation itself; instead, it + controls subsequent alignment operation(s). + + The first argument to AlignCtrl is a string which may contain one or + more alignment control settings. Most of the settings are specified + by single letters; the exceptions are the p# and P# commands which + interpret a digit following the p or P as specifying padding about the + separator. + + The typical text line is considered to be composed of two or more + fields separated by one or more separator pattern(s): > + + ws field ws separator ws field ws separator ... +< + where "ws" stands for "white space" such as blanks and/or tabs. + + + SEPARATORS *alignctrl-separators* {{{3 + + As a result, separators may not have white space (tabs or blanks) on + their outsides (ie. ": :" is fine as a separator, but " :: " is + not). Usually such separators are not needed, although a map has been + provided which works around this limitation and aligns on whitespace + (see |alignmap-tsp|). + + However, if you really need to have separators with leading or + trailing whitespace, consider handling them by performing a substitute + first (ie. s/ :: /@/g), do the alignment on the temporary pattern + (ie. @), and then perform a substitute to revert the separators back + to their desired condition (ie. s/@/ :: /g). + + The Align#Align() function will first convert tabs over the region into + spaces and then apply alignment control. Except for initial white + space, white space surrounding the fields is ignored. One has three + options just for handling initial white space: + + + --- *alignctrl-w* + wWI INITIAL WHITE SPACE *alignctrl-W* {{{3 + --- *alignctrl-I* + w : ignore all selected lines' initial white space + W : retain all selected lines' initial white space + I : retain only the first line's initial white space and + re-use it for subsequent lines + + Example: Leading white space options: > + +---------------+-------------------+-----------------+ + |AlignCtrl w= :=| AlignCtrl W= := | AlignCtrl I= := | + +------------------+---------------+-------------------+-----------------+ + | Original | w option | W option | I option | + +------------------+---------------+-------------------+-----------------+ + | a := baaa |a := baaa | a : = baaa | a := baaa | + | caaaa := deeee |caaaa := deeee | caaaa : = deeee| caaaa := deeee| + | ee := f |ee := f | ee : = f | ee := f | + +------------------+---------------+-------------------+-----------------+ +< + The original has at least one leading white space on every line. + Using Align with w eliminated each line's leading white space. + Using Align with W preserved each line's leading white space. + Using Align with I applied the first line's leading white space + (three spaces) to each line. + + + ------ *alignctrl-l* + lrc-+: FIELD JUSTIFICATION *alignctrl-r* {{{3 + ------ *alignctrl-c* + + With "lrc", the fields will be left-justified, right-justified, or + centered as indicated by the justification specifiers (lrc). The + "lrc" options are re-used by cycling through them as needed: + + l means llllll.... + r means rrrrrr.... + lr means lrlrlr.... + llr means llrllr.... + + Example: Justification options: Align = > + +------------+-------------------+-------------------+-------------------+ + | Original | AlignCtrl l | AlignCtrl r | AlignCtrl lr | + +------------+-------------------+-------------------+-------------------+ + | a=bb=ccc=1 |a = bb = ccc = 1| a = bb = ccc = 1|a = bb = ccc = 1| + | ccc=a=bb=2 |ccc = a = bb = 2|ccc = a = bb = 2|ccc = a = bb = 2| + | dd=eee=f=3 |dd = eee = f = 3| dd = eee = f = 3|dd = eee = f = 3| + +------------+-------------------+-------------------+-------------------+ + | Alignment |l l l l| r r r r|l r l r| + +------------+-------------------+-------------------+-------------------+ +< + AlignCtrl l : The = separator is repeatedly re-used, as the + cycle only consists of one character (the "l"). + Every time left-justification is used for fields. + AlignCtrl r : The = separator is repeatedly re-used, as the + cycle only consists of one character (the "l"). + Every time right-justification is used for fields + AlignCtrl lr: Again, the "=" separator is repeatedly re-used, + but the fields are justified alternately between + left and right. + + Even more separator control is available. With "-+:": + + - : skip treating the separator as a separator. *alignctrl--* + + : repeat use of the last "lrc" justification *alignctrl-+* + : : treat the rest of the line as a single field *alignctrl-:* + + Example: More justification options: Align = > + +------------+---------------+--------------------+---------------+ + | Original | AlignCtrl -l | AlignCtrl rl+ | AlignCtrl l: | + +------------+---------------+--------------------+---------------+ + | a=bb=ccc=1 |a=bb = ccc=1 | a = bb = ccc = 1 |a = bb=ccc=1 | + | ccc=a=bb=2 |ccc=a = bb=2 |ccc = a = bb = 2 |ccc = a=bb=2 | + | dd=eee=f=3 |dd=eee = f=3 | dd = eee = f = 3 |dd = eee=f=3 | + +------------+---------------+--------------------+---------------+ + | Alignment |l l | r l l l |l l | + +------------+---------------+--------------------+---------------+ +< + In the first example in "More justification options": + + The first "=" separator is skipped by the "-" specification, + and so "a=bb", "ccc=a", and "dd=eee" are considered as single fields. + + The next "=" separator has its (left side) field left-justified. + Due to the cyclic nature of separator patterns, the "-l" + specification is equivalent to "-l-l-l ...". + + Hence the next specification is a "skip", so "ccc=1", etc are fields. + + In the second example in "More justification options": + + The first field is right-justified, the second field is left + justified, and all remaining fields repeat the last justification + command (ie. they are left justified, too). + + Hence rl+ is equivalent to rlllllllll ... + (whereas plain rl is equivalent to rlrlrlrlrl ... ). + + In the third example in "More justification options": + + The text following the first separator is treated as a single field. + + Thus using the - and : operators one can apply justification to a + single separator. + + ex. 1st separator only: AlignCtrl l: + 2nd separator only: AlignCtrl -l: + 3rd separator only: AlignCtrl --l: + etc. + + + --- *alignctrl-=* + =C CYCLIC VS ALL-ACTIVE SEPARATORS *alignctrl-C* {{{3 + --- + + The separators themselves may be considered as equivalent and + simultaneously active ("=") or sequentially cycled through ("C"). + Separators are regular expressions (|regexp|) and are specified as the + second, third, etc arguments. When the separator patterns are + equivalent and simultaneously active, there will be one pattern + constructed: > + + AlignCtrl ... pat1 pat2 pat3 + \(pat1\|pat2\|pat3\) +< + Each separator pattern is thus equivalent and simultaneously active. + The cyclic separator AlignCtrl option stores a list of patterns, only + one of which is active for each field at a time. + + Example: Equivalent/Simultaneously-Active vs Cyclic Separators > + +-------------+------------------+---------------------+----------------------+ + | Original | AlignCtrl = = + -| AlignCtrl = = | AlignCtrl C = + - | + +-------------+------------------+---------------------+----------------------+ + |a = b + c - d|a = b + c - d |a = b + c - d |a = b + c - d | + |x = y = z + 2|x = y = z + 2 |x = y = z + 2|x = y = z + 2 | + |w = s - t = 0|w = s - t = 0 |w = s - t = 0 |w = s - t = 0 | + +-------------+------------------+---------------------+----------------------+ +< + The original is initially aligned with all operators (=+-) being + considered as equivalent and simultaneously active field separators. + Thus the "AlignCtrl = = + -" example shows no change. + + The second example only accepts the '=' as a field separator; + consequently "b + c - d" is now a single field. + + The third example illustrates cyclic field separators and is analyzed + in the following illustration: > + + field1 separator field2 separator field3 separator field4 + a = b + c - d + x = y = z + 2 + w = s - t = 0 +< + The word "cyclic" is used because the patterns form a cycle of use; in + the above case, its = + - = + - = + - = + -... + + Example: Cyclic separators > + Label : this is some text discussing ":"s | ex. abc:def:ghi + Label : this is some text with a ":" in it | ex. abc:def +< + apply AlignCtrl lWC : | | + (select lines)Align > + Label : this is some text discussing ":"s | ex. abc:def:ghi + Label : this is some text with a ":" in it | ex. abcd:efg +< + In the current example, + : is the first separator So the first ":"s are aligned + | is the second separator but subsequent ":"s are not. + | is the third separator The "|"s are aligned, too. + : is the fourth separator Since there aren't two bars, + | is the fifth separator the subsequent potential cycles + | is the sixth separator don't appear. + ... + + In this case it would probably have been a better idea to have used > + AlignCtrl WCl: : | +< as that alignment control would guarantee that no more cycling + would be used after the vertical bar. + + Example: Cyclic separators + + Original: > + a| b&c | (d|e) & f-g-h + aa| bb&cc | (dd|ee) & ff-gg-hh + aaa| bbb&ccc | (ddd|eee) & fff-ggg-hhh +< + AlignCtrl C | | & - > + a | b&c | (d|e) & f - g-h + aa | bb&cc | (dd|ee) & ff - gg-hh + aaa | bbb&ccc | (ddd|eee) & fff - ggg-hhh +< + In this example, + the first and second separators are "|", + the third separator is "&", and + the fourth separator is "-", + + (cycling) + the fifth and sixth separators are "|", + the seventh separator is "&", and + the eighth separator is "-", etc. + + Thus the first "&"s are (not yet) separators, and hence are treated as + part of the field. Ignoring white space for the moment, the AlignCtrl + shown here means that Align will work with > + + field | field | field & field - field | field | field & field - ... +< + + --- *alignctrl-<* + <>| SEPARATOR JUSTIFICATION *alignctrl->* {{{3 + --- *alignctrl-|* + + Separators may be of differing lengths as shown in the example below. + Hence they too may be justified left, right, or centered. + Furthermore, separator justification specifications are cyclic: + + < means <<<<<... justify separator(s) to the left + > means >>>>>... justify separator(s) to the right + | means |||||... center separator(s) + + Example: Separator Justification: Align -\+ > + +-----------------+ + | Original | + +-----------------+ + | a - bbb - c | + | aa -- bb -- ccc | + | aaa --- b --- cc| + +---------------------+-+-----------------+-+---------------------+ + | AlignCtrl < | AlignCtrl > | AlignCtrl | | + +---------------------+---------------------+---------------------+ + | a - bbb - c | a - bbb - c | a - bbb - c | + | aa -- bb -- ccc | aa -- bb -- ccc | aa -- bb -- ccc | + | aaa --- b --- cc | aaa --- b --- cc | aaa --- b --- cc | + +---------------------+---------------------+---------------------+ +< + + --- *alignctrl-g* + gv SELECTIVE APPLICATION *alignctrl-v* {{{3 + --- + + + These two options provide a way to select (g) or to deselect (v) lines + based on a pattern. Ideally :g/pat/Align would work; unfortunately + it results in Align#Align() being called on each line satisfying the + pattern separately. > + + AlignCtrl g pattern +< + Align will only consider those lines which have the given pattern. > + + AlignCtrl v pattern +< + Align will only consider those lines without the given pattern. As an + example of use, consider the following example: > + + :AlignCtrl v ^\s*/\* + Original :Align = :Align = + +----------------+------------------+----------------+ + |one= 2; |one = 2; |one = 2; | + |three= 4; |three = 4; |three = 4; | + |/* skip=this */ |/* skip = this */ |/* skip=this */ | + |five= 6; |five = 6; |five = 6; | + +----------------+------------------+----------------+ +< + The first "Align =" aligned with all "="s, including that one in the + "skip=this" comment. + + The second "Align =" had a AlignCtrl v-pattern which caused it to skip + (ignore) the "skip=this" line when aligning. + + To remove AlignCtrl's g and v patterns, use (as appropriate) > + + AlignCtrl g + AlignCtrl v +< + To see what g/v patterns are currently active, just use the reporting + capability of an unadorned call to AlignCtrl: > + + AlignCtrl +< + + --- + m MAP SUPPORT *alignctrl-m* {{{3 + --- + + This option primarily supports the development of maps. The + Align#AlignCtrl() call will first do an Align#AlignPush() (ie. retain + current alignment control settings). The next Align#Align() will, in + addition to its alignment job, finish up with an Align#AlignPop(). + Thus the Align#AlignCtrl settings that follow the "m" are only + temporarily in effect for just the next Align#Align(). + + + --- + p### *alignctrl-p* + P### PADDING *alignctrl-P* {{{3 + --- + + These two options control pre-padding and post-padding with blanks + about the separator. One may pad separators with zero to nine spaces; + the padding number(s) is/are treated as a cyclic parameter. Thus one + may specify padding separately for each field or re-use a padding + pattern. > + + Example: AlignCtrl p102P0 + +---------+----------------------------------+ + | Original| a=b=c=d=e=f=g=h=1 | + | Align = | a =b=c =d =e=f =g =h=1 | + +---------+----------------------------------+ + | prepad | 1 0 2 1 0 2 1 0 | + +---------+----------------------------------+ +< + This example will cause Align to: + + pre-pad the first "=" with a single blank, + pre-pad the second "=" with no blanks, + pre-pad the third "=" with two blanks, + pre-pad the fourth "=" with a single blank, + pre-pad the fifth "=" with no blanks, + pre-pad the sixth "=" with two blanks, + etc. + + --------------- *alignctrl-settings* + No option given DISPLAY STATUS *alignctrl-* {{{3 + --------------- *alignctrl-no-option* + + AlignCtrl, when called with no arguments, will display the current + alignment control settings. A typical display is shown below: > + + AlignCtrl<=> qty=1 AlignStyle Padding<1|1> + Pat1<\(=\)> +< + Interpreting, this means that the separator patterns are all + equivalent; in this case, there's only one (qty=1). Fields will be + padded on the right with spaces (left justification), and separators + will be padded on each side with a single space. + + To change one of these items, see: + + AlignCtrl......|alignctrl| + qty............|align-concept| + AlignStyle.....|alignctrl--| |alignctrl-+| |alignctrl-:||alignctrl-c| + Padding........|alignctrl-p| |alignctrl-P| + + One may get a string which can be fed back into AlignCtrl: > + + :let alignctrl= Align#AlignCtrl() +< + This form will put a string describing the current AlignCtrl options, + except for the "g" and "v" patterns, into a variable. The + Align#AlignCtrl() function will still echo its settings, however. One + can feed any non-supported "option" to AlignCtrl() to prevent this, + however: > + + :let alignctrl= Align#AlignCtrl("d") +< + +ALIGNMENT *align-align* {{{2 + + Once the alignment control has been determined, the user specifies a + range of lines for the Align command/function to do its thing. + Alignment is often done on a line-range basis, but one may also + restrict alignment to a visual block using ctrl-v. For any visual + mode, one types the colon (:) and then "Align". One may, of course, + specify a range of lines: > + + :[range]Align [list-of-separators] +< + where the |:range| is the usual Vim-powered set of possibilities; the + list of separators is the same as the AlignCtrl capability. There is + only one list of separators, but either AlignCtrl or Align can be used + to specify that list. + + An alternative form of the Align command can handle both alignment + control and the separator list: > + + :[range]Align! [alignment-control-string] [list-of-separators] +< + The alignment control string will be applied only for this particular + application of Align (it uses |alignctrl-m|). The "g pattern" and + "v pattern" alignment controls (see |alignctrl-g| and |alignctrl-v|) + are also available via this form of the Align command. + + Align makes two passes over the text to be aligned. The first pass + determines how many fields there are and determines the maximum sizes + of each field; these sizes are then stored in a vector. The second + pass pads the field (left/right/centered as specified) to bring its + length up to the maximum size of the field. Then the separator and + its AlignCtrl-specified padding is appended. + + Pseudo-Code:~ + During pass 1 + | For all fields in the current line + || Determine current separator + || Examine field specified by current separator + || Determine length of field and save if largest thus far + Initialize newline based on initial whitespace option (wWI) + During pass 2 + | For all fields in current line + || Determine current separator + || Extract field specified by current separator + || Prepend/append padding as specified by AlignCtrl + || (right/left/center)-justify to fit field into max-size field + || Append separator with AlignCtrl-specified separator padding + || Delete current line, install newly aligned line + + The g and v AlignCtrl patterns cause the passes not to consider lines + for alignment, either by requiring that the g-pattern be present or + that the v-pattern not be present. + + The whitespace on either side of a separator is ignored. + + +============================================================================== +4. Alignment Maps *alignmaps* *align-maps* {{{1 + + There are a number of maps using Align#AlignCtrl() and Align#Align() + in the file. This file may also be put into the + plugins subdirectory. Since AlignCtrl and Align supercede textab and + its file, the maps either have a leading "t" (for + "textab") or the more complicated ones an "a" (for "alignment") for + backwards compatibility. + + The maps are shown below with a leading backslash (\). Actually, the + construct is used (see |mapleader|), so the maps' leading + kick-off character is easily customized. + + Furthermore, all AlignMapsPlugin.vim maps use the construct (see + ||and |usr_41.txt|). Hence, if one wishes to override the + mapping entirely, one may do that, too. As an example: > + map ACOM AM_acom +< would have \ACOM do what \acom previously did (assuming that the + mapleader has been left at its default value of a backslash). + + \a, : useful for breaking up comma-separated + declarations prior to \adec |alignmap-a,| + \a( : aligns ( and , (useful for prototypes) *alignmap-a(* + \a? : aligns (...)? ...:... expressions on ? and : |alignmap-a?| + \a< : aligns << and >> for c++ |alignmap-a<| + \a= : aligns := assignments |alignmap-a=| + \abox : draw a C-style comment box around text lines |alignmap-abox| + \acom : useful for aligning comments |alignmap-acom| + \adcom: useful for aligning comments in declarations |alignmap-adcom| + \anum : useful for aligning numbers |alignmap-anum| + NOTE: For the visual-mode use of \anum, is needed! + See http://mysite.verizon.net/astronaut/vim/index.html#VIS + \aenum: align a European-style number |alignmap-anum| + \aunum: align a USA-style number |alignmap-anum| + \adec : useful for aligning declarations |alignmap-adec| + \adef : useful for aligning definitions |alignmap-adef| + \afnc : useful for aligning ansi-c style functions' + argument lists |alignmap-afnc| + \adcom: a variant of \acom, restricted to comment |alignmap-adcom| + containing lines only, but also only for + those which don't begin with a comment. + Good for certain declaration styles. + \aocom: a variant of \acom, restricted to comment |alignmap-aocom| + containing lines only + \tab : align a table based on tabs *alignmap-tab* + (converts to spaces) + \tml : useful for aligning the trailing backslashes |alignmap-tml| + used to continue lines (shell programming, etc) + \tsp : use Align to make a table separated by blanks |alignmap-tsp| + (left justified) + \ts, : like \t, but swaps whitespace on the right of *alignmap-ts,* + the commas to their left + \ts: : like \t: but swaps whitespace on the right of *alignmap-ts:* + the colons to their left + \ts< : like \t< but swaps whitespace on the right of *alignmap-ts<* + the less-than signs to their left + \ts= : like \t= but swaps whitespace on the right of *alignmap-ts=* + the equals signs to their left + \Tsp : use Align to make a table separated by blanks |alignmap-Tsp| + (right justified) + \tsq : use Align to make a table separated by blanks |alignmap-tsq| + (left justified) -- "strings" are not split up + \tt : useful for aligning LaTeX tabular tables |alignmap-tt| + \Htd : tabularizes html tables: |alignmap-Htd| + ...field... ...field... + + *alignmap-t|* *alignmap-t#* *alignmap-t,* *alignmap-t:* + *alignmap-t;* *alignmap-t<* *alignmap-t?* *alignmap-t~* + *alignmap-m=* + \tx : make a left-justified alignment on + character "x" where "x" is: ,:<=@|# |alignmap-t=| + \Tx : make a right-justified alignment on + character "x" where "x" is: ,:<=@# |alignmap-T=| + \m= : like \t= but aligns with %... style comments + + The leading backslash is actually (see |mapleader| for how to + customize the leader to be whatever you like). These maps use the + package and are defined in the file. + Although the maps use AlignCtrl options, they typically use the "m" + option which pushes the options (AlignPush). The associated Align + call which follows will then AlignPop the user's original options + back. + + ALIGNMENT MAP USE WITH MARK AND MOVE~ + In the examples below, one may select the text with a "ma" at the + first line, move to the last line, then execute the map. + + ALIGNMENT MAP USE WITH VISUAL MODE~ + Alternatively, one may select the text with the "V" visual mode + command. + + ALIGNMENT MAP USE WITH MENUS~ + One may use the mark-and-move style (ma, move, use the menu) or + the visual mode style (use the V visual mode, move, then select + the alignment map with menu selection). The alignment map menu + items are under DrChip.AlignMaps . + + One may even change the top level menu name to whatever is wished; by + default, its > + let g:DrChipTopLvlMenu= "DrChip." +< If you set the variable to the empty string (""), then no menu items + will be produced. Of course, one must have a vim with +menu, the gui + must be running, and |'go'| must have the menu bar suboption (ie. m + must be included). + + COMPLEX ALIGNMENT MAP METHOD~ + + For those complex alignment maps which do alignment on constructs + (e.g. \acom, \adec, etc), a series of substitutes is used to insert + "@" symbols in appropriate locations. Align#Align() is then used to + do alignment directly on "@"s; then it is followed by further + substitutes to do clean-up. However, the maps \WS and \WE, used by + every map supported by AlignMaps, protect any original embedded "@" + symbols by first converting them to characters, doing the + requested job, and then converting them back. > + + \WS calls AlignMaps#WrapperStart() + \WE calls AlignMaps#WrapperEnd() +< + + --------------------------- + Alignment Map Examples: \a, *alignmap-a,* {{{3 + --------------------------- + + Original: illustrates comma-separated declaration splitting: > + int a,b,c; + struct ABC_str abc,def; +< + Becomes: > + int a; + int b; + int c; + struct ABC_str abc; + struct ABC_str def; +< + + --------------------------- + Alignment Map Examples: \a? *alignmap-a?* {{{3 + --------------------------- + + Original: illustrates ()?: aligning > + printf("<%s>\n", + (x == ABC)? "abc" : + (x == DEFG)? "defg" : + (x == HIJKL)? "hijkl" : "???"); +< + Becomes: select "(x == ..." lines, then \a? > + printf("<%s>\n", + (x == ABC)? "abc" : + (x == DEFG)? "defg" : + (x == HIJKL)? "hijkl" : "???"); +< + + --------------------------- + Alignment Map Examples: \a< *alignmap-a<* {{{3 + --------------------------- + + Original: illustrating aligning of << and >> > + cin << x; + cin << y; + cout << "this is x=" << x; + cout << "but y=" << y << "is not"; +< + Becomes: select "(x == ..." lines, then \a< > + cin << x; + cin << y; + cout << "this is x=" << x; + cout << "but y=" << y << "is not"; +< + + --------------------------- + Alignment Map Examples: \a= *alignmap-a=* {{{3 + --------------------------- + + Original: illustrates how to align := assignments > + aa:=bb:=cc:=1; + a:=b:=c:=1; + aaa:=bbb:=ccc:=1; +< + Bcomes: select the three assignment lines, then \a:= > + aa := bb := cc := 1; + a := b := c := 1; + aaa := bbb := ccc := 1; +< + + --------------------------- + Alignment Map Examples: \abox *alignmap-abox* {{{3 + --------------------------- + + Original: illustrates how to comment-box some text > + This is some plain text + which will + soon be surrounded by a + comment box. +< + Becomes: Select "This..box." with ctrl-v, press \abox > + /*************************** + * This is some plain text * + * which will * + * soon be surrounded by a * + * comment box. * + ***************************/ +< + + --------------------------- + Alignment Map Examples: \acom *alignmap-acom* {{{3 + --------------------------- + + Original: illustrates aligning C-style comments (works for //, too) > + if(itworks) { /* this */ + then= dothis; /* is a */ + } /* set of three comments */ +< + Becomes: Select the three lines, press \acom > + if(itworks) { /* this */ + then= dothis; /* is a */ + } /* set of three comments */ +< + Also see |alignmap-aocom| + + + --------------------------- + Alignment Map Examples: \anum *alignmap-anum* {{{3 + --------------------------- + + Original: illustrates how to get numbers lined up > + -1.234 .5678 -.901e-4 + 1.234 5.678 9.01e-4 + 12.34 56.78 90.1e-4 + 123.4 567.8 901.e-4 +< + Becomes: Go to first line, ma. Go to last line, press \anum > + -1.234 .5678 -.901e-4 + 1.234 5.678 9.01e-4 + 12.34 56.78 90.1e-4 + 123.4 567.8 901.e-4 +< + Original: > + | -1.234 .5678 -.901e-4 | + | 1.234 5.678 9.01e-4 | + | 12.34 56.78 90.1e-4 | + | 123.4 567.8 901.e-4 | +< + Becomes: Select the numbers with ctrl-v (visual-block mode), > + press \anum + | -1.234 .5678 -.901e-4 | + | 1.234 5.678 9.01e-4 | + | 12.34 56.78 90.1e-4 | + | 123.4 567.8 901.e-4 | +< + Original: > + -1,234 ,5678 -,901e-4 + 1,234 5,678 9,01e-4 + 12,34 56,78 90,1e-4 + 123,4 567,8 901,e-4 +< + Becomes: Go to first line, ma. Go to last line, press \anum > + -1,234 ,5678 -,901e-4 + 1,234 5,678 9,01e-4 + 12,34 56,78 90,1e-4 + 123,4 567,8 901,e-4 +< + In addition: + \aenum is provided to support European-style numbers + \aunum is provided to support USA-style numbers + + One may get \aenum behavior for \anum > + let g:alignmaps_euronumber= 1 +< or \aunum behavior for \anum if one puts > + let g:alignmaps_usanumber= 1 +< in one's <.vimrc>. + + + --------------------------- + Alignment Map Examples: \ascom *alignmap-ascom* {{{3 + --------------------------- + + Original: > + /* A Title */ + int x; /* this is a comment */ + int yzw; /* this is another comment*/ +< + Becomes: Select the three lines, press \ascom > + /* A Title */ + int x; /* this is a comment */ + int yzw; /* this is another comment */ +< + + --------------------------- + Alignment Map Examples: \adec *alignmap-adec* {{{3 + --------------------------- + + Original: illustrates how to clean up C/C++ declarations > + int a; + float b; + double *c=NULL; + char x[5]; + struct abc_str abc; + struct abc_str *pabc; + int a; /* a */ + float b; /* b */ + double *c=NULL; /* b */ + char x[5]; /* x[5] */ + struct abc_str abc; /* abc */ + struct abc_str *pabc; /* pabc */ + static int a; /* a */ + static float b; /* b */ + static double *c=NULL; /* b */ + static char x[5]; /* x[5] */ + static struct abc_str abc; /* abc */ + static struct abc_str *pabc; /* pabc */ +< + Becomes: Select the declarations text, then \adec > + int a; + float b; + double *c = NULL; + char x[5]; + struct abc_str abc; + struct abc_str *pabc; + int a; /* a */ + float b; /* b */ + double *c = NULL; /* b */ + char x[5]; /* x[5] */ + struct abc_str abc; /* abc */ + struct abc_str *pabc; /* pabc */ + static int a; /* a */ + static float b; /* b */ + static double *c = NULL; /* b */ + static char x[5]; /* x[5] */ + static struct abc_str abc; /* abc */ + static struct abc_str *pabc; /* pabc */ +< + + --------------------------- + Alignment Map Examples: \adef *alignmap-adef* {{{3 + --------------------------- + + Original: illustrates how to line up #def'initions > + #define ONE 1 + #define TWO 22 + #define THREE 333 + #define FOUR 4444 +< + Becomes: Select four definition lines, apply \adef > + # define ONE 1 + # define TWO 22 + # define THREE 333 + # define FOUR 4444 +< + + --------------------------- + Alignment Map Examples: \afnc *alignmap-afnc* {{{3 + --------------------------- + + This map is an exception to the usual selection rules. + It uses "]]" to find the function body's leading "{". + Just put the cursor anywhere in the function arguments and + the entire function declaration should be processed. + + Because "]]" looks for that "{" in the first column, the + "original" and "becomes" examples are in the first column, + too. + + Original: illustrates lining up ansi-c style function definitions > + int f( + struct abc_str ***a, /* one */ + long *b, /* two */ + int c) /* three */ + { + } +< + Becomes: put cursor anywhere before the '{', press \afnc > + int f( + struct abc_str ***a, /* one */ + long *b, /* two */ + int c) /* three */ + { + } +< + + --------------------------- + Alignment Map Examples: \adcom *alignmap-adcom* {{{3 + --------------------------- + + Original: illustrates aligning comments that don't begin + lines (optionally after some whitespace). > + struct { + /* this is a test */ + int x; /* of how */ + double y; /* to use adcom */ + }; +< + Becomes: Select the inside lines of the structure, + then press \adcom. The comment-only + line is ignored but the other two comments + get aligned. > + struct { + /* this is a test */ + int x; /* of how */ + double y; /* to use adcom */ + }; +< + + --------------------------- + Alignment Map Examples: \aocom *alignmap-aocom* {{{3 + --------------------------- + + Original: illustrates how to align C-style comments (works for //, too) + but restricted only to aligning with those lines containing + comments. See the difference from \acom (|alignmap-acom|). > + if(itworks) { /* this comment */ + then= dothis; + } /* only appears on two lines */ +< + Becomes: Select the three lines, press \aocom > + if(itworks) { /* this comment */ + then= dothis; + } /* only appears on two lines */ +< + Also see |alignmap-acom| + + + --------------------------- *alignmap-Tsp* + Alignment Map Examples: \tsp *alignmap-tsp* {{{3 + --------------------------- + + Normally Align can't use white spaces for field separators as such + characters are ignored surrounding field separators. The \tsp and + \Tsp maps get around this limitation. + + Original: > + one two three four five + six seven eight nine ten + eleven twelve thirteen fourteen fifteen +< + Becomes: Select the lines, \tsp > + one two three four five + six seven eight nine ten + eleven twelve thirteen fourteen fifteen +< + Becomes: Select the lines, \Tsp > + one two three four five + six seven eight nine ten + eleven twelve thirteen fourteen fifteen +< + + --------------------------- + Alignment Map Examples: \tsq *alignmap-tsq* {{{3 + --------------------------- + + The \tsp map is useful for aligning tables based on white space, + but sometimes one wants double-quoted strings to act as a single + object in spite of embedded spaces. The \tsq map was invented + to support this. (thanks to Leif Wickland) + + Original: > + "one two" three + four "five six" +< + Becomes: Select the lines, \tsq > + "one two" three + four "five six" +< + + --------------------------- + Alignment Map Examples: \tt *alignmap-tt* {{{3 + --------------------------- + + Original: illustrates aligning a LaTex Table > + \begin{tabular}{||c|l|r||} + \hline\hline + one&two&three\\ \hline + four&five&six\\ + seven&eight&nine\\ + \hline\hline + \end{tabular} +< + Becomes: Select the three lines inside the table > + (ie. one..,four..,seven..) and press \tt + \begin{tabular}{||c|l|r||} + \hline\hline + one & two & three \\ \hline + four & five & six \\ + seven & eight & nine \\ + \hline\hline + \end{tabular} +< + + ---------------------------- + Alignment Map Examples: \tml *alignmap-tml* {{{3 + ---------------------------- + + Original: illustrates aligning multi-line continuation marks > + one \ + two three \ + four five six \ + seven \\ \ + eight \nine \ + ten \ +< + Becomes: > + one \ + two three \ + four five six \ + seven \\ \ + eight \nine \ + ten \ +< + + --------------------------- + Alignment Map Examples: \t= *alignmap-t=* {{{3 + --------------------------- + + Original: illustrates left-justified aligning of = > + aa=bb=cc=1;/*one*/ + a=b=c=1;/*two*/ + aaa=bbb=ccc=1;/*three*/ +< + Becomes: Select the three equations, press \t= > + aa = bb = cc = 1; /* one */ + a = b = c = 1; /* two */ + aaa = bbb = ccc = 1; /* three */ +< + + --------------------------- + Alignment Map Examples: \T= *alignmap-T=* {{{3 + --------------------------- + + Original: illustrates right-justified aligning of = > + aa=bb=cc=1; /* one */ + a=b=c=1; /* two */ + aaa=bbb=ccc=1; /* three */ +< + Becomes: Select the three equations, press \T= > + aa = bb = cc = 1; /* one */ + a = b = c = 1; /* two */ + aaa = bbb = ccc = 1; /* three */ +< + + --------------------------- + Alignment Map Examples: \Htd *alignmap-Htd* {{{3 + --------------------------- + + Original: for aligning tables with html > + ...field one......field two... + ...field three......field four... +< + Becomes: Select ... lines, press \Htd > + ...field one... ...field two... + ...field three... ...field four... +< +============================================================================== +4. Alignment Tools' History *align-history* {{{1 + +ALIGN HISTORY {{{2 + 35 : Nov 02, 2008 * g:loaded_AlignPlugin testing to prevent re-loading + installed + Nov 19, 2008 * new sanity check for an AlignStyle of just ":" + Jan 08, 2009 * save&restore of |'mod'| now done with local + variant + 34 : Jul 08, 2008 * using :AlignCtrl before entering any alignment + control commands was causing an error. + 33 : Sep 20, 2007 * s:Strlen() introduced to support various ways + used to represent characters and their effects + on string lengths. See |align-strlen|. + * Align now accepts "..." -- so it can accept + whitespace as separators. + 32 : Aug 18, 2007 * uses || instead of || plus a + custom argument splitter to allow patterns with + backslashes to slide in unaltered. + 31 : Aug 06, 2007 * :[range]Align! [AlignCtrl settings] pattern(s) + implemented. + 30 : Feb 12, 2007 * now uses |setline()| + 29 : Jan 18, 2006 * cecutil updated to use keepjumps + Feb 23, 2006 * Align now converted to vim 7.0 style using + auto-loading functions. + 28 : Aug 17, 2005 * report option workaround + Oct 24, 2005 * AlignCtrl l: wasn't behaving as expected; fixed + 27 : Apr 15, 2005 : cpo workaround + ignorecase workaround + 26 : Aug 20, 2004 : loaded_align now also indicates version number + GetLatestVimScripts :AutoInstall: now supported + 25 : Jul 27, 2004 : For debugging, uses Dfunc(), Dret(), and Decho() + 24 : Mar 03, 2004 : (should've done this earlier!) visualmode(1) + not supported until v6.2, now Align will avoid + calling it for earlier versions. Visualmode + clearing won't take place then, of course. + 23 : Oct 07, 2003 : Included Leif Wickland's ReplaceQuotedSpaces() + function which supports \tsq + 22 : Jan 29, 2003 : Now requires 6.1.308 or later to clear visualmode() + 21 : Jan 10, 2003 : BugFix: similar problem to #19; new code + bypasses "norm! v\" until initialization + is over. + 20 : Dec 30, 2002 : BugFix: more on "unable to highlight" fixed + 19 : Nov 21, 2002 : BugFix: some terminals gave an "unable to highlight" + message at startup; Hari Krishna Dara tracked it + down; a silent! now included to prevent noise. + 18 : Nov 04, 2002 : BugFix: re-enabled anti-repeated-loading + 17 : Nov 04, 2002 : BugFix: forgot to have AlignPush() push s:AlignSep + AlignCtrl now clears visual-block mode when used so + that Align won't try to use old visual-block + selection marks '< '> + 16 : Sep 18, 2002 : AlignCtrl <>| options implemented (separator + justification) + 15 : Aug 22, 2002 : bug fix: AlignCtrl's ":" now acts as a modifier of + the preceding alignment operator (lrc) + 14 : Aug 20, 2002 : bug fix: AlignCtrl default now keeps &ic unchanged + bug fix: Align, on end-field, wasn't using correct + alignop bug fix: Align, on end-field, was appending + padding + 13 : Aug 19, 2002 : bug fix: zero-length g/v patterns are accepted + bug fix: always skip blank lines + bug fix: AlignCtrl default now also clears g and v + patterns + 12 : Aug 16, 2002 : moved keep_ic above zero-length pattern checks + added "AlignCtrl default" + fixed bug with last field getting separator spaces + at end line + 11 : Jul 08, 2002 : prevent separator patterns which match zero length + -+: included as additional alignment/justification + styles + 10 : Jun 26, 2002 : =~# used instead of =~ (for matching case) + ignorecase option handled + 9 : Jun 25, 2002 : implemented cyclic padding + +ALIGNMENT MAP HISTORY *alignmap-history* {{{2 + v41 Nov 02, 2008 * g:loaded_AlignMapsPlugin testing to prevent + re-loading installed + * AlignMaps now use 0x0f (ctrl-p) for special + character substitutions (instead of 0xff). + Seems to avoid some problems with having to + use Strlen(). + * bug fixed with \ts, + * new maps: \ts; \ts, \ts: \ts< \ts= \a( + v40 Oct 21, 2008 * Modified AlignMaps so that its maps use s + and