Index: /issm/branches/trunk-larour-NatClimateChange2016/Makefile.am =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/Makefile.am (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/Makefile.am (revision 21239) @@ -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-larour-NatClimateChange2016/README =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/README (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/README (revision 21239) @@ -0,0 +1,45 @@ +------------------------------------------------------------------------------ + +ISSM +Ice Sheet System Modeling: a framework for modeling ice flow on ice sheet/ice shelf +systems using Finite Elemenent Analysis, and parallel technologies. + +Email: issm@jpl.nasa.gov +Website: http://issm.jpl.nasa.gov/ + +------------------------------------------------------------------------------ + +License + +ISSM is California Institute of Technology Copyright, Distributed under BSD Three Clause License. + + +Copyright (c) 2002-2014, 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-larour-NatClimateChange2016/configs/config-arm-linux.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-arm-linux.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-arm-linux.sh (revision 21239) @@ -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-larour-NatClimateChange2016/configs/config-discover-intel11.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-discover-intel11.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-discover-intel11.sh (revision 21239) @@ -0,0 +1,24 @@ +#!/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-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-scalapack-dir="/usr/local/intel/mkl/10.1.2.024/lib/64/" \ + --with-blas-lapack-dir="/usr/local/intel/mkl/10.1.2.024/lib/64/" \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-O3 -xS -DMPICH_IGNORE_CXX_SEEK" \ + --with-vendor=intel-discover + Index: /issm/branches/trunk-larour-NatClimateChange2016/configs/config-discover-intel13.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-discover-intel13.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-discover-intel13.sh (revision 21239) @@ -0,0 +1,23 @@ +#!/bin/csh + +#PETSc 3.2 +#MPI /usr/local/other/SLES11.1/mvapich2/1.8.1/intel-13.1.2.183/lib + +./configure \ + --prefix=$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-mkl-dir="/usr/local/intel/Composer/composer_xe_2013.3.163/mkl/" \ + --with-mpi-include="/usr/local/other/SLES11.1/mvapich2/1.8.1/intel-13.1.2.183/include" \ + --with-mpi-libflags="-L/usr/local/other/SLES11.1/mvapich2/1.8.1/intel-13.1.2.183/lib -lmpich -lopa -lmpl -lfmpich -lmpichcxx -lmpichf90 -lpthread -lrdmacm -libverbs -libumad -lrt -lnuma" \ + --with-petsc-arch=$ISSM_ARCH \ + --with-blacs-dir="/usr/local/intel/Composer/composer_xe_2013.3.163/mkl/" \ + --with-blas-lapack-dir="/usr/local/intel/Composer/composer_xe_2013.3.163/mkl/" \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-cxxoptflags="-O3 -xS -DMPICH_IGNORE_CXX_SEEK" \ + --with-vendor=intel-discover + + # --with-esmf-dir=$ESMF_INSTALL_DIRECTORY \ + Index: /issm/branches/trunk-larour-NatClimateChange2016/configs/config-ios-armv7.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-ios-armv7.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-ios-armv7.sh (revision 21239) @@ -0,0 +1,32 @@ +#!/bin/sh +set -eu + +export DEVROOT=`xcode-select --print-path` +export SDKROOT="$DEVROOT/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS7.1.sdk" +export CLANG="$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang" +export CLANGXX="$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++" +export CC=$CLANG +export LD=$DEVROOT/usr/bin/ld +export CPPFLAGS="-isysroot $SDKROOT/usr/include" +export CXX=$CLANGXX +export CXXFLAGS="-O -arch armv7 -isysroot $SDKROOT -I$SDKROOT/usr/include" +export CFLAGS="-O -arch armv7 -isysroot $SDKROOT -I$SDKROOT/usr/include" +export AR=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/ar +export AS=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/as +export LDFLAGS="-lstdc++ -arch armv7 -isysroot $SDKROOT" +export LIBTOOL=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/libtool +export STRIP=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/strip +export RANLIB=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib + +./configure \ + --prefix=$ISSM_DIR \ + --build="i386-apple-darwin13.1.0" \ + --host="armv7-apple-darwin14.0.0" \ + --enable-shared \ + --with-ios=yes \ + --with-Gia=no \ + --without-fortran \ + --without-wrappers \ + --without-kriging \ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ Index: /issm/branches/trunk-larour-NatClimateChange2016/configs/config-ios-armv7s.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-ios-armv7s.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-ios-armv7s.sh (revision 21239) @@ -0,0 +1,32 @@ +#!/bin/sh +set -eu + +export DEVROOT=`xcode-select --print-path` +export SDKROOT="$DEVROOT/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS7.1.sdk" +export CLANG="$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang" +export CLANGXX="$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++" +export CC=$CLANG +export LD=$DEVROOT/usr/bin/ld +export CPPFLAGS="-isysroot $SDKROOT/usr/include" +export CXX=$CLANGXX +export CXXFLAGS="-O -arch armv7s -isysroot $SDKROOT -I$SDKROOT/usr/include" +export CFLAGS="-O -arch armv7s -isysroot $SDKROOT -I$SDKROOT/usr/include" +export AR=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/ar +export AS=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/as +export LDFLAGS="-lstdc++ -arch armv7s -isysroot $SDKROOT" +export LIBTOOL=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/libtool +export STRIP=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/strip +export RANLIB=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib + +./configure \ + --prefix=$ISSM_DIR \ + --build="i386-apple-darwin13.1.0" \ + --host="armv7s-apple-darwin14.0.0" \ + --enable-shared \ + --with-ios=yes \ + --with-Gia=no \ + --without-fortran \ + --without-wrappers \ + --without-kriging \ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ Index: /issm/branches/trunk-larour-NatClimateChange2016/configs/config-ios-linux.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-ios-linux.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-ios-linux.sh (revision 21239) @@ -0,0 +1,28 @@ +#!/bin/sh + +export DEVROOT="/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/" +export SDKROOT="$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=$ISSM_DIR/externalpackages/triangle/install \ Index: /issm/branches/trunk-larour-NatClimateChange2016/configs/config-ios-simulator.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-ios-simulator.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-ios-simulator.sh (revision 21239) @@ -0,0 +1,31 @@ +#!/bin/sh +set -eu + +export DEVROOT=`xcode-select --print-path` +export SDKROOT="$DEVROOT/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator7.1.sdk" +export CLANG="$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang" +export CLANGXX="$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++" +export CC=$CLANG +export CXX=$CLANGXX +export LD=$DEVROOT/usr/bin/ld +export CPPFLAGS="-isysroot $SDKROOT/usr/include" +export CXXFLAGS="-O -arch i386 -miphoneos-version-min=7.1 -isysroot $SDKROOT -I$SDKROOT/usr/include" +export CFLAGS="-O -arch i386 -miphoneos-version-min=7.1 -isysroot $SDKROOT -I$SDKROOT/usr/include" +export AR=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/ar +export AS=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/as +export LDFLAGS="-lstdc++ -arch i386 -isysroot $SDKROOT" +export LIBTOOL=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/libtool +export STRIP=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/strip +export RANLIB=$DEVROOT/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib + +./configure \ + --prefix=$ISSM_DIR \ + --target="i386-apple-darwin13.1.0" \ + --enable-shared \ + --with-ios=yes \ + --with-Gia=no \ + --without-fortran \ + --without-wrappers \ + --without-kriging \ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ Index: /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-acenet.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-acenet.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-acenet.sh (revision 21239) @@ -0,0 +1,17 @@ +#!/bin/bash + +./configure \ + --prefix=/home/klemorza/issm/trunk-jpl \ + --with-metis-dir=$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=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-cxxoptflags="-O2" \ + --with-numthreads=32 \ + --with-serial=no \ + --with-modules=no \ + --enable-debugging CC=mpicc CXX=mpiCC F77=mpif77 Index: /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-cloud.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-cloud.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-cloud.sh (revision 21239) @@ -0,0 +1,18 @@ +#!/bin/sh + +#External packages versions: +#petsc 3.1 or 3.2 +#mpich 1.4 + +./configure \ + --prefix=$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-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-cxxoptflags=" -O2 -fpermissive" Index: /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-cyclone.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-cyclone.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-cyclone.sh (revision 21239) @@ -0,0 +1,22 @@ +#!/bin/sh + +#Default configuration script +#automake 1.14 +#petsc 3.6 +#mpich 3.0 + +./configure \ + --prefix=$ISSM_DIR \ + --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \ + --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \ + --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \ + --with-mpi-include="$ISSM_DIR/externalpackages/mpich/install/include" \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib/ -lmpich -lmpl" \ + --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install/" \ + --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install/" \ + --with-fortran-lib="-L/opt/intel/intelcompiler-12.04/composerxe-2011.4.191/compiler/lib/intel64 -lifport -lifcore -limf -lsvml -lintlc "\ + --enable-development \ + CC=mpicc \ + CXX=mpic++ Index: /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-hexagon.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-hexagon.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-hexagon.sh (revision 21239) @@ -0,0 +1,14 @@ +#!/bin/sh + +#need to swap to GNU environment +#need to change the petsc libflag to lcraypetsc... +./configure \ + --prefix=/work/bfl022/issm_install \ + --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \ + --with-petsc-dir=$PETSC_DIR \ + --with-metis-dir=$CRAY_TPSL_PREFIX_DIR \ + --with-mumps-dir=$CRAY_TPSL_PREFIX_DIR \ + --with-mpi-include="$CRAY_MPICH2_DIR/include" \ + --with-mpi-libflags="-L$CRAY_MPICH2_DIR/lib -lmpich -lmpl -lfmpich -lmpichcxx -lmpichf90" \ + --with-gsl-dir="/work/apps/gsl/1.16-gnu/" \ + --enable-development Index: /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-murdo-ad.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-murdo-ad.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-murdo-ad.sh (revision 21239) @@ -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=$ISSM_DIR/externalpackages/triangle/install Index: /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-pleiades-ampi-gcc.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-pleiades-ampi-gcc.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-pleiades-ampi-gcc.sh (revision 21239) @@ -0,0 +1,22 @@ +#!/bin/csh +./configure \ + --prefix=$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="$ISSM_DIR/externalpackages/petsc/install" \ + --with-graphics-lib="/usr/lib64/libX11.so" \ + --with-cxxoptflags=" -O3 -march=corei7-avx" \ + --with-vendor="intel-pleiades-gcc" \ + CFLAGS="-O3 -march=corei7-avx" \ + CXXFLAGS="-O3 -march=corei7-avx" \ + FFLAGS="-O3 -march=corei7-avx" Index: /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-pleiades-ampi.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-pleiades-ampi.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-pleiades-ampi.sh (revision 21239) @@ -0,0 +1,19 @@ +#!/bin/csh +./configure \ + --prefix=$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-larour-NatClimateChange2016/configs/config-linux64-pleiades-gcc-4.4.4.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-pleiades-gcc-4.4.4.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-pleiades-gcc-4.4.4.sh (revision 21239) @@ -0,0 +1,16 @@ +#!/bin/csh +./configure \ + --prefix=$ISSM_DIR \ + --without-kriging \ + --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-triangle-dir="$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-larour-NatClimateChange2016/configs/config-linux64-pleiades-gcc-4.7.0.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-pleiades-gcc-4.7.0.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-pleiades-gcc-4.7.0.sh (revision 21239) @@ -0,0 +1,17 @@ +#!/bin/csh +./configure \ + --prefix=$ISSM_DIR \ + --without-kriging \ + --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-triangle-dir="$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="$ISSM_DIR/externalpackages/petsc/install" \ + --with-graphics-lib="/usr/lib64/libX11.so" \ + --with-cxxoptflags="-g -O2" \ + --with-vendor="intel-pleiades-gcc" Index: /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-pleiades-intel2012.0.032-mpt.2.06rp16.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-pleiades-intel2012.0.032-mpt.2.06rp16.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-pleiades-intel2012.0.032-mpt.2.06rp16.sh (revision 21239) @@ -0,0 +1,17 @@ +#!/bin/csh +./configure \ + --prefix=$ISSM_DIR \ + --without-kriging \ + --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \ + --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-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="$ISSM_DIR/externalpackages/petsc/install" \ + --with-graphics-lib="/usr/lib64/libX11.so" \ + --with-cxxoptflags="-g -O2" \ + --with-vendor="intel-pleiades" Index: /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-pleiades-intel2015.0.090-mpt.2.11r13.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-pleiades-intel2015.0.090-mpt.2.11r13.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-pleiades-intel2015.0.090-mpt.2.11r13.sh (revision 21239) @@ -0,0 +1,15 @@ +#!/bin/csh +./configure \ + --prefix=$ISSM_DIR \ + --without-kriging \ + --with-wrappers=no \ + --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \ + --with-mpi-include="/nasa/sgi/mpt/2.11r13/include" \ + --with-mpi-libflags="-L/nasa/sgi/mpt/2.11r13/ -lmpi" \ + --with-mkl-dir="/nasa/intel/Compiler/2015.0.090/composer_xe_2015.0.090/mkl/" \ + --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-cxxoptflags="-O3 -axAVX" \ + --with-vendor="intel-pleiades" Index: /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-skylla.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-skylla.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-skylla.sh (revision 21239) @@ -0,0 +1,22 @@ +#!/bin/sh + +#External packages versions: +#petsc 3.4 +#mpich 3.0 + +./configure \ + --prefix=$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-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-larour-NatClimateChange2016/configs/config-linux64-vilje.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-vilje.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-linux64-vilje.sh (revision 21239) @@ -0,0 +1,23 @@ +#!/bin/sh +#Vilje configuration script +#this uses system stuff, you need to load the following: +#module load intelcomp/15.0.1 mpt/2.10 petsc/3.5.3d +#module load parmetis/4.0.3 mumps/5.0.0 +#module load automake + +./configure \ + --prefix=$ISSM_DIR \ + --without-kriging \ + --with-wrappers=no \ + --with-petsc-dir="/sw/sdev/Modules/petsc/petsc-3.5.3" \ + --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \ + --with-mpi-include="/sw/sgi/mpt/mpt-2.10/include/" \ + --with-mpi-libflags="-L/sw/sgi/mpt/mpt-2.10/lib -lmpi -lmpi++" \ + --with-metis-dir="/sw/sdev/Modules/parmetis/parmetis-4.0.3/include" \ + --with-mumps-dir="/sw/sdev/Modules/mumps/mumps-5.0.0/lib" \ + --with-cxxoptflags="-O2 -xAVX" \ + --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \ + --enable-development \ + CC=/sw/sdev/Modules/intelcomp/psxe_2015/bin/icc \ + CXX=/sw/sdev/Modules/intelcomp/psxe_2015/bin/icpc \ + F77=/sw/sdev/Modules/intelcomp/psxe_2015/bin/ifort Index: /issm/branches/trunk-larour-NatClimateChange2016/configs/config-macosx64-ad.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-macosx64-ad.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-macosx64-ad.sh (revision 21239) @@ -0,0 +1,18 @@ +#!/bin/sh + +./configure \ + --prefix=$ISSM_DIR \ + --without-wrappers\ + --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install\ + --without-thermal \ + --without-control \ + --without-hydrology \ + --without-stressbalance \ + --without-balanced \ + --without-responses \ + --without-slope \ + --without-rifts \ + --without-steadystate \ + --without-transient \ + --without-3d \ + --without-groundingline Index: /issm/branches/trunk-larour-NatClimateChange2016/configs/config-macosx64-dakota.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-macosx64-dakota.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-macosx64-dakota.sh (revision 21239) @@ -0,0 +1,26 @@ +#!/bin/sh + +#petsc 3.6 +#mpich 3.0 yosemite +#boost 1.55 yosemite +#dakota 5.3.1 yosemite +export F77='/usr/local/gfortran/bin/gfortran' +export CC=/usr/local/gfortran/bin/gcc +export CXX=/usr/local/gfortran/bin/g++ + +./configure \ + --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-boost-dir=$ISSM_DIR/externalpackages/boost/install \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/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 $ISSM_DIR/externalpackages/mpich/install/lib/libmpl.a " \ + --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ + --with-numthreads=8 + Index: /issm/branches/trunk-larour-NatClimateChange2016/configs/config-macosx64.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-macosx64.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-macosx64.sh (revision 21239) @@ -0,0 +1,19 @@ +#!/bin/sh + +#petsc 3.4 +#mpich 3.0.4 + +./configure \ + --prefix=$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 $ISSM_DIR/externalpackages/mpich/install/lib/libmpl.a " \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-fortran-lib="/usr/lib/gcc/i686-apple-darwin10/4.2.1/x86_64/libgfortran.a" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-numthreads=8 Index: /issm/branches/trunk-larour-NatClimateChange2016/configs/config-pleiades-petsc3.4.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-pleiades-petsc3.4.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-pleiades-petsc3.4.sh (revision 21239) @@ -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-larour-NatClimateChange2016/configs/config-pleiades-petscdev.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-pleiades-petscdev.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-pleiades-petscdev.sh (revision 21239) @@ -0,0 +1,23 @@ +#!/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=$ISSM_DIR/externalpackages/tao/install \ + --with-mpi-include=/nasa/sgi/mpt/2.04/include \ + --with-mpi-libflags="-L/nasa/sgi/mpt/2.04/lib/ -lmpi -lpthread -lgfortran" \ + --with-dakota-dir=$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-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=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-O3" \ + --with-vendor=intel-pleiades Index: /issm/branches/trunk-larour-NatClimateChange2016/configs/config-win10.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/config-win10.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/config-win10.sh (revision 21239) @@ -0,0 +1,19 @@ +#!/bin/bash + +./configure --prefix=$ISSM_DIR \ + --with-vendor=MSVC-Win64 \ + --with-cxxoptflags='' \ + --disable-static \ + --enable-standalone-libraries \ + --with-fortran=no \ + --without-Gia \ + --without-kriging \ + --without-kml \ + --with-matlab-dir=$MATLAB_PATH \ + --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \ + --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/lib/ \ + --with-mpi-libdir="$ISSM_DIR/externalpackages/petsc/install/lib" \ + --with-mpi-libflags="-Wl,libpetsc.lib" \ + --with-mpi-include="$ISSM_DIR/externalpackages/petsc/install/include/petsc/mpiuni" Index: /issm/branches/trunk-larour-NatClimateChange2016/configs/configure.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configs/configure.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configs/configure.sh (revision 21239) @@ -0,0 +1,17 @@ +#!/bin/sh + +#Default configuration script +#petsc 3.4 +#mpich 1.4 + +./configure \ + --prefix=$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="$ISSM_DIR/externalpackages/petsc/install" \ + --with-metis-dir="$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-larour-NatClimateChange2016/configure.ac =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/configure.ac (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/configure.ac (revision 21239) @@ -0,0 +1,51 @@ +# Process this file with autoconf to produce a configure script. + +#AUTOCONF +AC_INIT([Ice Sheet System Model (ISSM)],[4.11],[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]) + +#print header +AC_MSG_NOTICE(============================================================================) +AC_MSG_NOTICE(= AC_PACKAGE_NAME AC_PACKAGE_VERSION configuration =) +AC_MSG_NOTICE(============================================================================) + +#Determine System type and OS +AC_CANONICAL_TARGET + +#Compilers +AC_PROG_CC([icc cl icl gcc]) +AC_PROG_CPP +AC_PROG_CXX([icpc cl icl g++]) +AC_PROG_F77([ifort g77 gfortran]) + +#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_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/wrappers/javascript/Makefile + src/mobile/Makefile + src/mobile/native/Makefile + src/m/Makefile + ]) + +#End of configure.ac +AC_OUTPUT Index: /issm/branches/trunk-larour-NatClimateChange2016/etc/environment.csh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/etc/environment.csh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/etc/environment.csh (revision 21239) @@ -0,0 +1,116 @@ +#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 (-e $MATLAB_DIR) then +# setenv MATLAB_DIR {$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 $DAKOTA_DIR) then + setenv PATH {$DAKOTA_DIR}/bin:{$PATH} + setenv MANPATH {$MANPATH}:{$MPI_DIR}/man:{$DAKOTA_DIR}/docs/man:{$DAKOTA_DIR}/docs/man-ref +endif + +#Boost +set BOOST_DIR="$ISSM_DIR/externalpackages/boost/install" +set BOOSTROOT="$ISSM_DIR/externalpackages/boost/install" +if (-d $BOOST_DIR) then + setenv PATH {$BOOST_DIR}/bin:{$PATH} +endif + +#Doxygen +set DOXYGEN_DIR="$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 $SHELL2JUNIT_DIR) then + setenv PATH {$SHELL2JUNIT_DIR}/install:{$PATH} +endif + +#GMT +set GMT_DIR="$ISSM_DIR/externalpackages/gmt" +if (-d $GMT_DIR) then + setenv PATH {$GMT_DIR}/install/bin/:{$PATH} +endif Index: /issm/branches/trunk-larour-NatClimateChange2016/etc/environment.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/etc/environment.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/etc/environment.sh (revision 21239) @@ -0,0 +1,329 @@ +#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 "$MATLAB_DIR/lib" + +#GMT +GMT_DIR="$ISSM_DIR/externalpackages/gmt/install" +export GMT_DIR +pathprepend "$GMT_DIR/bin" +libpathappend "$GMT_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" +if [ -d "$PETSC_DIR" ]; then + export PETSC_DIR + libpathappend "$PETSC_DIR/lib" +fi + +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 "$BOOST_DIR" ]; then + export BOOSTROOT + export BOOST_DIR + libpathprepend "$BOOST_DIR/lib" + dylibpathprepend "$BOOST_DIR/lib" + pathprepend "$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" + +CVS_DIR="$ISSM_DIR/externalpackages/cvs/install" +pathprepend "$CVS_DIR/bin" + +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 "$ISSM_DIR/externalpackages/expat/install" + +#GMSH +pathappend "$ISSM_DIR/externalpackages/gmsh/install" + +#CURL +libpathprepend "$ISSM_DIR/externalpackages/curl/install/lib" +dylibpathprepend "$ISSM_DIR/externalpackages/curl/install/lib" +pathprepend "$ISSM_DIR/externalpackages/curl/install/bin" + +#GMT +pathprepend "$ISSM_DIR/externalpackages/gmt/install/bin" Index: /issm/branches/trunk-larour-NatClimateChange2016/examples/Data/Download.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/Data/Download.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/Data/Download.sh (revision 21239) @@ -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" +$ISSM_DIR/scripts/DownloadExternalPackage2.py 'ftp://n5eil01u.ecs.nsidc.org/SAN/MEASURES/NSIDC-0484.001/1996.01.01/antarctica_ice_velocity_900m.nc' 'Antarctica_ice_velocity.nc' + +echo "Downloading PIG errors" +$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/examples/Box_Greenland_SMB_monthly_1840-2012_5km_cal_ver20141007.nc' 'Box_Greenland_SMB_monthly_1840-2012_5km_cal_ver20141007.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-larour-NatClimateChange2016/examples/Greenland/CheatSheet.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/Greenland/CheatSheet.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/Greenland/CheatSheet.m (revision 21239) @@ -0,0 +1,72 @@ +if any(steps==7) + disp(' Step 7: Historical Relaxation run'); + md = loadmodel('./Models/Greenland.Control_drag'); + + load smbbox + + %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); + + %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.smb.mass_balance = [smb;1 ]; + + %Set transient options, run for 20 years, saving every 5 timesteps + md.timestepping.time_step=0.2; + md.timestepping.final_time=200; + md.settings.output_frequency=5; + + %Additional options + md.inversion.iscontrol=0; + md.transient.requested_outputs={'IceVolume','TotalSmb', ... + 'SmbMassBalance'}; + md.verbose=verbose('solution',true,'module',true); + + %Go solve + md.cluster=generic('name',oshostname,'np',2); + md=solve(md,'Transient'); + + save ./Models/Greenland.HistoricTransient_200yr md; +end + +if any(steps==8) + disp(' Step 8: Plotting exercise'); + + %Load historic transient model + md = loadmodel('./Models/Greenland.HistoricTransient_200yr'); + + %Create Line Plots of relaxation run. Create a figure. + figure + + %Save surface mass balance, by looping through 200 years (1000 steps) + % Note, the first output will always contain output from time step 1 + surfmb=[]; for i=2:201; surfmb=[surfmb ... + md.results.TransientSolution(i).SmbMassBalance]; end + + %Plot surface mass balance time series in first subplot + subplot(3,1,1); plot([1:200],mean(surfmb)); + + %Title this plot Mean surface mass balance + title('Mean Surface mass balance'); + + %Save velocity by looping through 200 years + vel=[]; for i=2:201; vel=[vel md.results.TransientSolution(i).Vel]; end + + %Plot velocity time series in second subplot + subplot(3,1,2); plot([1:200],mean(vel)); + + %Title this plot Mean Velocity + title('Mean Velocity'); + + %Save Ice Volume by looping through 200 years + volume=[]; for i=2:201; volume=[volume md.results.TransientSolution(i).IceVolume]; end + + %Plot volume time series in third subplot + subplot(3,1,3); plot([1:200],volume); + + %Title this plot Mean Velocity and add an x label of years + title('Ice Volume'); xlabel('years'); +end Index: /issm/branches/trunk-larour-NatClimateChange2016/examples/Greenland/DomainOutline.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/Greenland/DomainOutline.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/Greenland/DomainOutline.exp (revision 21239) @@ -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 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+66950.2394150000 -2594124.2461040001 +57598.7572140000 -2581101.0214539999 +53117.8386600000 -2598131.3921500002 +41818.1310010000 -2586610.8472679998 +30810.6571600000 -2599133.1786610000 +44253.4128240000 -2608650.1505200001 +47662.8073760000 -2621047.2585999998 + Index: /issm/branches/trunk-larour-NatClimateChange2016/examples/Greenland/Greenland.par =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/Greenland/Greenland.par (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/Greenland/Greenland.par (revision 21239) @@ -0,0 +1,77 @@ +%Name and Coordinate system +md.miscellaneous.name='SeaRISEgreenland'; +md.mesh.epsg=3413; + +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.smb.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); +md.smb.mass_balance=md.smb.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 constraints'); +%Initialize single point constraint arrays +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); + Index: /issm/branches/trunk-larour-NatClimateChange2016/examples/Greenland/runme.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/Greenland/runme.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/Greenland/runme.m (revision 21239) @@ -0,0 +1,329 @@ +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,'Stressbalance'); + + %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.smb.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', ... + 'SmbMassBalance'}; + md.verbose=verbose('solution',true,'module',true,'convergence',true); + + %Go solve + md.cluster=generic('name',oshostname,'np',2); + md=solve(md,'Transient'); + + save ./Models/Greenland.Transient md; +end + +if any(steps==5) + disp(' Step 5: Plotting'); + md = loadmodel('./Models/Greenland.Transient'); + + %Planview plots + plotmodel(md,'data',md.results.TransientSolution(end).Vel,'log#1', 10, ... + 'caxis#1', [1e-1 1e4], ... + 'title#1', 'Velocity (m/y)',... + 'data',md.results.TransientSolution(1).SmbMassBalance,... + 'title#2', 'Surface Mass Balance (m/y)',... + 'data',md.results.TransientSolution(end).Thickness,... + 'title', 'Thickness (m)',... + 'data',md.results.TransientSolution(end).Surface,... + 'title', 'Surface (m)'); + + %Line Plots + figure + + %Plot surface mass balance + surfmb=[]; for i=1:100; surfmb=[surfmb ... + md.results.TransientSolution(i).SmbMassBalance]; 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: Extract Box SMB'); + md = loadmodel('./Models/Greenland.Transient'); + + ncbox='../Data/Box_Greenland_SMB_monthly_1840-2012_5km_cal_ver20141007.nc'; + + %Set surface mass balance + lat = ncread(ncbox,'lat'); + lon = ncread(ncbox,'lon'); + smbbox = ncread(ncbox,'MassFlux'); + [x1 y1]=ll2xy(lat,lon,+1,45,70); + + years_of_simulation = 1840:2012; + t = [years_of_simulation(1):1/12:years_of_simulation(end)+11/12]; + + %Area of grid for 5km box + area_of_grid=5000*5000; + totalsmb=reshape(sum(sum(smbbox/1000,1),2),length(t),1)*area_of_grid; + + %save surface mass balance mat dataset + smbmean = mean(mean(smbbox,3),4); + save -v7.3 smbbox smbmean totalsmb smbbox x1 y1 t; + + %plot a time series of total SMB + figure; plot(t,totalsmb/1e9); title('Total Surface mass balance, Gt'); xlabel('year'); ylabel('Gt/yr'); + + clear smbbox + +end + +if any(steps==7) + disp(' Step 7: Historical Relaxation run'); + md = loadmodel('./Models/Greenland.Control_drag'); + + load smbbox + + %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); + + %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.smb.mass_balance = [smb;1 ]; + + %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', ... + 'SmbMassBalance'}; + md.verbose=verbose('solution',true,'module',true); + + %Go solve + md.cluster=generic('name',oshostname,'np',2); + md=solve(md,'Transient'); + + save ./Models/Greenland.HistoricTransient md; +end + +if any(steps==8) + disp(' Step 8: Plotting exercise'); + + %Load historic transient model + + + %Create Line Plots of relaxation run. Create a figure. + + + %Save surface mass balance, by looping through 200 years (1000 steps) + % Note, the first output will always contain output from time step 1 + + + %Plot surface mass balance time series in first subplot + + + %Title this plot Mean surface mass balance + + + %Save velocity by looping through 200 years + + + %Plot velocity time series in second subplot + + + %Title this plot Mean Velocity + + + %Save Ice Volume by looping through 200 years + + + %Plot volume time series in third subplot + + + %Title this plot Mean Velocity and add an x label of years + +end + +if any(steps==9) + disp(' Step 9: Box Transient run'); + md = loadmodel('./Models/Greenland.HistoricTransient_200yr'); + + %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.smb.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', ... + 'SmbMassBalance'}; + md.verbose=verbose('solution',true,'module',true); + + %Go solve + md.cluster=generic('name',oshostname,'np',2); + md=solve(md,'Transient'); + + save ./Models/Greenland.BoxTransient md; +end + +if any(steps==10) + disp(' Step 10: 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-larour-NatClimateChange2016/examples/ISMIP/CheatyIsmipA.par =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/ISMIP/CheatyIsmipA.par (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/ISMIP/CheatyIsmipA.par (revision 21239) @@ -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-larour-NatClimateChange2016/examples/ISMIP/CheatyIsmipF.par =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/ISMIP/CheatyIsmipF.par (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/ISMIP/CheatyIsmipF.par (revision 21239) @@ -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-larour-NatClimateChange2016/examples/ISMIP/CheatyRunme.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/ISMIP/CheatyRunme.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/ISMIP/CheatyRunme.m (revision 21239) @@ -0,0 +1,221 @@ +%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 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,'Stressbalance'); + % 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,'Transient'); + % 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-larour-NatClimateChange2016/examples/ISMIP/IsmipA.par =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/ISMIP/IsmipA.par (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/ISMIP/IsmipA.par (revision 21239) @@ -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-larour-NatClimateChange2016/examples/ISMIP/IsmipF.par =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/ISMIP/IsmipF.par (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/ISMIP/IsmipF.par (revision 21239) @@ -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-larour-NatClimateChange2016/examples/ISMIP/runme.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/ISMIP/runme.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/ISMIP/runme.m (revision 21239) @@ -0,0 +1,215 @@ +%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-larour-NatClimateChange2016/examples/IceBridge/DomainOutline.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/IceBridge/DomainOutline.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/IceBridge/DomainOutline.exp (revision 21239) @@ -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 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-2607648.3640089999 +92277.1703750000 -2603641.2179629998 +97537.3791130000 -2587111.7405229998 +88380.7194580000 -2573587.6226180000 +74743.1412490000 -2567076.0102940002 +61105.5630390000 -2577093.8754090001 +66950.2394150000 -2594124.2461040001 +57598.7572140000 -2581101.0214539999 +53117.8386600000 -2598131.3921500002 +41818.1310010000 -2586610.8472679998 +30810.6571600000 -2599133.1786610000 +44253.4128240000 -2608650.1505200001 +47662.8073760000 -2621047.2585999998 + Index: /issm/branches/trunk-larour-NatClimateChange2016/examples/IceBridge/Greenland.par =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/IceBridge/Greenland.par (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/IceBridge/Greenland.par (revision 21239) @@ -0,0 +1,99 @@ +%Name and Coordinate system +md.miscellaneous.name='SeaRISEgreenland'; +md.mesh.epsg=3413; + +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; + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%Reading IceBridge data for Jakobshavn +disp(' reading IceBridge Jakobshavn bedrock'); +fid = fopen('../Data/Jakobshavn_2008_2011_Composite_XYZGrid.txt'); +titles = fgets(fid); +data = fscanf(fid,'%g,%g,%g,%g,%g',[5 266400])'; +fclose(fid); + +[xi,yi]= ll2xy(md.mesh.lat,md.mesh.long,+1,45,70); +bed = flipud(reshape(data(:,5),[360 740])); bed(find(bed==-9999))=NaN; +bedy = flipud(reshape(data(:,1),[360 740])); +bedx = flipud(reshape(data(:,2),[360 740])); + +%Insert Icebridge bed and recalculate thickness +bed_jks=InterpFromGridToMesh(bedx(1,:)',bedy(:,1),bed,xi,yi,NaN); +in=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,... + 'Jak_grounded.exp','node',1); +bed_jks(~in)=NaN; +pos=find(~isnan(bed_jks)); +md.geometry.base(pos)=bed_jks(pos); +md.geometry.thickness=md.geometry.surface-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.smb.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); +md.smb.mass_balance=md.smb.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.groundedice_melting_rate = zeros(md.mesh.numberofvertices,1); +md.basalforcings.floatingice_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 constraints'); +%Initialize single point constraint arrays +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); Index: /issm/branches/trunk-larour-NatClimateChange2016/examples/IceBridge/Greenland_noOIB.par =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/IceBridge/Greenland_noOIB.par (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/IceBridge/Greenland_noOIB.par (revision 21239) @@ -0,0 +1,82 @@ +%Name and Coordinate system +md.miscellaneous.name='SeaRISEgreenland'; +md.mesh.epsg=3413; + +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.smb.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); +md.smb.mass_balance=md.smb.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.groundedice_melting_rate = zeros(md.mesh.numberofvertices,1); +md.basalforcings.floatingice_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-larour-NatClimateChange2016/examples/IceBridge/Greenland_solution.par =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/IceBridge/Greenland_solution.par (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/IceBridge/Greenland_solution.par (revision 21239) @@ -0,0 +1,103 @@ +%Name and Coordinate system +md.miscellaneous.name='SeaRISEgreenland'; +md.mesh.epsg=3413; + +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; + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%Reading IceBridge data for Jakobshavn +disp(' reading IceBridge Jakobshavn bedrock'); +fid = fopen('../Data/Jakobshavn_2008_2011_Composite_XYZGrid.txt'); +titles = fgets(fid); +data = fscanf(fid,'%g,%g,%g,%g,%g',[5 266400])'; +fclose(fid); + +[xi,yi]= ll2xy(md.mesh.lat,md.mesh.long,+1,45,70); +bed = flipud(reshape(data(:,5),[360 740])); bed(find(bed==-9999))=NaN; +surf = flipud(reshape(data(:,4),[360 740])); surf(find(surf==-9999))=NaN; +bedy = flipud(reshape(data(:,1),[360 740])); +bedx = flipud(reshape(data(:,2),[360 740])); + +%Insert Icebridge bed and recalculate thickness +bed_jks=InterpFromGridToMesh(bedx(1,:)',bedy(:,1),bed,xi,yi,NaN); +surf_jks=InterpFromGridToMesh(bedx(1,:)',bedy(:,1),surf,xi,yi,NaN); +in=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,... + 'Jak_grounded.exp','node',1); +bed_jks(~in)=NaN; +surf_jks(~in)=NaN; +pos=find(~isnan(bed_jks)); +md.geometry.base(pos)=bed_jks(pos); +md.geometry.surface(pos)=surf_jks(pos); +md.geometry.thickness=md.geometry.surface-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.smb.mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); +md.smb.mass_balance=md.smb.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.groundedice_melting_rate = zeros(md.mesh.numberofvertices,1); +md.basalforcings.floatingice_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 constraints'); +%Initialize single point constraint arrays +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); Index: /issm/branches/trunk-larour-NatClimateChange2016/examples/IceBridge/Jak_grounded.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/IceBridge/Jak_grounded.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/IceBridge/Jak_grounded.exp (revision 21239) @@ -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-larour-NatClimateChange2016/examples/IceBridge/Jak_outline.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/IceBridge/Jak_outline.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/IceBridge/Jak_outline.exp (revision 21239) @@ -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-larour-NatClimateChange2016/examples/IceBridge/data_gaps.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/IceBridge/data_gaps.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/IceBridge/data_gaps.exp (revision 21239) @@ -0,0 +1,70 @@ +## Name:data_gaps +## Icon:0 +# Points Count Value +13 1.000000 +# X pos Y pos +-183076.0390091268 -1794119.5324780210 +-233886.6983670916 -1838953.5447257366 +-239864.4229974404 -2006333.8571172084 +-299641.6693009282 -2081057.2108634012 +-269753.0461491842 -2116924.4206615738 +-257797.5968884868 -2185669.9061080711 +-278719.6330947075 -2248437.5232548732 +-254808.7345733123 -2266371.1281539593 +-224920.1114215683 -2167736.3012089850 +-198020.3505849990 -2093012.9474627920 +-123298.7927056390 -1967477.7131691882 +-180087.1766939524 -1797108.4666278686 +-183076.0390091268 -1794119.5324780210 + +## Name:data_gaps +## Icon:0 +# Points Count Value +12 1.000000 +# X pos Y pos +-90421.3072387208 -1824008.8739764981 +-117321.0680752902 -1946555.1741202541 +-156176.2781725575 -2075079.3425637058 +-177098.3143787782 -2203603.5110071572 +-174109.4520636038 -2314194.0745515227 +-72488.1333476745 -2293271.5355025884 +-93410.1695538952 -2203603.5110071572 +-30644.0609352330 -2206592.4451570050 +-6733.1624138379 -2081057.2108634012 +44077.4969441269 -1967477.7131691882 +-93410.1695538952 -1824008.8739764981 +-90421.3072387208 -1824008.8739764981 + +## Name:data_gaps +## Icon:0 +# Points Count Value +15 1.000000 +# X pos Y pos +-87432.4449235464 -2365005.9550989335 +-287686.2200402305 -2639987.8968849229 +-284697.3577250564 -2879102.6288727401 +-470006.8212658686 -2983715.3241174100 +-538750.6545148797 -3157073.5048085772 +-356430.0532892416 -3267664.0683529424 +-189053.7636394757 -3270653.0025027902 +-272741.9084643587 -3243752.5951541606 +-218942.3867912197 -3076372.2827626891 +-236875.5606822660 -3019582.5339155826 +-117321.0680752902 -2834268.6166250245 +20166.5984227317 -2669877.2383834003 +-12710.8870441865 -2469618.6503436035 +-87432.4449235464 -2367994.8892487814 +-87432.4449235464 -2365005.9550989335 + +## Name:data_gaps +## Icon:0 +# Points Count Value +6 1.000000 +# X pos Y pos +-186064.9013243013 -1555004.8004902040 +-177098.3143787782 -1695484.7055330465 +-81454.7202931975 -1698473.6396828941 +-36621.7855655816 -1513159.7223923360 +-186064.9013243013 -1552015.8663403564 +-186064.9013243013 -1555004.8004902040 + Index: /issm/branches/trunk-larour-NatClimateChange2016/examples/IceBridge/runme.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/IceBridge/runme.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/IceBridge/runme.m (revision 21239) @@ -0,0 +1,157 @@ +clear all; +close 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 without refinement in Jak basin + md=bamg(md,'hmax',400000,'hmin',5000,'gradation',1.7,'field',vel,'err',8); + return; + + %Refine mesh in the region of Jakobshavn (resolution = 3000 m) + hmaxVertices=NaN*ones(md.mesh.numberofvertices,1); + in=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,... + 'Jak_outline.exp','node',1); + hmaxVertices(find(in))=3000; + md=bamg(md,'hmax',400000,'hmin',5000,'gradation',1.7,'field',vel,... + 'err',8,'hmaxVertices',hmaxVertices); + + %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; +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.Parameterization2 md; +end + +if any(steps==3) + disp(' Step 3: Control method friction'); + md = loadmodel('./Models/Greenland.Parameterization2'); + + %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); + 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)=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); + in=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,... + 'data_gaps.exp','node',1); + md.inversion.cost_functions_coefficients(find(in),1)=0.0; + md.inversion.cost_functions_coefficients(find(in),2)=0.0; + + %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.verbose=verbose('solution',true,'control',true); + md=solve(md,'Stressbalance'); + + %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)*1000/md.materials.rho_ice; + smb = [smb smb smb-1.0]; + md.smb.mass_balance = [smb;1 10 20]; + + %Set transient options, run for 20 years, saving every year + md.timestepping.time_step=0.2; %This must be reduced for finer resolutions + md.timestepping.final_time=20; + md.settings.output_frequency=1; + + %Additional options + md.inversion.iscontrol=0; + md.transient.requested_outputs={'IceVolume','TotalSmb','SmbMassBalance'}; + md.verbose=verbose('solution',true,'module',true,'convergence',true); + + %Go solve + md.cluster=generic('name',oshostname,'np',2); + md=solve(md,'Transient'); + + save ./Models/Greenland.Transient md; +end + +if any(steps==5) + disp(' Step 5: Plotting'); + md = loadmodel('./Models/Greenland.Transient'); + + %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(end).SmbMassBalance, ... + '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 + time_plot=md.results.TransientSolution(1).time:md.timestepping.time_step:md.timestepping.final_time; + + %Plot surface mass balance + surfmb=[]; for i=1:100; surfmb=[surfmb ... + md.results.TransientSolution(i).SmbMassBalance]; end + subplot(3,1,1); plot(time_plot,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(time_plot,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(time_plot,volume); title('Ice Volume'); + xlabel('years') +end Index: /issm/branches/trunk-larour-NatClimateChange2016/examples/IceflowModels/Contour.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/IceflowModels/Contour.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/IceflowModels/Contour.exp (revision 21239) @@ -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-larour-NatClimateChange2016/examples/IceflowModels/EISMINT.par =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/IceflowModels/EISMINT.par (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/IceflowModels/EISMINT.par (revision 21239) @@ -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.smb.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-larour-NatClimateChange2016/examples/IceflowModels/RoundFront.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/IceflowModels/RoundFront.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/IceflowModels/RoundFront.exp (revision 21239) @@ -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-larour-NatClimateChange2016/examples/IceflowModels/Square.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/IceflowModels/Square.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/IceflowModels/Square.exp (revision 21239) @@ -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-larour-NatClimateChange2016/examples/IceflowModels/SquareFront.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/IceflowModels/SquareFront.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/IceflowModels/SquareFront.exp (revision 21239) @@ -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-larour-NatClimateChange2016/examples/IceflowModels/SquareShelf.par =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/IceflowModels/SquareShelf.par (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/IceflowModels/SquareShelf.par (revision 21239) @@ -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-larour-NatClimateChange2016/examples/IceflowModels/eismint.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/IceflowModels/eismint.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/IceflowModels/eismint.m (revision 21239) @@ -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,'Stressbalance'); +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 ice sheet (m)'); +ylabel('velocity (m/yr)'); +legend('calculated velocity','exact velocity'); +axis([0 750000 0 200]); +hold off; Index: /issm/branches/trunk-larour-NatClimateChange2016/examples/IceflowModels/runme.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/IceflowModels/runme.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/IceflowModels/runme.m (revision 21239) @@ -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,'Stressbalance'); Index: /issm/branches/trunk-larour-NatClimateChange2016/examples/Inversion/DomainOutline.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/Inversion/DomainOutline.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/Inversion/DomainOutline.exp (revision 21239) @@ -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-larour-NatClimateChange2016/examples/Inversion/Front.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/Inversion/Front.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/Inversion/Front.exp (revision 21239) @@ -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-larour-NatClimateChange2016/examples/Inversion/Square.par =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/Inversion/Square.par (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/Inversion/Square.par (revision 21239) @@ -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.x=-18.0e5); +x_pig = x(posx); +posy = find(y<=1.0e5 & y>-4.0e5); +y_pig = flipud(y(posy)); + +vx_pig = flipud(vx(posx,posy)'); +vy_pig = flipud(vy(posx,posy)'); +vel_pig = sqrt(vx_pig.^2+vy_pig.^2); + +imagesc(x_pig,y_pig,log(vel_pig+1)); +axis xy equal tight; Index: /issm/branches/trunk-larour-NatClimateChange2016/examples/Pig/runme.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/Pig/runme.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/Pig/runme.m (revision 21239) @@ -0,0 +1,198 @@ +steps=[1]; + +if any(steps==1) %Mesh Generation #1 + %Mesh parameters + domain =['./DomainOutline.exp']; + hinit=10000; % element size for the initial mesh + hmax=40000; % maximum element size of the final mesh + hmin=5000; % minimum element size of the final 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); + + %ploting + plotmodel(md,'data','mesh') + return; + + % Load Velocities + nsidc_vel='../Data/Antarctica_ice_velocity.nc'; + + % Get necessary data to build up the velocity grid + xmin = ncreadatt(nsidc_vel,'/','xmin'); + ymax = ncreadatt(nsidc_vel,'/','ymax'); + spacing = ncreadatt(nsidc_vel,'/','spacing'); + nx = double(ncreadatt(nsidc_vel,'/','nx')); + ny = double(ncreadatt(nsidc_vel,'/','ny')); + vx = double(ncread(nsidc_vel,'vx')); + vy = double(ncread(nsidc_vel,'vy')); + + % Read coordinates + xmin = strtrim(xmin); + xmin = str2num(xmin(1:end-2)); + ymax = strtrim(ymax); + ymax = str2num(ymax(1:end-2)); + spacing = strtrim(spacing); + spacing = str2num(spacing(1:end-2)); + + % Build the coordinates + x=xmin+(0:1:nx)'*spacing; + y=(ymax-ny*spacing)+(0:1:ny)'*spacing; + + % 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') + + % Save model + save ./Models/PIG_Mesh_generation md; +end + +if any(steps==2) %Masks #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 + +if any(steps==3) %Parameterization #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 + +if any(steps==4) %Control Method #4 + + md = loadmodel('./Models/PIG_Parameterization'); + + % Control general + md.inversion.iscontrol=1; + md.inversion.maxstepss=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,'Stressbalance'); + + % 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 + +if any(steps==5) %Plot #5 + + md = loadmodel('./Models/PIG_Control_drag'); + + plotmodel(md,'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 + +if any(steps==6) %Higher-Order #6 + + % Load Model + + % Disable inversion + + % Extrude Mesh + + % Set Flowequation + + % Solve + + % Save Model + +end + +if any(steps==7) %Plot #7 + + mdHO = loadmodel('./Models/PIG_ModelHO'); + mdSSA = loadmodel('./Models/PIG_Control_drag'); + + basal=find(mdHO.mesh.vertexonbase); + surf=find(mdHO.mesh.vertexonsurface); + + plotmodel(mdHO,'nlines',3,'ncols',2,'axis#all','equal',... + 'xlim#all',[min(mdHO.mesh.x) max(mdHO.mesh.x)]/10^3,... + 'ylim#all',[min(mdHO.mesh.y) max(mdHO.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-larour-NatClimateChange2016/examples/PigSensitivity/FrontRetreat.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/PigSensitivity/FrontRetreat.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/PigSensitivity/FrontRetreat.exp (revision 21239) @@ -0,0 +1,17 @@ +## Name:FrontRetreat +## Icon:0 +# Points Count Value +11 1.000000 +# X pos Y pos +-1626858.6376043619 -327176.4356578548 +-1605190.4936934854 -325911.1425827671 +-1604716.0087903275 -316263.2828852235 +-1607088.4333061168 -312625.5652943464 +-1612465.9288752396 -311676.5954880306 +-1618476.0709819060 -312467.4036599604 +-1624011.7281854146 -313890.8583694341 +-1626858.6376043619 -315788.7979820656 +-1627807.6074106777 -319268.3539385567 +-1628756.5772169936 -322589.7482606619 +-1626858.6376043619 -327176.4356578548 + Index: /issm/branches/trunk-larour-NatClimateChange2016/examples/PigSensitivity/Help.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/PigSensitivity/Help.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/PigSensitivity/Help.m (revision 21239) @@ -0,0 +1,22 @@ +if step==4 + %Load model + md = loadmodel('./Models/PIG_Transient'); + + %Change external forcing basal melting rate and surface mass balance) + md.basalforcings.groundedice_melting_rate=zeros(md.mesh.numberofvertices,1); + md.basalforcings.floatingice_melting_rate=25*ones(md.mesh.numberofvertices,1); + md.smb.mass_balance=2*md.smb.mass_balance; + + %Define time steps and time span of the simulation + md.timestepping.time_step=0.1; + md.timestepping.final_time=10; + + %Request additional outputs + md.transient.requested_outputs={'default','IceVolume','IceVolumeAboveFloatation'}; + + %Solve + md=solve(md,'Transient'); + + %Save model + save ./Models/PIG_SMB md; +end Index: /issm/branches/trunk-larour-NatClimateChange2016/examples/PigSensitivity/runme.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/PigSensitivity/runme.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/PigSensitivity/runme.m (revision 21239) @@ -0,0 +1,75 @@ +steps=[1]; + +if any(steps==1) %Transient Run #1 + + md = loadmodel('../Pig/Models/PIG_Control_drag'); + + md.inversion.iscontrol=0; + md.transient.ismasstransport=1; + md.transient.isstressbalance=1; + md.transient.isgroundingline=1; + md.transient.ismovingfront=0; + md.transient.isthermal=0; + + pos=find(md.mask.groundedice_levelset<0); + md.basalforcings.groundedice_melting_rate=zeros(md.mesh.numberofvertices,1); + md.basalforcings.floatingice_melting_rate=25*ones(md.mesh.numberofvertices,1); + + md.timestepping.time_step=0.1; + md.timestepping.final_time=10; + md.transient.requested_outputs={'default','IceVolume','IceVolumeAboveFloatation'}; + + md=solve(md,'Transient'); + + % Save model + save ./Models/PIG_Transient md; +end + +if any(steps==2) %High Melt #2 + md = loadmodel('./Models/PIG_Transient'); + + md.basalforcings.groundedice_melting_rate=zeros(md.mesh.numberofvertices,1); + md.basalforcings.floatingice_melting_rate=60*ones(md.mesh.numberofvertices,1); + + md.timestepping.time_step=0.1; + md.timestepping.final_time=10; + md.transient.requested_outputs={'default','IceVolume','IceVolumeAboveFloatation'}; + + md=solve(md,'Transient'); + + save ./Models/PIG_HighMelt md; +end + +if any(steps==3) %Ice Front retreat + md = loadmodel('./Models/PIG_Transient'); + + md2=extract(md,'~FrontRetreat.exp'); + + md2=SetMarineIceSheetBC(md2); + + md2.basalforcings.groundedice_melting_rate=zeros(md2.mesh.numberofvertices,1); + md2.basalforcings.floatingice_melting_rate=25*ones(md2.mesh.numberofvertices,1); + + md2.timestepping.time_step=0.1; + md2.timestepping.final_time=10; + md2.transient.requested_outputs={'default','IceVolume','IceVolumeAboveFloatation'}; + + md2=solve(md2,'Transient'); + + save ./Models/PIG_FrontRetreat md2; +end + +if any(steps==4) %High surface mass balance #3 + %Load model + + %Change external forcing basal melting rate and surface mass balance) + + %Refine time steps and time span of the simulation + + %Request additional outputs + + %Solve + + %Save model + +end Index: /issm/branches/trunk-larour-NatClimateChange2016/examples/README.txt =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/README.txt (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/README.txt (revision 21239) @@ -0,0 +1,6 @@ +To run the following examples see the accompanying tutorials that can be found within the +documentation tab on the ISSM webpage. The tutorials were created to be parallel to lectures given, +but the tutorials are up to date on their version of ISSM. However within the workshop directory you +can find the lecture tutorials which will give a more in depth technical overview. If more help is +needed see the Usermanual also found under the documentation tab. If you don't want to complete the +tutorials in chronological order make sure to see Jakobshavn to run the download script. Index: /issm/branches/trunk-larour-NatClimateChange2016/examples/SquareIceShelf/DomainOutline.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/SquareIceShelf/DomainOutline.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/SquareIceShelf/DomainOutline.exp (revision 21239) @@ -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-larour-NatClimateChange2016/examples/SquareIceShelf/Front.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/SquareIceShelf/Front.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/SquareIceShelf/Front.exp (revision 21239) @@ -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-larour-NatClimateChange2016/examples/SquareIceShelf/Square.par =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/SquareIceShelf/Square.par (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/SquareIceShelf/Square.par (revision 21239) @@ -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-larour-NatClimateChange2016/examples/SquareIceShelf/runme.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/SquareIceShelf/runme.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/SquareIceShelf/runme.m (revision 21239) @@ -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,'Stressbalance'); Index: /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/ErrorContour.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/ErrorContour.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/ErrorContour.exp (revision 21239) @@ -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-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux1.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux1.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux1.exp (revision 21239) @@ -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-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux10.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux10.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux10.exp (revision 21239) @@ -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-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux11.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux11.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux11.exp (revision 21239) @@ -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-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux12.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux12.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux12.exp (revision 21239) @@ -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-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux13.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux13.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux13.exp (revision 21239) @@ -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-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux14.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux14.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux14.exp (revision 21239) @@ -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-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux15.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux15.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux15.exp (revision 21239) @@ -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 +-1675803.3920552148 -352985.6713725598 +-1672935.8509424068 -352801.1873251720 +-1668529.5198238282 -353048.3463822120 +-1666370.5689502691 -354473.4893832008 +-1665423.6161039397 -356733.4691418489 +-1662720.0686237188 -357334.8975107344 +-1660276.4961961196 -357869.6209268258 +-1657124.6115999895 -361080.6428832713 +-1655993.6074009922 -363193.2597271361 +-1653688.2093358042 -364017.9494011777 +-1654435.7188006472 -361506.6539926908 +-1652050.9793420888 -355295.4585798742 +-1649364.4081354018 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+-1586738.4648190001 -266671.8935250000 +-1586491.5239589999 -266628.3511920000 +-1586244.5830989999 -266584.8088590000 +-1585997.6422389999 -266541.2665270000 +-1585750.7013790000 -266497.7241940000 +-1585256.8196590000 -266410.6395280000 +-1585009.8787990001 -266367.0971960000 +-1584762.9379400001 -266323.5548630000 +-1584472.4547470000 -266526.9533900000 +-1584428.9124139999 -266773.8942500000 +-1584138.4292210001 -266977.2927780000 +-1583804.4036960001 -267427.6321650000 +-1583760.8613630000 -267674.5730250000 +-1583470.3781699999 -267877.9715530000 +-1583179.8949770001 -268081.3700800000 +-1583136.3526450000 -268328.3109400000 +-1582845.8694519999 -268531.7094680000 +-1582802.3271190000 -268778.6503280000 +-1582468.3015940001 -269228.9897150000 +-1582424.7592610000 -269475.9305750000 +-1582134.2760679999 -269679.3291030000 +-1582090.7337350000 -269926.2699630000 +-1581800.2505419999 -270129.6684900000 +-1581509.7673500001 -270333.0670180000 +-1581219.2841570000 -270536.4655450000 +-1581132.1994910000 -271030.3472650000 +-1580841.7162990000 -271233.7457930000 +-1580551.2331060001 -271437.1443200000 +-1580507.6907730000 -271684.0851800000 +-1580217.2075799999 -271887.4837080000 +-1580173.6652470001 -272134.4245680000 +-1579839.6397220001 -272584.7639550000 +-1579796.0973890000 -272831.7048160000 +-1579505.6141959999 -273035.1033430000 +-1579462.0718640001 -273282.0442030000 +-1579418.5295309999 -273528.9850630000 +-1579128.0463380001 -273732.3835910000 +-1579084.5040050000 -273979.3244510000 +-1578750.4784800000 -274429.6638380000 +-1578706.9361469999 -274676.6046980000 + Index: /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux3.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux3.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux3.exp (revision 21239) @@ -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-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux4.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux4.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux4.exp (revision 21239) @@ -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-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux5.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux5.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux5.exp (revision 21239) @@ -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-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux6.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux6.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux6.exp (revision 21239) @@ -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-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux7.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux7.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux7.exp (revision 21239) @@ -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-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux8.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux8.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux8.exp (revision 21239) @@ -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-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux9.exp =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux9.exp (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/MassFluxes/MassFlux9.exp (revision 21239) @@ -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-larour-NatClimateChange2016/examples/UncertaintyQuantification/runme.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/runme.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/examples/UncertaintyQuantification/runme.m (revision 21239) @@ -0,0 +1,312 @@ +%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.direct=true; + md.qmu.params.analysis_driver=''; + md.qmu.params.analysis_components=''; + md.qmu.params.evaluation_concurrency=1; + md.qmu.params.tabular_graphics_data=true; + + md.stressbalance.restol=10^-5; %tighten tolerances for UQ analyses + + %Turn off verbosity + md.verbose=verbose(0); + + %Here, we choose to run with 4 processors, 3 for DAKOTA + % while one serves as the master + md.cluster=generic('name',oshostname,'np',4); + + %Dakota runs in parallel with a master/slave configuration. + % At least 2 cpu's are needed to run the UQ + md.qmu.params.evaluation_scheduling='master'; + md.qmu.params.processors_per_evaluation=md.cluster.np-1; + + %Turn dakota on + md.qmu.isdakota=1; md.inversion.iscontrol=0; + md=solve(md,'Stressbalance','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.direct=true; + md.qmu.params.analysis_driver=''; + md.qmu.params.analysis_components=''; + md.qmu.params.evaluation_concurrency=1; + md.qmu.params.tabular_graphics_data=false; + + md.stressbalance.restol=10^-5; %tighten for qmu analyses + + %Here, we choose to run with 2 processors, 1 for DAKOTA + % while one serves as the master + md.cluster=generic('name',oshostname,'np',2); + + %Dakota runs in parallel with a master/slave configuration. + % At least 2 cpu's are needed to run the UQ + md.qmu.params.evaluation_scheduling='master'; + md.qmu.params.processors_per_evaluation=md.cluster.np-1; + + %Clear results and turn dakota on + md.results=[]; + md.qmu.isdakota=1; md.inversion.iscontrol=0; + md.verbose=verbose('qmu',true); + md=solve(md,'Stressbalance','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',... + 'linewidth',2, 'axis#all','image','unit','km','colorbar','off',... + 'title','Partition Edges on ISSM mesh','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,... + 'title','Sensitivities: H, \alpha, B'); + + %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,... + 'title','Importance Factors: H, \alpha, B'); + +end Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/README =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/README (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/README (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/adic/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adic/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adic/install.sh (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/adic/tests/notes =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adic/tests/notes (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adic/tests/notes (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/adjoinablempi/install-macosx64.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adjoinablempi/install-macosx64.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adjoinablempi/install-macosx64.sh (revision 21239) @@ -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 $1 +fi +make install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adjoinablempi/install-pleaides-gcc.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adjoinablempi/install-pleaides-gcc.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adjoinablempi/install-pleaides-gcc.sh (revision 21239) @@ -0,0 +1,27 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install + +#Mercurial cloning: +hg clone http://mercurial.mcs.anl.gov//ad/AdjoinableMPI src + +#Configure adjoinablempi +cd src +autoreconf -fi + +./configure \ + --prefix="$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 $1 +fi +make install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adjoinablempi/install-pleaides.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adjoinablempi/install-pleaides.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adjoinablempi/install-pleaides.sh (revision 21239) @@ -0,0 +1,27 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install + +#Mercurial cloning: +hg clone http://mercurial.mcs.anl.gov//ad/AdjoinableMPI src + +#Configure adjoinablempi +cd src +autoreconf -fi + +./configure \ + --prefix="$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 $1 +fi +make install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adjoinablempi/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adjoinablempi/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adjoinablempi/install.sh (revision 21239) @@ -0,0 +1,27 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install + +#Mercurial cloning: +hg clone http://mercurial.mcs.anl.gov//ad/AdjoinableMPI src + +#Configure adjoinablempi +cd src +autoreconf -fi + +./configure \ + --prefix="$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 $1 +fi +make install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adolc/install-withampi-macosx64.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adolc/install-withampi-macosx64.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adolc/install-withampi-macosx64.sh (revision 21239) @@ -0,0 +1,32 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src + +git clone https://gitlab.com/adol-c/adol-c.git src +#git clone -b ampi git://git.mcs.anl.gov/adol-c.git src +#git reset --hard b254b2a001a1b7a024a9184cd087ae06eb975cad + +#Compile ADOL-C +cd src +autoreconf -f -i + +export CFLAGS="-O2 -L$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 $1 V=1 +fi +make V=1 install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adolc/install-withampi-pleiades-gcc.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adolc/install-withampi-pleiades-gcc.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adolc/install-withampi-pleiades-gcc.sh (revision 21239) @@ -0,0 +1,28 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src + +git clone -b ampi git://git.mcs.anl.gov/adol-c.git src +#git reset --hard b254b2a001a1b7a024a9184cd087ae06eb975cad + +#Compile ADOL-C +cd src +autoreconf -f -i + +./configure --prefix=$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 $1 V=1 +fi +make V=1 install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adolc/install-withampi-pleiades.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adolc/install-withampi-pleiades.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adolc/install-withampi-pleiades.sh (revision 21239) @@ -0,0 +1,28 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src + +git clone -b ampi git://git.mcs.anl.gov/adol-c.git src +#git reset --hard b254b2a001a1b7a024a9184cd087ae06eb975cad + +#Compile ADOL-C +cd src +autoreconf -f -i + +./configure --prefix=$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 $1 V=1 +fi +make V=1 install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adolc/install-withampi.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adolc/install-withampi.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adolc/install-withampi.sh (revision 21239) @@ -0,0 +1,28 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src + +git clone https://gitlab.com/adol-c/adol-c.git src +#git reset --hard b254b2a001a1b7a024a9184cd087ae06eb975cad + +#Compile ADOL-C +cd src +autoreconf -f -i + +./configure --prefix=$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 $1 V=1 +fi +make V=1 install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adolc/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adolc/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adolc/install.sh (revision 21239) @@ -0,0 +1,22 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src + +git clone https://gitlab.com/adol-c/adol-c.git src +#git reset --hard b254b2a001a1b7a024a9184cd087ae06eb975cad + +#Compile ADOL-C +cd src + +autoreconf -f -i +./configure --prefix=$ISSM_DIR/externalpackages/adolc/install \ + --libdir=$ISSM_DIR/externalpackages/adolc/install/lib + +if [ $# -eq 0 ]; then + make V=1 +else + make -j $1 V=1 +fi +make V=1 install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adolc/old/install-2.2.0.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adolc/old/install-2.2.0.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adolc/old/install-2.2.0.sh (revision 21239) @@ -0,0 +1,60 @@ +#!/bin/bash +set -eu + +#some issues on macosx64 with ISSM's autoconf. you might want to run native to mac on this. + +#Some cleanup +rm -rf install ADOL-C-2.2.0 src trunk + +#Create install directories +mkdir install src + +#Download from ISSM server +$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 $1 +fi +make install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adolc/old/update.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adolc/old/update.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adolc/old/update.sh (revision 21239) @@ -0,0 +1,14 @@ +#!/bin/bash + +cd adolc_issm +git pull + +autoreconf -f -i +./configure --prefix=$ISSM_DIR/externalpackages/adolc/install + +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adolc/update-existing.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adolc/update-existing.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/adolc/update-existing.sh (revision 21239) @@ -0,0 +1,29 @@ +#!/bin/bash +set -eu + +#This script is very specific to the larour larsen nightly using adolc. +#It relies on just an update of adolc, and symlink to an existing adolc +#repo. + +#Some cleanup +rm -rf install src + +#symlink: +ln -s /proj/ice/larour2/issm-uci/trunk-jpl/externalpackages/adolc/adolc_issm ./src + +#update and compile +cd src +git pull origin +git checkout ampi +#git reset --hard b254b2a001a1b7a024a9184cd087ae06eb975cad + +autoreconf -f -i +./configure --prefix=$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-larour-NatClimateChange2016/externalpackages/android/android-ndk/android_aux.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/android/android-ndk/android_aux.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/android/android-ndk/android_aux.sh (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/android/android-ndk/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/android/android-ndk/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/android/android-ndk/install.sh (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/android/android-ndk/installNDK-linux-x86.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/android/android-ndk/installNDK-linux-x86.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/android/android-ndk/installNDK-linux-x86.sh (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/android/android-sdk/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/android/android-sdk/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/android/android-sdk/install.sh (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/android/android-sdk/installSDK-linux-x86.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/android/android-sdk/installSDK-linux-x86.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/android/android-sdk/installSDK-linux-x86.sh (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/android/android_aux.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/android/android_aux.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/android/android_aux.sh (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/angel/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/angel/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/angel/install.sh (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/appscan/bin/genouncemakePFile.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/appscan/bin/genouncemakePFile.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/appscan/bin/genouncemakePFile.sh (revision 21239) @@ -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 $? + ;; +esac +echo "[ P R O C E S S C O M P L E T E !!! ]" +echo Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/appscan/hostname =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/appscan/hostname (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/appscan/hostname (revision 21239) @@ -0,0 +1,1 @@ +jplsec-codescan.jpl.nasa.gov Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/appscan/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/appscan/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/appscan/install.sh (revision 21239) @@ -0,0 +1,10 @@ +#!/bin/bash +set -eu + +#AppScan install directory. Just symlink to your existing AppScan software + +#Erase symlink +rm -rf install + +#Select or create a new simlink +ln -s /opt/IBM/AppScan_Source ./install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/apr-util/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/apr-util/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/apr-util/install.sh (revision 21239) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf apr-util-1.4.1 +mkdir src install + +#Download from ISSM server +$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 $1 +fi +make install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/apr/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/apr/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/apr/install.sh (revision 21239) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf apr-1.4.6 +mkdir src install + +#Download from ISSM server +$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-larour-NatClimateChange2016/externalpackages/aspell/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/aspell/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/aspell/install.sh (revision 21239) @@ -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 + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/aspell5-en-6.0.0.tar.gz' 'aspell5-en-6.0.0.tar.gz' + + #Untar + tar -zxvf aspell5-en-6.0.0.tar.gz + + #Move aspell into src directory + mv aspell5-en-6.0.0 dicts + + #install + cd dicts/aspell5-en-6.0.0 + ./configure + make install +fi Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/atlas/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/atlas/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/atlas/install.sh (revision 21239) @@ -0,0 +1,32 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install ATLAS build +mkdir src install build + +#Download from ISSM server +$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 $1 +fi +make install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/autotools/install-win.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/autotools/install-win.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/autotools/install-win.sh (revision 21239) @@ -0,0 +1,53 @@ +#!/bin/bash +set -eu + +rm -rf install +mkdir install + +export PATH="$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="$ISSM_DIR/externalpackages/autotools/install" +make +make install +cd .. + +# This patch takes care of removing options passed to the linker that casuse +# the build to fail, as well as changing some flags to match up to Microsoft +# compilers. +patch ./install/share/aclocal/libtool.m4 < ./patches/libtool.m4.patch + +# Small change to Automake in order to get the right flags for Microsoft's +# compiler. +patch ./install/bin/automake < ./patches/automake.patch Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/autotools/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/autotools/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/autotools/install.sh (revision 21239) @@ -0,0 +1,56 @@ +#!/bin/bash +set -eu + +rm -rf install +mkdir install + +export PATH="$ISSM_DIR/externalpackages/autotools/install/bin:$PATH" + +#install m4 +echo " === INSTALLING M4 ==" +rm -rf src +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/m4-1.4.17.tar.gz' 'm4-1.4.17.tar.gz' +tar -zxvf m4-1.4.17.tar.gz +mv m4-1.4.17 src +cd src +./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" +make +make install +cd .. + +#install autoconf +echo " === INSTALLING AUTOCONF ==" +rm -rf src +$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="$ISSM_DIR/externalpackages/autotools/install" +make +make install +cd .. Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/autotools/patches/automake.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/autotools/patches/automake.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/autotools/patches/automake.patch (revision 21239) @@ -0,0 +1,13 @@ +--- ./externalpackages/autotools/install/bin/automake 2015-09-24 19:26:11.796659200 -0700 ++++ /home/daeden/tmp/automake 2015-09-25 11:32:53.557609300 -0700 +@@ -702,8 +702,8 @@ + 'compile' => "\$(CXX) @cpplike_flags \$(AM_CXXFLAGS) \$(CXXFLAGS)", + 'ccer' => 'CXX', + 'compiler' => 'CXXCOMPILE', +- 'compile_flag' => '-c', +- 'output_flag' => '-o', ++ 'compile_flag' => '/c', ++ 'output_flag' => '/Fo:', + 'libtool_tag' => 'CXX', + 'lder' => 'CXXLD', + 'ld' => '$(CXX)', Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/autotools/patches/libtool.m4.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/autotools/patches/libtool.m4.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/autotools/patches/libtool.m4.patch (revision 21239) @@ -0,0 +1,74 @@ +--- ./install/share/aclocal/libtool.m4 2015-09-25 15:51:40.870862200 -0700 ++++ /home/daeden/tmp/libtool.m4 2015-09-25 15:42:15.385935100 -0700 +@@ -2382,7 +2382,7 @@ + # Native MSVC + libname_spec='$name' + soname_spec='${libname}`echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext}' +- library_names_spec='${libname}.dll.lib' ++ library_names_spec='${libname}${shrext_cmds}' + + case $build_os in + mingw*) +@@ -3142,7 +3142,7 @@ + case $host_os in + cygwin* | mingw* | pw32* | cegcc*) + if test "$GCC" != yes; then +- reload_cmds=false ++ reload_cmds='lib /OUT:$output$reload_objs' + fi + ;; + darwin*) +@@ -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 $compiler_flags /OUT:$output_objdir/$soname ' + # 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 $compiler_flags /OUT:$output_objdir/$soname ' + else + _LT_TAGVAR(ld_shlibs, $1)=no + fi +@@ -5136,7 +5136,7 @@ + else + sed -e 's/\\\\\\\(.*\\\\\\\)/-link\\\ -EXPORT:\\\\\\\1/' < $export_symbols > $output_objdir/$soname.exp; + fi~ +- $CC -o $tool_output_objdir$soname $libobjs $compiler_flags $deplibs "@$tool_output_objdir$soname.exp" -Wl,-DLL,-IMPLIB:"$tool_output_objdir$libname.dll.lib"~ ++ $CC -o $tool_output_objdir$soname $libobjs $compiler_flags $deplibs~ + linknames=' + # The linker will not automatically build a static lib if we build a DLL. + # _LT_TAGVAR(old_archive_from_new_cmds, $1)='true' +@@ -6135,7 +6135,7 @@ + else + $SED -e 's/\\\\\\\(.*\\\\\\\)/-link\\\ -EXPORT:\\\\\\\1/' < $export_symbols > $output_objdir/$soname.exp; + fi~ +- $CC -o $tool_output_objdir$soname $libobjs $compiler_flags $deplibs "@$tool_output_objdir$soname.exp" -Wl,-DLL,-IMPLIB:"$tool_output_objdir$libname.dll.lib"~ ++ $CC -o $tool_output_objdir$soname $libobjs $compiler_flags $deplibs~ + linknames=' + # The linker will not automatically build a static lib if we build a DLL. + # _LT_TAGVAR(old_archive_from_new_cmds, $1)='true' +@@ -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 $compiler_flags /OUT:$output_objdir/$soname ' + # 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 $compiler_flags /OUT:$output_objdir/$soname ' + else + _LT_TAGVAR(ld_shlibs, $1)=no + fi Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/bbftp/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/bbftp/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/bbftp/install.sh (revision 21239) @@ -0,0 +1,27 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install bbftp-client-3.2.0 + +#Download from ISSM server +$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-larour-NatClimateChange2016/externalpackages/blas/configs/linux64/make.inc =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/blas/configs/linux64/make.inc (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/blas/configs/linux64/make.inc (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/blas/configs/macosx64/make.inc =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/blas/configs/macosx64/make.inc (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/blas/configs/macosx64/make.inc (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/blas/install-linux64.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/blas/install-linux64.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/blas/install-linux64.sh (revision 21239) @@ -0,0 +1,29 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install BLAS blas.tgz +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/blas.tgz' 'blas.tgz' + +#Untar +tar -zxvf blas.tgz + +#Move blas into install directory +mv BLAS/* src +rm -rf BLAS + +#install +cd src +cp ../configs/linux64/make.inc ./ +make + +#Compile +cd ../install +mkdir lib +cd lib +cp ../../src/*.a . +ln -s blas_LINUX.a blas.a +ln -s blas_LINUX.a libblas.a Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/blas/install-macosx64.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/blas/install-macosx64.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/blas/install-macosx64.sh (revision 21239) @@ -0,0 +1,29 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install BLAS blas.tgz +mkdir install src + +#Download from ISSM server +$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-larour-NatClimateChange2016/externalpackages/boost/configs/1.55/adl.hpp.lonestar.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/configs/1.55/adl.hpp.lonestar.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/configs/1.55/adl.hpp.lonestar.patch (revision 21239) @@ -0,0 +1,7 @@ +33,34c33,35 +< || BOOST_WORKAROUND(BOOST_INTEL_CXX_VERSION, BOOST_TESTED_AT(810)) \ +< ) +--- +> ) +> // || BOOST_WORKAROUND(BOOST_INTEL_CXX_VERSION, BOOST_TESTED_AT(810)) \ +> // ) Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/configs/1.55/adl.hpp.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/configs/1.55/adl.hpp.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/configs/1.55/adl.hpp.patch (revision 21239) @@ -0,0 +1,7 @@ +33,34c33,35 +< || BOOST_WORKAROUND(BOOST_INTEL_CXX_VERSION, BOOST_TESTED_AT(810)) \ +< ) +--- +> ) +> // || BOOST_WORKAROUND(BOOST_INTEL_CXX_VERSION, BOOST_TESTED_AT(810)) \ +> // ) Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/configs/1.55/cas128strong.hpp.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/configs/1.55/cas128strong.hpp.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/configs/1.55/cas128strong.hpp.patch (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/boost/configs/1.55/darwin.jam.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/configs/1.55/darwin.jam.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/configs/1.55/darwin.jam.patch (revision 21239) @@ -0,0 +1,4 @@ +587c587 +< "$(.LIBTOOL)" -static -o "$(<:T)" $(ARFLAGS) "$(>:T)" +--- +> /usr/bin/libtool -static -o "$(<:T)" $(ARFLAGS) "$(>:T)" Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/configs/1.55/darwin.py.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/configs/1.55/darwin.py.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/configs/1.55/darwin.py.patch (revision 21239) @@ -0,0 +1,4 @@ +40c40 +< toolset.flags ('darwin.compile', 'OPTIONS', None, ['-Wno-long-double', '-no-cpp-precomp']) +--- +> toolset.flags ('darwin.compile', 'OPTIONS', None, ['-Wno-long-double']) Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/configs/1.55/gcc-atomic.hpp.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/configs/1.55/gcc-atomic.hpp.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/configs/1.55/gcc-atomic.hpp.patch (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/boost/configs/1.55/user-config.jam.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/configs/1.55/user-config.jam.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/configs/1.55/user-config.jam.patch (revision 21239) @@ -0,0 +1,4 @@ +42c42 +< # using gcc ; +--- +> using darwin : std0x : "/usr/local/gfortran/bin/x86_64-apple-darwin10-g++" : -std=gnu++0x; Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.49-linux.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.49-linux.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.49-linux.sh (revision 21239) @@ -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=python2.7 \ + --with-python-root="$ISSM_DIR/externalpackages/python/install" + +#Compile boost +./bjam install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.49-macosx-snowleopard.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.49-macosx-snowleopard.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.49-macosx-snowleopard.sh (revision 21239) @@ -0,0 +1,35 @@ +#!/bin/bash + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_49_0 src +mkdir install src + +#Download from ISSM server +$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-larour-NatClimateChange2016/externalpackages/boost/install-1.55-discover.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-discover.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-discover.sh (revision 21239) @@ -0,0 +1,38 @@ +#!/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 +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' + +#Untar +tar -zxvf boost_1_55_0.tar.gz + +#Move boost into install directory +mv boost_1_55_0/* src +rm -rf boost_1_55_0 + +patch src/boost/mpl/aux_/config/adl.hpp ./configs/1.55/adl.hpp.patch + +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python2.7 \ + --with-python-root="$ISSM_DIR/externalpackages/python/install" + +#Compile boost +./bjam install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-linux.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-linux.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-linux.sh (revision 21239) @@ -0,0 +1,39 @@ +#!/bin/bash +set -eu + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_55_0 src +mkdir install src + +#Download from ISSM server +$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 + +#Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost +export CXXFLAGS='-std=c++98' + +#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 +./bjam install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-lonestar.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-lonestar.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-lonestar.sh (revision 21239) @@ -0,0 +1,38 @@ +#!/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 +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' + +#Untar +tar -zxvf boost_1_55_0.tar.gz + +#Move boost into install directory +mv boost_1_55_0/* src +rm -rf boost_1_55_0 + +patch src/boost/mpl/aux_/config/adl.hpp ./configs/1.55/adl.hpp.lonestar.patch + +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python3.2 \ + --with-python-root="$ISSM_DIR/externalpackages/python/install" + +#Compile boost +./bjam install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-macosx-el_capitan.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-macosx-el_capitan.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-macosx-el_capitan.sh (revision 21239) @@ -0,0 +1,44 @@ +#!/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 +python2.7 $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' + +#Untar +tar -zxvf boost_1_55_0.tar.gz + +#Move boost into install directory +mv boost_1_55_0/* src +rm -rf boost_1_55_0 + +patch src/boost/atomic/detail/cas128strong.hpp ./configs/1.55/cas128strong.hpp.patch +patch src/boost/atomic/detail/gcc-atomic.hpp ./configs/1.55/gcc-atomic.hpp.patch +patch src/tools/build/v2/user-config.jam ./configs/1.55/user-config.jam.patch +patch src/tools/build/v2/tools/darwin.jam ./configs/1.55/darwin.jam.patch +patch src/tools/build/v2/tools/darwin.py ./configs/1.55/darwin.py.patch + +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python + +#Compile boost +# Need gcc with iconv installed in a location that has been added to your path +# export CC=/usr/local/gfortan/bin/gcc +# export CXX=/usr/local/gfortran/bin/g++ +./bjam toolset=darwin link=static install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-macosx-mavericks.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-macosx-mavericks.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-macosx-mavericks.sh (revision 21239) @@ -0,0 +1,45 @@ +#!/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 +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' + +#Untar +tar -zxvf boost_1_55_0.tar.gz + +#Move boost into install directory +mv boost_1_55_0/* src +rm -rf boost_1_55_0 + +#patch src/boost/atomic/detail/cas128strong.hpp ./configs/1.55/cas128strong.hpp.patch +#patch src/boost/atomic/detail/gcc-atomic.hpp ./configs/1.55/gcc-atomic.hpp.patch +patch src/tools/build/v2/user-config.jam ./configs/1.55/user-config.jam.patch +patch src/tools/build/v2/tools/darwin.jam ./configs/1.55/darwin.jam.patch +patch src/tools/build/v2/tools/darwin.py ./configs/1.55/darwin.py.patch + +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python2.7 \ + --with-python-root="$ISSM_DIR/externalpackages/python/install" + +#Compile boost +# Need gcc with iconv installed in a location that has been added to your path +./bjam toolset=darwin-std0x link=static install + +#./b2 toolset=clang cxxflags=-stdlib=libstdc++ linkflags=-stdlib=libstdc++ -j2 variant=release link=static threading=multi instal + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-macosx-snowleopard.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-macosx-snowleopard.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-macosx-snowleopard.sh (revision 21239) @@ -0,0 +1,45 @@ +#!/bin/bash +set -eu + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_55_0 src +mkdir install src + +#Download from ISSM server +$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 +patch src/tools/build/v2/user-config.jam ./configs/1.55/user-config.jam.patch +patch src/tools/build/v2/tools/darwin.jam ./configs/1.55/darwin.jam.patch +patch src/tools/build/v2/tools/darwin.py ./configs/1.55/darwin.py.patch + +#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 +# Need gcc with iconv installed in a location that has been added to your path +./bjam toolset=darwin-std0x link=static install + +#./b2 toolset=clang cxxflags=-stdlib=libstdc++ linkflags=-stdlib=libstdc++ -j2 variant=release link=static threading=multi instal + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-macosx-yosemite.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-macosx-yosemite.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-macosx-yosemite.sh (revision 21239) @@ -0,0 +1,46 @@ +#!/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 +python2.7 $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' + +#Untar +tar -zxvf boost_1_55_0.tar.gz + +#Move boost into install directory +mv boost_1_55_0/* src +rm -rf boost_1_55_0 + +patch src/boost/atomic/detail/cas128strong.hpp ./configs/1.55/cas128strong.hpp.patch +patch src/boost/atomic/detail/gcc-atomic.hpp ./configs/1.55/gcc-atomic.hpp.patch +patch src/tools/build/v2/user-config.jam ./configs/1.55/user-config.jam.patch +patch src/tools/build/v2/tools/darwin.jam ./configs/1.55/darwin.jam.patch +patch src/tools/build/v2/tools/darwin.py ./configs/1.55/darwin.py.patch + +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python + +#Compile boost +# Need gcc with iconv installed in a location that has been added to your path +#./bjam toolset=darwin-std0x link=static install + +export CC=/usr/local/gfortan/bin/gcc +export CXX=/usr/local/gfortran/bin/g++ +./b2 toolset=clang cxxflags=-stdlib=libstdc++ linkflags=-stdlib=libstdc++ -j2 architecture=x86 variant=release link=static threading=multi install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-pleiades.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-pleiades.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-pleiades.sh (revision 21239) @@ -0,0 +1,47 @@ +#!/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 +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' + +#Untar +tar -zxvf boost_1_55_0.tar.gz + +#Move boost into install directory +mv boost_1_55_0/* src +rm -rf boost_1_55_0 + +#patch src/boost/atomic/detail/cas128strong.hpp ./configs/1.55/cas128strong.hpp.patch +#patch src/boost/atomic/detail/gcc-atomic.hpp ./configs/1.55/gcc-atomic.hpp.patch +#patch src/tools/build/v2/user-config.jam ./configs/1.55/user-config.jam.patch +#patch src/tools/build/v2/tools/darwin.jam ./configs/1.55/darwin.jam.patch +#patch src/tools/build/v2/tools/darwin.py ./configs/1.55/darwin.py.patch + +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python2.7 \ + --with-python-root="$ISSM_DIR/externalpackages/python/install" \ + --with-toolset=intel-linux + +#Compile boost +# Need gcc with iconv installed in a location that has been added to your path +./b2 toolset=intel-linux cxxflags=-static-libstdc++ linkflags=-static-libstdc++ threading=multi install +#./bjam install + +#./b2 toolset=clang cxxflags=-stdlib=libstdc++ linkflags=-stdlib=libstdc++ -j2 variant=release link=static threading=multi instal + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-pleiades_dakota6.2.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-pleiades_dakota6.2.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install-1.55-pleiades_dakota6.2.sh (revision 21239) @@ -0,0 +1,38 @@ +#!/bin/bash +set -eu + +#Note of caution: stop after boostrap phase, and run +#bjam --debug-configuration, to figure out which paths boost is using to include +#python. make sure everyone of these paths is covered by python. If not, just make +#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY +#to get the boost library to include python support without doing that. + +#Some cleanup +rm -rf install boost_1_55_0 src +mkdir install src + +#Download from ISSM server +$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/mpl/aux_/config/adl.hpp ./configs/1.55/adl.hpp.lonestar.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 +./bjam install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/boost/install.sh (revision 21239) @@ -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="$ISSM_DIR/externalpackages/python/install" + +#Compile boost +./bjam install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/bsdtar/install-win7.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/bsdtar/install-win7.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/bsdtar/install-win7.sh (revision 21239) @@ -0,0 +1,21 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src libarchive-3.0.3 +mkdir install src + +#Download from ISSM server +$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-larour-NatClimateChange2016/externalpackages/canos/InterX.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/canos/InterX.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/canos/InterX.m (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/canos/license.txt =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/canos/license.txt (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/canos/license.txt (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/canos/licenseNS.txt =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/canos/licenseNS.txt (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/canos/licenseNS.txt (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/canos/selfintersect.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/canos/selfintersect.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/canos/selfintersect.m (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/cccl/install-win7.orig.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cccl/install-win7.orig.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cccl/install-win7.orig.sh (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/cccl/install-win7.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cccl/install-win7.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cccl/install-win7.sh (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/cccl/issm/cccl =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cccl/issm/cccl (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cccl/issm/cccl (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/chaco/chaco.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/chaco.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/chaco.patch (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/chaco/chaco_README.txt =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/chaco_README.txt (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/chaco_README.txt (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/chaco/chaco_jes_notes.txt =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/chaco_jes_notes.txt (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/chaco_jes_notes.txt (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/chaco/chaco_njs_notes.txt =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/chaco_njs_notes.txt (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/chaco_njs_notes.txt (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/chaco/install-macosx64.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/install-macosx64.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/install-macosx64.sh (revision 21239) @@ -0,0 +1,55 @@ +#!/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 + +# Patch src/code/Makefile +patch ./src/code/Makefile ./patches/Makefile.patch + + +# Build chaco +cd src/code +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make chacominusblas.a + +# Clean up objects (but not library or executable) +make clean +cd ../.. + +# Populate install directory +cp -p src/exec/README install +cp -p src/exec/User_Params install +cp -p src/exec/*.coords install +cp -p src/exec/*.graph install +mkdir install/include +cp -p src/code/main/defs.h install/include/defs.h +cp -p src/code/main/params.h install/include/params.h +cp -p chaco.h install/include/chaco.h +mkdir install/lib +mv src/code/chaco.a install/lib/libchaco.a +mv src/code/chacominusblas.a install/lib/libchacominusblas.a +mkdir install/exec +mv src/exec/chaco install/exec Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/install.sh (revision 21239) @@ -0,0 +1,51 @@ +#!/bin/bash +set -eu + +# Some cleanup +rm -rf Chaco-2.2 +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$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-larour-NatClimateChange2016/externalpackages/chaco/mex/Chaco.c =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/mex/Chaco.c (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/mex/Chaco.c (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/chaco/mex/Chaco_m.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/mex/Chaco_m.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/mex/Chaco_m.m (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/chaco/mex/Chacox.c =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/mex/Chacox.c (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/mex/Chacox.c (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/chaco/mex/Makefile =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/mex/Makefile (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/mex/Makefile (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/chaco/mex/User_Params.debug =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/mex/User_Params.debug (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/mex/User_Params.debug (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/chaco/mex/User_Params.verbose =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/mex/User_Params.verbose (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/mex/User_Params.verbose (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/chaco/mex/user_params.c =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/mex/user_params.c (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/mex/user_params.c (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/chaco/mlchaco_README.txt =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/mlchaco_README.txt (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/mlchaco_README.txt (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/chaco/mlchaco_jes_notes.txt =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/mlchaco_jes_notes.txt (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/mlchaco_jes_notes.txt (revision 21239) @@ -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 ${CHACO}/main/defs.h so that local bail.c is + unnecessary. + +6/15/10: + +- separated chaco x-layer from meshpart build. + Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/patches/Makefile.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/patches/Makefile.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/chaco/patches/Makefile.patch (revision 21239) @@ -0,0 +1,11 @@ +--- ./src/code/Makefile 2016-02-16 19:39:30.000000000 -0800 ++++ ./Makefile 2016-02-16 19:37:49.000000000 -0800 +@@ -6,7 +6,7 @@ + #CFLAGS = -O2 + #OFLAGS = -O2 + #CFLAGS = -fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread -fexceptions +-CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g ++CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g -I/usr/include/malloc + #CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB + OFLAGS = -O2 + #AR = /usr/ccs/bin/ar rcv # for solaris 2 Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cmake/install-macosx64-snowleopard.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cmake/install-macosx64-snowleopard.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cmake/install-macosx64-snowleopard.sh (revision 21239) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu +VER="2.8.11.2" + +#Some cleanup +rm -rf install cmake-$VER +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/cmake-$VER.tar.gz" "cmake-$VER.tar.gz" + +#Untar +tar -zxvf cmake-$VER.tar.gz + +#Move cmake into install directory +mv cmake-$VER/* install +rm -rf cmake-$VER + +LDFLAGS="-L/usr/lib/ -lstdc++ -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/ -lgfortran" +F77="/usr/local/gfortran/bin/x86_64-apple-darwin10-gfortran" + +#Compile cmake +cd install +./bootstrap --prefix=$ISSM_DIR/externalpackages/cmake/install +if [ $# -eq 0 ]; then + make +else + make -j $1; +fi +make install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cmake/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cmake/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cmake/install.sh (revision 21239) @@ -0,0 +1,27 @@ +#!/bin/bash +set -eu +VER="3.6.2" + +#Some cleanup +rm -rf install cmake-$VER +mkdir install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/cmake-$VER.tar.gz" "cmake-$VER.tar.gz" + +#Untar +tar -zxvf cmake-$VER.tar.gz + +#Move cmake into install directory +mv cmake-$VER/* install +rm -rf cmake-$VER + +#Compile cmake +cd install +./bootstrap --prefix=$ISSM_DIR/externalpackages/cmake/install +if [ $# -eq 0 ]; then + make +else + make -j $1; +fi +make install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/colpack/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/colpack/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/colpack/install.sh (revision 21239) @@ -0,0 +1,26 @@ +#!/bin/bash +set -eu + +#Erase install +rm -rf install src ColPack + +#Download from ISSM server +$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-larour-NatClimateChange2016/externalpackages/cppcheck/install-dev.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cppcheck/install-dev.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cppcheck/install-dev.sh (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/cppcheck/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cppcheck/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cppcheck/install.sh (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/curl/install-macosx64.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/curl/install-macosx64.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/curl/install-macosx64.sh (revision 21239) @@ -0,0 +1,32 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install curl-7.39.0 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/curl-7.39.0.tar.gz' 'curl-7.39.0.tar.gz' + +#Untar +tar -zxvf curl-7.39.0.tar.gz + +#Move curl into src directory +mv curl-7.39.0/* src +rm -rf curl-7.39.0 + +#Configure curl +cd src + +export CFLAGS=" -arch x86_64" + +./configure \ + --prefix="$ISSM_DIR/externalpackages/curl/install" + +#Compile curl +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cvs/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cvs/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cvs/install.sh (revision 21239) @@ -0,0 +1,34 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf cvs-1.11.23 +mkdir src install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/cvs-1.11.23.tar.gz' 'cvs-1.11.23.tar.gz' + +#Untar +tar -zxvf cvs-1.11.23.tar.gz + +#Move subversion into src directory +mv cvs-1.11.23/* src +rm -rf cvs-1.11.23 + +#Patch getline +cd src +cat lib/getline.c | sed -e "s/getline /get_line /" > BACK && mv BACK lib/getline.c +cat lib/getline.h | sed -e "s/getline /get_line /" > BACK && mv BACK lib/getline.h + +#Configure +./configure --prefix="$ISSM_DIR/externalpackages/cvs/install" + +#Compile and install subversion +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cython/install-18.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cython/install-18.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cython/install-18.sh (revision 21239) @@ -0,0 +1,13 @@ +#!/bin/bash +set -eu + +#clean up +rm -rf Cython-0.18 + +#download numpy first +$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-larour-NatClimateChange2016/externalpackages/cython/install-19.2.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cython/install-19.2.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cython/install-19.2.sh (revision 21239) @@ -0,0 +1,13 @@ +#!/bin/bash +set -eu + +#clean up +rm -rf Cython-0.19.2 + +#download numpy first +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Cython-0.19.2.tar.gz' 'cython.tar.gz' + +#install numpy +tar -zxvf cython.tar.gz +cd Cython-0.19.2 +python setup.py install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cython/install-22.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cython/install-22.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cython/install-22.sh (revision 21239) @@ -0,0 +1,13 @@ +#!/bin/bash +set -eu + +#clean up +rm -rf Cython-0.22 + +#download numpy first +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Cython-0.22.tar.gz' 'cython.tar.gz' + +#install numpy +tar -zxvf cython.tar.gz +cd Cython-0.22 +python setup.py install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cython/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cython/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/cython/install.sh (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dakota/configs/4.2/LHSDriver.cpp.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/4.2/LHSDriver.cpp.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/4.2/LHSDriver.cpp.patch (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dakota/configs/4.2/NIDRProblemDescDB.C.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/4.2/NIDRProblemDescDB.C.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/4.2/NIDRProblemDescDB.C.patch (revision 21239) @@ -0,0 +1,4 @@ +95a96,98 +> +> //close the input file +> fclose(nidrin); Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/4.2/NonDLocalReliability.C.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/4.2/NonDLocalReliability.C.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/4.2/NonDLocalReliability.C.patch (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dakota/configs/4.2/NonDSampling.C.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/4.2/NonDSampling.C.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/4.2/NonDSampling.C.patch (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dakota/configs/4.2/NonDUnilevelRBDO.C.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/4.2/NonDUnilevelRBDO.C.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/4.2/NonDUnilevelRBDO.C.patch (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dakota/configs/4.2/ParallelLibrary.C.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/4.2/ParallelLibrary.C.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/4.2/ParallelLibrary.C.patch (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dakota/configs/4.2/ParallelLibrary.H.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/4.2/ParallelLibrary.H.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/4.2/ParallelLibrary.H.patch (revision 21239) @@ -0,0 +1,3 @@ +346a347,348 +> /// library mode constructor, serial mode +> ParallelLibrary(char* serial_mode); Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.2/NIDRProblemDescDB.C.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.2/NIDRProblemDescDB.C.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.2/NIDRProblemDescDB.C.patch (revision 21239) @@ -0,0 +1,5 @@ +109a110,113 +> +> //close the input file +> fclose(nidrin); +> Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.2/NonDLocalReliability.C.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.2/NonDLocalReliability.C.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.2/NonDLocalReliability.C.patch (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dakota/configs/5.2/NonDSampling.C.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.2/NonDSampling.C.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.2/NonDSampling.C.patch (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dakota/configs/5.2/NonDUnilevelRBDO.C.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.2/NonDUnilevelRBDO.C.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.2/NonDUnilevelRBDO.C.patch (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dakota/configs/5.2/ParallelLibrary.C.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.2/ParallelLibrary.C.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.2/ParallelLibrary.C.patch (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dakota/configs/5.2/ParallelLibrary.H.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.2/ParallelLibrary.H.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.2/ParallelLibrary.H.patch (revision 21239) @@ -0,0 +1,3 @@ +358a359,360 +> /// library mode constructor, serial mode (for the Issm software) +> ParallelLibrary(char* serial_mode); Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.2/Teuchos_ConfigDefs.hpp.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.2/Teuchos_ConfigDefs.hpp.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.2/Teuchos_ConfigDefs.hpp.patch (revision 21239) @@ -0,0 +1,2 @@ +87a88 +> #include Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.2/pecos_global_defs.hpp.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.2/pecos_global_defs.hpp.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.2/pecos_global_defs.hpp.patch (revision 21239) @@ -0,0 +1,4 @@ +24a25 +> #ifndef PI +25a27 +> #endif Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.mac.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.mac.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.mac.patch (revision 21239) @@ -0,0 +1,14 @@ +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) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.patch (revision 21239) @@ -0,0 +1,26 @@ +64,65c64,65 +< #set( DAKOTA_HAVE MPI ON +< # CACHE BOOL "Build with MPI enabled" FORCE) +--- +> set( DAKOTA_HAVE MPI OFF +> CACHE BOOL "Build with MPI disabled" FORCE) +73,77c73,77 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "$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 +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.pfe.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.pfe.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.pfe.patch (revision 21239) @@ -0,0 +1,26 @@ +64,65c64,65 +< #set( DAKOTA_HAVE MPI ON +< # CACHE BOOL "Build with MPI enabled" FORCE) +--- +> set( DAKOTA_HAVE MPI OFF +> CACHE BOOL "Build with MPI disabled" FORCE) +73,77c73,77 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "/nasa/boost/1.50.0" +> CACHE PATH "Use non-standard Boost install" FORCE) +> set( Boost_NO_SYSTEM_PATHS TRUE +> CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.lonestar.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.lonestar.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.lonestar.patch (revision 21239) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS "-L/opt/apps/intel/16.0.1.150/compilers_and_libraries_2016.1.150/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") +> set(LAPACK_LIBS "-L/opt/apps/intel/16.0.1.150/compilers_and_libraries_2016.1.150/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.patch (revision 21239) @@ -0,0 +1,4 @@ +47a48,50 +> set(BUILD_STATIC_LIBS ON CACHE BOOL "Set to ON to build static libraries" FORCE) +> set(BUILD_SHARED_LIBS OFF CACHE BOOL "Set to ON to build DSO libraries" FORCE) +> Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.pfe.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.pfe.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.pfe.patch (revision 21239) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS "-L/nasa/intel/Compiler/2015.0.090/composer_xe_2015.0.090/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm") +> set(LAPACK_LIBS "-L/nasa/intel/Compiler/2015.0.090/composer_xe_2015.0.090/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm") Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/DakotaDev.cmake.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/DakotaDev.cmake.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/DakotaDev.cmake.patch (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/NonDLocalReliability.cpp.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/NonDLocalReliability.cpp.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/NonDLocalReliability.cpp.patch (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/NonDSampling.cpp.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/NonDSampling.cpp.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/NonDSampling.cpp.patch (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/ParallelLibrary.cpp.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/ParallelLibrary.cpp.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/ParallelLibrary.cpp.patch (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/ParallelLibrary.hpp.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/ParallelLibrary.hpp.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/ParallelLibrary.hpp.patch (revision 21239) @@ -0,0 +1,3 @@ +358a359,360 +> /// library mode constructor, serial mode (for the ISSM software) +> ParallelLibrary(char* serial_mode); Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/pecos_global_defs.hpp.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/pecos_global_defs.hpp.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3.1/pecos_global_defs.hpp.patch (revision 21239) @@ -0,0 +1,4 @@ +25a26 +> #ifndef PI +26a28 +> #endif Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3/BuildDakotaCustom.cmake.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3/BuildDakotaCustom.cmake.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3/BuildDakotaCustom.cmake.patch (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3/DakotaDev.cmake.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3/DakotaDev.cmake.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3/DakotaDev.cmake.patch (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3/NonDLocalReliability.cpp.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3/NonDLocalReliability.cpp.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3/NonDLocalReliability.cpp.patch (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3/NonDSampling.cpp.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3/NonDSampling.cpp.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3/NonDSampling.cpp.patch (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3/ParallelLibrary.cpp.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3/ParallelLibrary.cpp.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3/ParallelLibrary.cpp.patch (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3/ParallelLibrary.hpp.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3/ParallelLibrary.hpp.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3/ParallelLibrary.hpp.patch (revision 21239) @@ -0,0 +1,3 @@ +358a359,360 +> /// library mode constructor, serial mode (for the ISSM software) +> ParallelLibrary(char* serial_mode); Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3/pecos_global_defs.hpp.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3/pecos_global_defs.hpp.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3/pecos_global_defs.hpp.patch (revision 21239) @@ -0,0 +1,4 @@ +25a26 +> #ifndef PI +26a28 +> #endif Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3/utilibExpat_patch.txt =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3/utilibExpat_patch.txt (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/5.3/utilibExpat_patch.txt (revision 21239) @@ -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 ${EXPAT_LIBRARIES}) + endif() + if(MSVC) + list(APPEND libs dbghelp) Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/BuildDakotaCustom.cmake.mac.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/BuildDakotaCustom.cmake.mac.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/BuildDakotaCustom.cmake.mac.patch (revision 21239) @@ -0,0 +1,14 @@ +64,65c64,65 +< #set( DAKOTA_HAVE_MPI ON +< # CACHE BOOL "Build with MPI enabled" FORCE) +--- +> set( DAKOTA_HAVE_MPI OFF +> CACHE BOOL "Build with MPI disabled" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/BuildDakotaCustom.cmake.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/BuildDakotaCustom.cmake.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/BuildDakotaCustom.cmake.patch (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/CMakeLists.txt.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/CMakeLists.txt.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/CMakeLists.txt.patch (revision 21239) @@ -0,0 +1,4 @@ +47a48,50 +> set(BUILD_STATIC_LIBS ON CACHE BOOL "Set to ON to build static libraries" FORCE) +> set(BUILD_SHARED_LIBS OFF CACHE BOOL "Set to ON to build DSO libraries" FORCE) +> Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/CMakeLists.txt.pfe.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/CMakeLists.txt.pfe.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/CMakeLists.txt.pfe.patch (revision 21239) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS "-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread") +> set(LAPACK_LIBS "-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread") Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/DakotaDev.cmake.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/DakotaDev.cmake.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/DakotaDev.cmake.patch (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/NonDLocalReliability.cpp.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/NonDLocalReliability.cpp.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/NonDLocalReliability.cpp.patch (revision 21239) @@ -0,0 +1,9 @@ +2645a2646 +> // add sensitivity output to importance factors (jes, 8/06/10) +2651c2652,2655 +< << 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-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/NonDSampling.cpp.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/NonDSampling.cpp.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/NonDSampling.cpp.patch (revision 21239) @@ -0,0 +1,25 @@ +780,786c780,787 +< 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, dsv_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, dsv_labels, drv_labels, +> // iteratedModel.response_labels()); +> // } +1277,1278c1278,1281 +< nonDSampCorr.print_correlations(s, cv_labels, div_labels, dsv_labels, +< drv_labels,iteratedModel.response_labels()); +--- +> +> //don't output for now. +> // nonDSampCorr.print_correlations(s, cv_labels, div_labels, dsv_labels, +> // drv_labels,iteratedModel.response_labels()); Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/ParallelLibrary.cpp.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/ParallelLibrary.cpp.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/ParallelLibrary.cpp.patch (revision 21239) @@ -0,0 +1,24 @@ +51a54,76 +> /** This constructor is provided for the ISSM software, to run serial +> * Dakota in a parallel MPI ring: */ +> ParallelLibrary::ParallelLibrary(char* serial_mode): +> mpiManager(dummy_mpi_mgr), programOptions(dummy_prg_opt), +> outputManager(dummy_out_mgr), dummyFlag(true), outputTimings(false) +> { +> 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 6.1 MPI executable in serial mode on CPU 0 for ISSM." << std::endl; +> #else // mpi not available +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota 6.1 serial executable in serial mode for ISSM." << std::endl; +> #endif // HAVE_MPI +> +> parallelLevels.push_back(pl); +> increment_parallel_configuration(); +> } +> +> Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/ParallelLibrary.hpp.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/ParallelLibrary.hpp.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/ParallelLibrary.hpp.patch (revision 21239) @@ -0,0 +1,3 @@ +475a476,477 +> /// library mode constructor, serial mode (for the ISSM software) +> ParallelLibrary(char* serial_mode); Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/pecos_global_defs.hpp.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/pecos_global_defs.hpp.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.1/pecos_global_defs.hpp.patch (revision 21239) @@ -0,0 +1,4 @@ +25a26 +> #ifndef PI +26a28 +> #endif Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.discover.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.discover.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.discover.patch (revision 21239) @@ -0,0 +1,35 @@ +54,55c54,55 +< #set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} " +< # CACHE STRING "CXX Flags for my platform" ) +--- +> set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DMPICH_IGNORE_CXX_SEEK" +> CACHE STRING "CXX Flags for my platform" ) +67a68,75 +> set( DAKOTA_HAVE_MPI ON +> CACHE BOOL "Always build with MPI enabled" FORCE) +> set( MPI_INCLUDE_PATH +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/include" +> CACHE FILEPATH "Use installed MPI headers" FORCE) +> set( MPI_LIBRARY +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/lib/libmpich.so" +> CACHE FILEPATH "Use installed MPI library" 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-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.mac.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.mac.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.mac.patch (revision 21239) @@ -0,0 +1,8 @@ +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.patch (revision 21239) @@ -0,0 +1,29 @@ +67a68,75 +> set( DAKOTA_HAVE_MPI ON +> CACHE BOOL "Always build with MPI enabled" FORCE) +> set( MPI_INCLUDE_PATH +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/include" +> CACHE FILEPATH "Use installed MPI headers" FORCE) +> set( MPI_LIBRARY +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/lib/libmpich.so" +> CACHE FILEPATH "Use installed MPI library" FORCE) +73,77c73,77 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "$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 +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.pfe.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.pfe.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.pfe.patch (revision 21239) @@ -0,0 +1,29 @@ +67a68,75 +> set( DAKOTA_HAVE_MPI ON +> CACHE BOOL "Always build with MPI enabled" FORCE) +> set( MPI_INCLUDE_PATH +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/include" +> CACHE FILEPATH "Use installed MPI headers" FORCE) +> set( MPI_LIBRARY +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/lib/libmpich.so" +> CACHE FILEPATH "Use installed MPI library" FORCE) +73,77c73,77 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "/nasa/boost/1.50.0" +> CACHE PATH "Use non-standard Boost install" FORCE) +> set( Boost_NO_SYSTEM_PATHS TRUE +> CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.yosemite.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.yosemite.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.yosemite.patch (revision 21239) @@ -0,0 +1,29 @@ +67a68,75 +> set( DAKOTA_HAVE_MPI ON +> CACHE BOOL "Always build with MPI enabled" FORCE) +> set( MPI_INCLUDE_PATH +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/include" +> CACHE FILEPATH "Use installed MPI headers" FORCE) +> set( MPI_LIBRARY +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/lib/libmpich.a" +> CACHE FILEPATH "Use installed MPI library" 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-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/CMakeLists.txt.discover.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/CMakeLists.txt.discover.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/CMakeLists.txt.discover.patch (revision 21239) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS "-L/usr/local/intel/Composer/composer_xe_2015.0.090/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") +> set(LAPACK_LIBS "-L/usr/local/intel/Composer/composer_xe_2015.0.090/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/CMakeLists.txt.lonestar.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/CMakeLists.txt.lonestar.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/CMakeLists.txt.lonestar.patch (revision 21239) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS "-L/opt/apps/intel/11.1/mkl/lib/em64t/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") +> set(LAPACK_LIBS "-L/opt/apps/intel/11.1/mkl/lib/em64t/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/CMakeLists.txt.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/CMakeLists.txt.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/CMakeLists.txt.patch (revision 21239) @@ -0,0 +1,4 @@ +47a48,50 +> set(BUILD_STATIC_LIBS ON CACHE BOOL "Set to ON to build static libraries" FORCE) +> set(BUILD_SHARED_LIBS OFF CACHE BOOL "Set to ON to build DSO libraries" FORCE) +> Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/CMakeLists.txt.pfe.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/CMakeLists.txt.pfe.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/CMakeLists.txt.pfe.patch (revision 21239) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS "-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread") +> set(LAPACK_LIBS "-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread") Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/DakotaDev.cmake.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/DakotaDev.cmake.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/DakotaDev.cmake.patch (revision 21239) @@ -0,0 +1,14 @@ +5,8c5,8 +< 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(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-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/NonDLocalReliability.cpp.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/NonDLocalReliability.cpp.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/NonDLocalReliability.cpp.patch (revision 21239) @@ -0,0 +1,9 @@ +2645a2646 +> // add sensitivity output to importance factors (jes, 8/06/10) +2651c2652,2655 +< << 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-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/NonDSampling.cpp.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/NonDSampling.cpp.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/NonDSampling.cpp.patch (revision 21239) @@ -0,0 +1,25 @@ +780,786c780,787 +< 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, dsv_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, dsv_labels, drv_labels, +> // iteratedModel.response_labels()); +> // } +1277,1278c1278,1281 +< nonDSampCorr.print_correlations(s, cv_labels, div_labels, dsv_labels, +< drv_labels,iteratedModel.response_labels()); +--- +> +> //don't output for now. +> // nonDSampCorr.print_correlations(s, cv_labels, div_labels, dsv_labels, +> // drv_labels,iteratedModel.response_labels()); Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/pecos_global_defs.hpp.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/pecos_global_defs.hpp.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/configs/6.2/pecos_global_defs.hpp.patch (revision 21239) @@ -0,0 +1,4 @@ +24a25 +> #ifndef PI +25a27 +> #endif Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-4.2-altix64-cosmos.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-4.2-altix64-cosmos.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-4.2-altix64-cosmos.sh (revision 21239) @@ -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 $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-4.2-discover.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-4.2-discover.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-4.2-discover.sh (revision 21239) @@ -0,0 +1,97 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$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 $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-4.2-linux64-cloud.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-4.2-linux64-cloud.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-4.2-linux64-cloud.sh (revision 21239) @@ -0,0 +1,97 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$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 $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-4.2-linux64-murdo.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-4.2-linux64-murdo.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-4.2-linux64-murdo.sh (revision 21239) @@ -0,0 +1,97 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$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 $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-4.2-macosx64.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-4.2-macosx64.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-4.2-macosx64.sh (revision 21239) @@ -0,0 +1,97 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$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 $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-4.2-pleiades-petsc3.3.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-4.2-pleiades-petsc3.3.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-4.2-pleiades-petsc3.3.sh (revision 21239) @@ -0,0 +1,103 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$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 $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-4.2-pleiades.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-4.2-pleiades.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-4.2-pleiades.sh (revision 21239) @@ -0,0 +1,97 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$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 $1 install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.2-discover.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.2-discover.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.2-discover.sh (revision 21239) @@ -0,0 +1,52 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$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 $1 install +fi +cd .. Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.2-linux64-caladan.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.2-linux64-caladan.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.2-linux64-caladan.sh (revision 21239) @@ -0,0 +1,48 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$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="$ISSM_DIR/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-blas="$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 $1 install +fi +cd .. Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.2-linux64-larsen.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.2-linux64-larsen.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.2-linux64-larsen.sh (revision 21239) @@ -0,0 +1,49 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$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 $1 install +fi +cd .. Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.2-macosx64.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.2-macosx64.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.2-macosx64.sh (revision 21239) @@ -0,0 +1,51 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$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 $1 install +fi +cd .. Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.2-pleiades-petsc3.3.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.2-pleiades-petsc3.3.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.2-pleiades-petsc3.3.sh (revision 21239) @@ -0,0 +1,59 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Download from ISSM server +$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 $1 install +fi +cd .. Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.3.1-linux64-caladan.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.3.1-linux64-caladan.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.3.1-linux64-caladan.sh (revision 21239) @@ -0,0 +1,51 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$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 +#patch $DAK_SRC/CMakeLists.txt configs/5.3.1/CMakeLists.txt.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 $DAK_SRC -DBLAS_LIBS=$ISSM_DIR/externalpackages/petsc/install/lib/libfblas.a -DLAPACK_LIBS=$ISSM_DIR/externalpackages/petsc/install/lib/libflapack.a +cd .. + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.3.1-linux64.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.3.1-linux64.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.3.1-linux64.sh (revision 21239) @@ -0,0 +1,51 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$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 +#patch $DAK_SRC/CMakeLists.txt configs/5.3.1/CMakeLists.txt.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 $1 install +fi +cd .. Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.3.1-lonestar.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.3.1-lonestar.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.3.1-lonestar.sh (revision 21239) @@ -0,0 +1,51 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$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 +patch $DAK_SRC/CMakeLists.txt configs/5.3.1/CMakeLists.txt.lonestar.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 $1 install +fi +cd .. Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.3.1-macosx64-snowleopard.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.3.1-macosx64-snowleopard.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.3.1-macosx64-snowleopard.sh (revision 21239) @@ -0,0 +1,62 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$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.mac.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/5.3.1/DakotaDev.cmake.patch + +#Apply patches +patch src/src/ParallelLibrary.cpp configs/5.3.1/ParallelLibrary.cpp.patch +patch src/src/ParallelLibrary.hpp configs/5.3.1/ParallelLibrary.hpp.patch +patch src/src/NonDSampling.cpp configs/5.3.1/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/5.3.1/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.3.1/pecos_global_defs.hpp.patch + +export BOOST_ROOT=$ISSM_DIR/externalpackages/boost/install + +#Configure dakota +# Set your local gcc compiler here +cd $DAK_BUILD +cmake -DBoost_NO_BOOST_CMAKE=TRUE \ + -DBoost_NO_SYSTEM_PATHS=TRUE \ + -DBOOST_ROOT:PATHNAME=$BOOST_ROOT \ + -DBoost_LIBRARY_DIRS:FILEPATH=${BOOST_ROOT}/lib \ + -DCMAKE_CXX_COMPILER=/usr/bin/g++ -DCMAKE_CC_COMPILER=/usr/bin/gcc \ + -DCMAKE_Fortran_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-gfortran \ + -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC + +#-DCMAKE_CXX_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-g++ -DCMAKE_Fortran_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-gfortran + +cd .. + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.3.1-macosx64-yosemite.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.3.1-macosx64-yosemite.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.3.1-macosx64-yosemite.sh (revision 21239) @@ -0,0 +1,51 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$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 +patch $DAK_SRC/CMakeLists.txt configs/5.3.1/CMakeLists.txt.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++ -D CMAKE_Fortran_COMPILER=/usr/local/gfortran/bin/gfortran -D LDFLAGS="-std=gnu++0x" -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 $1 install +fi +cd .. Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.3.1-macosx64.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.3.1-macosx64.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.3.1-macosx64.sh (revision 21239) @@ -0,0 +1,62 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$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.mac.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/5.3.1/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/5.3.1/CMakeLists.txt.patch + +#Apply patches +patch src/src/ParallelLibrary.cpp configs/5.3.1/ParallelLibrary.cpp.patch +patch src/src/ParallelLibrary.hpp configs/5.3.1/ParallelLibrary.hpp.patch +patch src/src/NonDSampling.cpp configs/5.3.1/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/5.3.1/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.3.1/pecos_global_defs.hpp.patch + +export BOOST_ROOT=$ISSM_DIR/externalpackages/boost/install + +#Configure dakota +# Set your local gcc compiler here +cd $DAK_BUILD +cmake -DBoost_NO_BOOST_CMAKE=TRUE \ + -DBoost_NO_SYSTEM_PATHS=TRUE \ + -DBOOST_ROOT:PATHNAME=$BOOST_ROOT \ + -DBoost_LIBRARY_DIRS:FILEPATH=${BOOST_ROOT}/lib \ + -DCMAKE_CXX_COMPILER=g++ -DCMAKE_CC_COMPILER=gcc \ + -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC + +#-DCMAKE_CXX_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-g++ -DCMAKE_Fortran_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-gfortran + +cd .. + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.3.1-pleiades.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.3.1-pleiades.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-5.3.1-pleiades.sh (revision 21239) @@ -0,0 +1,51 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$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.pfe.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/5.3.1/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/5.3.1/CMakeLists.txt.pfe.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 $1 install +fi +cd .. Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-6.2-intel15-discover.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-6.2-intel15-discover.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-6.2-intel15-discover.sh (revision 21239) @@ -0,0 +1,58 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz' + +#Untar +tar -zxvf dakota-6.2-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-6.2.0.src/* src +rm -rf dakota-6.2.0.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +export MPIHOME=$ISSM_DIR/externalpackages/mpich/install +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2/BuildDakotaCustom.cmake.discover.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.discover.patch + +#Apply patches +patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch + +#Configure dakota +cd $DAK_BUILD + +cmake -D CMAKE_C_COMPILER=mpicc \ + -D CMAKE_CXX_COMPILER=mpicxx \ + -D CMAKE_Fortran_COMPILER=/usr/bin/gfortran \ + -DHAVE_ACRO=off \ + -DHAVE_JEGA=off \ + -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 $1 install +fi +cd .. Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-6.2-linux64.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-6.2-linux64.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-6.2-linux64.sh (revision 21239) @@ -0,0 +1,60 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz' + +#Untar +tar -zxvf dakota-6.2-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-6.2.0.src/* src +rm -rf dakota-6.2.0.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +export MPIHOME=$ISSM_DIR/externalpackages/mpich/install +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2/BuildDakotaCustom.cmake.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch + +#Apply patches +patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch + +#Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost +export CXXFLAGS='-std=c++98' + +#Configure dakota +cd $DAK_BUILD + +cmake -D CMAKE_C_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicc \ + -D CMAKE_CXX_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicxx \ + -D CMAKE_Fortran_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpif77 \ + -DHAVE_ACRO=off \ + -DHAVE_JEGA=off \ + -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 $1 install +fi +cd .. Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-6.2-lonestar.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-6.2-lonestar.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-6.2-lonestar.sh (revision 21239) @@ -0,0 +1,58 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz' + +#Untar +tar -zxvf dakota-6.2-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-6.2.0.src/* src +rm -rf dakota-6.2.0.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +export MPIHOME=/opt/cray/mpt/default/gni/mpich-intel/14.0/ +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2/BuildDakotaCustom.cmake.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.lonestar.patch + +#Apply patches +patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch + +#Configure dakota +cd $DAK_BUILD + +cmake -D CMAKE_C_COMPILER=/opt/apps/intel16/cray_mpich/7.3.0/bin/mpicc \ + -D CMAKE_CXX_COMPILER=/opt/apps/intel16/cray_mpich/7.3.0/bin/mpicxx \ + -D CMAKE_Fortran_COMPILER=/opt/apps/intel16/cray_mpich/7.3.0/bin/mpif77 \ + -DHAVE_ACRO=off \ + -DHAVE_JEGA=off \ + -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 $1 install +fi +cd .. Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-6.2-macosx64-snowleopard.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-6.2-macosx64-snowleopard.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-6.2-macosx64-snowleopard.sh (revision 21239) @@ -0,0 +1,69 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz' + +#Untar +tar -zxvf dakota-6.2-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-6.2.0.src/* src +rm -rf dakota-6.2.0.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +export MPIHOME=$ISSM_DIR/externalpackages/mpich/install +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2/BuildDakotaCustom.cmake.mac.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.patch + +#Apply patches +patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch + +export BOOST_ROOT=$ISSM_DIR/externalpackages/boost/install + +#Configure dakota +# Set your local gcc compiler here +cd $DAK_BUILD +cmake -DBoost_NO_BOOST_CMAKE=TRUE \ + -DBoost_NO_SYSTEM_PATHS=TRUE \ + -DBOOST_ROOT:PATHNAME=$BOOST_ROOT \ + -DBoost_LIBRARY_DIRS:FILEPATH=${BOOST_ROOT}/lib \ + -D CMAKE_C_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicc \ + -D CMAKE_CXX_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicxx \ + -D CMAKE_Fortran_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpif77 \ + -DHAVE_ACRO=off \ + -DHAVE_JEGA=off \ + -D LDFLAGS="-L/usr/lib/ -lstdc++ -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/ -lgfortran" \ + -C $DAK_SRC/cmake/BuildDakotaCustom.cmake \ + -C $DAK_SRC/cmake/DakotaDev.cmake \ + $DAK_SRC +cd .. + +# Snowleopard: Mpi should be made with these compilers +#-DCMAKE_CXX_COMPILER=/usr/bin/g++ -DCMAKE_CC_COMPILER=/usr/bin/gcc \ +#-DCMAKE_Fortran_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-gfortran \ + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-6.2-macosx64-yosemite.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-6.2-macosx64-yosemite.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-6.2-macosx64-yosemite.sh (revision 21239) @@ -0,0 +1,63 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz' + +#Untar +tar -zxvf dakota-6.2-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-6.2.0.src/* src +rm -rf dakota-6.2.0.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +export MPIHOME=$ISSM_DIR/externalpackages/mpich/install +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2/BuildDakotaCustom.cmake.yosemite.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.patch + +#Apply patches +patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch + +#Configure dakota +cd $DAK_BUILD + +cmake -D CMAKE_C_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicc \ + -D CMAKE_CXX_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicxx \ + -D CMAKE_Fortran_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpif77 \ + -DHAVE_ACRO=off \ + -DHAVE_JEGA=off \ + -DBLAS_LIBS=$ISSM_DIR/externalpackages/petsc/install/lib/libfblas.a \ + -DLAPACK_LIBS=$ISSM_DIR/externalpackages/petsc/install/lib/libflapack.a \ + -C $DAK_SRC/cmake/BuildDakotaCustom.cmake \ + -C $DAK_SRC/cmake/DakotaDev.cmake \ + $DAK_SRC +cd .. + +#Make sure to include --download-fblaslapack=1 \ in petsc configure script to use the petsc blas and dlapack libs +#-DBLAS_LIBS=$ISSM_DIR/externalpackages/petsc/install/lib/libfblas.a -DLAPACK_LIBS=$ISSM_DIR/externalpackages/petsc/install/lib/libflapack.a + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-6.2-macosx64.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-6.2-macosx64.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-6.2-macosx64.sh (revision 21239) @@ -0,0 +1,69 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz' + +#Untar +tar -zxvf dakota-6.2-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-6.2.0.src/* src +rm -rf dakota-6.2.0.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +export MPIHOME=$ISSM_DIR/externalpackages/mpich/install +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2/BuildDakotaCustom.cmake.mac.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.patch + +#Apply patches +patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch + +export BOOST_ROOT=$ISSM_DIR/externalpackages/boost/install + +#Configure dakota +# Set your local gcc compiler here +cd $DAK_BUILD +cmake -DBoost_NO_BOOST_CMAKE=TRUE \ + -DBoost_NO_SYSTEM_PATHS=TRUE \ + -DBOOST_ROOT:PATHNAME=$BOOST_ROOT \ + -DBoost_LIBRARY_DIRS:FILEPATH=${BOOST_ROOT}/lib \ + -D CMAKE_C_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicc \ + -D CMAKE_CXX_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicxx \ + -D CMAKE_Fortran_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpif77 \ + -D CMAKE_CXX_FLAGS=-fdelayed-template-parsing \ + -DHAVE_ACRO=off \ + -DHAVE_JEGA=off \ + -C $DAK_SRC/cmake/BuildDakotaCustom.cmake \ + -C $DAK_SRC/cmake/DakotaDev.cmake \ + $DAK_SRC +cd .. + +# Snowleopard: Mpi should be made with these compilers +#-DCMAKE_CXX_COMPILER=/usr/bin/g++ -DCMAKE_CC_COMPILER=/usr/bin/gcc \ +#-DCMAKE_Fortran_COMPILER=/usr/local/gfortran/bin/x86_64-apple-darwin10-gfortran \ + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-6.2-pleiades.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-6.2-pleiades.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/install-6.2-pleiades.sh (revision 21239) @@ -0,0 +1,58 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz' + +#Untar +tar -zxvf dakota-6.2-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-6.2.0.src/* src +rm -rf dakota-6.2.0.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +export MPIHOME=$ISSM_DIR/externalpackages/mpich/install +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2/BuildDakotaCustom.cmake.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.pfe.patch + +#Apply patches +patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch + +#Configure dakota +cd $DAK_BUILD + +cmake -D CMAKE_C_COMPILER=mpicc \ + -D CMAKE_CXX_COMPILER=mpicxx \ + -D CMAKE_Fortran_COMPILER=/usr/bin/gfortran \ + -DHAVE_ACRO=off \ + -DHAVE_JEGA=off \ + -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-larour-NatClimateChange2016/externalpackages/dakota/tests/test.in =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/tests/test.in (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/tests/test.in (revision 21239) @@ -0,0 +1,36 @@ +method, + nond_sampling + seed = 1234 + rng rnum2 + samples = 2000 + sample_type lhs + distribution cumulative + num_probability_levels = 9 + probability_levels = + 0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 + 0.9999 + +model, + single + +variables, + normal_uncertain = 2 + nuv_means = + 1 1 + nuv_std_deviations = + 0.1 0.1 + nuv_descriptors = + 'x1' 'x2' + +interface, + direct + analysis_driver = 'plugin_text_book' + evaluation_scheduling master + processors_per_evaluation = 3 + +responses, + num_response_functions = 1 + response_descriptors = + 'MaxVel' + no_gradients + no_hessians Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/tests/test2.in =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/tests/test2.in (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dakota/tests/test2.in (revision 21239) @@ -0,0 +1,36 @@ +method, + nond_sampling + seed = 1234 + rng rnum2 + samples = 3 + sample_type lhs + distribution cumulative + num_probability_levels = 9 + probability_levels = + 0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 + 0.9999 + +model, + single + +variables, + normal_uncertain = 2 + nuv_means = + 1 1 + nuv_std_deviations = + 0.1 0.1 + nuv_descriptors = + 'x1' 'x2' + +interface, + direct + analysis_driver = 'plugin_text_book' + evaluation_scheduling master + processors_per_evaluation = 1 + +responses, + num_response_functions = 1 + response_descriptors = + 'MaxVel' + no_gradients + no_hessians Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dem/dem.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dem/dem.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dem/dem.m (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dem/landcolor.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dem/landcolor.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dem/landcolor.m (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dem/license.txt =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dem/license.txt (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dem/license.txt (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dem/seacolor.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dem/seacolor.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dem/seacolor.m (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/distribute/README =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/distribute/README (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/distribute/README (revision 21239) @@ -0,0 +1,9 @@ +At: https://pypi.python.org/pypi/setuptools + +Installation Instructions + +The recommended way to bootstrap setuptools on any system is to download ez_setup.py and run it using the target Python environment. Different operating systems have different recommended techniques to accomplish this basic routine, so below are some examples to get you started. + +Setuptools requires Python 2.6 or later. To install setuptools on Python 2.4 or Python 2.5, use the bootstrap script for Setuptools 1.x. + +The link provided to ez_setup.py is a bookmark to bootstrap script for the latest known stable release. Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/distribute/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/distribute/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/distribute/install.sh (revision 21239) @@ -0,0 +1,6 @@ +#!/bin/bash +set -eu + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://python-distribute.org/distribute_setup.py' 'distribute_setup.py' +python distribute_setup.py Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/doxygen/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/doxygen/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/doxygen/install.sh (revision 21239) @@ -0,0 +1,21 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +mkdir install + +#Download latest version +svn co https://svn.code.sf.net/p/doxygen/code/trunk src + +#Configure doxygen +cd src && ./configure --prefix "$ISSM_DIR/externalpackages/doxygen/install" +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi + +#Install doxygen +make install +make install_docs Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dyson/ldap.pl =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dyson/ldap.pl (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dyson/ldap.pl (revision 21239) @@ -0,0 +1,25 @@ +#!/usr/bin/perl +# +# LDAP.PL - Acquire JPL LDAP data and pare down to user IDs - 2011-08-01 +# +$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-larour-NatClimateChange2016/externalpackages/dyson/readme.txt =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dyson/readme.txt (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dyson/readme.txt (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/dyson/source_seek.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dyson/source_seek.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/dyson/source_seek.sh (revision 21239) @@ -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: $0 \n"; +fi +# +# EOF - 2011-08-05 - Jay Dyson Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/ec2ami/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/ec2ami/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/ec2ami/install.sh (revision 21239) @@ -0,0 +1,12 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf ec2-api-tools.zip +rm -rf ec2-api-tools-1.4.0.7 + +#Download from ISSM server +$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-larour-NatClimateChange2016/externalpackages/ec2api/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/ec2api/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/ec2api/install.sh (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/emscripten/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/emscripten/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/emscripten/install.sh (revision 21239) @@ -0,0 +1,21 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/emsdk-portable.tar.gz' 'emsdk-portable.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf emsdk-portable.tar.gz +mv emsdk_portable src + +cd src + +export CXX=g++ +export CC=gcc + +./emsdk update +./emsdk install latest +./emsdk activate latest Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/esmf/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/esmf/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/esmf/install.sh (revision 21239) @@ -0,0 +1,31 @@ +#!/bin/bash +set -eu + +export ESMF_DIR=$ISSM_DIR/externalpackages/esmf/esmf +export ESMF_INSTALL_PREFIX=$ISSM_DIR/externalpackages/esmf/install +export ESMF_COMPILER=gfortran +export ESMF_COMM=mpich2 + +#Some cleanup +rm -rf esmf_6_3_0rp1 +rm -rf esmf + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/esmf_6_3_0rp1_src.tar.gz' 'esmf_6_3_0rp1_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_6_3_0rp1_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 Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/LICENSE =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/LICENSE (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/LICENSE (revision 21239) @@ -0,0 +1,27 @@ +Copyright (c) 2014, Oliver J. 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. + +* Neither the name of the {organization} 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 COPYRIGHT HOLDER 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-larour-NatClimateChange2016/externalpackages/export_fig/README.md =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/README.md (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/README.md (revision 21239) @@ -0,0 +1,259 @@ +export_fig +========== + +A toolbox for exporting figures from MATLAB to standard image and document formats nicely. + +### Overview +Exporting a figure from MATLAB the way you want it (hopefully the way it looks on screen), can be a real headache for the unitiated, thanks to all the settings that are required, and also due to some eccentricities (a.k.a. features and bugs) of functions such as `print`. The first goal of export_fig is to make transferring a plot from screen to document, just the way you expect (again, assuming that's as it appears on screen), a doddle. + +The second goal is to make the output media suitable for publication, allowing you to publish your results in the full glory that you originally intended. This includes embedding fonts, setting image compression levels (including lossless), anti-aliasing, cropping, setting the colourspace, alpha-blending and getting the right resolution. + +Perhaps the best way to demonstrate what export_fig can do is with some examples. + +### Examples +**Visual accuracy** - MATLAB's exporting functions, namely `saveas` and `print`, change many visual properties of a figure, such as size, axes limits and ticks, and background colour, in unexpected and unintended ways. Export_fig aims to faithfully reproduce the figure as it appears on screen. For example: +```Matlab +plot(cos(linspace(0, 7, 1000))); +set(gcf, 'Position', [100 100 150 150]); +saveas(gcf, 'test.png'); +export_fig test2.png +``` +generates the following: + +| Figure: | test.png: | test2.png: | +|:-------:|:---------:|:----------:| +|![](https://farm6.staticflickr.com/5616/15589249291_16e485c29a_o_d.png)|![](https://farm4.staticflickr.com/3944/15406302850_4d2e1c7afa_o_d.png)|![](https://farm6.staticflickr.com/5607/15568225476_8ce9bd5f6b_o_d.png)| + +Note that the size and background colour of test2.png (the output of export_fig) are the same as those of the on screen figure, in contrast to test.png. Of course, if you want want the figure background to be white (or any other colour) in the exported file then you can set this prior to exporting using: +```Matlab +set(gcf, 'Color', 'w'); +``` + +Notice also that export_fig crops and anti-aliases (smooths, for bitmaps only) the output by default. However, these options can be disabled; see the Tips section below for details. + +**Resolution** - by default, export_fig exports bitmaps at screen resolution. However, you may wish to save them at a different resolution. You can do this using either of two options: `-m`, where is a positive real number, magnifies the figure by the factor for export, e.g. `-m2` produces an image double the size (in pixels) of the on screen figure; `-r`, again where is a positive real number, specifies the output bitmap to have pixels per inch, the dimensions of the figure (in inches) being those of the on screen figure. For example, using: +```Matlab +export_fig test.png -m2.5 +``` +on the figure from the example above generates: + +![](https://farm4.staticflickr.com/3937/15591910915_dc7040c477_o_d.png) + +Sometimes you might have a figure with an image in. For example: +```Matlab +imshow(imread('cameraman.tif')) +hold on +plot(0:255, sin(linspace(0, 10, 256))*127+128); +set(gcf, 'Position', [100 100 150 150]); +``` +generates this figure: + +![](https://farm4.staticflickr.com/3942/15589249581_ff87a56a3f_o_d.png) + +Here the image is displayed in the figure at resolution lower than its native resolution. However, you might want to export the figure at a resolution such that the image is output at its native (i.e. original) size (in pixels). Ordinarily this would require some non-trivial computation to work out what that resolution should be, but export_fig has an option to do this for you. Using: +```Matlab +export_fig test.png -native +``` +produces: + +![](https://farm6.staticflickr.com/5604/15589249591_da2b2652e4_o_d.png) + +with the image being the size (in pixels) of the original image. Note that if you want an image to be a particular size, in pixels, in the output (other than its original size) then you can resize it to this size and use the `-native` option to achieve this. + +All resolution options (`-m`, `-q` and `-native`) correctly set the resolution information in PNG and TIFF files, as if the image were the dimensions of the on screen figure. + +**Shrinking dots & dashes** - when exporting figures with dashed or dotted lines using either the ZBuffer or OpenGL (default for bitmaps) renderers, the dots and dashes can appear much shorter, even non-existent, in the output file, especially if the lines are thick and/or the resolution is high. For example: +```Matlab +plot(sin(linspace(0, 10, 1000)), 'b:', 'LineWidth', 4); +hold on +plot(cos(linspace(0, 7, 1000)), 'r--', 'LineWidth', 3); +grid on +export_fig test.png +``` +generates: + +![](https://farm4.staticflickr.com/3956/15592747732_f943d4aa0a_o_d.png) + +This problem can be overcome by using the painters renderer. For example: +```Matlab +export_fig test.png -painters +``` +used on the same figure generates: + +![](https://farm4.staticflickr.com/3945/14971168504_77692f11f5_o_d.png) + +Note that not only are the plot lines correct, but the grid lines are too. + +**Transparency** - sometimes you might want a figure and axes' backgrounds to be transparent, so that you can see through them to a document (for example a presentation slide, with coloured or textured background) that the exported figure is placed in. To achieve this, first (optionally) set the axes' colour to 'none' prior to exporting, using: +```Matlab +set(gca, 'Color', 'none'); % Sets axes background +``` + +then use export_fig's `-transparent` option when exporting: +```Matlab +export_fig test.png -transparent +``` + +This will make the background transparent in PDF, EPS and PNG outputs. You can additionally save fully alpha-blended semi-transparent patch objects to the PNG format. For example: + +```Matlab +logo; +alpha(0.5); +``` + +generates a figure like this: + +![](https://farm4.staticflickr.com/3933/15405290339_b08de33528_o_d.png) + +If you then export this to PNG using the `-transparent` option you can then put the resulting image into, for example, a presentation slide with fancy, textured background, like so: + +![](https://farm6.staticflickr.com/5599/15406302920_59beaefff1_o_d.png) + +and the image blends seamlessly with the background. + +**Image quality** - when publishing images of your results, you want them to look as good as possible. By default, when outputting to lossy file formats (PDF, EPS and JPEG), export_fig uses a high quality setting, i.e. low compression, for images, so little information is lost. This is in contrast to MATLAB's print and saveas functions, whose default quality settings are poor. For example: +```Matlab +A = im2double(imread('peppers.png')); +B = randn(ceil(size(A, 1)/6), ceil(size(A, 2)/6), 3) * 0.1; +B = cat(3, kron(B(:,:,1), ones(6)), kron(B(:,:,2), ones(6)), kron(B(:,:,3), ones(6))); +B = A + B(1:size(A, 1),1:size(A, 2),:); +imshow(B); +print -dpdf test.pdf +``` +generates a PDF file, a sub-window of which looks (when zoomed in) like this: + +![](https://farm6.staticflickr.com/5613/15405290309_881b2774d6_o_d.png) + +while the command + +```Matlab +export_fig test.pdf +``` +on the same figure produces this: + +![](https://farm4.staticflickr.com/3947/14971168174_687473133f_o_d.png) + +While much better, the image still contains some compression artifacts (see the low level noise around the edge of the pepper). You may prefer to export with no artifacts at all, i.e. lossless compression. Alternatively, you might need a smaller file, and be willing to accept more compression. Either way, export_fig has an option that can suit your needs: `-q`, where is a number from 0-100, will set the level of lossy image compression (again in PDF, EPS and JPEG outputs only; other formats are lossless), from high compression (0) to low compression/high quality (100). If you want lossless compression in any of those formats then specify a greater than 100. For example: +```Matlab +export_fig test.pdf -q101 +``` +again on the same figure, produces this: + +![](https://farm6.staticflickr.com/5608/15405803908_934512c1fe_o_d.png) + +Notice that all the noise has gone. + +### Tips +**Anti-aliasing** - the anti-aliasing which export_fig applies to bitmap outputs by default makes the images look nice, but it can also blur images and increase exporting time and memory requirements, so you might not always want it. You can set the level of anti-aliasing by using the `-a` option, where is 1 (no anti-aliasing), 2, 3 (default) or 4 (maximum anti-aliasing). + +**Cropping** - by default, export_fig crops its output to minimize the amount of empty space around the figure. If you'd prefer the figure to be uncropped, and instead have the same appearance (in terms of border width) as the on screen figure, then use the `-nocrop` option. + +**Colourspace** - by default, export_fig generates files in the RGB [colourspace](http://en.wikipedia.org/wiki/Color_space). However, you can also export in greyscale or the CMYK colourspace, using the `-grey` (or `-gray`) and `-cmyk` options respectively. The CMYK option is useful for publishers who require documents in this colourspace, but the option is only supported for PDF, EPS and TIFF files. + +**Specifying a target directory** - you can get export_fig to save output files to any directory (for which you have write permission), simply by specifying the full or relative path in the filename. For example: +```Matlab +export_fig ../subdir/fig.png; +export_fig('C:/Users/Me/Documents/figures/myfig', '-pdf', '-png'); +``` + +**Variable file names** - often you might want to save a series of figures in a for loop, each with a different name. For this you can use the functional form of input arguments, i.e. `export_fig(arg1, arg2)`, and construct the filename string in a variable. Here's an example of this: +```Matlab +for a = 1:5 + plot(rand(5, 2)); + export_fig(sprintf('plot%d.png', a)); +end +``` +When using the functional form like this, be sure to put string variables in quotes: +```Matlab +export_fig(sprintf('plot%d', a), '-a1', '-pdf', '-png'); +``` + +**Specifying the figure/axes** - if you have mutiple figures open you can specify which figure to export using its handle: +```Matlab +export_fig(figure_handle, 'filename.fmt'); +``` +Equally, if your figure contains several subplots then you can export just one of them by giving export_fig the handle to the relevant axes: +```Matlab +export_fig(axes_handle, 'filename.fmt'); +``` + +**Multiple formats** - save time by exporting to multiple formats simultaneously. E.g.: +```Matlab +export_fig filename -pdf -eps -png -jpg -tiff +``` + +**Other file formats** - if you'd like to save your figure to a bitmap format that is not supported by export_fig, e.g. animated GIF, PPM file or a frame in a movie, then you can use export_fig to output the image, and optionally an alpha-matte, to the workspace. E.g.: +```Matlab +frame = export_fig; +``` +or +```Matlab +[frame, alpha] = export_fig; +``` +These variables can then be saved to other image formats using other functions, such as imwrite. + +**Appending to a file** - you can use the `-append` option to append the figure to the end of an image/document, if it already exists. This is supported for PDF and TIFF files only. Note that if you wish to append a lot of figures consecutively to a PDF, it can be more efficient to save all the figures to PDF separately then append them all in one go at the end (e.g. using [append_pdfs](http://www.mathworks.com/matlabcentral/fileexchange/31215-appendpdfs)). + +**Font size** - if you want to place an exported figure in a document with the font a particular size then you need to set the font to that size in the figure, and not resize the output of export_fig in the document. To avoid resizing, simply make sure that the on screen figure is the size you want the output to be in the document before exporting. + +**Renderers** - MATLAB has three renderers for displaying and exporting figures: painters, OpenGL and ZBuffer. The different renderers have different [features](http://www.mathworks.com/access/helpdesk/help/techdoc/creating_plots/f3-84337.html#f3-102410), so if you aren't happy with the result from one renderer try another. By default, vector formats (i.e. PDF and EPS outputs) use the painters renderer, while other formats use the OpenGL renderer. Non-default renderers can be selected by using one of these three export_fig input options: `-painters`, `-opengl`, `-zbuffer`. + +**Artifacts** - sometimes the output that you get from export_fig is not what you expected. If an output file contains artifacts that aren't in the on screen figure then make sure that the renderer used for rendering the figure on screen is the same as that used for exporting. To set the renderer used to display the figure, use: +```Matlab +set(figure_handle, 'Renderer', 'opengl'); +``` +After matching the two renderers, if the artifact appears in the on screen figure then you'll need to fix that before exporting. Alternatively you can try changing the renderer used by export_fig. Finally check that it isn't one of the known issues mentioned in the section below. + +**Smoothed/interpolated images in output PDF** - if you produce a PDF using export_fig and images in the PDF look overly smoothed or interpolated, this is because the software you are using to view the PDF is smoothing or interpolating the image data. The image is not smoothed in the PDF file itself. If the software has an option to disable this feature, you should select it. Alternatively, use another PDF viewer that doesn't exhibit this problem. + +**Locating Ghostscript/pdftops** - You may find a dialogue box appears when using export_fig, asking you to locate either [Ghostscript](http://www.ghostscript.com) or [pdftops](http://www.foolabs.com/xpdf). These are separate applications which export_fig requires to perform certain functions. If such a dialogue appears it is because export_fig can't find the application automatically. This is because you either haven't installed it, or it isn't in the normal place. Make sure you install the applications correctly first. They can be downloaded from the following places: + 1. Ghostscript: [www.ghostscript.com](http://www.ghostscript.com) + 2. pdftops (install the Xpdf package): [www.foolabs.com/xpdf](http://www.foolabs.com/xpdf) + +If you choose to install them in a non-default location then point export_fig +to this location using the dialogue box. + +**Undefined function errors** - If you download and run export_fig and get an error similar to this: +```Matlab +??? Undefined function or method 'print2array' for input arguments of type 'double'. +``` +then you are missing one or more of the files that come in the export_fig package. Make sure that you click the "Get from GitHub" button at the top-right of the download [page](http://www.mathworks.co.uk/matlabcentral/fileexchange/23629-exportfig), then extract all the files in the zip file to the same directory. You should then have all the necessary files. + +### Known issues +There are lots of problems with MATLAB's exporting functions, and unfortunately export_fig, which is simply a glorified wrapper for MATLAB's print function, doesn't solve all of them (yet?). Some of the problems I know about are: + +**Fonts** - when using the painters renderer, MATLAB can only export a small number of fonts, details of which can be found [here](http://www.mathworks.com/access/helpdesk/help/techdoc/creating_plots/f3-103191.html#f3-96545). Export_fig attempts to correct font names in the resulting EPS file (for upto a maximum of 11 different fonts in one figure), but this is not always guaranteed to work. In particular, the text positions will be affected. It also does not work for text blocks where the 'Interpreter' property is set to 'latex'. + +Also, when using the painters renderer, ghostscript will sometimes throw an error such as `Error: /undefined in /findfont`. This suggests that ghostscript could not find a definition file for one of your fonts. One possible fix for this is to make sure the file `EXPORT_FIG_PATH/.ignore/gs_font_path.txt` exists and contains a list of paths to the folder(s) containing the necessary font definitions (make sure they're TrueType definitions), separated by a semicolon. + +**RGB color data not yet supported in Painter's mode** - you will see this as a warning if you try to export a figure which contains patch objects whose face or vertex colors are specified as a an RGB colour, rather than an index into the colormap, using the painters renderer (the default renderer for vector output). This problem can arise if you use `pcolor`, for example. This is a problem with MATLAB's painters renderer, which also affects `print`; there is currently no fix available in export_fig (other than to export to bitmap). The suggested workaround is to avoid colouring patches using RGB. First, try to use colours in the figure's colourmap (instructions [here](http://www.mathworks.co.uk/support/solutions/en/data/1-6OTPQE/)) - change the colourmap, if necessary. If you are using `pcolor`, try using [uimagesc](http://www.mathworks.com/matlabcentral/fileexchange/11368) (on the file exchange) instead. + +**Dashed contour lines appear solid** - when using the painters renderer, MATLAB cannot generate dashed lines using the `contour` function (either on screen or in exported PDF and EPS files). Details can be found [here](http://www.mathworks.com/support/solutions/en/data/1-14PPHB/?solution=1-14PPHB). + +**Text size** - when using the OpenGL or ZBuffer renderers, large text can be resized relative to the figure when exporting at non-screen-resolution (including using anti-alising at screen resolution). This is a feature of MATLAB's `print `function. In this case, try using the `-painters` option. + +**Lighting and transparency** - when using the painters renderer, transparency and lighting effects are not supported. Sorry, but this is a feature of the renderer. To find out more about the capabilities of each rendering method, see [here](http://www.mathworks.com/access/helpdesk/help/techdoc/creating_plots/f3-84337.html#f3-102410). You can still export transparent objects to vector format (SVG) using the excellent [plot2svg](http://www.mathworks.com/matlabcentral/fileexchange/7401) package, then convert this to PDF, for example using [Inkscape](http://inkscape.org/). However, it can't handle lighting. + +**Lines in patch objects** - when exporting patch objects to PDF using the painters renderer (default), sometimes the output can appear to have lines across the middle of rectangular patches; these lines are the colour of the background, as if there is a crack in the patch, allowing you to see through. This issue is a feature of the software used to display the PDF, rather than the PDF itself. Sometimes disabling anti-aliasing in this software can get rid of the lines. + +**Out of memory** - if you run into memory issues when using export_fig, some ways to get round this are: + 1. Reduce the level of anti-aliasing. + 2. Reduce the size of the on screen figure. + 3. Reduce the resolution (dpi) the figure is exported at. + +**Errors** - the other common type of errors people get with export_fig are OpenGL errors. This isn't a fault of export_fig, but either a bug in MATLAB's `print`, or your graphics driver getting itself into a state. Always make sure your graphics driver is up-to-date. If it still doesn't work, try using the ZBuffer renderer. + +### Raising issues +If you think you have found a genuine error or issue with export_fig **that is not listed above**, first ensure that the figure looks correct on screen when rendered using the renderer that export_fig is set to use (e.g. if exporting to PDF or EPS, does the figure look correct on screen using the painters renderer, or if exporting to bitmap, does the figure look correct on screen using the OpenGL renderer?). If it looks wrong then the problem is there, and I cannot help (other than to suggest you try exporting using a different renderer). + +Secondly, if exporting to bitmap, do try all the renderers (i.e. try the options `-opengl`, `-zbuffer` and `-painters` separately), to see if one of them does produce an acceptable output, and if so, use that. + +If the figure looks correct on screen, but an error exists in the exported output (which cannot be solved using a different renderer) then please feel free to raise an [issue](https://github.com/ojwoodford/export_fig/issues). Please be sure to include the .fig file, the export_fig command you use, the output you get, and a description of what you expected. I can't promise anything, but if it's easy to fix I probably will do it. Often I will find that the error is due to a bug in MATLAB's print function, in which case I will suggest you submit it as a bug to TheMathWorks, and inform me of any fix they suggest. Also, if there's a feature you'd like that isn't supported please tell me what it is and I'll consider implementing it. + +### And finally... + +![](https://farm4.staticflickr.com/3956/15591911455_b9008bd77e_o_d.jpg) + +If you've ever wondered what's going on in the icon on the export_fig download page (reproduced on the left), then this explanantion is for you. The icon is designed to demonstrate as many of export_fig's features as possible. Given a +figure containing a translucent mesh (top right), export_fig can export to pdf (bottom centre), which allows the figure to be zoomed in without losing quality (because it's a vector graphic), but isn't able to reproduce the translucency, and also, depending on the viewer, creates small gaps between the patches, which are seen here as thin white lines. By contrast, when exporting to png (top left), translucency is preserved (see how the graphic below shows through), the figure is anti-aliased, but zooming in does not reveal more detail. + Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/append_pdfs.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/append_pdfs.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/append_pdfs.m (revision 21239) @@ -0,0 +1,58 @@ +%APPEND_PDFS Appends/concatenates multiple PDF files +% +% Example: +% append_pdfs(output, input1, input2, ...) +% append_pdfs(output, input_list{:}) +% append_pdfs test.pdf temp1.pdf temp2.pdf +% +% This function appends multiple PDF files to an existing PDF file, or +% concatenates them into a PDF file if the output file doesn't yet exist. +% +% This function requires that you have ghostscript installed on your +% system. Ghostscript can be downloaded from: http://www.ghostscript.com +% +% IN: +% output - string of output file name (including the extension, .pdf). +% If it exists it is appended to; if not, it is created. +% input1 - string of an input file name (including the extension, .pdf). +% All input files are appended in order. +% input_list - cell array list of input file name strings. All input +% files are appended in order. + +% Copyright: Oliver Woodford, 2011 + +% Thanks to Reinhard Knoll for pointing out that appending multiple pdfs in +% one go is much faster than appending them one at a time. + +% Thanks to Michael Teo for reporting the issue of a too long command line. +% Issue resolved on 5/5/2011, by passing gs a command file. + +% Thanks to Martin Wittmann for pointing out the quality issue when +% appending multiple bitmaps. +% Issue resolved (to best of my ability) 1/6/2011, using the prepress +% setting + +function append_pdfs(varargin) +% Are we appending or creating a new file +append = exist(varargin{1}, 'file') == 2; +if append + output = [tempname '.pdf']; +else + output = varargin{1}; + varargin = varargin(2:end); +end +% Create the command file +cmdfile = [tempname '.txt']; +fh = fopen(cmdfile, 'w'); +fprintf(fh, '-q -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -dPDFSETTINGS=/prepress -sOutputFile="%s" -f', output); +fprintf(fh, ' "%s"', varargin{:}); +fclose(fh); +% Call ghostscript +ghostscript(['@"' cmdfile '"']); +% Delete the command file +delete(cmdfile); +% Rename the file if needed +if append + movefile(output, varargin{1}); +end +end Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/copyfig.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/copyfig.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/copyfig.m (revision 21239) @@ -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(findall(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 +end Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/crop_borders.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/crop_borders.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/crop_borders.m (revision 21239) @@ -0,0 +1,81 @@ +%CROP_BORDERS Crop the borders of an image or stack of images +% +% [B, v] = crop_borders(A, bcol, [padding]) +% +%IN: +% A - HxWxCxN stack of images. +% bcol - Cx1 background colour vector. +% padding - scalar indicating how many pixels padding to have. Default: 0. +% +%OUT: +% B - JxKxCxN cropped stack of images. +% v - 1x4 vector of start and end indices for first two dimensions, s.t. +% B = A(v(1):v(2),v(3):v(4),:,:). + +function [A, v] = crop_borders(A, bcol, padding) +if nargin < 3 + padding = 0; +end +[h, w, c, n] = size(A); +if isscalar(bcol) + bcol = bcol(ones(c, 1)); +end +bail = false; +for l = 1:w + for a = 1:c + if ~all(col(A(:,l,a,:)) == bcol(a)) + bail = true; + break; + end + end + if bail + break; + end +end +bcol = A(ceil(end/2),w,:,1); +bail = false; +for r = w:-1:l + for a = 1:c + if ~all(col(A(:,r,a,:)) == bcol(a)) + bail = true; + break; + end + end + if bail + break; + end +end +bcol = A(1,ceil(end/2),:,1); +bail = false; +for t = 1:h + for a = 1:c + if ~all(col(A(t,:,a,:)) == bcol(a)) + bail = true; + break; + end + end + if bail + break; + end +end +bcol = A(h,ceil(end/2),:,1); +bail = false; +for b = h:-1:t + for a = 1:c + if ~all(col(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-padding, 1) min(b+padding, h) max(l-padding, 1) min(r+padding, w)]; +A = A(v(1):v(2),v(3):v(4),:,:); +end + +function A = col(A) +A = A(:); +end Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/eps2pdf.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/eps2pdf.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/eps2pdf.m (revision 21239) @@ -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 me + % Delete the intermediate file + delete(tmp_nam); + rethrow(me); + 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 +end + +% 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); +end Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/export_fig.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/export_fig.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/export_fig.m (revision 21239) @@ -0,0 +1,799 @@ +%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 ... -p +% 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 pixel dimensions by when generating bitmap +% outputs. Default: '-m1'. +% -r - option val indicates the resolution (in pixels per inch) to +% export bitmap and vector outputs at, keeping the dimensions +% of the on-screen figure. Default: '-r864' (for vector output +% only). Note that the -m option overides the -r option for +% bitmap outputs only. +% -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. +% -p - option to add a border of width val to eps and pdf files, +% where val is in units of the intermediate eps file. Default: +% 0 (i.e. no padding). +% -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: +% https://github.com/ojwoodford/export_fig +% +% See also PRINT, SAVEAS. + +% Copyright (C) Oliver Woodford 2008-2014 + +% 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. +% 25/09/13: Add support for changing resolution in vector formats. Thanks +% to Jan Jaap Meijer for suggesting it. +% 07/05/14: Add support for '~' at start of path. Thanks to Sally Warner +% 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'); +set_tick_mode(Hlims, 'X'); +set_tick_mode(Hlims, 'Y'); +set_tick_mode(Hlims, 'Z'); +% 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_borders(alpha, 0, 1); + 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_borders(A, tcol, 1); + 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, sprintf('-r%d', options.resolution)}; + if options.colourspace == 1 + p2eArgs = [p2eArgs {'-cmyk'}]; + end + if ~options.crop + p2eArgs = [p2eArgs {'-loose'}]; + end + try + % Generate an eps + print2eps(tmp_nam, fig, options.bb_padding, p2eArgs{:}); + % Remove the background, if desired + if options.transparent && ~isequal(get(fig, 'Color'), 'none') + eps_remove_background(tmp_nam, 1 + using_hg2(fig)); + 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 +end + +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', 0, ... + 'bb_padding', 0, ... + 'magnify', [], ... + 'resolution', [], ... + '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|p|P))-?\d*.?\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.resolution = val; + case 'q' + options.quality = max(val, 0); + case 'p' + options.bb_padding = val; + 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 + +% Set default anti-aliasing now we know the renderer +if options.aa_factor == 0 + options.aa_factor = 1 + 2 * (~(using_hg2(fig) && strcmp(get(ancestor(fig, 'figure'), 'GraphicsSmoothing'), 'on')) | (options.renderer == 3)); +end + +% Convert user dir '~' to full path +if numel(options.name) > 2 && options.name(1) == '~' && (options.name(2) == '/' || options.name(2) == '\') + options.name = fullfile(char(java.lang.System.getProperty('user.home')), options.name(2:end)); +end + +% Compute the magnification and resolution +if isempty(options.magnify) + if isempty(options.resolution) + options.magnify = 1; + options.resolution = 864; + else + options.magnify = options.resolution ./ get(0, 'ScreenPixelsPerInch'); + end +elseif isempty(options.resolution) + options.resolution = 864; +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(1), '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 +end + +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 +end + +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)); +end + +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 +end + +function eps_remove_background(fname, count) +% 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 count + % 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+ +r[fe] *[\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); + % Reduce the count + count = count - 1; + end +end +% Close the file +fclose(fh); +end + +function b = isvector(options) +b = options.pdf || options.eps; +end + +function b = isbitmap(options) +b = options.png || options.tif || options.jpg || options.bmp || options.im || options.alpha; +end + +% Helper function +function A = make_cell(A) +if ~iscell(A) + A = {A}; +end +end + +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); +end + +function set_tick_mode(Hlims, ax) +% Set the tick mode of linear axes to manual +% Leave log axes alone as these are tricky +M = get(Hlims, [ax 'Scale']); +if ~iscell(M) + M = {M}; +end +M = cellfun(@(c) strcmp(c, 'linear'), M); +set(Hlims(M), [ax 'TickMode'], 'manual'); +end Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/fix_lines.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/fix_lines.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/fix_lines.m (revision 21239) @@ -0,0 +1,143 @@ +%FIX_LINES Improves the line style of eps files generated by print +% +% Examples: +% fix_lines fname +% fix_lines fname fname2 +% fstrm_out = fixlines(fstrm_in) +% +% 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. +% fstrm_in - File contents of a MATLAB-generated eps file. +% +%OUT: +% fstrm_out - Contents of the eps file with line styles fixed. + +% Copyright: (C) Oliver Woodford, 2008-2014 + +% 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. + +function fstrm = fix_lines(fstrm, fname2) + +if nargout == 0 || nargin > 1 + if nargin < 2 + % Overwrite the input file + fname2 = fstrm; + end + % Read in the file + fstrm = read_write_entire_textfile(fstrm); +end + +% 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 + +% Construct the output +fstrm = [fstrm(1:first_sec) second_sec sprintf('%s\r', new_style{:}) remaining]; + +% Write the output file +if nargout == 0 || nargin > 1 + read_write_entire_textfile(fname2, fstrm); +end +end Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/ghostscript.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/ghostscript.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/ghostscript.m (revision 21239) @@ -0,0 +1,158 @@ +%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, 2009-2013 + +% 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. +% 28/6/13 - Fix error using GS 9.07 in Linux. Many thanks to Jannick +% Steinbring for proposing the fix. +% 24/10/13 - Fix error using GS 9.07 in Linux. Many thanks to Johannes +% for the fix. +% 23/01/2014 - Add full path to ghostscript.txt in warning. Thanks to Koen +% Vermeer for raising the issue. + +function varargout = ghostscript(cmd) +% Initialize any required system calls before calling ghostscript +shell_cmd = ''; +if isunix + shell_cmd = 'export LD_LIBRARY_PATH=""; '; % Avoids an error on Linux with GS 9.07 +end +if ismac + shell_cmd = 'export DYLD_LIBRARY_PATH=""; '; % Avoids an error on Mac with GS 9.07 +end +% Call ghostscript +[varargout{1:nargout}] = system(sprintf('%s"%s" %s', shell_cmd, gs_path, cmd)); +end + +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 + executable = {'/usr/bin/gs', '/usr/local/bin/gs'}; + for a = 1:numel(executable) + path_ = executable{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?'); +end + +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 %s.', fullfile(fileparts(which('user_string.m')), '.ignore', 'ghostscript.txt')); + return +end +end + +function good = check_gs_path(path_) +% Check the path is valid +shell_cmd = ''; +if ismac + shell_cmd = 'export DYLD_LIBRARY_PATH=""; '; % Avoids an error on Mac with GS 9.07 +end +[good, message] = system(sprintf('%s"%s" -h', shell_cmd, path_)); +good = good == 0; +end Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/im2gif.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/im2gif.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/im2gif.m (revision 21239) @@ -0,0 +1,186 @@ +%IM2GIF Convert a multiframe image to an animated GIF file +% +% Examples: +% im2gif infile +% im2gif infile outfile +% im2gif(A, outfile) +% im2gif(..., '-nocrop') +% im2gif(..., '-nodither') +% im2gif(..., '-ncolors', n) +% im2gif(..., '-loops', n) +% im2gif(..., '-delay', n) +% +% This function converts a multiframe image to an animated GIF. +% +% To create an animation from a series of figures, export to a multiframe +% TIFF file using export_fig, then convert to a GIF, as follows: +% +% for a = 2 .^ (3:6) +% peaks(a); +% export_fig test.tif -nocrop -append +% end +% im2gif('test.tif', '-delay', 0.5); +% +%IN: +% infile - string containing the name of the input image. +% outfile - string containing the name of the output image (must have the +% .gif extension). Default: infile, with .gif extension. +% A - HxWxCxN array of input images, stacked along fourth dimension, to +% be converted to gif. +% -nocrop - option indicating that the borders of the output are not to +% be cropped. +% -nodither - option indicating that dithering is not to be used when +% converting the image. +% -ncolors - option pair, the value of which indicates the maximum number +% of colors the GIF can have. This can also be a quantization +% tolerance, between 0 and 1. Default/maximum: 256. +% -loops - option pair, the value of which gives the number of times the +% animation is to be looped. Default: 65535. +% -delay - option pair, the value of which gives the time, in seconds, +% between frames. Default: 1/15. + +% Copyright (C) Oliver Woodford 2011 + +function im2gif(A, varargin) + +% Parse the input arguments +[A, options] = parse_args(A, varargin{:}); + +if options.crop ~= 0 + % Crop + A = crop_borders(A, A(ceil(end/2),1,:,1)); +end + +% Convert to indexed image +[h, w, c, n] = size(A); +A = reshape(permute(A, [1 2 4 3]), h, w*n, c); +map = unique(reshape(A, h*w*n, c), 'rows'); +if size(map, 1) > 256 + dither_str = {'dither', 'nodither'}; + dither_str = dither_str{1+(options.dither==0)}; + if options.ncolors <= 1 + [B, map] = rgb2ind(A, options.ncolors, dither_str); + if size(map, 1) > 256 + [B, map] = rgb2ind(A, 256, dither_str); + end + else + [B, map] = rgb2ind(A, min(round(options.ncolors), 256), dither_str); + end +else + if max(map(:)) > 1 + map = double(map) / 255; + A = double(A) / 255; + end + B = rgb2ind(im2double(A), map); +end +B = reshape(B, h, w, 1, n); + +% Bug fix to rgb2ind +map(B(1)+1,:) = im2double(A(1,1,:)); + +% Save as a gif +imwrite(B, map, options.outfile, 'LoopCount', round(options.loops(1)), 'DelayTime', options.delay); +end + +%% Parse the input arguments +function [A, options] = parse_args(A, varargin) +% Set the defaults +options = struct('outfile', '', ... + 'dither', true, ... + 'crop', true, ... + 'ncolors', 256, ... + 'loops', 65535, ... + 'delay', 1/15); + +% Go through the arguments +a = 0; +n = numel(varargin); +while a < n + a = a + 1; + if ischar(varargin{a}) && ~isempty(varargin{a}) + if varargin{a}(1) == '-' + opt = lower(varargin{a}(2:end)); + switch opt + case 'nocrop' + options.crop = false; + case 'nodither' + options.dither = false; + otherwise + if ~isfield(options, opt) + error('Option %s not recognized', varargin{a}); + end + a = a + 1; + if ischar(varargin{a}) && ~ischar(options.(opt)) + options.(opt) = str2double(varargin{a}); + else + options.(opt) = varargin{a}; + end + end + else + options.outfile = varargin{a}; + end + end +end + +if isempty(options.outfile) + if ~ischar(A) + error('No output filename given.'); + end + % Generate the output filename from the input filename + [path, outfile] = fileparts(A); + options.outfile = fullfile(path, [outfile '.gif']); +end + +if ischar(A) + % Read in the image + A = imread_rgb(A); +end +end + +%% Read image to uint8 rgb array +function [A, alpha] = imread_rgb(name) +% Get file info +info = imfinfo(name); +% Special case formats +switch lower(info(1).Format) + case 'gif' + [A, map] = imread(name, 'frames', 'all'); + if ~isempty(map) + map = uint8(map * 256 - 0.5); % Convert to uint8 for storage + A = reshape(map(uint32(A)+1,:), [size(A) size(map, 2)]); % Assume indexed from 0 + A = permute(A, [1 2 5 4 3]); + end + case {'tif', 'tiff'} + A = cell(numel(info), 1); + for a = 1:numel(A) + [A{a}, map] = imread(name, 'Index', a, 'Info', info); + if ~isempty(map) + map = uint8(map * 256 - 0.5); % Convert to uint8 for storage + A{a} = reshape(map(uint32(A{a})+1,:), [size(A) size(map, 2)]); % Assume indexed from 0 + end + if size(A{a}, 3) == 4 + % TIFF in CMYK colourspace - convert to RGB + if isfloat(A{a}) + A{a} = A{a} * 255; + else + A{a} = single(A{a}); + end + A{a} = 255 - A{a}; + A{a}(:,:,4) = A{a}(:,:,4) / 255; + A{a} = uint8(A(:,:,1:3) .* A{a}(:,:,[4 4 4])); + end + end + A = cat(4, A{:}); + otherwise + [A, map, alpha] = imread(name); + A = A(:,:,:,1); % Keep only first frame of multi-frame files + if ~isempty(map) + map = uint8(map * 256 - 0.5); % Convert to uint8 for storage + A = reshape(map(uint32(A)+1,:), [size(A) size(map, 2)]); % Assume indexed from 0 + elseif size(A, 3) == 4 + % Assume 4th channel is an alpha matte + alpha = A(:,:,4); + A = A(:,:,1:3); + end +end +end Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/isolate_axes.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/isolate_axes.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/isolate_axes.m (revision 21239) @@ -0,0 +1,119 @@ +%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 2011-2013 + +% 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. +% 08/10/13 - Bug fix to allchildren suggested by Will Grant (many thanks!). +% 05/12/13 - Bug fix to axes having different units. Thanks to Remington +% Reid for reporting the issue. + +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 + set([ah(:); lh(:)], 'Units', 'normalized'); + 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); + ax_pos = shiftdim(ax_pos, -1); + % Overlap test + M = bsxfun(@lt, leg_pos(:,1), ax_pos(:,:,3)) & ... + bsxfun(@lt, leg_pos(:,2), ax_pos(:,:,4)) & ... + bsxfun(@gt, leg_pos(:,3), ax_pos(:,:,1)) & ... + bsxfun(@gt, leg_pos(:,4), ax_pos(:,:,2)); + ah = [ah; lh(any(M, 2))]; +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)]))); +end + +function ah = allchildren(ah) +ah = findall(ah); +if iscell(ah) + ah = cell2mat(ah); +end +ah = ah(:); +end + +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 +end Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/license.txt =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/license.txt (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/license.txt (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/export_fig/pdf2eps.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/pdf2eps.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/pdf2eps.m (revision 21239) @@ -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); +end + Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/pdftops.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/pdftops.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/pdftops.m (revision 21239) @@ -0,0 +1,109 @@ +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. +% 23/01/2014 - Add full path to pdftops.txt in warning. + +% Call pdftops +[varargout{1:nargout}] = system(sprintf('"%s" %s', xpdf_path, cmd)); +end + +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.'); +end + +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 %s.', fullfile(fileparts(which('user_string.m')), '.ignore', 'pdftops.txt')); + return +end +end + +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')); +end Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/print2array.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/print2array.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/print2array.m (revision 21239) @@ -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, 0, 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 +end + +% 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); +end Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/print2eps.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/print2eps.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/print2eps.m (revision 21239) @@ -0,0 +1,213 @@ +%PRINT2EPS Prints figures to eps with improved line styles +% +% Examples: +% print2eps filename +% print2eps(filename, fig_handle) +% print2eps(filename, fig_handle, bb_padding) +% print2eps(filename, fig_handle, bb_padding, 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(). +% bb_padding - Scalar value of amount of padding to add to border around +% the figure, in points. Can be negative as well as +% positive. Default: 0. +% options - Additional parameter strings to be passed to print. + +% Copyright (C) Oliver Woodford 2008-2014 + +% 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. +% 23/07/13: Bug fix to font swapping. Thanks to George for reporting the +% issue. +% 13/08/13: Fix MATLAB feature of not exporting white lines correctly. +% Thanks to Sebastian Heßlinger for reporting it. + +function print2eps(name, fig, bb_padding, varargin) +options = {'-depsc2'}; +if nargin > 3 + options = [options varargin]; +elseif nargin < 3 + bb_padding = 0; + if nargin < 2 + fig = gcf(); + end +end +% Construct the filename +if numel(name) < 5 || ~strcmpi(name(end-3:end), '.eps') + name = [name '.eps']; % Add the missing extension +end +% Set paper size +old_pos_mode = get(fig, 'PaperPositionMode'); +old_orientation = get(fig, 'PaperOrientation'); +set(fig, 'PaperPositionMode', 'auto', 'PaperOrientation', 'portrait'); +% 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,a}(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 +% 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); +% MATLAB bug fix - white lines can come out funny sometimes +% Find the white lines +white_line_handles = findobj(fig, 'Type', 'line'); +M = get(white_line_handles, 'Color'); +if iscell(M) + M = cell2mat(M); +end +white_line_handles = white_line_handles(sum(M, 2) == 3); +% Set the line color slightly off white +set(white_line_handles, 'Color', [1 1 1] - 0.00001); +% Print to eps file +print(fig, options{:}, name); +% Reset the font and line colors +set(black_text_handles, 'Color', [0 0 0]); +set(white_text_handles, 'Color', [1 1 1]); +set(white_line_handles, 'Color', [1 1 1]); +% Reset paper size +set(fig, 'PaperPositionMode', old_pos_mode, 'PaperOrientation', old_orientation); +% Reset the font names in the figure +if ~isempty(font_swap) + for a = update + set(font_handles(a), 'FontName', fonts{a}, 'FontSize', fonts_size(a)); + end +end +% Do post-processing on the eps file +try + fstrm = read_write_entire_textfile(name); +catch + warning('Loading EPS file failed, so unable to perform post-processing. This is usually because the figure contains a large number of patch objects. Consider exporting to a bitmap format in this case.'); + return +end +% Replace the font names +if ~isempty(font_swap) + for a = 1:size(font_swap, 2) + %fstrm = regexprep(fstrm, [font_swap{1,a} '-?[a-zA-Z]*\>'], font_swap{3,a}(~isspace(font_swap{3,a}))); + fstrm = regexprep(fstrm, font_swap{2,a}, font_swap{3,a}(~isspace(font_swap{3,a}))); + end +end +if using_hg2(fig) + % Convert miter joins to line joins + fstrm = regexprep(fstrm, '10.0 ML\n', '1 LJ\n'); + % Move the bounding box to the top of the file + [s, e] = regexp(fstrm, '%%BoundingBox: [\w\s()]*%%'); + if numel(s) == 2 + fstrm = fstrm([1:s(1)-1 s(2):e(2)-2 e(1)-1:s(2)-1 e(2)-1:end]); + end +else + % Fix the line styles + fstrm = fix_lines(fstrm); +end +% Apply the bounding box padding +if bb_padding + add_padding = @(n1, n2, n3, n4) sprintf(' %d', str2double({n1, n2, n3, n4}) + [-bb_padding -bb_padding bb_padding bb_padding]); + fstrm = regexprep(fstrm, '%%BoundingBox:[ ]+([-]?\d+)[ ]+([-]?\d+)[ ]+([-]?\d+)[ ]+([-]?\d+)', '%%BoundingBox:${add_padding($1, $2, $3, $4)}'); +end +% Write out the fixed eps file +read_write_entire_textfile(name, fstrm); +end Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/read_write_entire_textfile.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/read_write_entire_textfile.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/read_write_entire_textfile.m (revision 21239) @@ -0,0 +1,37 @@ +%READ_WRITE_ENTIRE_TEXTFILE Read or write a whole text file to/from memory +% +% Read or write an entire text file to/from memory, without leaving the +% file open if an error occurs. +% +% Reading: +% fstrm = read_write_entire_textfile(fname) +% Writing: +% read_write_entire_textfile(fname, fstrm) +% +%IN: +% fname - Pathname of text file to be read in. +% fstrm - String to be written to the file, including carriage returns. +% +%OUT: +% fstrm - String read from the file. If an fstrm input is given the +% output is the same as that input. + +function fstrm = read_write_entire_textfile(fname, fstrm) +modes = {'rt', 'wt'}; +writing = nargin > 1; +fh = fopen(fname, modes{1+writing}); +if fh == -1 + error('Unable to open file %s.', fname); +end +try + if writing + fwrite(fh, fstrm, 'char*1'); + else + fstrm = fread(fh, '*char')'; + end +catch ex + fclose(fh); + rethrow(ex); +end +fclose(fh); +end Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/user_string.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/user_string.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/user_string.m (revision 21239) @@ -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 +end Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/using_hg2.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/using_hg2.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/export_fig/using_hg2.m (revision 21239) @@ -0,0 +1,18 @@ +%USING_HG2 Determine if the HG2 graphics pipeline is used +% +% tf = using_hg2(fig) +% +%IN: +% fig - handle to the figure in question. +% +%OUT: +% tf - boolean indicating whether the HG2 graphics pipeline is being used +% (true) or not (false). + +function tf = using_hg2(fig) +try + tf = ~graphicsversion(fig, 'handlegraphics'); +catch + tf = false; +end +end Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/ffmpeg/install-macosx64.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/ffmpeg/install-macosx64.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/ffmpeg/install-macosx64.sh (revision 21239) @@ -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 $1 +fi +make install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/findbugs/README =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/findbugs/README (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/findbugs/README (revision 21239) @@ -0,0 +1,2 @@ +Fingbugs for Java programs. +Downloaded from http://findbugs.sourceforge.net/downloads.html Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/findbugs/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/findbugs/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/findbugs/install.sh (revision 21239) @@ -0,0 +1,13 @@ +#!/bin/bash +set -eu + +#Erase install +rm -rf install findbugs-1.3.9 +mkdir install + +#Download from ISSM server +$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-larour-NatClimateChange2016/externalpackages/flaim/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/flaim/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/flaim/install.sh (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/freetype/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/freetype/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/freetype/install.sh (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/fti/Makefile =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/fti/Makefile (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/fti/Makefile (revision 21239) @@ -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) $(STATIC) doc install uninstall clean Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/fti/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/fti/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/fti/install.sh (revision 21239) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install fti-0.9.2 +mkdir install + +#Download from ISSM server +$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-larour-NatClimateChange2016/externalpackages/gdal/configs/GDALmake.opt.patch.murdo =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gdal/configs/GDALmake.opt.patch.murdo (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gdal/configs/GDALmake.opt.patch.murdo (revision 21239) @@ -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) $(CURL_LIB) \ +225c225 +< CURL_LIB = -L/usr/kerberos/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz +--- +> CURL_LIB = -L/usr/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gdal/install-1.10-linux64.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gdal/install-1.10-linux64.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gdal/install-1.10-linux64.sh (revision 21239) @@ -0,0 +1,45 @@ +#!/bin/bash +set -eu + +#WARNING: you need to have python installed in externalpackages + +#Some cleanup +rm -rf src +rm -rf install +rm -rf gdal-1.10.0 +mkdir src install + +#Download from ISSM server +$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 + +export CFLAGS=-D_HAVE_STRNDUP +export CXXFLAGS=-D_HAVE_STRNDUP + +#Configure gdal +cd src +./configure \ + --prefix="$ISSM_DIR/externalpackages/gdal/install" \ + --with-python="$ISSM_DIR/externalpackages/python/install/bin/python" \ + --with-netcdf=no \ + --with-jasper=no \ + --without-hdf5 + +#Compile and install gdal +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install + +#For some reasons, on thwaites, one needs to do the following to get the python bindings: +#cd src/swig/python/ +# python setup.py build +# python setup.py install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gdal/install-1.10-macosx64.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gdal/install-1.10-macosx64.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gdal/install-1.10-macosx64.sh (revision 21239) @@ -0,0 +1,38 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf gdal-1.10.0 +mkdir src install + +#Download from ISSM server +$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 $1 +fi +make install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gdal/install-1.6-linux64-murdo.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gdal/install-1.6-linux64-murdo.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gdal/install-1.6-linux64-murdo.sh (revision 21239) @@ -0,0 +1,39 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf gdal-1.6.0 +mkdir src install + +#Download from ISSM server +$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 $1 +fi +make install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gdal/install-1.6-macosx64.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gdal/install-1.6-macosx64.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gdal/install-1.6-macosx64.sh (revision 21239) @@ -0,0 +1,39 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf install +rm -rf gdal-1.6.0 +mkdir src install + +#Download from ISSM server +$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 $1 +fi +make install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/geocode/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/geocode/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/geocode/install.sh (revision 21239) @@ -0,0 +1,2 @@ +#/bin/bash +unzip geoCode.zip Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/geos5/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/geos5/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/geos5/install.sh (revision 21239) @@ -0,0 +1,7 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf GEOSagcm +#svn download +svn --username eric.larour@jpl.nasa.gov checkout http://geos5.org/svn/branches/Fortuna-2_5_p1 GEOSagcm Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/git/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/git/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/git/install.sh (revision 21239) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install git-1.7.10.2 +mkdir install src + +#Download from ISSM server +$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-larour-NatClimateChange2016/externalpackages/gmake/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gmake/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gmake/install.sh (revision 21239) @@ -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 $1 install; +fi Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gmp/install-linux64.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gmp/install-linux64.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gmp/install-linux64.sh (revision 21239) @@ -0,0 +1,29 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install gmp-5.0.5 +mkdir install src + +#Download from ISSM server +$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 $1 +fi +make install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gmsh/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gmsh/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gmsh/install.sh (revision 21239) @@ -0,0 +1,21 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install src +mkdir install + +#Download latest version +svn co --username gmsh --password gmsh https://geuz.org/svn/gmsh/trunk src + +#Configure +cd install +cmake ../src -DCMAKE_INSTALL_PREFIX="$ISSM_DIR/externalpackages/gmsh/install" + +#Compile and install +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gmt/configs/ConfigUser.cmake =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gmt/configs/ConfigUser.cmake (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gmt/configs/ConfigUser.cmake (revision 21239) @@ -0,0 +1,240 @@ +# +# $Id: ConfigUserTemplate.cmake 12904 2014-02-17 20:52:35Z fwobbe $ +# +# Copyright (c) 1991-2014 by P. Wessel, W. H. F. Smith, R. Scharroo, J. Luis and F. Wobbe +# See LICENSE.TXT file for copying and redistribution conditions. +# +# This program is free software; you can redistribute it and/or modify it +# under the terms of the GNU Lesser General Public License as published by the +# Free Software Foundation; version 3 or 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 Lesser General Public License +# for more details. +# +# Contact info: gmt.soest.hawaii.edu +# ---------------------------------------------------------------------------- + +# Use this file to override variables in 'ConfigDefault.cmake' on a per-user +# basis. First copy 'ConfigUserTemplate.cmake' to 'ConfigUser.cmake', then +# edit 'ConfigUser.cmake'. 'ConfigUser.cmake' is not version controlled +# (currently listed in svn:ignore property) +# +# Note: CMake considers an empty string, "FALSE", "OFF", "NO", or any string +# ending in "-NOTFOUND" to be false (this happens to be case-insensitive, so +# "False", "off", "no", and "something-NotFound" are all false). Other values +# are true. Thus it does not matter whether you use TRUE and FALSE, ON and +# OFF, or YES and NO for your booleans. + +## +## Section 1: Installation paths +## + +# ============================================================================ +# Basic setup begins here. All settings are optional. In most cases, setting +# CMAKE_INSTALL_PREFIX should be all you need to do in order to build GMT with +# reasonable defaults enabled. +# ============================================================================ + +# Installation path (usually defaults to /usr/local) [auto]: +set (CMAKE_INSTALL_PREFIX "$ENV{ISSM_DIR}/externalpackages/gmt/install") + +# Set install name suffix used for directories and gmt executables +# [undefined]: +#set (GMT_INSTALL_NAME_SUFFIX "suffix") + +# Install into traditional directory structure. Disable to install a +# distribution type directory structure (doc and share separated) [on]: +#set (GMT_INSTALL_TRADITIONAL_FOLDERNAMES OFF) + +# Install convenience links for GMT modules. Disable to install only the main +# gmt program and access modules as "gmt modulename options" [TRUE]: +#set (GMT_INSTALL_MODULE_LINKS FALSE) + +# Make executables relocatable on supported platforms (relative RPATH) [TRUE]: +#set (GMT_INSTALL_RELOCATABLE FALSE) + +# ============================================================================ +# Advanced configuration begins here. Usually it is not necessary to edit any +# settings below. You should know what you are doing if you do though. Note: +# installation paths are relative to ${CMAKE_INSTALL_PREFIX} unless absolute +# path is given. +# ============================================================================ + +# Set binary installation path [bin]: +#set (GMT_BINDIR "bin") + +# Set library installation path [lib or lib64]: +#set (GMT_LIBDIR "lib") + +# Set include installation path [include/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_INCLUDEDIR "include/gmt") + +# Set share installation path [share or share/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_DATADIR "share/gmt") + +# Set doc installation path [share/doc or +# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_DOCDIR "share/doc/gmt") + +# Set manpage installation path [share/man or +# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}/man]: +#set (GMT_MANDIR "share/doc/gmt/man") + +# Install documentation files from this external location instead of creating +# new PDF and HTML documents from scratch [${GMT_SOURCE_DIR}/doc_release]: +#set (GMT_INSTALL_EXTERNAL_DOC OFF) + +# Install manual pages from this external location instead of creating the +# manpages from scratch [${GMT_SOURCE_DIR}/man_release]: +#set (GMT_INSTALL_EXTERNAL_MAN OFF) + +## +## Section 2: Build dependencies (should only be needed if CMake cannot +## automatically detect the rights version or path.) +## + +# Set path to GSHHG Shoreline Database [auto]: +set (GSHHG_ROOT "$ENV{ISSM_DIR}/externalpackages/gshhg/install") + +# Copy GSHHG files to $/coast [FALSE]: +#set (COPY_GSHHG TRUE) + +# Set path to DCW Digital Chart of the World for GMT [auto]: +#set (DCW_ROOT "dcw-gmt_path") + +# Copy DCW files to $/dcw [FALSE]: +#set (COPY_DCW TRUE) + +# Set location of NetCDF (can be root directory, path to header file or path +# to nc-config) [auto]: +set (NETCDF_ROOT "$ENV{ISSM_DIR}/externalpackages/netcdf/install") + +# Set location of GDAL (can be root directory, path to header file or path to +# gdal-config) [auto]: +set (GDAL_ROOT "$ENV{ISSM_DIR}/externalpackages/gdal/install") + +# Set location of PCRE (can be root directory, path to header file or path to +# pcre-config) [auto]: +#set (PCRE_ROOT "pcre_install_prefix") + +# Set location of single precision FFTW (can be root directory or path to +# header file) [auto]: +#set (FFTW3_ROOT "fftw_install_prefix") + +# Set location of ZLIB (can be root directory or path to header file) [auto]: +#set (ZLIB_ROOT "zlib_install_prefix") + +## +## Section 3: GMT features +## + +# Enforce GPL or LGPL conformity. Use this to disable routines that cannot be +# redistributed under the terms of the GPL or LGPL such as Shewchuk's +# triangulation (valid values are GPL, LGPL and off) [off]: +#set (LICENSE_RESTRICTED GPL) + +# Configure default units (possible values are SI and US) [SI]: +#set (UNITS "US") + +# Enable building of shared libraries [TRUE] (disable to use static libraries; +# not recommended): +#set (BUILD_SHARED_LIBS FALSE) + +# Build GMT shared lib with supplemental modules [TRUE]: +#set (BUILD_SUPPLEMENTS FALSE) + +## +## Section 4: Advanced tweaking +## + +# +# Testing and development +# + +# Enable running examples/tests with "ctest" or "make check" (out-of-source). +# Need to set either DO_EXAMPLES, DO_TESTS or both and uncomment the following +# line. +#enable_testing() +#set (DO_EXAMPLES TRUE) +#set (DO_TESTS TRUE) +# Number of parallel test jobs with "make check": +#set (N_TEST_JOBS 4) + +# Enable this option to run GMT programs from within ${GMT_BINARY_DIR} without +# installing or setting GMT_SHAREDIR and GMT_USERDIR first. This is required +# for testing [OFF]: +#set (SUPPORT_EXEC_IN_BINARY_DIR ON) + +# List extra sub-dirs of 'src' with a CMakeList.txt to build non-module codes +# that link against the full gmt libs (not just the API; for building codes +# that only need the GMT API, see the gmtextension project). +#set (EXTRA_BUILD_DIRS apidemo) + +# Directory in which to install the release sources per default +# [${GMT_BINARY_DIR}/gmt-${GMT_PACKAGE_VERSION}]: +#set (GMT_RELEASE_PREFIX "release-src-prefix") + +# If set to false, image conversion from PS images to PNG and PDF does +# not depend on the gmt binary target. Note: "make gmt" is then required +# before docs_depends [TRUE]. +#set (GMT_DOCS_DEPEND_ON_GMT FALSE) + +# +# Debugging +# + +# Set build type can be: empty, Debug, Release, RelWithDebInfo or MinSizeRel +# [Release]: +#set (CMAKE_BUILD_TYPE Debug) + +# Extra debugging for developers: +#add_definitions(-DDEBUG) +#add_definitions(-DMEMDEBUG) # Turn on memory tracking see gmt_support.c for extra info +#set (CMAKE_C_FLAGS "-Wall -Wdeclaration-after-statement") # recommended even for release build +#set (CMAKE_C_FLAGS "-Wextra ${CMAKE_C_FLAGS}") # extra warnings +#set (CMAKE_C_FLAGS_DEBUG -ggdb3) # gdb debugging symbols +#set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized") # check uninitialized variables +#set (CMAKE_LINK_DEPENDS_DEBUG_MODE TRUE) # debug link dependencies + +# +# System specific tweaks +# + +# This is for GCC on Solaris to avoid "relocations remain against allocatable +# but non-writable sections" problems: +#set (USER_GMTLIB_LINK_FLAGS -mimpure-text) + +# This may be needed to enable strdup and extended math functions with GCC and +# Suncc on Solaris: +#set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D__EXTENSIONS__") + +# Do not warn when building with Windows SDK or Visual Studio Express: +#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS ON) + +# Manually select runtime library when compiling with Windows SDK or Visual +# Studio Express: +#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS c:/Windows/System32/msvcr100.dll) + +# If your NetCDF library is static (not recommended, applies to Windows only) +#set (NETCDF_STATIC TRUE) + +# If want to rename the DLLs to something else than the default (e.g. to +# append the bitness - Windows only) +#if (WIN32) +# set (BITAGE 32) +# # Detect if we are building a 32 or 64 bits version +# if (CMAKE_SIZEOF_VOID_P EQUAL 8) +# set (BITAGE 64) +# endif () +# set (GMT_DLL_RENAME gmt_w${BITAGE}) +# set (PSL_DLL_RENAME psl_w${BITAGE}) +#endif(WIN32) + +# On Windows Visual C 2012 needs _ALLOW_KEYWORD_MACROS to build +#if(MSVC11) +# add_definitions(/D_ALLOW_KEYWORD_MACROS) +#endif(MSVC11) + +# vim: textwidth=78 noexpandtab tabstop=2 softtabstop=2 shiftwidth=2 Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gmt/configs/ConfigUser.cmake-jenkins =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gmt/configs/ConfigUser.cmake-jenkins (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gmt/configs/ConfigUser.cmake-jenkins (revision 21239) @@ -0,0 +1,240 @@ +# +# $Id: ConfigUserTemplate.cmake 12904 2014-02-17 20:52:35Z fwobbe $ +# +# Copyright (c) 1991-2014 by P. Wessel, W. H. F. Smith, R. Scharroo, J. Luis and F. Wobbe +# See LICENSE.TXT file for copying and redistribution conditions. +# +# This program is free software; you can redistribute it and/or modify it +# under the terms of the GNU Lesser General Public License as published by the +# Free Software Foundation; version 3 or 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 Lesser General Public License +# for more details. +# +# Contact info: gmt.soest.hawaii.edu +# ---------------------------------------------------------------------------- + +# Use this file to override variables in 'ConfigDefault.cmake' on a per-user +# basis. First copy 'ConfigUserTemplate.cmake' to 'ConfigUser.cmake', then +# edit 'ConfigUser.cmake'. 'ConfigUser.cmake' is not version controlled +# (currently listed in svn:ignore property) +# +# Note: CMake considers an empty string, "FALSE", "OFF", "NO", or any string +# ending in "-NOTFOUND" to be false (this happens to be case-insensitive, so +# "False", "off", "no", and "something-NotFound" are all false). Other values +# are true. Thus it does not matter whether you use TRUE and FALSE, ON and +# OFF, or YES and NO for your booleans. + +## +## Section 1: Installation paths +## + +# ============================================================================ +# Basic setup begins here. All settings are optional. In most cases, setting +# CMAKE_INSTALL_PREFIX should be all you need to do in order to build GMT with +# reasonable defaults enabled. +# ============================================================================ + +# Installation path (usually defaults to /usr/local) [auto]: +set (CMAKE_INSTALL_PREFIX "$ENV{ISSM_DIR}/externalpackages/gmt/install") + +# Set install name suffix used for directories and gmt executables +# [undefined]: +#set (GMT_INSTALL_NAME_SUFFIX "suffix") + +# Install into traditional directory structure. Disable to install a +# distribution type directory structure (doc and share separated) [on]: +#set (GMT_INSTALL_TRADITIONAL_FOLDERNAMES OFF) + +# Install convenience links for GMT modules. Disable to install only the main +# gmt program and access modules as "gmt modulename options" [TRUE]: +#set (GMT_INSTALL_MODULE_LINKS FALSE) + +# Make executables relocatable on supported platforms (relative RPATH) [TRUE]: +#set (GMT_INSTALL_RELOCATABLE FALSE) + +# ============================================================================ +# Advanced configuration begins here. Usually it is not necessary to edit any +# settings below. You should know what you are doing if you do though. Note: +# installation paths are relative to ${CMAKE_INSTALL_PREFIX} unless absolute +# path is given. +# ============================================================================ + +# Set binary installation path [bin]: +#set (GMT_BINDIR "bin") + +# Set library installation path [lib or lib64]: +#set (GMT_LIBDIR "lib") + +# Set include installation path [include/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_INCLUDEDIR "include/gmt") + +# Set share installation path [share or share/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_DATADIR "share/gmt") + +# Set doc installation path [share/doc or +# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_DOCDIR "share/doc/gmt") + +# Set manpage installation path [share/man or +# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}/man]: +#set (GMT_MANDIR "share/doc/gmt/man") + +# Install documentation files from this external location instead of creating +# new PDF and HTML documents from scratch [${GMT_SOURCE_DIR}/doc_release]: +#set (GMT_INSTALL_EXTERNAL_DOC OFF) + +# Install manual pages from this external location instead of creating the +# manpages from scratch [${GMT_SOURCE_DIR}/man_release]: +#set (GMT_INSTALL_EXTERNAL_MAN OFF) + +## +## Section 2: Build dependencies (should only be needed if CMake cannot +## automatically detect the rights version or path.) +## + +# Set path to GSHHG Shoreline Database [auto]: +set (GSHHG_ROOT "$ENV{ISSM_DIR}/externalpackages/gshhg/install") + +# Copy GSHHG files to $/coast [FALSE]: +#set (COPY_GSHHG TRUE) + +# Set path to DCW Digital Chart of the World for GMT [auto]: +#set (DCW_ROOT "dcw-gmt_path") + +# Copy DCW files to $/dcw [FALSE]: +#set (COPY_DCW TRUE) + +# Set location of NetCDF (can be root directory, path to header file or path +# to nc-config) [auto]: +set (NETCDF_ROOT "/") + +# Set location of GDAL (can be root directory, path to header file or path to +# gdal-config) [auto]: +set (GDAL_ROOT "$ENV{ISSM_DIR}/externalpackages/gdal/install") + +# Set location of PCRE (can be root directory, path to header file or path to +# pcre-config) [auto]: +#set (PCRE_ROOT "pcre_install_prefix") + +# Set location of single precision FFTW (can be root directory or path to +# header file) [auto]: +#set (FFTW3_ROOT "fftw_install_prefix") + +# Set location of ZLIB (can be root directory or path to header file) [auto]: +#set (ZLIB_ROOT "zlib_install_prefix") + +## +## Section 3: GMT features +## + +# Enforce GPL or LGPL conformity. Use this to disable routines that cannot be +# redistributed under the terms of the GPL or LGPL such as Shewchuk's +# triangulation (valid values are GPL, LGPL and off) [off]: +#set (LICENSE_RESTRICTED GPL) + +# Configure default units (possible values are SI and US) [SI]: +#set (UNITS "US") + +# Enable building of shared libraries [TRUE] (disable to use static libraries; +# not recommended): +#set (BUILD_SHARED_LIBS FALSE) + +# Build GMT shared lib with supplemental modules [TRUE]: +#set (BUILD_SUPPLEMENTS FALSE) + +## +## Section 4: Advanced tweaking +## + +# +# Testing and development +# + +# Enable running examples/tests with "ctest" or "make check" (out-of-source). +# Need to set either DO_EXAMPLES, DO_TESTS or both and uncomment the following +# line. +#enable_testing() +#set (DO_EXAMPLES TRUE) +#set (DO_TESTS TRUE) +# Number of parallel test jobs with "make check": +#set (N_TEST_JOBS 4) + +# Enable this option to run GMT programs from within ${GMT_BINARY_DIR} without +# installing or setting GMT_SHAREDIR and GMT_USERDIR first. This is required +# for testing [OFF]: +#set (SUPPORT_EXEC_IN_BINARY_DIR ON) + +# List extra sub-dirs of 'src' with a CMakeList.txt to build non-module codes +# that link against the full gmt libs (not just the API; for building codes +# that only need the GMT API, see the gmtextension project). +#set (EXTRA_BUILD_DIRS apidemo) + +# Directory in which to install the release sources per default +# [${GMT_BINARY_DIR}/gmt-${GMT_PACKAGE_VERSION}]: +#set (GMT_RELEASE_PREFIX "release-src-prefix") + +# If set to false, image conversion from PS images to PNG and PDF does +# not depend on the gmt binary target. Note: "make gmt" is then required +# before docs_depends [TRUE]. +#set (GMT_DOCS_DEPEND_ON_GMT FALSE) + +# +# Debugging +# + +# Set build type can be: empty, Debug, Release, RelWithDebInfo or MinSizeRel +# [Release]: +#set (CMAKE_BUILD_TYPE Debug) + +# Extra debugging for developers: +#add_definitions(-DDEBUG) +#add_definitions(-DMEMDEBUG) # Turn on memory tracking see gmt_support.c for extra info +#set (CMAKE_C_FLAGS "-Wall -Wdeclaration-after-statement") # recommended even for release build +#set (CMAKE_C_FLAGS "-Wextra ${CMAKE_C_FLAGS}") # extra warnings +#set (CMAKE_C_FLAGS_DEBUG -ggdb3) # gdb debugging symbols +#set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized") # check uninitialized variables +#set (CMAKE_LINK_DEPENDS_DEBUG_MODE TRUE) # debug link dependencies + +# +# System specific tweaks +# + +# This is for GCC on Solaris to avoid "relocations remain against allocatable +# but non-writable sections" problems: +#set (USER_GMTLIB_LINK_FLAGS -mimpure-text) + +# This may be needed to enable strdup and extended math functions with GCC and +# Suncc on Solaris: +#set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D__EXTENSIONS__") + +# Do not warn when building with Windows SDK or Visual Studio Express: +#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS ON) + +# Manually select runtime library when compiling with Windows SDK or Visual +# Studio Express: +#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS c:/Windows/System32/msvcr100.dll) + +# If your NetCDF library is static (not recommended, applies to Windows only) +#set (NETCDF_STATIC TRUE) + +# If want to rename the DLLs to something else than the default (e.g. to +# append the bitness - Windows only) +#if (WIN32) +# set (BITAGE 32) +# # Detect if we are building a 32 or 64 bits version +# if (CMAKE_SIZEOF_VOID_P EQUAL 8) +# set (BITAGE 64) +# endif () +# set (GMT_DLL_RENAME gmt_w${BITAGE}) +# set (PSL_DLL_RENAME psl_w${BITAGE}) +#endif(WIN32) + +# On Windows Visual C 2012 needs _ALLOW_KEYWORD_MACROS to build +#if(MSVC11) +# add_definitions(/D_ALLOW_KEYWORD_MACROS) +#endif(MSVC11) + +# vim: textwidth=78 noexpandtab tabstop=2 softtabstop=2 shiftwidth=2 Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gmt/install-jenkins.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gmt/install-jenkins.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gmt/install-jenkins.sh (revision 21239) @@ -0,0 +1,32 @@ +#!/bin/bash +set -eu + +#Erase install +rm -rf install src gmt + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gmt-5.1.1.tar.gz' 'gmt-5.1.1.tar.gz' + +#install directory +mkdir src +tar -zxvf gmt-5.1.1.tar.gz +mv gmt-5.1.1/* src +rm -rf gmt-5.1.1 + +#configure: +cp configs/ConfigUser.cmake-jenkins ./src/cmake/ConfigUser.cmake + +cd src +mkdir build +cd build +cmake ../ + +#compile +if [ $# -eq 0 ]; then + make install +else + make -j $1 install +fi + +#come back: +cd ../../ Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gmt/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gmt/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gmt/install.sh (revision 21239) @@ -0,0 +1,32 @@ +#!/bin/bash +set -eu + +#Erase install +rm -rf install src gmt + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gmt-5.1.1.tar.gz' 'gmt-5.1.1.tar.gz' + +#install directory +mkdir src +tar -zxvf gmt-5.1.1.tar.gz +mv gmt-5.1.1/* src +rm -rf gmt-5.1.1 + +#configure: +cp configs/ConfigUser.cmake ./src/cmake + +cd src +mkdir build +cd build +cmake ../ + +#compile +if [ $# -eq 0 ]; then + make install +else + make -j $1 install +fi + +#come back: +cd ../../ Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/googleearthtoolbox/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/googleearthtoolbox/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/googleearthtoolbox/install.sh (revision 21239) @@ -0,0 +1,8 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install + +#Download code: +svn checkout http://googleearthtoolbox.googlecode.com/svn/trunk/ install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gshhg/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gshhg/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gshhg/install.sh (revision 21239) @@ -0,0 +1,16 @@ +#!/bin/bash +set -eu + +rm -rf gssh-gmt-2.3.4.tar.gz src install + +#get gssh database from noaa's website: http://www.ngdc.noaa.gov/mgg/shorelines/gshhs.html +#curl http://www.ngdc.noaa.gov/mgg/shorelines/data/gshhg/latest/gshhg-gmt-2.3.4.tar.gz > gshhg-gmt-2.3.4.tar.gz + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gshhg-gmt-2.3.4.tar.gz' 'gshhg-gmt-2.3.4.tar.gz' + +#untar: +tar -zxvf gshhg-gmt-2.3.4.tar.gz + +#move: +mv gshhg-gmt-2.3.4 install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/Makefile.am.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/Makefile.am.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/Makefile.am.patch (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/gsl/README =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/README (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/README (revision 21239) @@ -0,0 +1,1 @@ +GNU Scientfic Library, obtained from: http://www.gnu.org/software/gsl/ Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/finite.patch =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/finite.patch (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/finite.patch (revision 21239) @@ -0,0 +1,354 @@ +diff -ruN src/gsl_math.h src-mod/gsl_math.h +--- src/gsl_math.h 2010-12-26 09:57:08.000000000 -0800 ++++ src-mod/gsl_math.h 2014-05-27 18:47:26.000000000 -0700 +@@ -116,7 +116,7 @@ + #define GSL_SIGN(x) ((x) >= 0.0 ? 1 : -1) + + /* Return nonzero if x is a real number, i.e. non NaN or infinite. */ +-#define GSL_IS_REAL(x) (gsl_finite(x)) ++#define GSL_IS_REAL(x) (isfinite(x)) + + /* Definition of an arbitrary function with parameters */ + +diff -ruN src/integration/cquad.c src-mod/integration/cquad.c +--- src/integration/cquad.c 2011-05-01 11:46:28.000000000 -0700 ++++ src-mod/integration/cquad.c 2014-05-27 18:47:26.000000000 -0700 +@@ -235,7 +235,7 @@ + { + iv->fx[i] = GSL_FN_EVAL (f, m + xi[i] * h); + neval++; +- if (!finite (iv->fx[i])) ++ if (!isfinite (iv->fx[i])) + { + nans[nnans++] = i; + iv->fx[i] = 0.0; +@@ -319,7 +319,7 @@ + nnans = 0; + for (i = 0; i <= 32; i += skip[d]) + { +- if (!finite (iv->fx[i])) ++ if (!isfinite (iv->fx[i])) + { + nans[nnans++] = i; + iv->fx[i] = 0.0; +@@ -444,7 +444,7 @@ + nnans = 0; + for (i = 0; i <= 32; i += skip[0]) + { +- if (!finite (ivl->fx[i])) ++ if (!isfinite (ivl->fx[i])) + { + nans[nnans++] = i; + ivl->fx[i] = 0.0; +@@ -510,7 +510,7 @@ + nnans = 0; + for (i = 0; i <= 32; i += skip[0]) + { +- if (!finite (ivr->fx[i])) ++ if (!isfinite (ivr->fx[i])) + { + nans[nnans++] = i; + ivr->fx[i] = 0.0; +diff -ruN src/linalg/balance.c src-mod/linalg/balance.c +--- src/linalg/balance.c 2010-12-26 09:57:08.000000000 -0800 ++++ src-mod/linalg/balance.c 2014-05-27 18:47:27.000000000 -0700 +@@ -54,7 +54,7 @@ + + double f = 1.0; + +- if (s == 0.0 || !gsl_finite(s)) ++ if (s == 0.0 || !isfinite(s)) + { + gsl_vector_set (D, j, f); + continue; +diff -ruN src/min/min.h src-mod/min/min.h +--- src/min/min.h 2010-12-26 09:57:08.000000000 -0800 ++++ src-mod/min/min.h 2014-05-27 18:47:27.000000000 -0700 +@@ -20,6 +20,6 @@ + #define SAFE_FUNC_CALL(f, x, yp) \ + do { \ + *yp = GSL_FN_EVAL(f,x); \ +- if (!gsl_finite(*yp)) \ ++ if (!isfinite(*yp)) \ + GSL_ERROR("computed function value is infinite or NaN", GSL_EBADFUNC); \ + } while (0) +diff -ruN src/multimin/simplex.c src-mod/multimin/simplex.c +--- src/multimin/simplex.c 2010-12-26 09:57:08.000000000 -0800 ++++ src-mod/multimin/simplex.c 2014-05-27 18:47:27.000000000 -0700 +@@ -122,7 +122,7 @@ + we finish the contraction (and do not abort) to allow the user + to handle the situation */ + +- if(!gsl_finite(newval)) ++ if(!isfinite(newval)) + { + status = GSL_EBADFUNC; + } +@@ -260,7 +260,7 @@ + + val = GSL_MULTIMIN_FN_EVAL (f, x); + +- if (!gsl_finite(val)) ++ if (!isfinite(val)) + { + GSL_ERROR("non-finite function value encountered", GSL_EBADFUNC); + } +@@ -283,7 +283,7 @@ + gsl_vector_set (xtemp, i, val); + val = GSL_MULTIMIN_FN_EVAL (f, xtemp); + +- if (!gsl_finite(val)) ++ if (!isfinite(val)) + { + GSL_ERROR("non-finite function value encountered", GSL_EBADFUNC); + } +@@ -374,14 +374,14 @@ + + val = nmsimplex_move_corner (-1.0, state, hi, xc, f); + +- if (gsl_finite(val) && val < gsl_vector_get (y1, lo)) ++ if (isfinite(val) && val < gsl_vector_get (y1, lo)) + { + + /* reflected point becomes lowest point, try expansion */ + + val2 = nmsimplex_move_corner (-2.0, state, hi, xc2, f); + +- if (gsl_finite(val2) && val2 < gsl_vector_get (y1, lo)) ++ if (isfinite(val2) && val2 < gsl_vector_get (y1, lo)) + { + gsl_matrix_set_row (x1, hi, xc2); + gsl_vector_set (y1, hi, val2); +@@ -397,9 +397,9 @@ + or + we got a non-finite (illegal) function value */ + +- else if (!gsl_finite(val) || val > gsl_vector_get (y1, s_hi)) ++ else if (!isfinite(val) || val > gsl_vector_get (y1, s_hi)) + { +- if (gsl_finite(val) && val <= gsl_vector_get (y1, hi)) ++ if (isfinite(val) && val <= gsl_vector_get (y1, hi)) + { + + /* if trial point is better than highest point, replace +@@ -413,7 +413,7 @@ + + val2 = nmsimplex_move_corner (0.5, state, hi, xc2, f); + +- if (gsl_finite(val2) && val2 <= gsl_vector_get (y1, hi)) ++ if (isfinite(val2) && val2 <= gsl_vector_get (y1, hi)) + { + gsl_matrix_set_row (state->x1, hi, xc2); + gsl_vector_set (y1, hi, val2); +diff -ruN src/multimin/simplex2.c src-mod/multimin/simplex2.c +--- src/multimin/simplex2.c 2010-12-26 09:57:08.000000000 -0800 ++++ src-mod/multimin/simplex2.c 2014-05-27 18:47:27.000000000 -0700 +@@ -171,7 +171,7 @@ + we finish the contraction (and do not abort) to allow the user + to handle the situation */ + +- if (!gsl_finite (newval)) ++ if (!isfinite (newval)) + { + status = GSL_EBADFUNC; + } +@@ -367,7 +367,7 @@ + + val = GSL_MULTIMIN_FN_EVAL (f, x); + +- if (!gsl_finite (val)) ++ if (!isfinite (val)) + { + GSL_ERROR ("non-finite function value encountered", GSL_EBADFUNC); + } +@@ -394,7 +394,7 @@ + val = GSL_MULTIMIN_FN_EVAL (f, xtemp); + } + +- if (!gsl_finite (val)) ++ if (!isfinite (val)) + { + GSL_ERROR ("non-finite function value encountered", GSL_EBADFUNC); + } +@@ -477,13 +477,13 @@ + + val = try_corner_move (-1.0, state, hi, xc, f); + +- if (gsl_finite (val) && val < gsl_vector_get (y1, lo)) ++ if (isfinite (val) && val < gsl_vector_get (y1, lo)) + { + /* reflected point is lowest, try expansion */ + + val2 = try_corner_move (-2.0, state, hi, xc2, f); + +- if (gsl_finite (val2) && val2 < gsl_vector_get (y1, lo)) ++ if (isfinite (val2) && val2 < gsl_vector_get (y1, lo)) + { + update_point (state, hi, xc2, val2); + } +@@ -492,12 +492,12 @@ + update_point (state, hi, xc, val); + } + } +- else if (!gsl_finite (val) || val > gsl_vector_get (y1, s_hi)) ++ else if (!isfinite (val) || val > gsl_vector_get (y1, s_hi)) + { + /* reflection does not improve things enough, or we got a + non-finite function value */ + +- if (gsl_finite (val) && val <= gsl_vector_get (y1, hi)) ++ if (isfinite (val) && val <= gsl_vector_get (y1, hi)) + { + /* if trial point is better than highest point, replace + highest point */ +@@ -509,7 +509,7 @@ + + val2 = try_corner_move (0.5, state, hi, xc2, f); + +- if (gsl_finite (val2) && val2 <= gsl_vector_get (y1, hi)) ++ if (isfinite (val2) && val2 <= gsl_vector_get (y1, hi)) + { + update_point (state, hi, xc2, val2); + } +@@ -605,7 +605,7 @@ + + val = GSL_MULTIMIN_FN_EVAL (f, x); + +- if (!gsl_finite (val)) ++ if (!isfinite (val)) + { + GSL_ERROR ("non-finite function value encountered", GSL_EBADFUNC); + } +@@ -669,7 +669,7 @@ + + val = GSL_MULTIMIN_FN_EVAL (f, &r_i.vector); + +- if (!gsl_finite (val)) ++ if (!isfinite (val)) + { + GSL_ERROR ("non-finite function value encountered", GSL_EBADFUNC); + } +diff -ruN src/roots/newton.c src-mod/roots/newton.c +--- src/roots/newton.c 2010-12-26 09:57:08.000000000 -0800 ++++ src-mod/roots/newton.c 2014-05-27 18:47:27.000000000 -0700 +@@ -83,12 +83,12 @@ + state->f = f_new ; + state->df = df_new ; + +- if (!gsl_finite(f_new)) ++ if (!isfinite(f_new)) + { + GSL_ERROR ("function value is not finite", GSL_EBADFUNC); + } + +- if (!gsl_finite (df_new)) ++ if (!isfinite (df_new)) + { + GSL_ERROR ("derivative value is not finite", GSL_EBADFUNC); + } +diff -ruN src/roots/roots.h src-mod/roots/roots.h +--- src/roots/roots.h 2010-12-26 09:57:08.000000000 -0800 ++++ src-mod/roots/roots.h 2014-05-27 18:47:27.000000000 -0700 +@@ -28,7 +28,7 @@ + #define SAFE_FUNC_CALL(f, x, yp) \ + do { \ + *yp = GSL_FN_EVAL(f,x); \ +- if (!gsl_finite(*yp)) \ ++ if (!isfinite(*yp)) \ + GSL_ERROR("function value is not finite", GSL_EBADFUNC); \ + } while (0) + +diff -ruN src/roots/secant.c src-mod/roots/secant.c +--- src/roots/secant.c 2010-12-26 09:57:08.000000000 -0800 ++++ src-mod/roots/secant.c 2014-05-27 18:47:27.000000000 -0700 +@@ -94,12 +94,12 @@ + state->f = f_new ; + state->df = df_new ; + +- if (!gsl_finite (f_new)) ++ if (!isfinite (f_new)) + { + GSL_ERROR ("function value is not finite", GSL_EBADFUNC); + } + +- if (!gsl_finite (df_new)) ++ if (!isfinite (df_new)) + { + GSL_ERROR ("derivative value is not finite", GSL_EBADFUNC); + } +diff -ruN src/roots/steffenson.c src-mod/roots/steffenson.c +--- src/roots/steffenson.c 2010-12-26 09:57:08.000000000 -0800 ++++ src-mod/roots/steffenson.c 2014-05-27 18:47:27.000000000 -0700 +@@ -105,7 +105,7 @@ + state->f = f_new ; + state->df = df_new ; + +- if (!gsl_finite (f_new)) ++ if (!isfinite (f_new)) + { + GSL_ERROR ("function value is not finite", GSL_EBADFUNC); + } +@@ -126,7 +126,7 @@ + *root = x_1 - u * u / v ; /* accelerated value */ + } + +- if (!gsl_finite (df_new)) ++ if (!isfinite (df_new)) + { + GSL_ERROR ("derivative value is not finite", GSL_EBADFUNC); + } +diff -ruN src/specfunc/hyperg_U.c src-mod/specfunc/hyperg_U.c +--- src/specfunc/hyperg_U.c 2010-12-26 09:57:08.000000000 -0800 ++++ src-mod/specfunc/hyperg_U.c 2014-05-27 18:47:28.000000000 -0700 +@@ -524,7 +524,7 @@ + t_err = a0_err + b0_err; + dchu_val += t_val; + dchu_err += t_err; +- if(!finite(t_val) || fabs(t_val) < EPS*fabs(dchu_val)) break; ++ if(!isfinite(t_val) || fabs(t_val) < EPS*fabs(dchu_val)) break; + } + + result->val = dchu_val; +diff -ruN src/sys/ldfrexp.c src-mod/sys/ldfrexp.c +--- src/sys/ldfrexp.c 2010-12-26 09:57:08.000000000 -0800 ++++ src-mod/sys/ldfrexp.c 2014-05-27 18:47:28.000000000 -0700 +@@ -60,7 +60,7 @@ + *e = 0; + return 0.0; + } +- else if (!finite (x)) ++ else if (!isfinite (x)) + { + *e = 0; + return x; +@@ -85,7 +85,7 @@ + + f = x * pow (2.0, -ei); + +- if (!finite (f)) ++ if (!isfinite (f)) + { + /* This should not happen */ + *e = 0; +diff -ruN src/test/results.c src-mod/test/results.c +--- src/test/results.c 2010-12-26 09:57:08.000000000 -0800 ++++ src-mod/test/results.c 2014-05-27 18:47:28.000000000 -0700 +@@ -24,7 +24,10 @@ + #include + #include + #include ++#include ++#define STDC_HEADERS + ++/* + #if HAVE_VPRINTF + #ifdef STDC_HEADERS + #include +@@ -32,6 +35,7 @@ + #include + #endif + #endif ++*/ + + #include + Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/install-android.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/install-android.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/install-android.sh (revision 21239) @@ -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 $j + fi + + make install +fi + Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/install-greenplanet.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/install-greenplanet.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/install-greenplanet.sh (revision 21239) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install gsl-1.15 +mkdir src install + +#Download from ISSM server +$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-larour-NatClimateChange2016/externalpackages/gsl/install-ios.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/install-ios.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/install-ios.sh (revision 21239) @@ -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 $j + fi + + make install +fi + Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/install-javascript.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/install-javascript.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/install-javascript.sh (revision 21239) @@ -0,0 +1,35 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src-javascript install-javascript gsl-1.15 +mkdir src-javascript install-javascript + +#Download from ISSM server +$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-javascript +rm -rf gsl-1.15 + +#Configure gsl +cd src-javascript + +export CC=emcc +export CXX=em++ + +# Issue with variadic function signatures. +export CFLAGS=-DSTDC_HEADERS + +./configure --prefix="$ISSM_DIR/externalpackages/gsl/install-javascript" + +#Compile gsl +if [ $# -eq 0 ]; then + make +else + make -j $1 +fi +make install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/install-linux64.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/install-linux64.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/install-linux64.sh (revision 21239) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install gsl-1.15 +mkdir src install + +#Download from ISSM server +$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 $1 +fi +make install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/install-macosx64.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/install-macosx64.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/install-macosx64.sh (revision 21239) @@ -0,0 +1,32 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install gsl-1.15 +mkdir src install + +#Download from ISSM server +$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 $1 +fi +make install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/install-pleiades.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/install-pleiades.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/install-pleiades.sh (revision 21239) @@ -0,0 +1,30 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install gsl-1.15 +mkdir src install + +#Download from ISSM server +$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 $1 +fi +make install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/install-walgreen.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/install-walgreen.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gsl/install-walgreen.sh (revision 21239) @@ -0,0 +1,31 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install gsl-1.15 +mkdir src install + +#Download from ISSM server +$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 $1 +fi +make install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gslib/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gslib/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/gslib/install.sh (revision 21239) @@ -0,0 +1,24 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install +mkdir install + +#Download from ISSM server +$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=ifort/g" > Makefile.bak +mv Makefile.bak Makefile +cat gslib/Makefile | sed -e "s/FC=g95/FC=ifort/g" > Makefile.bak +mv Makefile.bak gslib/Makefile +make Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/h5py/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/h5py/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/h5py/install.sh (revision 21239) @@ -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=$ISSM_DIR/externalpackages/hdf5/install +python setup.py install Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/hdf5/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/hdf5/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/hdf5/install.sh (revision 21239) @@ -0,0 +1,33 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src install hdf5-1.8.9 +mkdir src install + +#Download from ISSM server +$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 + +# This project uses C code with C++ style comment default C standard used by +# GNU's C compiler's default C standard does not support C++ style comments. +# As such, we need to specify a standard that does. +export CFLAGS='-std=c99' + +#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-larour-NatClimateChange2016/externalpackages/howatmask/enviread.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/howatmask/enviread.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/howatmask/enviread.m (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/howatmask/subsetGimpIceMask.m =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/howatmask/subsetGimpIceMask.m (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/howatmask/subsetGimpIceMask.m (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/inishell/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/inishell/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/inishell/install.sh (revision 21239) @@ -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-larour-NatClimateChange2016/externalpackages/inishell/scripts/inishell =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/inishell/scripts/inishell (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/inishell/scripts/inishell (revision 21239) @@ -0,0 +1,3 @@ +#/bin/bash + +java -jar $ISSM_DIR/externalpackages/inishell/install/inishell.jar Index: /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/ipython/install.sh =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/ipython/install.sh (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/ipython/install.sh (revision 21239) @@ -0,0 +1,22 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf src +rm -rf ipython-1.0.0 +mkdir src + +#Download from ISSM server +$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-larour-NatClimateChange2016/externalpackages/javascript/src/gauge.min.js =================================================================== --- /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/javascript/src/gauge.min.js (revision 21239) +++ /issm/branches/trunk-larour-NatClimateChange2016/externalpackages/javascript/src/gauge.min.js (revision 21239) @@ -0,0 +1,1 @@ +(function(){var a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q={}.hasOwnProperty,r=function(a,b){function c(){this.constructor=a}for(var d in b)q.call(b,d)&&(a[d]=b[d]);return c.prototype=b.prototype,a.prototype=new 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MacKenzie IV + * @version 2.3.2 + */ + +/* Copyright (c) 2015, Brandon Jones, Colin MacKenzie IV. + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. */ + +!function(t,a){if("object"==typeof exports&&"object"==typeof module)module.exports=a();else if("function"==typeof define&&define.amd)define(a);else{var n=a();for(var r in n)("object"==typeof exports?exports:t)[r]=n[r]}}(this,function(){return function(t){function a(r){if(n[r])return n[r].exports;var o=n[r]={exports:{},id:r,loaded:!1};return t[r].call(o.exports,o,o.exports,a),o.loaded=!0,o.exports}var n={};return a.m=t,a.c=n,a.p="",a(0)}([function(t,a,n){a.glMatrix=n(1),a.mat2=n(2),a.mat2d=n(3),a.mat3=n(4),a.mat4=n(5),a.quat=n(6),a.vec2=n(9),a.vec3=n(7),a.vec4=n(8)},function(t,a){var n={};n.EPSILON=1e-6,n.ARRAY_TYPE="undefined"!=typeof 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r=a[0],o=a[1],l=a[2],u=a[3],e=a[4],M=a[5],i=n[0],s=n[1];return t[0]=r*i,t[1]=o*i,t[2]=l*s,t[3]=u*s,t[4]=e,t[5]=M,t},o.translate=function(t,a,n){var r=a[0],o=a[1],l=a[2],u=a[3],e=a[4],M=a[5],i=n[0],s=n[1];return t[0]=r,t[1]=o,t[2]=l,t[3]=u,t[4]=r*i+l*s+e,t[5]=o*i+u*s+M,t},o.fromRotation=function(t,a){var n=Math.sin(a),r=Math.cos(a);return t[0]=r,t[1]=n,t[2]=-n,t[3]=r,t[4]=0,t[5]=0,t},o.fromScaling=function(t,a){return t[0]=a[0],t[1]=0,t[2]=0,t[3]=a[1],t[4]=0,t[5]=0,t},o.fromTranslation=function(t,a){return t[0]=1,t[1]=0,t[2]=0,t[3]=1,t[4]=a[0],t[5]=a[1],t},o.str=function(t){return"mat2d("+t[0]+", "+t[1]+", "+t[2]+", "+t[3]+", "+t[4]+", "+t[5]+")"},o.frob=function(t){return Math.sqrt(Math.pow(t[0],2)+Math.pow(t[1],2)+Math.pow(t[2],2)+Math.pow(t[3],2)+Math.pow(t[4],2)+Math.pow(t[5],2)+1)},t.exports=o},function(t,a,n){var r=n(1),o={};o.create=function(){var t=new r.ARRAY_TYPE(9);return t[0]=1,t[1]=0,t[2]=0,t[3]=0,t[4]=1,t[5]=0,t[6]=0,t[7]=0,t[8]=1,t},o.fromMat4=function(t,a){return t[0]=a[0],t[1]=a[1],t[2]=a[2],t[3]=a[4],t[4]=a[5],t[5]=a[6],t[6]=a[8],t[7]=a[9],t[8]=a[10],t},o.clone=function(t){var a=new r.ARRAY_TYPE(9);return a[0]=t[0],a[1]=t[1],a[2]=t[2],a[3]=t[3],a[4]=t[4],a[5]=t[5],a[6]=t[6],a[7]=t[7],a[8]=t[8],a},o.copy=function(t,a){return t[0]=a[0],t[1]=a[1],t[2]=a[2],t[3]=a[3],t[4]=a[4],t[5]=a[5],t[6]=a[6],t[7]=a[7],t[8]=a[8],t},o.identity=function(t){return t[0]=1,t[1]=0,t[2]=0,t[3]=0,t[4]=1,t[5]=0,t[6]=0,t[7]=0,t[8]=1,t},o.transpose=function(t,a){if(t===a){var n=a[1],r=a[2],o=a[5];t[1]=a[3],t[2]=a[6],t[3]=n,t[5]=a[7],t[6]=r,t[7]=o}else t[0]=a[0],t[1]=a[3],t[2]=a[6],t[3]=a[1],t[4]=a[4],t[5]=a[7],t[6]=a[2],t[7]=a[5],t[8]=a[8];return t},o.invert=function(t,a){var n=a[0],r=a[1],o=a[2],l=a[3],u=a[4],e=a[5],M=a[6],i=a[7],s=a[8],c=s*u-e*i,D=-s*l+e*M,S=i*l-u*M,I=n*c+r*D+o*S;return I?(I=1/I,t[0]=c*I,t[1]=(-s*r+o*i)*I,t[2]=(e*r-o*u)*I,t[3]=D*I,t[4]=(s*n-o*M)*I,t[5]=(-e*n+o*l)*I,t[6]=S*I,t[7]=(-i*n+r*M)*I,t[8]=(u*n-r*l)*I,t):null},o.adjoint=function(t,a){var n=a[0],r=a[1],o=a[2],l=a[3],u=a[4],e=a[5],M=a[6],i=a[7],s=a[8];return t[0]=u*s-e*i,t[1]=o*i-r*s,t[2]=r*e-o*u,t[3]=e*M-l*s,t[4]=n*s-o*M,t[5]=o*l-n*e,t[6]=l*i-u*M,t[7]=r*M-n*i,t[8]=n*u-r*l,t},o.determinant=function(t){var a=t[0],n=t[1],r=t[2],o=t[3],l=t[4],u=t[5],e=t[6],M=t[7],i=t[8];return a*(i*l-u*M)+n*(-i*o+u*e)+r*(M*o-l*e)},o.multiply=function(t,a,n){var r=a[0],o=a[1],l=a[2],u=a[3],e=a[4],M=a[5],i=a[6],s=a[7],c=a[8],D=n[0],S=n[1],I=n[2],x=n[3],f=n[4],F=n[5],m=n[6],h=n[7],d=n[8];return t[0]=D*r+S*u+I*i,t[1]=D*o+S*e+I*s,t[2]=D*l+S*M+I*c,t[3]=x*r+f*u+F*i,t[4]=x*o+f*e+F*s,t[5]=x*l+f*M+F*c,t[6]=m*r+h*u+d*i,t[7]=m*o+h*e+d*s,t[8]=m*l+h*M+d*c,t},o.mul=o.multiply,o.translate=function(t,a,n){var r=a[0],o=a[1],l=a[2],u=a[3],e=a[4],M=a[5],i=a[6],s=a[7],c=a[8],D=n[0],S=n[1];return t[0]=r,t[1]=o,t[2]=l,t[3]=u,t[4]=e,t[5]=M,t[6]=D*r+S*u+i,t[7]=D*o+S*e+s,t[8]=D*l+S*M+c,t},o.rotate=function(t,a,n){var r=a[0],o=a[1],l=a[2],u=a[3],e=a[4],M=a[5],i=a[6],s=a[7],c=a[8],D=Math.sin(n),S=Math.cos(n);return t[0]=S*r+D*u,t[1]=S*o+D*e,t[2]=S*l+D*M,t[3]=S*u-D*r,t[4]=S*e-D*o,t[5]=S*M-D*l,t[6]=i,t[7]=s,t[8]=c,t},o.scale=function(t,a,n){var r=n[0],o=n[1];return t[0]=r*a[0],t[1]=r*a[1],t[2]=r*a[2],t[3]=o*a[3],t[4]=o*a[4],t[5]=o*a[5],t[6]=a[6],t[7]=a[7],t[8]=a[8],t},o.fromTranslation=function(t,a){return t[0]=1,t[1]=0,t[2]=0,t[3]=0,t[4]=1,t[5]=0,t[6]=a[0],t[7]=a[1],t[8]=1,t},o.fromRotation=function(t,a){var n=Math.sin(a),r=Math.cos(a);return t[0]=r,t[1]=n,t[2]=0,t[3]=-n,t[4]=r,t[5]=0,t[6]=0,t[7]=0,t[8]=1,t},o.fromScaling=function(t,a){return t[0]=a[0],t[1]=0,t[2]=0,t[3]=0,t[4]=a[1],t[5]=0,t[6]=0,t[7]=0,t[8]=1,t},o.fromMat2d=function(t,a){return t[0]=a[0],t[1]=a[1],t[2]=0,t[3]=a[2],t[4]=a[3],t[5]=0,t[6]=a[4],t[7]=a[5],t[8]=1,t},o.fromQuat=function(t,a){var n=a[0],r=a[1],o=a[2],l=a[3],u=n+n,e=r+r,M=o+o,i=n*u,s=r*u,c=r*e,D=o*u,S=o*e,I=o*M,x=l*u,f=l*e,F=l*M;return t[0]=1-c-I,t[3]=s-F,t[6]=D+f,t[1]=s+F,t[4]=1-i-I,t[7]=S-x,t[2]=D-f,t[5]=S+x,t[8]=1-i-c,t},o.normalFromMat4=function(t,a){var n=a[0],r=a[1],o=a[2],l=a[3],u=a[4],e=a[5],M=a[6],i=a[7],s=a[8],c=a[9],D=a[10],S=a[11],I=a[12],x=a[13],f=a[14],F=a[15],m=n*e-r*u,h=n*M-o*u,d=n*i-l*u,v=r*M-o*e,z=r*i-l*e,p=o*i-l*M,w=s*x-c*I,A=s*f-D*I,R=s*F-S*I,b=c*f-D*x,Y=c*F-S*x,q=D*F-S*f,y=m*q-h*Y+d*b+v*R-z*A+p*w;return y?(y=1/y,t[0]=(e*q-M*Y+i*b)*y,t[1]=(M*R-u*q-i*A)*y,t[2]=(u*Y-e*R+i*w)*y,t[3]=(o*Y-r*q-l*b)*y,t[4]=(n*q-o*R+l*A)*y,t[5]=(r*R-n*Y-l*w)*y,t[6]=(x*p-f*z+F*v)*y,t[7]=(f*d-I*p-F*h)*y,t[8]=(I*z-x*d+F*m)*y,t):null},o.str=function(t){return"mat3("+t[0]+", "+t[1]+", "+t[2]+", "+t[3]+", "+t[4]+", "+t[5]+", "+t[6]+", "+t[7]+", "+t[8]+")"},o.frob=function(t){return Math.sqrt(Math.pow(t[0],2)+Math.pow(t[1],2)+Math.pow(t[2],2)+Math.pow(t[3],2)+Math.pow(t[4],2)+Math.pow(t[5],2)+Math.pow(t[6],2)+Math.pow(t[7],2)+Math.pow(t[8],2))},t.exports=o},function(t,a,n){var r=n(1),o={scalar:{},SIMD:{}};o.create=function(){var t=new r.ARRAY_TYPE(16);return t[0]=1,t[1]=0,t[2]=0,t[3]=0,t[4]=0,t[5]=1,t[6]=0,t[7]=0,t[8]=0,t[9]=0,t[10]=1,t[11]=0,t[12]=0,t[13]=0,t[14]=0,t[15]=1,t},o.clone=function(t){var a=new r.ARRAY_TYPE(16);return a[0]=t[0],a[1]=t[1],a[2]=t[2],a[3]=t[3],a[4]=t[4],a[5]=t[5],a[6]=t[6],a[7]=t[7],a[8]=t[8],a[9]=t[9],a[10]=t[10],a[11]=t[11],a[12]=t[12],a[13]=t[13],a[14]=t[14],a[15]=t[15],a},o.copy=function(t,a){return t[0]=a[0],t[1]=a[1],t[2]=a[2],t[3]=a[3],t[4]=a[4],t[5]=a[5],t[6]=a[6],t[7]=a[7],t[8]=a[8],t[9]=a[9],t[10]=a[10],t[11]=a[11],t[12]=a[12],t[13]=a[13],t[14]=a[14],t[15]=a[15],t},o.identity=function(t){return t[0]=1,t[1]=0,t[2]=0,t[3]=0,t[4]=0,t[5]=1,t[6]=0,t[7]=0,t[8]=0,t[9]=0,t[10]=1,t[11]=0,t[12]=0,t[13]=0,t[14]=0,t[15]=1,t},o.scalar.transpose=function(t,a){if(t===a){var n=a[1],r=a[2],o=a[3],l=a[6],u=a[7],e=a[11];t[1]=a[4],t[2]=a[8],t[3]=a[12],t[4]=n,t[6]=a[9],t[7]=a[13],t[8]=r,t[9]=l,t[11]=a[14],t[12]=o,t[13]=u,t[14]=e}else t[0]=a[0],t[1]=a[4],t[2]=a[8],t[3]=a[12],t[4]=a[1],t[5]=a[5],t[6]=a[9],t[7]=a[13],t[8]=a[2],t[9]=a[6],t[10]=a[10],t[11]=a[14],t[12]=a[3],t[13]=a[7],t[14]=a[11],t[15]=a[15];return t},o.SIMD.transpose=function(t,a){var n,r,o,l,u,e,M,i,s,c;return n=SIMD.Float32x4.load(a,0),r=SIMD.Float32x4.load(a,4),o=SIMD.Float32x4.load(a,8),l=SIMD.Float32x4.load(a,12),u=SIMD.Float32x4.shuffle(n,r,0,1,4,5),e=SIMD.Float32x4.shuffle(o,l,0,1,4,5),M=SIMD.Float32x4.shuffle(u,e,0,2,4,6),i=SIMD.Float32x4.shuffle(u,e,1,3,5,7),SIMD.Float32x4.store(t,0,M),SIMD.Float32x4.store(t,4,i),u=SIMD.Float32x4.shuffle(n,r,2,3,6,7),e=SIMD.Float32x4.shuffle(o,l,2,3,6,7),s=SIMD.Float32x4.shuffle(u,e,0,2,4,6),c=SIMD.Float32x4.shuffle(u,e,1,3,5,7),SIMD.Float32x4.store(t,8,s),SIMD.Float32x4.store(t,12,c),t},o.transpose=r.USE_SIMD?o.SIMD.transpose:o.scalar.transpose,o.scalar.invert=function(t,a){var n=a[0],r=a[1],o=a[2],l=a[3],u=a[4],e=a[5],M=a[6],i=a[7],s=a[8],c=a[9],D=a[10],S=a[11],I=a[12],x=a[13],f=a[14],F=a[15],m=n*e-r*u,h=n*M-o*u,d=n*i-l*u,v=r*M-o*e,z=r*i-l*e,p=o*i-l*M,w=s*x-c*I,A=s*f-D*I,R=s*F-S*I,b=c*f-D*x,Y=c*F-S*x,q=D*F-S*f,y=m*q-h*Y+d*b+v*R-z*A+p*w;return y?(y=1/y,t[0]=(e*q-M*Y+i*b)*y,t[1]=(o*Y-r*q-l*b)*y,t[2]=(x*p-f*z+F*v)*y,t[3]=(D*z-c*p-S*v)*y,t[4]=(M*R-u*q-i*A)*y,t[5]=(n*q-o*R+l*A)*y,t[6]=(f*d-I*p-F*h)*y,t[7]=(s*p-D*d+S*h)*y,t[8]=(u*Y-e*R+i*w)*y,t[9]=(r*R-n*Y-l*w)*y,t[10]=(I*z-x*d+F*m)*y,t[11]=(c*d-s*z-S*m)*y,t[12]=(e*A-u*b-M*w)*y,t[13]=(n*b-r*A+o*w)*y,t[14]=(x*h-I*v-f*m)*y,t[15]=(s*v-c*h+D*m)*y,t):null},o.SIMD.invert=function(t,a){var n,r,o,l,u,e,M,i,s,c,D=SIMD.Float32x4.load(a,0),S=SIMD.Float32x4.load(a,4),I=SIMD.Float32x4.load(a,8),x=SIMD.Float32x4.load(a,12);return u=SIMD.Float32x4.shuffle(D,S,0,1,4,5),r=SIMD.Float32x4.shuffle(I,x,0,1,4,5),n=SIMD.Float32x4.shuffle(u,r,0,2,4,6),r=SIMD.Float32x4.shuffle(r,u,1,3,5,7),u=SIMD.Float32x4.shuffle(D,S,2,3,6,7),l=SIMD.Float32x4.shuffle(I,x,2,3,6,7),o=SIMD.Float32x4.shuffle(u,l,0,2,4,6),l=SIMD.Float32x4.shuffle(l,u,1,3,5,7),u=SIMD.Float32x4.mul(o,l),u=SIMD.Float32x4.swizzle(u,1,0,3,2),e=SIMD.Float32x4.mul(r,u),M=SIMD.Float32x4.mul(n,u),u=SIMD.Float32x4.swizzle(u,2,3,0,1),e=SIMD.Float32x4.sub(SIMD.Float32x4.mul(r,u),e),M=SIMD.Float32x4.sub(SIMD.Float32x4.mul(n,u),M),M=SIMD.Float32x4.swizzle(M,2,3,0,1),u=SIMD.Float32x4.mul(r,o),u=SIMD.Float32x4.swizzle(u,1,0,3,2),e=SIMD.Float32x4.add(SIMD.Float32x4.mul(l,u),e),s=SIMD.Float32x4.mul(n,u),u=SIMD.Float32x4.swizzle(u,2,3,0,1),e=SIMD.Float32x4.sub(e,SIMD.Float32x4.mul(l,u)),s=SIMD.Float32x4.sub(SIMD.Float32x4.mul(n,u),s),s=SIMD.Float32x4.swizzle(s,2,3,0,1),u=SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(r,2,3,0,1),l),u=SIMD.Float32x4.swizzle(u,1,0,3,2),o=SIMD.Float32x4.swizzle(o,2,3,0,1),e=SIMD.Float32x4.add(SIMD.Float32x4.mul(o,u),e),i=SIMD.Float32x4.mul(n,u),u=SIMD.Float32x4.swizzle(u,2,3,0,1),e=SIMD.Float32x4.sub(e,SIMD.Float32x4.mul(o,u)),i=SIMD.Float32x4.sub(SIMD.Float32x4.mul(n,u),i),i=SIMD.Float32x4.swizzle(i,2,3,0,1),u=SIMD.Float32x4.mul(n,r),u=SIMD.Float32x4.swizzle(u,1,0,3,2),i=SIMD.Float32x4.add(SIMD.Float32x4.mul(l,u),i),s=SIMD.Float32x4.sub(SIMD.Float32x4.mul(o,u),s),u=SIMD.Float32x4.swizzle(u,2,3,0,1),i=SIMD.Float32x4.sub(SIMD.Float32x4.mul(l,u),i),s=SIMD.Float32x4.sub(s,SIMD.Float32x4.mul(o,u)),u=SIMD.Float32x4.mul(n,l),u=SIMD.Float32x4.swizzle(u,1,0,3,2),M=SIMD.Float32x4.sub(M,SIMD.Float32x4.mul(o,u)),i=SIMD.Float32x4.add(SIMD.Float32x4.mul(r,u),i),u=SIMD.Float32x4.swizzle(u,2,3,0,1),M=SIMD.Float32x4.add(SIMD.Float32x4.mul(o,u),M),i=SIMD.Float32x4.sub(i,SIMD.Float32x4.mul(r,u)),u=SIMD.Float32x4.mul(n,o),u=SIMD.Float32x4.swizzle(u,1,0,3,2),M=SIMD.Float32x4.add(SIMD.Float32x4.mul(l,u),M),s=SIMD.Float32x4.sub(s,SIMD.Float32x4.mul(r,u)),u=SIMD.Float32x4.swizzle(u,2,3,0,1),M=SIMD.Float32x4.sub(M,SIMD.Float32x4.mul(l,u)),s=SIMD.Float32x4.add(SIMD.Float32x4.mul(r,u),s),c=SIMD.Float32x4.mul(n,e),c=SIMD.Float32x4.add(SIMD.Float32x4.swizzle(c,2,3,0,1),c),c=SIMD.Float32x4.add(SIMD.Float32x4.swizzle(c,1,0,3,2),c),u=SIMD.Float32x4.reciprocalApproximation(c),c=SIMD.Float32x4.sub(SIMD.Float32x4.add(u,u),SIMD.Float32x4.mul(c,SIMD.Float32x4.mul(u,u))),(c=SIMD.Float32x4.swizzle(c,0,0,0,0))?(SIMD.Float32x4.store(t,0,SIMD.Float32x4.mul(c,e)),SIMD.Float32x4.store(t,4,SIMD.Float32x4.mul(c,M)),SIMD.Float32x4.store(t,8,SIMD.Float32x4.mul(c,i)),SIMD.Float32x4.store(t,12,SIMD.Float32x4.mul(c,s)),t):null},o.invert=r.USE_SIMD?o.SIMD.invert:o.scalar.invert,o.scalar.adjoint=function(t,a){var n=a[0],r=a[1],o=a[2],l=a[3],u=a[4],e=a[5],M=a[6],i=a[7],s=a[8],c=a[9],D=a[10],S=a[11],I=a[12],x=a[13],f=a[14],F=a[15];return t[0]=e*(D*F-S*f)-c*(M*F-i*f)+x*(M*S-i*D),t[1]=-(r*(D*F-S*f)-c*(o*F-l*f)+x*(o*S-l*D)),t[2]=r*(M*F-i*f)-e*(o*F-l*f)+x*(o*i-l*M),t[3]=-(r*(M*S-i*D)-e*(o*S-l*D)+c*(o*i-l*M)),t[4]=-(u*(D*F-S*f)-s*(M*F-i*f)+I*(M*S-i*D)),t[5]=n*(D*F-S*f)-s*(o*F-l*f)+I*(o*S-l*D),t[6]=-(n*(M*F-i*f)-u*(o*F-l*f)+I*(o*i-l*M)),t[7]=n*(M*S-i*D)-u*(o*S-l*D)+s*(o*i-l*M),t[8]=u*(c*F-S*x)-s*(e*F-i*x)+I*(e*S-i*c),t[9]=-(n*(c*F-S*x)-s*(r*F-l*x)+I*(r*S-l*c)),t[10]=n*(e*F-i*x)-u*(r*F-l*x)+I*(r*i-l*e),t[11]=-(n*(e*S-i*c)-u*(r*S-l*c)+s*(r*i-l*e)),t[12]=-(u*(c*f-D*x)-s*(e*f-M*x)+I*(e*D-M*c)),t[13]=n*(c*f-D*x)-s*(r*f-o*x)+I*(r*D-o*c),t[14]=-(n*(e*f-M*x)-u*(r*f-o*x)+I*(r*M-o*e)),t[15]=n*(e*D-M*c)-u*(r*D-o*c)+s*(r*M-o*e),t},o.SIMD.adjoint=function(t,a){var n,r,o,l,u,e,M,i,s,c,D,S,I,n=SIMD.Float32x4.load(a,0),r=SIMD.Float32x4.load(a,4),o=SIMD.Float32x4.load(a,8),l=SIMD.Float32x4.load(a,12);return s=SIMD.Float32x4.shuffle(n,r,0,1,4,5),e=SIMD.Float32x4.shuffle(o,l,0,1,4,5),u=SIMD.Float32x4.shuffle(s,e,0,2,4,6),e=SIMD.Float32x4.shuffle(e,s,1,3,5,7),s=SIMD.Float32x4.shuffle(n,r,2,3,6,7),i=SIMD.Float32x4.shuffle(o,l,2,3,6,7),M=SIMD.Float32x4.shuffle(s,i,0,2,4,6),i=SIMD.Float32x4.shuffle(i,s,1,3,5,7),s=SIMD.Float32x4.mul(M,i),s=SIMD.Float32x4.swizzle(s,1,0,3,2),c=SIMD.Float32x4.mul(e,s),D=SIMD.Float32x4.mul(u,s),s=SIMD.Float32x4.swizzle(s,2,3,0,1),c=SIMD.Float32x4.sub(SIMD.Float32x4.mul(e,s),c),D=SIMD.Float32x4.sub(SIMD.Float32x4.mul(u,s),D),D=SIMD.Float32x4.swizzle(D,2,3,0,1),s=SIMD.Float32x4.mul(e,M),s=SIMD.Float32x4.swizzle(s,1,0,3,2),c=SIMD.Float32x4.add(SIMD.Float32x4.mul(i,s),c),I=SIMD.Float32x4.mul(u,s),s=SIMD.Float32x4.swizzle(s,2,3,0,1),c=SIMD.Float32x4.sub(c,SIMD.Float32x4.mul(i,s)),I=SIMD.Float32x4.sub(SIMD.Float32x4.mul(u,s),I),I=SIMD.Float32x4.swizzle(I,2,3,0,1),s=SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(e,2,3,0,1),i),s=SIMD.Float32x4.swizzle(s,1,0,3,2),M=SIMD.Float32x4.swizzle(M,2,3,0,1),c=SIMD.Float32x4.add(SIMD.Float32x4.mul(M,s),c),S=SIMD.Float32x4.mul(u,s),s=SIMD.Float32x4.swizzle(s,2,3,0,1),c=SIMD.Float32x4.sub(c,SIMD.Float32x4.mul(M,s)),S=SIMD.Float32x4.sub(SIMD.Float32x4.mul(u,s),S),S=SIMD.Float32x4.swizzle(S,2,3,0,1),s=SIMD.Float32x4.mul(u,e),s=SIMD.Float32x4.swizzle(s,1,0,3,2),S=SIMD.Float32x4.add(SIMD.Float32x4.mul(i,s),S),I=SIMD.Float32x4.sub(SIMD.Float32x4.mul(M,s),I),s=SIMD.Float32x4.swizzle(s,2,3,0,1),S=SIMD.Float32x4.sub(SIMD.Float32x4.mul(i,s),S),I=SIMD.Float32x4.sub(I,SIMD.Float32x4.mul(M,s)),s=SIMD.Float32x4.mul(u,i),s=SIMD.Float32x4.swizzle(s,1,0,3,2),D=SIMD.Float32x4.sub(D,SIMD.Float32x4.mul(M,s)),S=SIMD.Float32x4.add(SIMD.Float32x4.mul(e,s),S),s=SIMD.Float32x4.swizzle(s,2,3,0,1),D=SIMD.Float32x4.add(SIMD.Float32x4.mul(M,s),D),S=SIMD.Float32x4.sub(S,SIMD.Float32x4.mul(e,s)),s=SIMD.Float32x4.mul(u,M),s=SIMD.Float32x4.swizzle(s,1,0,3,2),D=SIMD.Float32x4.add(SIMD.Float32x4.mul(i,s),D),I=SIMD.Float32x4.sub(I,SIMD.Float32x4.mul(e,s)),s=SIMD.Float32x4.swizzle(s,2,3,0,1),D=SIMD.Float32x4.sub(D,SIMD.Float32x4.mul(i,s)),I=SIMD.Float32x4.add(SIMD.Float32x4.mul(e,s),I),SIMD.Float32x4.store(t,0,c),SIMD.Float32x4.store(t,4,D),SIMD.Float32x4.store(t,8,S),SIMD.Float32x4.store(t,12,I),t},o.adjoint=r.USE_SIMD?o.SIMD.adjoint:o.scalar.adjoint,o.determinant=function(t){var a=t[0],n=t[1],r=t[2],o=t[3],l=t[4],u=t[5],e=t[6],M=t[7],i=t[8],s=t[9],c=t[10],D=t[11],S=t[12],I=t[13],x=t[14],f=t[15],F=a*u-n*l,m=a*e-r*l,h=a*M-o*l,d=n*e-r*u,v=n*M-o*u,z=r*M-o*e,p=i*I-s*S,w=i*x-c*S,A=i*f-D*S,R=s*x-c*I,b=s*f-D*I,Y=c*f-D*x;return F*Y-m*b+h*R+d*A-v*w+z*p},o.SIMD.multiply=function(t,a,n){var r=SIMD.Float32x4.load(a,0),o=SIMD.Float32x4.load(a,4),l=SIMD.Float32x4.load(a,8),u=SIMD.Float32x4.load(a,12),e=SIMD.Float32x4.load(n,0),M=SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(e,0,0,0,0),r),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(e,1,1,1,1),o),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(e,2,2,2,2),l),SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(e,3,3,3,3),u))));SIMD.Float32x4.store(t,0,M);var i=SIMD.Float32x4.load(n,4),s=SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(i,0,0,0,0),r),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(i,1,1,1,1),o),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(i,2,2,2,2),l),SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(i,3,3,3,3),u))));SIMD.Float32x4.store(t,4,s);var c=SIMD.Float32x4.load(n,8),D=SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(c,0,0,0,0),r),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(c,1,1,1,1),o),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(c,2,2,2,2),l),SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(c,3,3,3,3),u))));SIMD.Float32x4.store(t,8,D);var S=SIMD.Float32x4.load(n,12),I=SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(S,0,0,0,0),r),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(S,1,1,1,1),o),SIMD.Float32x4.add(SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(S,2,2,2,2),l),SIMD.Float32x4.mul(SIMD.Float32x4.swizzle(S,3,3,3,3),u))));return SIMD.Float32x4.store(t,12,I),t},o.scalar.multiply=function(t,a,n){var r=a[0],o=a[1],l=a[2],u=a[3],e=a[4],M=a[5],i=a[6],s=a[7],c=a[8],D=a[9],S=a[10],I=a[11],x=a[12],f=a[13],F=a[14],m=a[15],h=n[0],d=n[1],v=n[2],z=n[3];return t[0]=h*r+d*e+v*c+z*x,t[1]=h*o+d*M+v*D+z*f,t[2]=h*l+d*i+v*S+z*F,t[3]=h*u+d*s+v*I+z*m,h=n[4],d=n[5],v=n[6],z=n[7],t[4]=h*r+d*e+v*c+z*x,t[5]=h*o+d*M+v*D+z*f,t[6]=h*l+d*i+v*S+z*F,t[7]=h*u+d*s+v*I+z*m,h=n[8],d=n[9],v=n[10],z=n[11],t[8]=h*r+d*e+v*c+z*x,t[9]=h*o+d*M+v*D+z*f,t[10]=h*l+d*i+v*S+z*F,t[11]=h*u+d*s+v*I+z*m,h=n[12],d=n[13],v=n[14],z=n[15],t[12]=h*r+d*e+v*c+z*x,t[13]=h*o+d*M+v*D+z*f,t[14]=h*l+d*i+v*S+z*F,t[15]=h*u+d*s+v*I+z*m,t},o.multiply=r.USE_SIMD?o.SIMD.multiply:o.scalar.multiply,o.mul=o.multiply,o.scalar.translate=function(t,a,n){var r,o,l,u,e,M,i,s,c,D,S,I,x=n[0],f=n[1],F=n[2];return a===t?(t[12]=a[0]*x+a[4]*f+a[8]*F+a[12],t[13]=a[1]*x+a[5]*f+a[9]*F+a[13],t[14]=a[2]*x+a[6]*f+a[10]*F+a[14],t[15]=a[3]*x+a[7]*f+a[11]*F+a[15]):(r=a[0],o=a[1],l=a[2],u=a[3],e=a[4],M=a[5],i=a[6],s=a[7],c=a[8],D=a[9],S=a[10],I=a[11],t[0]=r,t[1]=o,t[2]=l,t[3]=u,t[4]=e,t[5]=M,t[6]=i,t[7]=s,t[8]=c,t[9]=D,t[10]=S,t[11]=I,t[12]=r*x+e*f+c*F+a[12],t[13]=o*x+M*f+D*F+a[13],t[14]=l*x+i*f+S*F+a[14],t[15]=u*x+s*f+I*F+a[15]),t},o.SIMD.translate=function(t,a,n){var r=SIMD.Float32x4.load(a,0),o=SIMD.Float32x4.load(a,4),l=SIMD.Float32x4.load(a,8),u=SIMD.Float32x4.load(a,12),e=SIMD.Float32x4(n[0],n[1],n[2],0);a!==t&&(t[0]=a[0],t[1]=a[1],t[2]=a[2],t[3]=a[3],t[4]=a[4],t[5]=a[5],t[6]=a[6],t[7]=a[7],t[8]=a[8],t[9]=a[9],t[10]=a[10],t[11]=a[11]),r=SIMD.Float32x4.mul(r,SIMD.Float32x4.swizzle(e,0,0,0,0)),o=SIMD.Float32x4.mul(o,SIMD.Float32x4.swizzle(e,1,1,1,1)),l=SIMD.Float32x4.mul(l,SIMD.Float32x4.swizzle(e,2,2,2,2));var M=SIMD.Float32x4.add(r,SIMD.Float32x4.add(o,SIMD.Float32x4.add(l,u)));return SIMD.Float32x4.store(t,12,M),t},o.translate=r.USE_SIMD?o.SIMD.translate:o.scalar.translate,o.scalar.scale=function(t,a,n){var r=n[0],o=n[1],l=n[2];return t[0]=a[0]*r,t[1]=a[1]*r,t[2]=a[2]*r,t[3]=a[3]*r,t[4]=a[4]*o,t[5]=a[5]*o,t[6]=a[6]*o,t[7]=a[7]*o,t[8]=a[8]*l,t[9]=a[9]*l,t[10]=a[10]*l,t[11]=a[11]*l,t[12]=a[12],t[13]=a[13],t[14]=a[14],t[15]=a[15],t},o.SIMD.scale=function(t,a,n){var r,o,l,u=SIMD.Float32x4(n[0],n[1],n[2],0);return r=SIMD.Float32x4.load(a,0),SIMD.Float32x4.store(t,0,SIMD.Float32x4.mul(r,SIMD.Float32x4.swizzle(u,0,0,0,0))),o=SIMD.Float32x4.load(a,4),SIMD.Float32x4.store(t,4,SIMD.Float32x4.mul(o,SIMD.Float32x4.swizzle(u,1,1,1,1))),l=SIMD.Float32x4.load(a,8),SIMD.Float32x4.store(t,8,SIMD.Float32x4.mul(l,SIMD.Float32x4.swizzle(u,2,2,2,2))),t[12]=a[12],t[13]=a[13],t[14]=a[14],t[15]=a[15],t},o.scale=r.USE_SIMD?o.SIMD.scale:o.scalar.scale,o.rotate=function(t,a,n,o){var l,u,e,M,i,s,c,D,S,I,x,f,F,m,h,d,v,z,p,w,A,R,b,Y,q=o[0],y=o[1],E=o[2],g=Math.sqrt(q*q+y*y+E*E);return 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