Index: /issm/trunk/configure.ac
===================================================================
--- /issm/trunk/configure.ac (revision 27231)
+++ /issm/trunk/configure.ac (revision 27232)
@@ -2,5 +2,5 @@
#AUTOCONF
-AC_INIT([Ice-sheet and Sea-level System Model (ISSM)],[4.20],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure
+AC_INIT([Ice-sheet and Sea-level System Model (ISSM)],[4.21],[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
Index: /issm/trunk/etc/environment.sh
===================================================================
--- /issm/trunk/etc/environment.sh (revision 27231)
+++ /issm/trunk/etc/environment.sh (revision 27232)
@@ -299,4 +299,13 @@
fi
+HDF5_ROOT="${ISSM_EXT_DIR}/hdf5/install"
+if [ -d "${HDF5_ROOT}" ]; then
+ export HDF5_ROOT # Used in installation of NetCDF, GDAL
+ cpath_append "${HDF5_ROOT}/include"
+ library_path_append "${HDF5_ROOT}/lib"
+ dyld_library_path_append "${HDF5_ROOT}/lib"
+ ld_library_path_append "${HDF5_ROOT}/lib"
+fi
+
LAPACK_ROOT="${ISSM_EXT_DIR}/lapack/install"
if [ -d "${LAPACK_ROOT}" ]; then
@@ -308,4 +317,8 @@
path_append "${LAPACK_ROOT}/lib" # Allows dynamic loader to find DLLs
fi
+
+ if ls ${LAPACK_ROOT}/lib/libblas.* 1> /dev/null 2>&1; then
+ export BLAS_ROOT="${LAPACK_ROOT}"
+ fi
fi
@@ -340,4 +353,11 @@
path_append "${PARMETIS_ROOT}/lib" # Allows dynamic loader to find DLLs
fi
+fi
+
+QD_ROOT="${ISSM_EXT_DIR}/qd/install"
+if [ -d "${QD_ROOT}" ]; then
+ export QD_ROOT # Used in installation of MPLAPACK
+ library_path_prepend "${QD_ROOT}/lib"
+ ld_library_path_prepend "${QD_ROOT}/lib"
fi
@@ -430,23 +450,4 @@
ld_library_path_append "${TAO_ROOT}/lib"
-DAKOTA_ROOT="${ISSM_EXT_DIR}/dakota/install"
-if [ -d "${DAKOTA_ROOT}" ]; then
- path_append "${DAKOTA_ROOT}/bin"
- ld_library_path_append "${DAKOTA_ROOT}/lib"
- dyld_library_path_prepend "${DAKOTA_ROOT}/lib"
-fi
-
-NCO_ROOT="${ISSM_EXT_DIR}/nco/install/bin"
-path_prepend "${NCO_ROOT}/bin"
-
-CPPCHECK_ROOT="${ISSM_EXT_DIR}/cppcheck/install"
-path_append "${CPPCHECK_ROOT}/bin"
-
-MERCURIAL_ROOT="${ISSM_EXT_DIR}/mercurial/install"
-if [ -d "${MERCURIAL_ROOT}" ]; then
- export PYTHONPATH="${PYTHONPATH}:${MERCURIAL_ROOT}/mercurial/pure/"
- path_append "${MERCURIAL_ROOT}"
-fi
-
BOOST_ROOT="${ISSM_EXT_DIR}/boost/install"
if [ -d "${BOOST_ROOT}" ]; then
@@ -454,8 +455,27 @@
export BOOST_DIR=${BOOST_ROOT}
export BOOSTROOT=${BOOST_ROOT}
- library_path_append "${BOOST_ROOT}/lib"
- ld_library_path_append "${BOOST_ROOT}/lib"
- dyld_library_path_append "${BOOST_ROOT}/lib"
path_append "${BOOST_ROOT}/bin"
+ library_path_prepend "${BOOST_ROOT}/lib"
+ ld_library_path_prepend "${BOOST_ROOT}/lib"
+ dyld_library_path_prepend "${BOOST_ROOT}/lib"
+fi
+
+DAKOTA_ROOT="${ISSM_EXT_DIR}/dakota/install"
+if [ -d "${DAKOTA_ROOT}" ]; then
+ path_append "${DAKOTA_ROOT}/bin"
+ ld_library_path_prepend "${DAKOTA_ROOT}/lib"
+ dyld_library_path_prepend "${DAKOTA_ROOT}/lib"
+fi
+
+NCO_ROOT="${ISSM_EXT_DIR}/nco/install/bin"
+path_prepend "${NCO_ROOT}/bin"
+
+CPPCHECK_ROOT="${ISSM_EXT_DIR}/cppcheck/install"
+path_append "${CPPCHECK_ROOT}/bin"
+
+MERCURIAL_ROOT="${ISSM_EXT_DIR}/mercurial/install"
+if [ -d "${MERCURIAL_ROOT}" ]; then
+ export PYTHONPATH="${PYTHONPATH}:${MERCURIAL_ROOT}/mercurial/pure/"
+ path_append "${MERCURIAL_ROOT}"
fi
@@ -469,9 +489,9 @@
if [ -d "${NETCDF_ROOT}" ]; then
export NETCDF_ROOT # Used in installation of GDAL, GMT
- path_append "${NETCDF_ROOT}/bin"
- cpath_append "${NETCDF_ROOT}/include"
- library_path_append "${NETCDF_ROOT}/lib"
- dyld_library_path_append "${NETCDF_ROOT}/lib"
- ld_library_path_append "${NETCDF_ROOT}/lib"
+ path_prepend "${NETCDF_ROOT}/bin"
+ cpath_prepend "${NETCDF_ROOT}/include"
+ library_path_prepend "${NETCDF_ROOT}/lib"
+ dyld_library_path_prepend "${NETCDF_ROOT}/lib"
+ ld_library_path_prepend "${NETCDF_ROOT}/lib"
fi
@@ -491,16 +511,8 @@
if [ -d "${CURL_ROOT}" ]; then
export CURL_ROOT # Used in installation of NetCDF, GDAL, GMT
- ld_library_path_append "${CURL_ROOT}/lib"
- dyld_library_path_append "${CURL_ROOT}/lib"
+ cpath_prepend "${CURL_ROOT}/include"
+ ld_library_path_prepend "${CURL_ROOT}/lib"
+ dyld_library_path_prepend "${CURL_ROOT}/lib"
path_append "${CURL_ROOT}/bin"
-fi
-
-HDF5_ROOT="${ISSM_EXT_DIR}/hdf5/install"
-if [ -d "${HDF5_ROOT}" ]; then
- export HDF5_ROOT # Used in installation of NetCDF, GDAL
- cpath_append "${HDF5_ROOT}/include"
- library_path_append "${HDF5_ROOT}/lib"
- dyld_library_path_append "${HDF5_ROOT}/lib"
- ld_library_path_append "${HDF5_ROOT}/lib"
fi
Index: /issm/trunk/examples/Greenland/runme.m
===================================================================
--- /issm/trunk/examples/Greenland/runme.m (revision 27231)
+++ /issm/trunk/examples/Greenland/runme.m (revision 27232)
@@ -21,5 +21,5 @@
%Mesh Greenland
- md=bamg(md,'hmax',400000,'hmin',5000,'gradation',1.7,'field',vel,'err',8);
+ md=bamg(md,'hmax',400000,'hmin',5000,'gradation',1.4,'field',vel,'err',8);
%convert x,y coordinates (Polar stereo) to lat/lon
@@ -56,5 +56,5 @@
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(:,2)=0.2;
md.inversion.cost_functions_coefficients(:,3)=2e-6;
Index: /issm/trunk/examples/Greenland/runme.py
===================================================================
--- /issm/trunk/examples/Greenland/runme.py (revision 27231)
+++ /issm/trunk/examples/Greenland/runme.py (revision 27232)
@@ -42,5 +42,5 @@
#Mesh Greenland
- md = bamg(md, 'hmax', 400000, 'hmin', 5000, 'gradation', 1.7, 'field', vel, 'err', 8)
+ md = bamg(md, 'hmax', 400000, 'hmin', 5000, 'gradation', 1.4, 'field', vel, 'err', 8)
#convert x, y coordinates (Polar stereo) to lat / lon
@@ -77,5 +77,5 @@
md.inversion.cost_functions_coefficients = np.ones((md.mesh.numberofvertices, 3))
md.inversion.cost_functions_coefficients[:, 0] = 350
- md.inversion.cost_functions_coefficients[:, 1] = 0.6
+ md.inversion.cost_functions_coefficients[:, 1] = 0.2
md.inversion.cost_functions_coefficients[:, 2] = 2e-6
Index: /issm/trunk/examples/Inversion/runme.m
===================================================================
--- /issm/trunk/examples/Inversion/runme.m (revision 27231)
+++ /issm/trunk/examples/Inversion/runme.m (revision 27232)
@@ -1,3 +1,3 @@
-steps=[4];
+steps=[1];
if any(steps==1)
Index: /issm/trunk/examples/UncertaintyQuantification/runme.m
===================================================================
--- /issm/trunk/examples/UncertaintyQuantification/runme.m (revision 27231)
+++ /issm/trunk/examples/UncertaintyQuantification/runme.m (revision 27232)
@@ -5,4 +5,5 @@
disp(' Step 1: plot flux gates');
+ % NOTE: Need to run all steps of ../Pig/runme.m first!
md = loadmodel('../Pig/Models/PIG_Control_drag');
Index: /issm/trunk/externalpackages/autotools/install-linux.sh
===================================================================
--- /issm/trunk/externalpackages/autotools/install-linux.sh (revision 27231)
+++ /issm/trunk/externalpackages/autotools/install-linux.sh (revision 27232)
@@ -60,4 +60,5 @@
fi
cd ..
+
# Install Automake
echo " === INSTALLING AUTOMAKE ==="
Index: /issm/trunk/externalpackages/boost/install-1.7-mac.sh
===================================================================
--- /issm/trunk/externalpackages/boost/install-1.7-mac.sh (revision 27231)
+++ /issm/trunk/externalpackages/boost/install-1.7-mac.sh (revision 27232)
@@ -54,2 +54,10 @@
install_name_tool -id ${PREFIX}/lib/${name} ${name} 2>/dev/null
done
+
+if [ "${VER}" == "1_79_0" ]; then
+ ## Patch install names for certain libraries
+ #
+ # TODO: Figure out how to reconfigure source to apply these install names at compile time
+ #
+ install_name_tool -change @rpath/libboost_atomic.dylib ${PREFIX}/lib/libboost_atomic.dylib libboost_filesystem.dylib
+fi
Index: /issm/trunk/externalpackages/chaco/install.sh
===================================================================
--- /issm/trunk/externalpackages/chaco/install.sh (revision 27231)
+++ /issm/trunk/externalpackages/chaco/install.sh (revision 27232)
@@ -8,4 +8,8 @@
PREFIX="${ISSM_DIR}/externalpackages/chaco/install" # Set to location where external package should be installed
+
+## Environment
+#
+export CFLAGS="-Wno-error=implicit-function-declaration"
# Cleanup
Index: /issm/trunk/externalpackages/curl/install-7-linux-static.sh
===================================================================
--- /issm/trunk/externalpackages/curl/install-7-linux-static.sh (revision 27231)
+++ /issm/trunk/externalpackages/curl/install-7-linux-static.sh (revision 27232)
@@ -34,4 +34,5 @@
--disable-ldaps \
--with-zlib="${ZLIB_ROOT}" \
+ --without-zstd \
--without-libidn2 \
--without-nghttp2 \
Index: /issm/trunk/externalpackages/curl/install-7-mac-static.sh
===================================================================
--- /issm/trunk/externalpackages/curl/install-7-mac-static.sh (revision 27231)
+++ /issm/trunk/externalpackages/curl/install-7-mac-static.sh (revision 27232)
@@ -38,4 +38,5 @@
--disable-ldaps \
--with-zlib="${ZLIB_ROOT}" \
+ --without-zstd \
--without-libidn2 \
--without-nghttp2 \
Index: /issm/trunk/externalpackages/dakota/install-6.2-linux-static.sh
===================================================================
--- /issm/trunk/externalpackages/dakota/install-6.2-linux-static.sh (revision 27231)
+++ /issm/trunk/externalpackages/dakota/install-6.2-linux-static.sh (revision 27232)
@@ -9,12 +9,20 @@
PREFIX="${ISSM_DIR}/externalpackages/dakota/install" # Set to location where external package should be installed
+# Find libgfortran and libgcc so we do not have to hardcode them
+#
+# TODO:
+# - Move this to etc/environment.sh
+#
+LIBGFORTRAN=$(find /usr -name libgfortran* | egrep -n libgfortran.a | sed "s/[0-9]*://g" | head -1)
+LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*}
+LIBGCC=$(find ${LIBGFORTRAN_ROOT} -name libgcc* | egrep -n libgcc.a | sed "s/[0-9]*://g" | head -1
+
## Environment
#
-export BLAS_LIBS="-L${BLAS_ROOT}/lib -lfblas -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
-export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with MATLAB's Boost (absolutely necessary for this version)
+export BLAS_LIBS="-L${BLAS_ROOT}/lib -lfblas ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
export DAK_BUILD=${ISSM_DIR}/externalpackages/dakota/build # DO NOT CHANGE THIS
export DAK_INSTALL=${PREFIX} # DO NOT CHANGE THIS
export DAK_SRC=${ISSM_DIR}/externalpackages/dakota/src # DO NOT CHANGE THIS
-export LAPACK_LIBS="-L${LAPACK_ROOT}/lib -lflapack -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
+export LAPACK_LIBS="-L${LAPACK_ROOT}/lib -lflapack -L/usr/lib/x86_64-linux-gnu ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
# Cleanup
@@ -45,4 +53,7 @@
cp configs/${VER}/linux/cmake/DakotaDev.cmake ${DAK_SRC}/cmake
+# Disable requirement of Python 2 for TriBITS
+sed -i'' -e 's|SET(PythonInterp_FIND_VERSION|#SET(PythonInterp_FIND_VERSION|' ${DAK_SRC}/packages/teuchos/cmake/tribits/package_arch/TribitsFindPythonInterp.cmake
+
# Configure
cd ${DAK_BUILD}
@@ -54,4 +65,5 @@
-DCMAKE_CXX_COMPILER=${MPI_HOME}/bin/mpicxx \
-DCMAKE_CXX_FLAGS="-fPIC" \
+ -DCMAKE_CXX_STANDARD="11" \
-DCMAKE_Fortran_COMPILER=${MPI_HOME}/bin/mpif77 \
-DBoost_NO_BOOST_CMAKE=TRUE \
Index: /issm/trunk/externalpackages/dakota/install-6.2-linux.sh
===================================================================
--- /issm/trunk/externalpackages/dakota/install-6.2-linux.sh (revision 27231)
+++ /issm/trunk/externalpackages/dakota/install-6.2-linux.sh (revision 27232)
@@ -12,6 +12,4 @@
#
export BLAS_LIBS="-L${BLAS_ROOT}/lib -lfblas -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
-export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with MATLAB's Boost (absolutely necessary for this version)
-#export CXXFLAGS='-std=c++11'
export DAK_BUILD=${ISSM_DIR}/externalpackages/dakota/build # DO NOT CHANGE THIS
export DAK_INSTALL=${PREFIX} # DO NOT CHANGE THIS
@@ -46,4 +44,7 @@
cp configs/${VER}/linux/cmake/DakotaDev.cmake ${DAK_SRC}/cmake
+# Disable requirement of Python 2 for TriBITS
+sed -i'' -e 's|SET(PythonInterp_FIND_VERSION|#SET(PythonInterp_FIND_VERSION|' ${DAK_SRC}/packages/teuchos/cmake/tribits/package_arch/TribitsFindPythonInterp.cmake
+
# Configure
cd ${DAK_BUILD}
@@ -54,4 +55,5 @@
-DCMAKE_C_FLAGS="-Wno-error=implicit-function-declaration" \
-DCMAKE_CXX_COMPILER=${MPI_HOME}/bin/mpicxx \
+ -DCMAKE_CXX_STANDARD="11" \
-DCMAKE_Fortran_COMPILER=${MPI_HOME}/bin/mpif77 \
-DBoost_NO_BOOST_CMAKE=TRUE \
Index: /issm/trunk/externalpackages/dakota/install-6.2-mac-static.sh
===================================================================
--- /issm/trunk/externalpackages/dakota/install-6.2-mac-static.sh (revision 27231)
+++ /issm/trunk/externalpackages/dakota/install-6.2-mac-static.sh (revision 27232)
@@ -8,7 +8,4 @@
PREFIX="${ISSM_DIR}/externalpackages/dakota/install" # Set to location where external package should be installed
-
-## Environment
-#
# Find libgfortran and libgcc so we do not have to hardcode them.
@@ -22,8 +19,10 @@
# - Otherwise, refactor this to work with other gfortran installations
#
-LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | grep -n libgfortran.a | grep -v i386 | sed "s/[0-9]*://g" | head -1)
+LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1)
LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*}
-LIBGCC=$(mdfind -onlyin ${LIBGFORTRAN_ROOT} -name libgcc | grep -n libgcc.a | grep -v i386 | sed "s/[0-9]*://g" | head -1)
+LIBGCC=$(mdfind -onlyin ${LIBGFORTRAN_ROOT} -name libgcc | egrep -n libgcc.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1)
+## Environment
+#
export BLAS_LIBS="-L${BLAS_ROOT}/lib -lfblas ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
export DAK_BUILD=${ISSM_DIR}/externalpackages/dakota/build # DO NOT CHANGE THIS
@@ -72,4 +71,7 @@
# cp configs/${VER}/mac/static/packages/nidr/nidr-scanner.c ${DAK_SRC}/packages/nidr
+# Disable requirement of Python 2 for TriBITS
+sed -i'' -e 's|SET(PythonInterp_FIND_VERSION|#SET(PythonInterp_FIND_VERSION|' ${DAK_SRC}/packages/teuchos/cmake/tribits/package_arch/TribitsFindPythonInterp.cmake
+
# Configure
cd ${DAK_BUILD}
@@ -81,4 +83,5 @@
-DCMAKE_CXX_COMPILER=${MPI_HOME}/bin/mpicxx \
-DCMAKE_CXX_FLAGS="-fPIC -fdelayed-template-parsing" \
+ -DCMAKE_CXX_STANDARD="11" \
-DCMAKE_Fortran_COMPILER=${MPI_HOME}/bin/mpif77 \
-DCMAKE_Fortran_FLAGS="-fPIC -fallow-argument-mismatch" \
Index: /issm/trunk/externalpackages/dakota/install-6.2-mac.sh
===================================================================
--- /issm/trunk/externalpackages/dakota/install-6.2-mac.sh (revision 27231)
+++ /issm/trunk/externalpackages/dakota/install-6.2-mac.sh (revision 27232)
@@ -9,7 +9,4 @@
PREFIX="${ISSM_DIR}/externalpackages/dakota/install" # Set to location where external package should be installed
-## Environment
-#
-
# Find libgfortran so that we do not have to hardcode it.
#
@@ -20,7 +17,9 @@
# - Move this to etc/environment.sh
#
-LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | grep -n libgfortran.a | grep -v i386 | sed "s/[0-9]*://g" | head -1)
+LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1)
LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*}
+## Environment
+#
export BLAS_LIBS="-L${BLAS_ROOT}/lib -lfblas -L${LIBGFORTRAN_ROOT} -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
export DAK_BUILD=${ISSM_DIR}/externalpackages/dakota/build # DO NOT CHANGE THIS
@@ -57,4 +56,7 @@
cp configs/${VER}/mac/cmake/InstallDarwinDylibs.cmake ${DAK_SRC}/cmake
+# Disable requirement of Python 2 for TriBITS
+sed -i'' -e 's|SET(PythonInterp_FIND_VERSION|#SET(PythonInterp_FIND_VERSION|' ${DAK_SRC}/packages/teuchos/cmake/tribits/package_arch/TribitsFindPythonInterp.cmake
+
# Configure
cd ${DAK_BUILD}
@@ -65,6 +67,6 @@
-DCMAKE_CXX_COMPILER=${MPI_HOME}/bin/mpicxx \
-DCMAKE_CXX_FLAGS="-fdelayed-template-parsing" \
+ -DCMAKE_CXX_STANDARD="11" \
-DCMAKE_Fortran_COMPILER=${MPI_HOME}/bin/mpif77 \
- -DCMAKE_Fortran_FLAGS="-fallow-argument-mismatch" \
-DBoost_NO_BOOST_CMAKE=TRUE \
-DHAVE_ACRO=OFF \
Index: /issm/trunk/externalpackages/gdal/install-3-python-static.sh
===================================================================
--- /issm/trunk/externalpackages/gdal/install-3-python-static.sh (revision 27231)
+++ /issm/trunk/externalpackages/gdal/install-3-python-static.sh (revision 27232)
@@ -9,5 +9,5 @@
## Constants
#
-VER="3.1.1"
+VER="3.5.1"
## Environment
@@ -42,10 +42,15 @@
--enable-static \
--with-pic \
- --with-python \
+ --with-python=python3 \
+ --with-curl="${CURL_ROOT}/bin/curl-config" \
+ --with-hdf5="${HDF5_ROOT}" \
+ --with-jpeg=internal \
--with-libz="${ZLIB_ROOT}" \
- --with-hdf5="${HDF5_ROOT}" \
--with-netcdf="${NETCDF_ROOT}" \
+ --with-pcre=no \
+ --with-pg=no \
+ --with-png=internal \
--with-proj="${PROJ_ROOT}" \
- --with-pg=no
+ --with-zstd=no
# Compile and install
Index: /issm/trunk/externalpackages/gdal/install-3-python.sh
===================================================================
--- /issm/trunk/externalpackages/gdal/install-3-python.sh (revision 27231)
+++ /issm/trunk/externalpackages/gdal/install-3-python.sh (revision 27232)
@@ -9,5 +9,5 @@
## Constants
#
-VER="3.1.1"
+VER="3.5.1"
## Environment
@@ -34,7 +34,7 @@
--prefix="${PREFIX}" \
--enable-fast-install \
- --with-python \
+ --with-python=python3 \
+ --with-hdf5="${HDF5_ROOT}" \
--with-libz="${ZLIB_ROOT}" \
- --with-hdf5="${HDF5_ROOT}" \
--with-netcdf="${NETCDF_ROOT}" \
--with-proj="${PROJ_ROOT}"
Index: /issm/trunk/externalpackages/gdal/install-3-static.sh
===================================================================
--- /issm/trunk/externalpackages/gdal/install-3-static.sh (revision 27231)
+++ /issm/trunk/externalpackages/gdal/install-3-static.sh (revision 27232)
@@ -9,5 +9,5 @@
## Constants
#
-VER="3.1.1"
+VER="3.5.1"
## Environment
@@ -42,9 +42,14 @@
--enable-static \
--with-pic \
+ --with-curl="${CURL_ROOT}/bin/curl-config" \
+ --with-hdf5="${HDF5_ROOT}" \
+ --with-jpeg=internal \
--with-libz="${ZLIB_ROOT}" \
- --with-hdf5="${HDF5_ROOT}" \
--with-netcdf="${NETCDF_ROOT}" \
+ --with-pcre=no \
+ --with-pg=no \
+ --with-png=internal \
--with-proj="${PROJ_ROOT}" \
- --with-pg=no
+ --with-zstd=no
# Compile and install
Index: /issm/trunk/externalpackages/gdal/install-3.sh
===================================================================
--- /issm/trunk/externalpackages/gdal/install-3.sh (revision 27231)
+++ /issm/trunk/externalpackages/gdal/install-3.sh (revision 27232)
@@ -5,5 +5,5 @@
## Constants
#
-VER="3.1.1"
+VER="3.5.1"
## Environment
@@ -30,6 +30,6 @@
--prefix="${PREFIX}" \
--enable-fast-install \
+ --with-hdf5="${HDF5_ROOT}" \
--with-libz="${ZLIB_ROOT}" \
- --with-hdf5="${HDF5_ROOT}" \
--with-netcdf="${NETCDF_ROOT}" \
--with-proj="${PROJ_ROOT}"
Index: /issm/trunk/externalpackages/gmsh/install-4-linux-static.sh
===================================================================
--- /issm/trunk/externalpackages/gmsh/install-4-linux-static.sh (revision 27232)
+++ /issm/trunk/externalpackages/gmsh/install-4-linux-static.sh (revision 27232)
@@ -0,0 +1,83 @@
+#!/bin/bash
+set -eu
+
+
+# TODO:
+# - Add support for,
+# - MUMPS
+# - PETSc
+#
+# See Also:
+# - configs/4/static/CMakeLists.txt
+# - http://gmsh.info/doc/texinfo/gmsh.html#Compiling-the-source-code
+#
+
+## Constants
+#
+VER="4.10.5"
+
+PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" # Set to location where external package should be installed
+
+# Find libgfortran and libgcc so we do not have to hardcode them
+#
+# TODO:
+# - Move this to etc/environment.sh
+#
+LIBGFORTRAN=$(find /usr -name libgfortran* | egrep -n libgfortran.a | sed "s/[0-9]*://g" | head -1)
+LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*}
+LIBGCC=$(find ${LIBGFORTRAN_ROOT} -name libgcc* | egrep -n libgcc.a | sed "s/[0-9]*://g" | head -1)
+
+# Cleanup
+rm -rf ${PREFIX} src
+mkdir -p ${PREFIX} src
+
+# Download source
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz"
+
+# Unpack source
+tar -xvzf gmsh-${VER}-source.tgz
+
+# Move source to 'src' directory
+mv gmsh-${VER}-source/* src
+rm -rf gmsh-${VER}-source
+
+# Configure
+#
+# NOTE:
+# - Option -DENABLE_FLTK=0 is used because we do not need GUI.
+# - Option -DENABLE_MPEG_ENCODE=0 is used because we do not need to record MPEG
+# movies.
+# - Option -DENABLE_OCC=0 is used because we do not need CAD kernel and are not
+# importing STEP/IGES files.
+# - Option -DENABLE_TOUCHBAR=0 is used because we do not have GUI, therefore we
+# do not need to support Apple Touch bar (does not affect compilation on
+# Linux).
+#
+cd src
+cmake \
+ -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+ -DENABLE_BUILD_LIB=1 \
+ -DBLAS_LAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib -lflapack -L${BLAS_ROOT}/lib -lfblas ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" \
+ -DENABLE_BLAS_LAPACK=1 \
+ -DENABLE_EIGEN=0 \
+ -DENABLE_FLTK=0 \
+ -DENABLE_MPEG_ENCODE=0 \
+ -DENABLE_MPI=1 \
+ -DENABLE_OCC=0 \
+ -DENABLE_TOUCHBAR=0 \
+ -DMETIS_ROOT="${METIS_ROOT}"
+
+# Compile and install
+if [ $# -eq 0 ]; then
+ make
+ make install
+else
+ make -j $1
+ make -j $1 install
+fi
+
+# Make necessary link on RHEL
+if [[ -d ${PREFIX}/lib64 && ! -d ${PREFIX}/lib ]]; then
+ cd ${PREFIX}
+ ln -s ./lib64 ./lib
+fi
Index: /issm/trunk/externalpackages/gmsh/install-4-linux.sh
===================================================================
--- /issm/trunk/externalpackages/gmsh/install-4-linux.sh (revision 27232)
+++ /issm/trunk/externalpackages/gmsh/install-4-linux.sh (revision 27232)
@@ -0,0 +1,83 @@
+#!/bin/bash
+set -eu
+
+
+# TODO:
+# - Add support for,
+# - MUMPS
+# - PETSc
+#
+# See Also:
+# - configs/4/static/CMakeLists.txt
+# - http://gmsh.info/doc/texinfo/gmsh.html#Compiling-the-source-code
+#
+
+## Constants
+#
+VER="4.10.5"
+
+PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" # Set to location where external package should be installed
+
+# Find libgfortran so that we do not have to hardcode it.
+#
+# TODO:
+# - Move this to etc/environment.sh
+#
+LIBGFORTRAN=$(find /usr -name libgfortran* | egrep -n libgfortran.a | sed "s/[0-9]*://g" | head -1)
+LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*}
+
+# Cleanup
+rm -rf ${PREFIX} src
+mkdir -p ${PREFIX} src
+
+# Download source
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz"
+
+# Unpack source
+tar -xvzf gmsh-${VER}-source.tgz
+
+# Move source to 'src' directory
+mv gmsh-${VER}-source/* src
+rm -rf gmsh-${VER}-source
+
+# Configure
+#
+# NOTE:
+# - Option -DENABLE_FLTK=0 is used because we do not need GUI.
+# - Option -DENABLE_MPEG_ENCODE=0 is used because we do not need to record MPEG
+# movies.
+# - Option -DENABLE_OCC=0 is used because we do not need CAD kernel and are not
+# importing STEP/IGES files.
+# - Option -DENABLE_TOUCHBAR=0 is used because we do not have GUI, therefore we
+# do not need to support Apple Touch bar (does not affect compilation on
+# Linux).
+#
+cd src
+cmake \
+ -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+ -DENABLE_BUILD_DYNAMIC=1 \
+ -DENABLE_BUILD_SHARED=1 \
+ -DBLAS_LAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib -lflapack -L${BLAS_ROOT}/lib -lfblas -L${LIBGFORTRAN_ROOT} -lgfortran" \
+ -DENABLE_BLAS_LAPACK=1 \
+ -DENABLE_EIGEN=0 \
+ -DENABLE_FLTK=0 \
+ -DENABLE_MPEG_ENCODE=0 \
+ -DENABLE_MPI=1 \
+ -DENABLE_OCC=0 \
+ -DENABLE_TOUCHBAR=0 \
+ -DMETIS_ROOT="${METIS_ROOT}"
+
+# Compile and install
+if [ $# -eq 0 ]; then
+ make
+ make install
+else
+ make -j $1
+ make -j $1 install
+fi
+
+# Make necessary link on RHEL
+if [[ -d ${PREFIX}/lib64 && ! -d ${PREFIX}/lib ]]; then
+ cd ${PREFIX}
+ ln -s ./lib64 ./lib
+fi
Index: /issm/trunk/externalpackages/gmsh/install-4-mac-static.sh
===================================================================
--- /issm/trunk/externalpackages/gmsh/install-4-mac-static.sh (revision 27232)
+++ /issm/trunk/externalpackages/gmsh/install-4-mac-static.sh (revision 27232)
@@ -0,0 +1,91 @@
+#!/bin/bash
+set -eu
+
+
+# TODO:
+# - Add support for,
+# - MUMPS
+# - PETSc
+#
+# See Also:
+# - configs/4/static/CMakeLists.txt
+# - http://gmsh.info/doc/texinfo/gmsh.html#Compiling-the-source-code
+#
+
+## Constants
+#
+VER="4.10.5"
+
+PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" # Set to location where external package should be installed
+
+
+# Find libgfortran and libgcc so we do not have to hardcode them
+#
+# Should retrieve a copy of gfortran that is compiled from source before returning one that is installed via package manager
+#
+# TODO:
+# - Move this to etc/environment.sh
+# - Test if -static-libgfortran flag will avoid all of this.
+# - Otherwise, refactor this to work with other gfortran installations.
+#
+LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1)
+LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*}
+LIBGCC=$(mdfind -onlyin ${LIBGFORTRAN_ROOT} -name libgcc | egrep -n libgcc.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1)
+
+# Cleanup
+rm -rf ${PREFIX} src
+mkdir -p ${PREFIX} src
+
+# Download source
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz"
+
+# Unpack source
+tar -xvzf gmsh-${VER}-source.tgz
+
+# Move source to 'src' directory
+mv gmsh-${VER}-source/* src
+rm -rf gmsh-${VER}-source
+
+# Copy customized source and config files to 'src' directory
+cp configs/${VER}/static/CMakeLists.txt src
+
+# Configure
+#
+# NOTE:
+# - Option -DENABLE_FLTK=0 is used because we do not need GUI.
+# - Option -DENABLE_MPEG_ENCODE=0 is used because we do not need to record MPEG
+# movies.
+# - Option -DENABLE_OCC=0 is used because we do not need CAD kernel and are not
+# importing STEP/IGES files.
+# - Option -DENABLE_TOUCHBAR=0 is used because we do not have GUI, therefore we
+# do not need to support Apple Touch bar (does not affect compilation on
+# Linux).
+#
+cd src
+cmake \
+ -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+ -DENABLE_BUILD_LIB=1 \
+ -DBLAS_LAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib -lflapack -L${BLAS_ROOT}/lib -lfblas ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" \
+ -DENABLE_BLAS_LAPACK=1 \
+ -DENABLE_EIGEN=0 \
+ -DENABLE_FLTK=0 \
+ -DENABLE_MPEG_ENCODE=0 \
+ -DENABLE_MPI=1 \
+ -DENABLE_OCC=0 \
+ -DENABLE_TOUCHBAR=0 \
+ -DMETIS_ROOT="${METIS_ROOT}"
+
+# Compile and install
+if [ $# -eq 0 ]; then
+ make
+ make install
+else
+ make -j $1
+ make -j $1 install
+fi
+
+# Make necessary link on RHEL
+if [[ -d ${PREFIX}/lib64 && ! -d ${PREFIX}/lib ]]; then
+ cd ${PREFIX}
+ ln -s ./lib64 ./lib
+fi
Index: /issm/trunk/externalpackages/gmsh/install-4-mac.sh
===================================================================
--- /issm/trunk/externalpackages/gmsh/install-4-mac.sh (revision 27232)
+++ /issm/trunk/externalpackages/gmsh/install-4-mac.sh (revision 27232)
@@ -0,0 +1,86 @@
+#!/bin/bash
+set -eu
+
+
+# TODO:
+# - Add support for,
+# - MUMPS
+# - PETSc
+#
+# See Also:
+# - configs/4/static/CMakeLists.txt
+# - http://gmsh.info/doc/texinfo/gmsh.html#Compiling-the-source-code
+#
+
+## Constants
+#
+VER="4.10.5"
+
+PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" # Set to location where external package should be installed
+
+# Find libgfortran so that we do not have to hardcode it.
+#
+# Should retrieve a copy of gfortran that is compiled from source before
+# returning one that is installed via package manager.
+#
+# TODO:
+# - Move this to etc/environment.sh
+#
+LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1)
+LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*}
+
+# Cleanup
+rm -rf ${PREFIX} src
+mkdir -p ${PREFIX} src
+
+# Download source
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz"
+
+# Unpack source
+tar -xvzf gmsh-${VER}-source.tgz
+
+# Move source to 'src' directory
+mv gmsh-${VER}-source/* src
+rm -rf gmsh-${VER}-source
+
+# Configure
+#
+# NOTE:
+# - Option -DENABLE_FLTK=0 is used because we do not need GUI.
+# - Option -DENABLE_MPEG_ENCODE=0 is used because we do not need to record MPEG
+# movies.
+# - Option -DENABLE_OCC=0 is used because we do not need CAD kernel and are not
+# importing STEP/IGES files.
+# - Option -DENABLE_TOUCHBAR=0 is used because we do not have GUI, therefore we
+# do not need to support Apple Touch bar (does not affect compilation on
+# Linux).
+#
+cd src
+cmake \
+ -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+ -DENABLE_BUILD_DYNAMIC=1 \
+ -DENABLE_BUILD_SHARED=1 \
+ -DBLAS_LAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib -lflapack -L${BLAS_ROOT}/lib -lfblas -L${LIBGFORTRAN_ROOT} -lgfortran" \
+ -DENABLE_BLAS_LAPACK=1 \
+ -DENABLE_EIGEN=0 \
+ -DENABLE_FLTK=0 \
+ -DENABLE_MPEG_ENCODE=0 \
+ -DENABLE_MPI=1 \
+ -DENABLE_OCC=0 \
+ -DENABLE_TOUCHBAR=0 \
+ -DMETIS_ROOT="${METIS_ROOT}"
+
+# Compile and install
+if [ $# -eq 0 ]; then
+ make
+ make install
+else
+ make -j $1
+ make -j $1 install
+fi
+
+# Make necessary link on RHEL
+if [[ -d ${PREFIX}/lib64 && ! -d ${PREFIX}/lib ]]; then
+ cd ${PREFIX}
+ ln -s ./lib64 ./lib
+fi
Index: sm/trunk/externalpackages/gmsh/install-4-static.sh
===================================================================
--- /issm/trunk/externalpackages/gmsh/install-4-static.sh (revision 27231)
+++ (revision )
@@ -1,72 +1,0 @@
-#!/bin/bash
-set -eu
-
-
-# TODO:
-# - Add support for,
-# - BLAS_LAPACK
-# - MUMPS
-# - PETSC
-# (see configs/4/static/CMakeLists.txt)
-#
-
-## Constants
-#
-VER="4.5.6"
-
-PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" # Set to location where external package should be installed
-
-# Cleanup
-rm -rf ${PREFIX} src
-mkdir -p ${PREFIX} src
-
-# Download source
-$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz"
-
-# Unpack source
-tar -xvzf gmsh-${VER}-source.tgz
-
-# Move source to 'src' directory
-mv gmsh-${VER}-source/* src
-rm -rf gmsh-${VER}-source
-
-# Copy customized source and config files to 'src' directory
-cp configs/${VER}/static/CMakeLists.txt src
-
-# Configure
-#
-# NOTE:
-# - Option -DENABLE_FLTK=0 is used because we do not need GUI.
-# - Option -DENABLE_MPEG_ENCODE=0 is used because we do not need to record MPEG
-# movies.
-# - Option -DENABLE_OCC=0 is used because we do not need CAD kernel and are not
-# importing STEP/IGES files.
-# - Option -DENABLE_TOUCHBAR=0 is used because we do not have GUI, therefore we
-# do not need to support Apple Touch bar (does not affect compilation on
-# Linux).
-#
-cd src
-cmake \
- -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
- -DENABLE_BUILD_LIB=1 \
- -DENABLE_FLTK=0 \
- -DENABLE_MPEG_ENCODE=0 \
- -DENABLE_MPI=1 \
- -DENABLE_OCC=0 \
- -DENABLE_TOUCHBAR=0 \
- -DMETIS_ROOT="${METIS_ROOT}"
-
-# Compile and install
-if [ $# -eq 0 ]; then
- make
- make install
-else
- make -j $1
- make -j $1 install
-fi
-
-# Make necessary link on RHEL
-if [[ -d ${PREFIX}/lib64 && ! -d ${PREFIX}/lib ]]; then
- cd ${PREFIX}
- ln -s ./lib64 ./lib
-fi
Index: sm/trunk/externalpackages/gmsh/install-4.sh
===================================================================
--- /issm/trunk/externalpackages/gmsh/install-4.sh (revision 27231)
+++ (revision )
@@ -1,70 +1,0 @@
-#!/bin/bash
-set -eu
-
-
-# TODO:
-# - Add support for,
-# - BLAS_LAPACK
-# - MUMPS
-# - PETSC
-# (see configs/4/static/CMakeLists.txt)
-#
-
-## Constants
-#
-VER="4.5.6"
-
-PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" # Set to location where external package should be installed
-
-# Cleanup
-rm -rf ${PREFIX} src
-mkdir -p ${PREFIX} src
-
-# Download source
-$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz"
-
-# Unpack source
-tar -xvzf gmsh-${VER}-source.tgz
-
-# Move source to 'src' directory
-mv gmsh-${VER}-source/* src
-rm -rf gmsh-${VER}-source
-
-# Configure
-#
-# NOTE:
-# - Option -DENABLE_FLTK=0 is used because we do not need GUI.
-# - Option -DENABLE_MPEG_ENCODE=0 is used because we do not need to record MPEG
-# movies.
-# - Option -DENABLE_OCC=0 is used because we do not need CAD kernel and are not
-# importing STEP/IGES files.
-# - Option -DENABLE_TOUCHBAR=0 is used because we do not have GUI, therefore we
-# do not need to support Apple Touch bar (does not affect compilation on
-# Linux).
-#
-cd src
-cmake \
- -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
- -DENABLE_BUILD_DYNAMIC=1 \
- -DENABLE_BUILD_SHARED=1 \
- -DENABLE_FLTK=0 \
- -DENABLE_MPEG_ENCODE=0 \
- -DENABLE_MPI=1 \
- -DENABLE_OCC=0 \
- -DENABLE_TOUCHBAR=0 \
- -DMETIS_ROOT="${METIS_ROOT}"
-
-# Compile and install
-if [ $# -eq 0 ]; then
- make
- make install
-else
- make -j $1
- make -j $1 install
-fi
-
-# Make necessary link on RHEL
-if [[ -d ${PREFIX}/lib64 && ! -d ${PREFIX}/lib ]]; then
- cd ${PREFIX}
- ln -s ./lib64 ./lib
-fi
Index: /issm/trunk/externalpackages/gmt/configs/6/static/cmake/modules/FindGDAL.cmake
===================================================================
--- /issm/trunk/externalpackages/gmt/configs/6/static/cmake/modules/FindGDAL.cmake (revision 27231)
+++ /issm/trunk/externalpackages/gmt/configs/6/static/cmake/modules/FindGDAL.cmake (revision 27232)
@@ -148,4 +148,6 @@
NAMES ${_extralib}
HINTS
+ ${NETCDF_ROOT}
+ $ENV{NETCDF_ROOT}
${HDF5_ROOT}
$ENV{HDF5_ROOT}
Index: /issm/trunk/externalpackages/gmt/configs/6/static/cmake/modules/FindNETCDF.cmake
===================================================================
--- /issm/trunk/externalpackages/gmt/configs/6/static/cmake/modules/FindNETCDF.cmake (revision 27231)
+++ /issm/trunk/externalpackages/gmt/configs/6/static/cmake/modules/FindNETCDF.cmake (revision 27232)
@@ -130,5 +130,5 @@
# find all manually-supplied libs
if (NETCDF_EXTRA_LIBS)
- # Ensure -l is precedeced by whitespace to not match
+ # Ensure -l is preceded by whitespace to not match
# '-l' in '-L/usr/lib/x86_64-linux-gnu/hdf5/serial'
string (REGEX MATCHALL "(^| )-l[^ ]+" _netcdf_extra_lib_dashl ${NETCDF_EXTRA_LIBS})
Index: /issm/trunk/externalpackages/gmt/configs/6/static/linux/cmake/ConfigUser.static.cmake
===================================================================
--- /issm/trunk/externalpackages/gmt/configs/6/static/linux/cmake/ConfigUser.static.cmake (revision 27231)
+++ /issm/trunk/externalpackages/gmt/configs/6/static/linux/cmake/ConfigUser.static.cmake (revision 27232)
@@ -58,6 +58,6 @@
# Exclude optional GDAL, PCRE, PCRE2, FFTW3, LAPACK, BLAS, ZLIB dependencies even if you have them installed [FALSE]
#set (GMT_EXCLUDE_GDAL TRUE)
-#set (GMT_EXCLUDE_PCRE TRUE)
-#set (GMT_EXCLUDE_PCRE2 TRUE)
+set (GMT_EXCLUDE_PCRE TRUE)
+set (GMT_EXCLUDE_PCRE2 TRUE)
#set (GMT_EXCLUDE_FFTW3 TRUE)
#set (GMT_EXCLUDE_LAPACK TRUE)
@@ -112,5 +112,5 @@
# Copy GSHHG files to ${GMT_DATADIR}/coast [FALSE]:
-#set (COPY_GSHHG TRUE)
+set (COPY_GSHHG TRUE)
# Set path to DCW Digital Chart of the World for GMT [auto]:
Index: /issm/trunk/externalpackages/gmt/configs/6/static/mac/cmake/ConfigUser.static.cmake
===================================================================
--- /issm/trunk/externalpackages/gmt/configs/6/static/mac/cmake/ConfigUser.static.cmake (revision 27231)
+++ /issm/trunk/externalpackages/gmt/configs/6/static/mac/cmake/ConfigUser.static.cmake (revision 27232)
@@ -58,6 +58,6 @@
# Exclude optional GDAL, PCRE, PCRE2, FFTW3, LAPACK, BLAS, ZLIB dependencies even if you have them installed [FALSE]
#set (GMT_EXCLUDE_GDAL TRUE)
-#set (GMT_EXCLUDE_PCRE TRUE)
-#set (GMT_EXCLUDE_PCRE2 TRUE)
+set (GMT_EXCLUDE_PCRE TRUE)
+set (GMT_EXCLUDE_PCRE2 TRUE)
#set (GMT_EXCLUDE_FFTW3 TRUE)
#set (GMT_EXCLUDE_LAPACK TRUE)
@@ -112,5 +112,5 @@
# Copy GSHHG files to ${GMT_DATADIR}/coast [FALSE]:
-#set (COPY_GSHHG TRUE)
+set (COPY_GSHHG TRUE)
# Set path to DCW Digital Chart of the World for GMT [auto]:
Index: /issm/trunk/externalpackages/gmt/install-6-linux-static.sh
===================================================================
--- /issm/trunk/externalpackages/gmt/install-6-linux-static.sh (revision 27231)
+++ /issm/trunk/externalpackages/gmt/install-6-linux-static.sh (revision 27232)
@@ -5,18 +5,14 @@
## Constants
#
-VER="6.0.0"
+VER="6.4.0"
# Find libgfortran and libgcc so we do not have to hardcode them
#
-# NOTE: For now, paths are hardcoded.
-#
# TODO:
# - Move this to etc/environment.sh
-# - Figure out how to find and grep for single result like we do with mdfind
-# under macOS.
#
-LIBGFORTRAN="/usr/lib/gcc/x86_64-linux-gnu/8/libgfortran.a"
+LIBGFORTRAN=$(find /usr -name libgfortran* | egrep -n libgfortran.a | sed "s/[0-9]*://g" | head -1)
LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*}
-LIBGCC="/usr/lib/gcc/x86_64-linux-gnu/8/libgcc.a"
+LIBGCC=$(find ${LIBGFORTRAN_ROOT} -name libgcc* | egrep -n libgcc.a | sed "s/[0-9]*://g" | head -1)
GDAL_EXTRA_LIBS="-lstdc++" # Determined by running `$GDAL_ROOT/bin/gdal-config --dep-libs` then removing duplicate libs
@@ -65,4 +61,6 @@
cmake \
-DBLAS_LIBRARIES="${BLAS_ROOT}/lib/libfblas.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \
+ -DCURL_INCLUDE_DIR="${CURL_ROOT}/include" \
+ -DCURL_LIBRARY="${CURL_ROOT}/lib/libcurl.a" \
-DGDAL_EXTRA_LIBS="${GDAL_EXTRA_LIBS}" \
-DHDF5_ROOT="${HDF5_ROOT}" \
Index: /issm/trunk/externalpackages/gmt/install-6-linux.sh
===================================================================
--- /issm/trunk/externalpackages/gmt/install-6-linux.sh (revision 27231)
+++ /issm/trunk/externalpackages/gmt/install-6-linux.sh (revision 27232)
@@ -5,5 +5,13 @@
## Constants
#
-VER="6.0.0"
+VER="6.4.0"
+
+# Find libgfortran so that we do not have to hardcode it.
+#
+# TODO:
+# - Move this to etc/environment.sh
+#
+LIBGFORTRAN=$(find /usr -name libgfortran* | egrep -n libgfortran.a | sed "s/[0-9]*://g" | head -1)
+LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*}
# Environment
@@ -42,6 +50,8 @@
#
cmake \
- -DCURL_LIBRARY="${CURL_ROOT}/lib" \
+ -DBLAS_LIBRARIES="-L${BLAS_ROOT}/lib;-lfblas;-L${LIBGFORTRAN_ROOT};-lgfortran" \
-DCURL_INCLUDE_DIR="${CURL_ROOT}/include" \
+ -DCURL_LIBRARY="-L${CURL_ROOT}/lib;-lcurl" \
+ -DLAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib;-lflapack;-L${LIBGFORTRAN_ROOT};-lgfortran" \
..
Index: /issm/trunk/externalpackages/gmt/install-6-mac-static.sh
===================================================================
--- /issm/trunk/externalpackages/gmt/install-6-mac-static.sh (revision 27231)
+++ /issm/trunk/externalpackages/gmt/install-6-mac-static.sh (revision 27232)
@@ -5,5 +5,5 @@
## Constants
#
-VER="6.0.0"
+VER="6.4.0"
# Find libgfortran and libgcc so we do not have to hardcode them
@@ -16,10 +16,10 @@
# - Otherwise, refactor this to work with other gfortran installations.
#
-LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | grep -n libgfortran.a | grep -v i386 | sed "s/[0-9]*://g" | head -1)
+LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1)
LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*}
-LIBGCC=$(mdfind -onlyin ${LIBGFORTRAN_ROOT} -name libgcc | grep -n libgcc.a | grep -v i386 | sed "s/[0-9]*://g" | head -1)
+LIBGCC=$(mdfind -onlyin ${LIBGFORTRAN_ROOT} -name libgcc | egrep -n libgcc.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1)
-GDAL_EXTRA_LIBS="-lc++" # `$GDAL_ROOT/bin/gdal-config --dep-libs` does not report need to link to libc++ (see also customized configuration file ./configs/6.0/static/cmake/modules/FindGDAL.cmake)
-NETCDF_EXTRA_LIBS="-lsqlite3 -lpthread -ldl -liconv" # `$NETCDF_ROOT/bin/nc-config --libs` does not report certain dependencies of certain static libraries (see also customized configuration file ./configs/6.0/static/cmake/modules/FindNETCDF.cmake)
+GDAL_EXTRA_LIBS="-lc++" # `$GDAL_ROOT/bin/gdal-config --dep-libs` does not report need to link to libc++ (see also customized configuration file ./configs/6/static/cmake/modules/FindGDAL.cmake)
+NETCDF_EXTRA_LIBS="-lsqlite3 -lpthread -ldl -liconv" # `$NETCDF_ROOT/bin/nc-config --libs` does not report certain dependencies of certain static libraries (see also customized configuration file ./configs/6/static/cmake/modules/FindNETCDF.cmake)
# Environment
@@ -65,4 +65,6 @@
cmake \
-DBLAS_LIBRARIES="${BLAS_ROOT}/lib/libfblas.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \
+ -DCURL_INCLUDE_DIR="${CURL_ROOT}/include" \
+ -DCURL_LIBRARY="${CURL_ROOT}/lib/libcurl.a" \
-DGDAL_EXTRA_LIBS="${GDAL_EXTRA_LIBS}" \
-DHDF5_ROOT="${HDF5_ROOT}" \
Index: /issm/trunk/externalpackages/gmt/install-6-mac.sh
===================================================================
--- /issm/trunk/externalpackages/gmt/install-6-mac.sh (revision 27231)
+++ /issm/trunk/externalpackages/gmt/install-6-mac.sh (revision 27232)
@@ -5,5 +5,16 @@
## Constants
#
-VER="6.0.0"
+VER="6.4.0"
+
+# Find libgfortran so that we do not have to hardcode it.
+#
+# Should retrieve a copy of gfortran that is compiled from source before
+# returning one that is installed via package manager.
+#
+# TODO:
+# - Move this to etc/environment.sh
+#
+LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1)
+LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*}
# Environment
@@ -42,6 +53,8 @@
#
cmake \
- -DCURL_LIBRARY="${CURL_ROOT}/lib" \
+ -DBLAS_LIBRARIES="-L${BLAS_ROOT}/lib;-lfblas;-L${LIBGFORTRAN_ROOT};-lgfortran" \
-DCURL_INCLUDE_DIR="${CURL_ROOT}/include" \
+ -DCURL_LIBRARY="-L${CURL_ROOT}/lib;-lcurl" \
+ -DLAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib;-lflapack;-L${LIBGFORTRAN_ROOT};-lgfortran" \
..
Index: /issm/trunk/externalpackages/gsl/install-javascript.sh
===================================================================
--- /issm/trunk/externalpackages/gsl/install-javascript.sh (revision 27231)
+++ /issm/trunk/externalpackages/gsl/install-javascript.sh (revision 27232)
@@ -3,12 +3,7 @@
-## TODO:
-# - Revisit enviroment variables (especially EMCC_CFLAGS) once support for
-# Fortran has been accomplished.
-#
-
## Constants
#
-VER="1.15"
+VER="2.7"
PREFIX="${ISSM_DIR}/externalpackages/gsl/install" # Set to location where external package should be installed
@@ -21,5 +16,4 @@
export RANLIB=emranlib
#export EMCC_DEBUG=1 # Uncomment to enable debugging
-export EMCC_CFLAGS="-s ERROR_ON_UNDEFINED_SYMBOLS=0" # Required after v1.38.14 to avoid undefined symbol warnings from our Fortran object files being treated as errors
# Source Emscripten environment
Index: /issm/trunk/externalpackages/gsl/install-static.sh
===================================================================
--- /issm/trunk/externalpackages/gsl/install-static.sh (revision 27231)
+++ /issm/trunk/externalpackages/gsl/install-static.sh (revision 27232)
@@ -5,5 +5,5 @@
## Constants
#
-VER="1.15"
+VER="2.7"
PREFIX="${ISSM_DIR}/externalpackages/gsl/install" # Set to location where external package should be installed
Index: /issm/trunk/externalpackages/gsl/install.sh
===================================================================
--- /issm/trunk/externalpackages/gsl/install.sh (revision 27231)
+++ /issm/trunk/externalpackages/gsl/install.sh (revision 27232)
@@ -3,7 +3,7 @@
-# Constants
+## Constants
#
-VER="1.15"
+VER="2.7"
PREFIX="${ISSM_DIR}/externalpackages/gsl/install" # Set to location where external package should be installed
Index: /issm/trunk/externalpackages/mplapack/install-1-linux.sh
===================================================================
--- /issm/trunk/externalpackages/mplapack/install-1-linux.sh (revision 27231)
+++ /issm/trunk/externalpackages/mplapack/install-1-linux.sh (revision 27232)
@@ -56,4 +56,5 @@
--enable-fast-install=yes \
--disable-dependency-tracking \
+ --enable-optimization=yes \
--enable-fortranwrapper=yes \
--enable-gmp=yes \
Index: /issm/trunk/externalpackages/mplapack/install-2-linux.sh
===================================================================
--- /issm/trunk/externalpackages/mplapack/install-2-linux.sh (revision 27232)
+++ /issm/trunk/externalpackages/mplapack/install-2-linux.sh (revision 27232)
@@ -0,0 +1,75 @@
+#!/bin/bash
+set -eu
+
+##
+# Source code and installation guidelines available at,
+#
+# https://github.com/nakatamaho/mplapack
+#
+# Note that original website (for MPACK) at,
+#
+# http://mplapack.sourceforge.net
+#
+# is not maintained.
+#
+
+## Constants
+#
+VER="2.0"
+
+PREFIX="${ISSM_DIR}/externalpackages/mplapack/install" # Set to location where external package should be installed
+
+## Environment
+#
+export CC=gcc
+export CXX=g++
+export FC=gfortran
+export F77=gfortran
+
+# Cleanup
+rm -rf ${PREFIX} src
+mkdir -p ${PREFIX} src
+
+# Download source
+${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/mplapack-${VER}.tar.gz" "mplapack-${VER}.tar.gz"
+
+# Unpack source
+tar -zxvf mplapack-${VER}.tar.gz
+
+# Move source to 'src' directory
+mv mplapack-${VER}/* src
+rm -rf mplapack-${VER}
+
+# Configure
+cd src
+pushd mplapack/test/compare
+bash gen.Makefile.am.sh
+popd
+autoreconf --force --install
+aclocal
+autoconf
+automake --add-missing
+autoreconf --force --install
+./configure \
+ --prefix="${PREFIX}" \
+ --disable-static \
+ --enable-fast-install=yes \
+ --disable-dependency-tracking \
+ --enable-optimization=yes \
+ --enable-fortranwrapper=yes \
+ --enable-gmp=yes \
+ --enable-mpfr=yes \
+ --enable-qd=yes \
+ --enable-dd=yes \
+ --enable-double=yes \
+ --enable-_Float128=yes \
+ --enable-_Float64x=yes
+
+# Compile and install
+if [ $# -eq 0 ]; then
+ make
+ make install
+else
+ make -j $1
+ make -j $1 install
+fi
Index: /issm/trunk/externalpackages/petsc/install-3.12-linux.sh
===================================================================
--- /issm/trunk/externalpackages/petsc/install-3.12-linux.sh (revision 27231)
+++ /issm/trunk/externalpackages/petsc/install-3.12-linux.sh (revision 27232)
@@ -18,5 +18,5 @@
# Cleanup
rm -rf ${PREFIX} ${PETSC_DIR}
-mkdir ${PETSC_DIR}
+mkdir -p ${PETSC_DIR}
# Move source to $PETSC_DIR
Index: /issm/trunk/externalpackages/petsc/install-3.12-lonestar.sh
===================================================================
--- /issm/trunk/externalpackages/petsc/install-3.12-lonestar.sh (revision 27231)
+++ /issm/trunk/externalpackages/petsc/install-3.12-lonestar.sh (revision 27232)
@@ -1,8 +1,12 @@
#!/bin/bash
set -eu
+
## Constants
#
VER="3.12.3"
+
+PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS
+PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed
# Download source
@@ -13,16 +17,16 @@
# Cleanup
-rm -rf install src
-mkdir install src
+rm -rf ${PREFIX} ${PETSC_DIR}
+mkdir -p ${PETSC_DIR}
-# Move source to 'src' directory
-mv petsc-${VER}/* src/
+# Move source to $PETSC_DIR
+mv petsc-${VER}/* ${PETSC_DIR}
rm -rf petsc-${VER}
-#configure
-cd src
+# Configure
+cd ${PETSC_DIR}
./config/configure.py \
- --prefix="$ISSM_DIR/externalpackages/petsc/install" \
- --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
+ --prefix="${PREFIX}" \
+ --PETSC_DIR="${PETSC_DIR}" \
--with-mpi-dir="/opt/cray/pe/mpt/7.7.3/gni/mpich-intel/16.0/" \
--with-blas-lapack-dir="$TACC_MKL_LIB" \
Index: /issm/trunk/externalpackages/petsc/install-3.12-mac.sh
===================================================================
--- /issm/trunk/externalpackages/petsc/install-3.12-mac.sh (revision 27231)
+++ /issm/trunk/externalpackages/petsc/install-3.12-mac.sh (revision 27232)
@@ -18,5 +18,5 @@
# Cleanup
rm -rf ${PREFIX} ${PETSC_DIR}
-mkdir ${PETSC_DIR}
+mkdir -p ${PETSC_DIR}
# Move source to $PETSC_DIR
Index: /issm/trunk/externalpackages/petsc/install-3.12-win-msys2-gcc-msmpi.sh
===================================================================
--- /issm/trunk/externalpackages/petsc/install-3.12-win-msys2-gcc-msmpi.sh (revision 27231)
+++ /issm/trunk/externalpackages/petsc/install-3.12-win-msys2-gcc-msmpi.sh (revision 27232)
@@ -18,5 +18,5 @@
# Cleanup
rm -rf ${PREFIX} ${PETSC_DIR}
-mkdir ${PETSC_DIR}
+mkdir -p ${PETSC_DIR}
# Move source to $PETSC_DIR
Index: /issm/trunk/externalpackages/petsc/install-3.13-pleiades.sh
===================================================================
--- /issm/trunk/externalpackages/petsc/install-3.13-pleiades.sh (revision 27231)
+++ /issm/trunk/externalpackages/petsc/install-3.13-pleiades.sh (revision 27232)
@@ -20,5 +20,5 @@
# Cleanup
rm -rf ${PREFIX} ${PETSC_DIR}
-mkdir ${PETSC_DIR}
+mkdir -p ${PETSC_DIR}
# Move source to $PETSC_DIR
Index: /issm/trunk/externalpackages/petsc/install-3.14-discover.sh
===================================================================
--- /issm/trunk/externalpackages/petsc/install-3.14-discover.sh (revision 27231)
+++ /issm/trunk/externalpackages/petsc/install-3.14-discover.sh (revision 27232)
@@ -3,15 +3,13 @@
-# NOTE: There is a single difference between the Linux and macOS
-# configurations, which is the addition of the -static-libgfortran
-# option to FFLAGS on the macOS static configurations. For the sake of
-# consistency, we maintain separate files for each, respective Linux and
-# macOS configuration.
-
-# Constants
+## Constants
+#
VER="3.14.6"
+PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS
+PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed
+
# Download source
-$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
# Unpack source
@@ -19,17 +17,17 @@
# Cleanup
-rm -rf install src
-mkdir install src
+rm -rf ${PREFIX} ${PETSC_DIR}
+mkdir -p ${PETSC_DIR}
-# Move source to 'src' directory
-mv petsc-${VER}/* src/
+# Move source to $PETSC_DIR
+mv petsc-${VER}/* ${PETSC_DIR}
rm -rf petsc-${VER}
# Configure
-cd src
+cd ${PETSC_DIR}
./config/configure.py \
COPTFLAGS="-g -O3" CXXOPTFLAGS="-g -O3" FOPTFLAGS="-g -O3" \
- --prefix="${ISSM_DIR}/externalpackages/petsc/install" \
- --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
+ --prefix="${PREFIX}" \
+ --PETSC_DIR="${PETSC_DIR}" \
--with-debugging=0 \
--with-valgrind=0 \
Index: /issm/trunk/externalpackages/petsc/install-3.14-greenplanet.sh
===================================================================
--- /issm/trunk/externalpackages/petsc/install-3.14-greenplanet.sh (revision 27231)
+++ /issm/trunk/externalpackages/petsc/install-3.14-greenplanet.sh (revision 27232)
@@ -2,24 +2,34 @@
set -eu
-#WARNING: make sure you have the right mpi
-#Some cleanup
-rm -rf install petsc-3.14.0 src
-mkdir install src
+# WARNING: Make sure you have the right MPI
-#Download from ISSM server
-$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.14.0.tar.gz' 'petsc-3.14.0.tar.gz'
+## Constants
+#
+VER="3.14.0"
-#Untar and move petsc to install directory
-tar -zxvf petsc-3.14.0.tar.gz
-mv petsc-3.14.0/* src/
-rm -rf petsc-3.14.0
+PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS
+PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed
+
+# Download source
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
+
+# Unpack source
+tar -zxvf petsc-${VER}.tar.gz
+
+# Cleanup
+rm -rf ${PREFIX} ${PETSC_DIR}
+mkdir -p ${PETSC_DIR}
+
+# Move source to $PETSC_DIR
+mv petsc-${VER}/* ${PETSC_DIR}
+rm -rf petsc-${VER}
#configure
-cd src
+cd ${PETSC_DIR}
./config/configure.py \
COPTFLAGS="-g -O3" CXXOPTFLAGS="-g -O3" FOPTFLAGS="-g -O3" \
- --prefix="$ISSM_DIR/externalpackages/petsc/install" \
- --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
+ --prefix="${PREFIX}" \
+ --PETSC_DIR="${PETSC_DIR}" \
--with-blas-lapack-dir="/sopt/INTEL/compilers_and_libraries_2018.3.222/linux/mkl/" \
--with-mpi-dir="/sopt/OpenMPI/3.1.2/intel-2018.3-slim/" \
Index: /issm/trunk/externalpackages/petsc/install-3.14-linux.sh
===================================================================
--- /issm/trunk/externalpackages/petsc/install-3.14-linux.sh (revision 27231)
+++ /issm/trunk/externalpackages/petsc/install-3.14-linux.sh (revision 27232)
@@ -18,5 +18,5 @@
# Cleanup
rm -rf ${PREFIX} ${PETSC_DIR}
-mkdir ${PETSC_DIR}
+mkdir -p ${PETSC_DIR}
# Move source to $PETSC_DIR
Index: /issm/trunk/externalpackages/petsc/install-3.14-mac-nohdf5.sh
===================================================================
--- /issm/trunk/externalpackages/petsc/install-3.14-mac-nohdf5.sh (revision 27231)
+++ /issm/trunk/externalpackages/petsc/install-3.14-mac-nohdf5.sh (revision 27232)
@@ -18,5 +18,5 @@
# Cleanup
rm -rf ${PREFIX} ${PETSC_DIR}
-mkdir ${PETSC_DIR}
+mkdir -p ${PETSC_DIR}
# Move source to $PETSC_DIR
Index: /issm/trunk/externalpackages/petsc/install-3.14-mac.sh
===================================================================
--- /issm/trunk/externalpackages/petsc/install-3.14-mac.sh (revision 27231)
+++ /issm/trunk/externalpackages/petsc/install-3.14-mac.sh (revision 27232)
@@ -18,5 +18,5 @@
# Cleanup
rm -rf ${PREFIX} ${PETSC_DIR}
-mkdir ${PETSC_DIR}
+mkdir -p ${PETSC_DIR}
# Move source to $PETSC_DIR
Index: /issm/trunk/externalpackages/petsc/install-3.14-pleiades.sh
===================================================================
--- /issm/trunk/externalpackages/petsc/install-3.14-pleiades.sh (revision 27231)
+++ /issm/trunk/externalpackages/petsc/install-3.14-pleiades.sh (revision 27232)
@@ -18,5 +18,5 @@
# Cleanup
rm -rf ${PREFIX} ${PETSC_DIR}
-mkdir ${PETSC_DIR}
+mkdir -p ${PETSC_DIR}
# Move source to $PETSC_DIR
Index: /issm/trunk/externalpackages/petsc/install-3.14-tetralith.sh
===================================================================
--- /issm/trunk/externalpackages/petsc/install-3.14-tetralith.sh (revision 27231)
+++ /issm/trunk/externalpackages/petsc/install-3.14-tetralith.sh (revision 27232)
@@ -3,12 +3,10 @@
-# NOTE: There is a single difference between the Linux and macOS
-# configurations, which is the addition of the -static-libgfortran
-# option to FFLAGS on the macOS static configurations. For the sake of
-# consistency, we maintain separate files for each, respective Linux and
-# macOS configuration.
+## Constants
+#
+VER="3.14.6"
-# Constants
-VER="3.14.6"
+PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS
+PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed
# Download source
@@ -19,17 +17,17 @@
# Cleanup
-rm -rf install src
-mkdir install src
+rm -rf ${PREFIX} ${PETSC_DIR}
+mkdir -p ${PETSC_DIR}
-# Move source to 'src' directory
-mv petsc-${VER}/* src/
+# Move source to $PETSC_DIR
+mv petsc-${VER}/* ${PETSC_DIR}
rm -rf petsc-${VER}
# Configure
-cd src
+cd ${PETSC_DIR}
./config/configure.py \
COPTFLAGS="-g -O2" CXXOPTFLAGS="-g -O2" FOPTFLAGS="-g -O2" \
- --prefix="${ISSM_DIR}/externalpackages/petsc/install" \
- --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
+ --prefix="${PREFIX}" \
+ --PETSC_DIR="${PETSC_DIR}" \
--with-debugging=0 \
--with-valgrind=0 \
Index: /issm/trunk/externalpackages/petsc/install-3.14-win-msys2-mingw-msmpi.sh
===================================================================
--- /issm/trunk/externalpackages/petsc/install-3.14-win-msys2-mingw-msmpi.sh (revision 27231)
+++ /issm/trunk/externalpackages/petsc/install-3.14-win-msys2-mingw-msmpi.sh (revision 27232)
@@ -32,5 +32,5 @@
# Cleanup
rm -rf ${PREFIX} ${PETSC_DIR}
-mkdir ${PETSC_DIR}
+mkdir -p ${PETSC_DIR}
# Move source to $PETSC_DIR
Index: /issm/trunk/externalpackages/petsc/install-3.15-babylon.sh
===================================================================
--- /issm/trunk/externalpackages/petsc/install-3.15-babylon.sh (revision 27231)
+++ /issm/trunk/externalpackages/petsc/install-3.15-babylon.sh (revision 27232)
@@ -11,5 +11,5 @@
# Download source
-$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
# Unpack source
@@ -18,5 +18,5 @@
# Cleanup
rm -rf ${PREFIX} ${PETSC_DIR}
-mkdir ${PETSC_DIR}
+mkdir -p ${PETSC_DIR}
# Move source to $PETSC_DIR
Index: /issm/trunk/externalpackages/petsc/install-3.15-discovery.sh
===================================================================
--- /issm/trunk/externalpackages/petsc/install-3.15-discovery.sh (revision 27231)
+++ /issm/trunk/externalpackages/petsc/install-3.15-discovery.sh (revision 27232)
@@ -3,8 +3,12 @@
## Constants
+#
VER="3.15.3"
+PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS
+PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed
+
# Download source
-$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
# Unpack source
@@ -12,16 +16,17 @@
# Cleanup
-rm -rf install src
-mkdir install src
+rm -rf ${PREFIX} ${PETSC_DIR}
+mkdir -p ${PETSC_DIR}
-# Move source to 'src' directory
-mv petsc-${VER}/* src/
+# Move source to $PETSC_DIR
+mv petsc-${VER}/* ${PETSC_DIR}
rm -rf petsc-${VER}
-cd src
+# Configure
+cd ${PETSC_DIR}
./config/configure.py \
COPTFLAGS="-g -O3" CXXOPTFLAGS="-g -O3" FOPTFLAGS="-g -O3" \
- --prefix="${ISSM_DIR}/externalpackages/petsc/install" \
- --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
+ --prefix="${PREFIX}" \
+ --PETSC_DIR="${PETSC_DIR}" \
--with-make-np=20 \
--with-blas-lapack-dir=$MKL_ROOT \
Index: /issm/trunk/externalpackages/petsc/install-3.15-pleiades.sh
===================================================================
--- /issm/trunk/externalpackages/petsc/install-3.15-pleiades.sh (revision 27231)
+++ /issm/trunk/externalpackages/petsc/install-3.15-pleiades.sh (revision 27232)
@@ -14,20 +14,21 @@
# Unpack source
-tar -zxvf petsc-3.15.0.tar.gz
+tar -zxvf petsc-${VER}.tar.gz
# Cleanup
-rm -rf install src
-mkdir install src
+rm -rf ${PREFIX} ${PETSC_DIR}
+mkdir -p ${PETSC_DIR}
# Move source to $PETSC_DIR
-mv petsc-3.15.0/* src/
-rm -rf petsc-3.15.0
-
+mv petsc-${VER}/* ${PETSC_DIR}
+rm -rf petsc-${VER}
# Configure
#
-# NOTE: Based on /nasa/petsc/3.7.5/intel_mpt/lib/petsc/conf/petscvariables; look for CONFIGURE_OPTIONS
+# NOTE:
+# - Based on /nasa/petsc/3.7.5/intel_mpt/lib/petsc/conf/petscvariables (look
+# for CONFIGURE_OPTIONS)
#
-cd src
+cd ${PETSC_DIR}
./config/configure.py \
--prefix="${PREFIX}" \
Index: /issm/trunk/externalpackages/petsc/install-3.16-linux.sh
===================================================================
--- /issm/trunk/externalpackages/petsc/install-3.16-linux.sh (revision 27231)
+++ /issm/trunk/externalpackages/petsc/install-3.16-linux.sh (revision 27232)
@@ -3,4 +3,5 @@
## Constants
+#
VER="3.16.0"
@@ -9,5 +10,5 @@
# Download source
-$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
# Unpack source
@@ -15,16 +16,16 @@
# Cleanup
-rm -rf install src
-mkdir install src
+rm -rf ${PREFIX} ${PETSC_DIR}
+mkdir -p ${PETSC_DIR}
# Move source to $PETSC_DIR
-mv petsc-${VER}/* src/
+mv petsc-${VER}/* ${PETSC_DIR}
rm -rf petsc-${VER}
# Configure
-cd src
+cd ${PETSC_DIR}
./config/configure.py \
- --prefix="${ISSM_DIR}/externalpackages/petsc/install" \
- --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
+ --prefix="${PREFIX}" \
+ --PETSC_DIR="${PETSC_DIR}" \
-COPTFLAGS="-g -O2" -CXXOPTFLAGS="-g -O2" -FOPTFLAGS="-g -O2" \
--with-debugging=0 \
Index: /issm/trunk/externalpackages/petsc/install-3.16-mac.sh
===================================================================
--- /issm/trunk/externalpackages/petsc/install-3.16-mac.sh (revision 27232)
+++ /issm/trunk/externalpackages/petsc/install-3.16-mac.sh (revision 27232)
@@ -0,0 +1,60 @@
+#!/bin/bash
+set -eu
+
+
+## Constants
+#
+VER="3.16.6"
+
+PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS
+PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed
+
+# Download source
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
+
+# Unpack source
+tar -zxvf petsc-${VER}.tar.gz
+
+# Cleanup
+rm -rf ${PREFIX} ${PETSC_DIR}
+mkdir -p ${PETSC_DIR}
+
+# Move source to $PETSC_DIR
+mv petsc-${VER}/* ${PETSC_DIR}
+rm -rf petsc-${VER}
+
+# Configure
+#
+# NOTE:
+# - Added -Wno-error=implicit-function-declaration to CFLAGS for Clang >= 12.
+# (may need to remove it for earlier versions not using the C99 standard).
+# - Added -fallow-argument-mismatch to FFLAGS in order to clear,
+#
+# error: The Fortran compiler gfortran will not compile files that call
+# the same routine with arguments of different types.
+#
+# for gfortran 10 or later (may need to remove it for earlier versions).
+#
+cd ${PETSC_DIR}
+./config/configure.py \
+ --prefix="${PREFIX}" \
+ --PETSC_DIR="${PETSC_DIR}" \
+ --CFLAGS="-Wno-error=implicit-function-declaration" \
+ --FFLAGS="-fallow-argument-mismatch" \
+ --with-debugging=0 \
+ --with-valgrind=0 \
+ --with-x=0 \
+ --with-ssl=0 \
+ --with-pic=1 \
+ --download-fblaslapack=1 \
+ --download-mpich=1 \
+ --download-metis=1 \
+ --download-parmetis=1 \
+ --download-scalapack=1 \
+ --download-mumps=1 \
+ --download-zlib=1 \
+ --download-hdf5=1
+
+# Compile and install
+make
+make install
Index: /issm/trunk/externalpackages/petsc/install-3.16-pleiades.sh
===================================================================
--- /issm/trunk/externalpackages/petsc/install-3.16-pleiades.sh (revision 27231)
+++ /issm/trunk/externalpackages/petsc/install-3.16-pleiades.sh (revision 27232)
@@ -17,9 +17,9 @@
# Cleanup
-rm -rf install src
-mkdir install src
+rm -rf ${PREFIX} ${PETSC_DIR}
+mkdir -p ${PETSC_DIR}
# Move source to $PETSC_DIR
-mv petsc-${VER}/* src/
+mv petsc-${VER}/* ${PETSC_DIR}
rm -rf petsc-${VER}
@@ -27,7 +27,9 @@
# Configure
#
-# NOTE: Based on /nasa/petsc/3.7.5/intel_mpt/lib/petsc/conf/petscvariables; look for CONFIGURE_OPTIONS
+# NOTE:
+# - Based on /nasa/petsc/3.7.5/intel_mpt/lib/petsc/conf/petscvariables (look
+# for CONFIGURE_OPTIONS)
#
-cd src
+cd ${PETSC_DIR}
./config/configure.py \
--prefix="${PREFIX}" \
Index: /issm/trunk/externalpackages/petsc/install-3.17-mac-intel.sh
===================================================================
--- /issm/trunk/externalpackages/petsc/install-3.17-mac-intel.sh (revision 27232)
+++ /issm/trunk/externalpackages/petsc/install-3.17-mac-intel.sh (revision 27232)
@@ -0,0 +1,48 @@
+#!/bin/bash
+set -eu
+
+
+## Constants
+#
+VER="3.17.4"
+
+PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS
+PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed
+
+# Download source
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
+
+# Unpack source
+tar -zxvf petsc-${VER}.tar.gz
+
+# Cleanup
+rm -rf ${PREFIX} ${PETSC_DIR}
+mkdir -p ${PETSC_DIR}
+
+# Move source to $PETSC_DIR
+mv petsc-${VER}/* ${PETSC_DIR}
+rm -rf petsc-${VER}
+
+# Configure
+cd ${PETSC_DIR}
+./configure \
+ --prefix="${PREFIX}" \
+ --PETSC_DIR="${PETSC_DIR}" \
+ --with-debugging=0 \
+ --with-valgrind=0 \
+ --with-x=0 \
+ --with-ssl=0 \
+ --with-pic=1 \
+ --download-fblaslapack=1 \
+ --download-mpich=1 \
+ --download-metis=1 \
+ --download-parmetis=1 \
+ --download-scalapack=1 \
+ --download-mumps=1 \
+ --download-zlib=1 \
+ --download-hdf5=1
+
+# Compile and install
+make
+make install
+
Index: /issm/trunk/externalpackages/petsc/install-3.17-mac-m1-static.sh
===================================================================
--- /issm/trunk/externalpackages/petsc/install-3.17-mac-m1-static.sh (revision 27232)
+++ /issm/trunk/externalpackages/petsc/install-3.17-mac-m1-static.sh (revision 27232)
@@ -0,0 +1,64 @@
+#!/bin/bash
+set -eu
+
+
+## Constants
+#
+VER="3.17.4"
+
+PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS
+PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed
+
+# Download source
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
+
+# Unpack source
+tar -zxvf petsc-${VER}.tar.gz
+
+# Cleanup
+rm -rf ${PREFIX} ${PETSC_DIR}
+mkdir -p ${PETSC_DIR}
+
+# Move source to $PETSC_DIR
+mv petsc-${VER}/* ${PETSC_DIR}
+rm -rf petsc-${VER}
+
+# Configure
+#
+# NOTE:
+# - Cannot use --with-fpic option when compiling static libs,
+#
+# Cannot determine compiler PIC flags if shared libraries is turned off
+# Either run using --with-shared-libraries or --with-pic=0 and supply the
+# compiler PIC flag via CFLAGS, CXXXFLAGS, and FCFLAGS
+#
+# - Added -fallow-argument-mismatch to FFLAGS in order to clear,
+#
+# error: The Fortran compiler gfortran will not compile files that call
+# the same routine with arguments of different types.
+#
+# for gfortran 10 or later (may need to remove it for earlier versions).
+cd ${PETSC_DIR}
+./config/configure.py \
+ --prefix="${PREFIX}" \
+ --PETSC_DIR="${PETSC_DIR}" \
+ --LDFLAGS="-Wl,-no_compact_unwind" \
+ --with-shared-libraries=0 \
+ --CFLAGS="-fPIC" \
+ --CXXFLAGS="-fPIC" \
+ --FFLAGS="-fPIC" \
+ --with-debugging=0 \
+ --with-valgrind=0 \
+ --with-x=0 \
+ --with-ssl=0 \
+ --download-fblaslapack=1 \
+ --download-mpich=1 \
+ --download-metis=1 \
+ --download-parmetis=1 \
+ --download-scalapack=1 \
+ --download-mumps=1 \
+ --download-zlib=1
+
+# Compile and install
+make
+make install
Index: /issm/trunk/externalpackages/petsc/install-3.17-mac-m1.sh
===================================================================
--- /issm/trunk/externalpackages/petsc/install-3.17-mac-m1.sh (revision 27231)
+++ /issm/trunk/externalpackages/petsc/install-3.17-mac-m1.sh (revision 27232)
@@ -4,8 +4,12 @@
## Constants
-VER="3.17.0"
+#
+VER="3.17.4"
+
+PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS
+PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed
# Download source
-$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
# Unpack source
@@ -13,15 +17,16 @@
# Cleanup
-rm -rf install src
-mkdir install src
+rm -rf ${PREFIX} ${PETSC_DIR}
+mkdir -p ${PETSC_DIR}
-# Move source to 'src' directory
-mv petsc-${VER}/* src/
+# Move source to $PETSC_DIR
+mv petsc-${VER}/* ${PETSC_DIR}
rm -rf petsc-${VER}
-cd src
+# Configure
+cd ${PETSC_DIR}
./config/configure.py \
- --prefix="${ISSM_DIR}/externalpackages/petsc/install" \
- --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
+ --prefix="${PREFIX}" \
+ --PETSC_DIR="${PETSC_DIR}" \
--LDFLAGS="-Wl,-no_compact_unwind" \
--with-debugging=0 \
Index: /issm/trunk/externalpackages/petsc/install-3.17-pleiades.sh
===================================================================
--- /issm/trunk/externalpackages/petsc/install-3.17-pleiades.sh (revision 27232)
+++ /issm/trunk/externalpackages/petsc/install-3.17-pleiades.sh (revision 27232)
@@ -0,0 +1,58 @@
+#!/bin/bash
+set -eu
+
+
+## Constants
+#
+VER="3.17.4"
+
+PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS
+PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed
+
+# Download source
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
+
+# Unpack source
+tar -zxvf petsc-${VER}.tar.gz
+
+# Cleanup
+rm -rf ${PREFIX} ${PETSC_DIR}
+mkdir -p ${PETSC_DIR}
+
+# Move source to $PETSC_DIR
+mv petsc-${VER}/* ${PETSC_DIR}
+rm -rf petsc-${VER}
+
+# Configure
+#
+# NOTE:
+# - Options from,
+#
+# cat /nasa/petsc/3.14.5_toss3/lib/petsc/conf/petscvariables | grep CONF
+#
+cd ${PETSC_DIR}
+./configure \
+ --prefix="${PREFIX}" \
+ --PETSC_DIR="${PETSC_DIR}" \
+ --with-blas-lapack-dir="/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl" \
+ --with-scalapack-include="/nasa/intel/Compiler/2018.3.222/mkl/include" \
+ --with-scalapack-lib="/nasa/intel/Compiler/2018.3.222/mkl/lib/intel64/libmkl_scalapack_lp64.so /nasa/intel/Compiler/2018.3.222/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.so" \
+ --CFLAGS="-g -O3" \
+ --CXXFLAGS="-g -O3" \
+ --FFLAGS="-g -O3" \
+ --with-make-np=10 \
+ --with-batch=1 \
+ --with-pic=1 \
+ --with-shared-libraries=1 \
+ --with-debugging=0 \
+ --with-valgrind=0 \
+ --with-x=0 \
+ --with-ssl=0 \
+ --download-make=1 \
+ --download-metis=1 \
+ --download-parmetis=1 \
+ --download-mumps=1
+
+# Compile and install
+make
+make install
Index: /issm/trunk/externalpackages/sqlite/install.sh
===================================================================
--- /issm/trunk/externalpackages/sqlite/install.sh (revision 27231)
+++ /issm/trunk/externalpackages/sqlite/install.sh (revision 27232)
@@ -8,4 +8,8 @@
PREFIX="${ISSM_DIR}/externalpackages/sqlite/install" # Set to location where external package should be installed
+
+# Environment
+#
+export CFLAGS="-DSQLITE_ENABLE_COLUMN_METADATA=1"
# Cleanup
Index: /issm/trunk/externalpackages/triangle/install-linux-javascript.sh
===================================================================
--- /issm/trunk/externalpackages/triangle/install-linux-javascript.sh (revision 27231)
+++ /issm/trunk/externalpackages/triangle/install-linux-javascript.sh (revision 27232)
@@ -2,9 +2,4 @@
set -eu
-
-# TODO:
-# - Revisit enviroment variables (especially EMCC_CFLAGS) once support for
-# Fortran has been accomplished.
-#
# Constants
@@ -19,5 +14,4 @@
export RANLIB=emranlib
#export EMCC_DEBUG=1 # Uncomment to enable debugging
-export EMCC_CFLAGS="-s ERROR_ON_UNDEFINED_SYMBOLS=0" # Required after v1.38.14 to avoid undefined symbol warnings from our Fortran object files being treated as errors
# Source Emscripten environment
@@ -26,5 +20,5 @@
# Cleanup
rm -rf ${PREFIX} src
-mkdir ${PREFIX} ${PREFIX}/include ${PREFIX}/share src
+mkdir -p ${PREFIX} ${PREFIX}/include ${PREFIX}/share src
# Download source
Index: /issm/trunk/jenkins/aws-amazon_linux-solid_earth
===================================================================
--- /issm/trunk/jenkins/aws-amazon_linux-solid_earth (revision 27231)
+++ /issm/trunk/jenkins/aws-amazon_linux-solid_earth (revision 27232)
@@ -46,5 +46,5 @@
gshhg install.sh
gmt install-6-linux.sh
- gmsh install-4.sh
+ gmsh install-4-linux.sh
shell2junit install.sh
"
Index: /issm/trunk/jenkins/examples_tests.sh
===================================================================
--- /issm/trunk/jenkins/examples_tests.sh (revision 27231)
+++ /issm/trunk/jenkins/examples_tests.sh (revision 27232)
@@ -40,4 +40,10 @@
for dir in ./* ; do
if [ -d "${dir}" ]; then
+ # # Temporary short circuit to check single example
+ # example="./AMR"
+ # if [ "${dir}" != "${example}" ]; then
+ # continue
+ # fi
+
# Some of the examples are incomplete (on purpose). As such, we will
# have to populate the missing steps in order to make sure that
@@ -45,5 +51,4 @@
cd ${dir}
-
if [ "${dir}" == "./AMR" ]; then
sed -i.bak -e '1 s|^.*$|try\n\n&|' $RUNME_FILE
Index: /issm/trunk/jenkins/jenkins.sh
===================================================================
--- /issm/trunk/jenkins/jenkins.sh (revision 27231)
+++ /issm/trunk/jenkins/jenkins.sh (revision 27232)
@@ -178,28 +178,40 @@
cd ${ISSM_DIR}/externalpackages/$PACKAGENAME
- echo "======================================================";
- echo " Installing $PACKAGENAME ";
- echo "======================================================";
-
- ./$PACKAGEINST $NUMCPUS_INSTALL &> compil.log
- if [ $? -ne 0 ] && [ "${PACKAGENAME}" != "boost" ]; then
- cat compil.log
+ # Do not install package if it already exists
+ #
+ # NOTE: Assumes PREFIX is defined in package installation script
+ #
+ PREFIX=$(egrep "PREFIX=" ./$PACKAGEINST | cut -d'"' -f 2 | envsubst)
+ if [ ! -d "${PREFIX}" ]; then
echo "======================================================";
- echo " ERROR: installation of $PACKAGENAME failed ";
+ echo " Installing $PACKAGENAME ";
echo "======================================================";
- echo "" >> $EXTERNAL_TEST_FILE
- echo 'External packages did not install right. Check it.' >> $EXTERNAL_TEST_FILE
- cat compil.log >> $EXTERNAL_TEST_FILE
- echo '' >> $EXTERNAL_TEST_FILE
- echo '' >> $EXTERNAL_TEST_FILE
- EXTERNALPACKAGES_FAILED=1;
+
+ ./$PACKAGEINST $NUMCPUS_INSTALL &> compil.log
+ if [ $? -ne 0 ] && [ "${PACKAGENAME}" != "boost" ]; then
+ cat compil.log
+ echo "======================================================";
+ echo " ERROR: installation of $PACKAGENAME failed ";
+ echo "======================================================";
+ echo "" >> $EXTERNAL_TEST_FILE
+ echo 'External packages did not install right. Check it.' >> $EXTERNAL_TEST_FILE
+ cat compil.log >> $EXTERNAL_TEST_FILE
+ echo '' >> $EXTERNAL_TEST_FILE
+ echo '' >> $EXTERNAL_TEST_FILE
+ EXTERNALPACKAGES_FAILED=1;
+ else
+ echo "" >> $EXTERNAL_TEST_FILE
+ fi
+ source ${ISSM_DIR}/etc/environment.sh
+
+ #If external package is rebuilt, we also need to recompile
+ ISSM_RECONFIGURE="yes"
+ ISSM_COMPILATION="yes"
else
+ echo "======================================================";
+ echo " Skipping $PACKAGENAME ";
+ echo "======================================================";
echo "" >> $EXTERNAL_TEST_FILE
fi
- source ${ISSM_DIR}/etc/environment.sh
-
- #If external package is rebuilt, we also need to recompile
- ISSM_RECONFIGURE="yes"
- ISSM_COMPILATION="yes"
else
echo "======================================================";
Index: /issm/trunk/jenkins/pine_island-mac-binaries-matlab
===================================================================
--- /issm/trunk/jenkins/pine_island-mac-binaries-matlab (revision 27231)
+++ /issm/trunk/jenkins/pine_island-mac-binaries-matlab (revision 27232)
@@ -56,5 +56,5 @@
gshhg install.sh
gmt install-6-mac-static.sh
- gmsh install-4-static.sh
+ gmsh install-4-mac-static.sh
triangle install-mac-static.sh
chaco install.sh
Index: /issm/trunk/jenkins/pine_island-mac-binaries-python-2
===================================================================
--- /issm/trunk/jenkins/pine_island-mac-binaries-python-2 (revision 27231)
+++ /issm/trunk/jenkins/pine_island-mac-binaries-python-2 (revision 27232)
@@ -54,5 +54,5 @@
gshhg install.sh
gmt install-6-mac-static.sh
- gmsh install-4-static.sh
+ gmsh install-4-mac-static.sh
triangle install-mac-static.sh
chaco install.sh
Index: /issm/trunk/jenkins/pine_island-mac-binaries-python-3
===================================================================
--- /issm/trunk/jenkins/pine_island-mac-binaries-python-3 (revision 27231)
+++ /issm/trunk/jenkins/pine_island-mac-binaries-python-3 (revision 27232)
@@ -55,5 +55,5 @@
gshhg install.sh
gmt install-6-mac-static.sh
- gmsh install-4-static.sh
+ gmsh install-4-mac-static.sh
triangle install-mac-static.sh
chaco install.sh
Index: /issm/trunk/jenkins/pine_island-mac-dakota
===================================================================
--- /issm/trunk/jenkins/pine_island-mac-dakota (revision 27231)
+++ /issm/trunk/jenkins/pine_island-mac-dakota (revision 27232)
@@ -56,5 +56,5 @@
gshhg install.sh
gmt install-6-mac.sh
- gmsh install-4.sh
+ gmsh install-4-mac.sh
triangle install-mac.sh
chaco install.sh
Index: /issm/trunk/jenkins/pine_island-mac-examples
===================================================================
--- /issm/trunk/jenkins/pine_island-mac-examples (revision 27231)
+++ /issm/trunk/jenkins/pine_island-mac-examples (revision 27232)
@@ -57,5 +57,5 @@
gshhg install.sh
gmt install-6-mac.sh
- gmsh install-4.sh
+ gmsh install-4-mac.sh
triangle install-mac.sh
chaco install.sh
Index: /issm/trunk/jenkins/pine_island-mac-full
===================================================================
--- /issm/trunk/jenkins/pine_island-mac-full (revision 27231)
+++ /issm/trunk/jenkins/pine_island-mac-full (revision 27232)
@@ -44,5 +44,5 @@
autotools install-mac.sh
cmake install.sh
- petsc install-3.12-mac.sh
+ petsc install-3.17-mac-intel.sh
gsl install.sh
boost install-1.7-mac.sh
@@ -54,5 +54,5 @@
gshhg install.sh
gmt install-6-mac.sh
- gmsh install-4.sh
+ gmsh install-4-mac.sh
triangle install-mac.sh
chaco install.sh
Index: /issm/trunk/jenkins/pine_island-mac-full-valgrind
===================================================================
--- /issm/trunk/jenkins/pine_island-mac-full-valgrind (revision 27231)
+++ /issm/trunk/jenkins/pine_island-mac-full-valgrind (revision 27232)
@@ -44,5 +44,5 @@
autotools install-mac.sh
cmake install.sh
- petsc install-3.12-mac.sh
+ petsc install-3.16-mac.sh
gsl install.sh
boost install-1.7-mac.sh
@@ -54,5 +54,5 @@
gshhg install.sh
gmt install-6-mac.sh
- gmsh install-4.sh
+ gmsh install-4-mac.sh
triangle install-mac.sh
chaco install.sh
Index: /issm/trunk/jenkins/pine_island-mac-solid_earth
===================================================================
--- /issm/trunk/jenkins/pine_island-mac-solid_earth (revision 27231)
+++ /issm/trunk/jenkins/pine_island-mac-solid_earth (revision 27232)
@@ -56,5 +56,5 @@
gshhg install.sh
gmt install-6-mac.sh
- gmsh install-4.sh
+ gmsh install-4-mac.sh
triangle install-mac.sh
chaco install.sh
Index: /issm/trunk/jenkins/pine_island-mac-solid_earth-lambert
===================================================================
--- /issm/trunk/jenkins/pine_island-mac-solid_earth-lambert (revision 27231)
+++ /issm/trunk/jenkins/pine_island-mac-solid_earth-lambert (revision 27232)
@@ -56,5 +56,5 @@
gshhg install.sh
gmt install-6-mac.sh
- gmsh install-4.sh
+ gmsh install-4-mac.sh
triangle install-mac.sh
chaco install.sh
Index: /issm/trunk/jenkins/pleiades-solid_earth
===================================================================
--- /issm/trunk/jenkins/pleiades-solid_earth (revision 27231)
+++ /issm/trunk/jenkins/pleiades-solid_earth (revision 27232)
@@ -49,5 +49,5 @@
gshhg install.sh
gmt install-6-linux.sh
- gmsh install-4.sh
+ gmsh install-4-linux.sh
triangle install-linux.sh
chaco install.sh
Index: /issm/trunk/jenkins/ross-debian_linux-binaries-matlab
===================================================================
--- /issm/trunk/jenkins/ross-debian_linux-binaries-matlab (revision 27231)
+++ /issm/trunk/jenkins/ross-debian_linux-binaries-matlab (revision 27232)
@@ -54,5 +54,5 @@
gshhg install.sh
gmt install-6-linux-static.sh
- gmsh install-4-static.sh
+ gmsh install-4-linux-static.sh
triangle install-linux-static.sh
chaco install.sh
Index: /issm/trunk/jenkins/ross-debian_linux-binaries-python-2
===================================================================
--- /issm/trunk/jenkins/ross-debian_linux-binaries-python-2 (revision 27231)
+++ /issm/trunk/jenkins/ross-debian_linux-binaries-python-2 (revision 27232)
@@ -54,5 +54,5 @@
gshhg install.sh
gmt install-6-linux-static.sh
- gmsh install-4-static.sh
+ gmsh install-4-linux-static.sh
triangle install-linux-static.sh
chaco install.sh
Index: /issm/trunk/jenkins/ross-debian_linux-binaries-python-3
===================================================================
--- /issm/trunk/jenkins/ross-debian_linux-binaries-python-3 (revision 27231)
+++ /issm/trunk/jenkins/ross-debian_linux-binaries-python-3 (revision 27232)
@@ -55,5 +55,5 @@
gshhg install.sh
gmt install-6-linux-static.sh
- gmsh install-4-static.sh
+ gmsh install-4-linux-static.sh
triangle install-linux-static.sh
chaco install.sh
Index: /issm/trunk/jenkins/ross-debian_linux-dakota
===================================================================
--- /issm/trunk/jenkins/ross-debian_linux-dakota (revision 27231)
+++ /issm/trunk/jenkins/ross-debian_linux-dakota (revision 27232)
@@ -53,5 +53,5 @@
gshhg install.sh
gmt install-6-linux.sh
- gmsh install-4.sh
+ gmsh install-4-linux.sh
triangle install-linux.sh
chaco install.sh
Index: /issm/trunk/jenkins/ross-debian_linux-full
===================================================================
--- /issm/trunk/jenkins/ross-debian_linux-full (revision 27231)
+++ /issm/trunk/jenkins/ross-debian_linux-full (revision 27232)
@@ -54,5 +54,5 @@
gshhg install.sh
gmt install-6-linux.sh
- gmsh install-4.sh
+ gmsh install-4-linux.sh
triangle install-linux.sh
chaco install.sh
Index: /issm/trunk/jenkins/ross-debian_linux-full-mplapack
===================================================================
--- /issm/trunk/jenkins/ross-debian_linux-full-mplapack (revision 27231)
+++ /issm/trunk/jenkins/ross-debian_linux-full-mplapack (revision 27232)
@@ -47,5 +47,5 @@
cmake install.sh
petsc install-3.12-linux.sh
- mplapack install-1-linux.sh
+ mplapack install-2-linux.sh
gsl install.sh
boost install-1.7-linux.sh
@@ -57,5 +57,5 @@
gshhg install.sh
gmt install-6-linux.sh
- gmsh install-4.sh
+ gmsh install-4-linux.sh
triangle install-linux.sh
chaco install.sh
Index: /issm/trunk/jenkins/ross-debian_linux-full-valgrind
===================================================================
--- /issm/trunk/jenkins/ross-debian_linux-full-valgrind (revision 27231)
+++ /issm/trunk/jenkins/ross-debian_linux-full-valgrind (revision 27232)
@@ -54,5 +54,5 @@
gshhg install.sh
gmt install-6-linux.sh
- gmsh install-4.sh
+ gmsh install-4-linux.sh
triangle install-linux.sh
chaco install.sh
Index: /issm/trunk/jenkins/ross-debian_linux-gia
===================================================================
--- /issm/trunk/jenkins/ross-debian_linux-gia (revision 27231)
+++ /issm/trunk/jenkins/ross-debian_linux-gia (revision 27232)
@@ -37,5 +37,5 @@
triangle install-linux.sh
math77 install.sh
- gmsh install-4.sh
+ gmsh install-4-linux.sh
shell2junit install.sh
"
Index: /issm/trunk/jenkins/ross-debian_linux-javascript
===================================================================
--- /issm/trunk/jenkins/ross-debian_linux-javascript (revision 27231)
+++ /issm/trunk/jenkins/ross-debian_linux-javascript (revision 27232)
@@ -8,4 +8,5 @@
--enable-development \
--enable-debugging \
+ --with-cxxoptflags="-g -O2 -fPIC -std=c++11" \
--with-javascript \
--without-fortran \
Index: /issm/trunk/jenkins/ross-debian_linux-python
===================================================================
--- /issm/trunk/jenkins/ross-debian_linux-python (revision 27231)
+++ /issm/trunk/jenkins/ross-debian_linux-python (revision 27232)
@@ -49,5 +49,5 @@
gshhg install.sh
gmt install-6-linux.sh
- gmsh install-4.sh
+ gmsh install-4-linux.sh
triangle install-linux.sh
chaco install.sh
Index: /issm/trunk/jenkins/ross-debian_linux-solid_earth
===================================================================
--- /issm/trunk/jenkins/ross-debian_linux-solid_earth (revision 27231)
+++ /issm/trunk/jenkins/ross-debian_linux-solid_earth (revision 27232)
@@ -51,5 +51,5 @@
gshhg install.sh
gmt install-6-linux.sh
- gmsh install-4.sh
+ gmsh install-4-linux.sh
triangle install-linux.sh
chaco install.sh
Index: /issm/trunk/m4/analyses.m4
===================================================================
--- /issm/trunk/m4/analyses.m4 (revision 27231)
+++ /issm/trunk/m4/analyses.m4 (revision 27232)
@@ -11,1068 +11,590 @@
dnl with-HydrologyTws{{{
-
AC_ARG_WITH([HydrologyTws],
-
AS_HELP_STRING([--with-HydrologyTws = YES], [compile with HydrologyTws capabilities (default is yes)]),
-
[HYDROLOGYTWS=$withval],[HYDROLOGYTWS=yes])
-
AC_MSG_CHECKING(for HydrologyTws capability compilation)
-
HAVE_HYDROLOGYTWS=no
-
if test "x$HYDROLOGYTWS" = "xyes"; then
-
HAVE_HYDROLOGYTWS=yes
-
AC_DEFINE([_HAVE_HYDROLOGYTWS_],[1],[with HydrologyTws capability])
-
-fi
-
+fi
AM_CONDITIONAL([HYDROLOGYTWS], [test x$HAVE_HYDROLOGYTWS = xyes])
-
AC_MSG_RESULT($HAVE_HYDROLOGYTWS)
-
dnl }}}
dnl with-AdjointBalancethickness2{{{
-
AC_ARG_WITH([AdjointBalancethickness2],
-
AS_HELP_STRING([--with-AdjointBalancethickness2 = YES], [compile with AdjointBalancethickness2 capabilities (default is yes)]),
-
[ADJOINTBALANCETHICKNESS2=$withval],[ADJOINTBALANCETHICKNESS2=yes])
-
AC_MSG_CHECKING(for AdjointBalancethickness2 capability compilation)
-
HAVE_ADJOINTBALANCETHICKNESS2=no
-
if test "x$ADJOINTBALANCETHICKNESS2" = "xyes"; then
-
HAVE_ADJOINTBALANCETHICKNESS2=yes
-
AC_DEFINE([_HAVE_ADJOINTBALANCETHICKNESS2_],[1],[with AdjointBalancethickness2 capability])
-
-fi
-
+fi
AM_CONDITIONAL([ADJOINTBALANCETHICKNESS2], [test x$HAVE_ADJOINTBALANCETHICKNESS2 = xyes])
-
AC_MSG_RESULT($HAVE_ADJOINTBALANCETHICKNESS2)
-
dnl }}}
dnl with-AdjointBalancethickness{{{
-
AC_ARG_WITH([AdjointBalancethickness],
-
AS_HELP_STRING([--with-AdjointBalancethickness = YES], [compile with AdjointBalancethickness capabilities (default is yes)]),
-
[ADJOINTBALANCETHICKNESS=$withval],[ADJOINTBALANCETHICKNESS=yes])
-
AC_MSG_CHECKING(for AdjointBalancethickness capability compilation)
-
HAVE_ADJOINTBALANCETHICKNESS=no
-
if test "x$ADJOINTBALANCETHICKNESS" = "xyes"; then
-
HAVE_ADJOINTBALANCETHICKNESS=yes
-
AC_DEFINE([_HAVE_ADJOINTBALANCETHICKNESS_],[1],[with AdjointBalancethickness capability])
-
-fi
-
+fi
AM_CONDITIONAL([ADJOINTBALANCETHICKNESS], [test x$HAVE_ADJOINTBALANCETHICKNESS = xyes])
-
AC_MSG_RESULT($HAVE_ADJOINTBALANCETHICKNESS)
-
dnl }}}
dnl with-AdjointHoriz{{{
-
AC_ARG_WITH([AdjointHoriz],
-
AS_HELP_STRING([--with-AdjointHoriz = YES], [compile with AdjointHoriz capabilities (default is yes)]),
-
[ADJOINTHORIZ=$withval],[ADJOINTHORIZ=yes])
-
AC_MSG_CHECKING(for AdjointHoriz capability compilation)
-
HAVE_ADJOINTHORIZ=no
-
if test "x$ADJOINTHORIZ" = "xyes"; then
-
HAVE_ADJOINTHORIZ=yes
-
AC_DEFINE([_HAVE_ADJOINTHORIZ_],[1],[with AdjointHoriz capability])
-
-fi
-
+fi
AM_CONDITIONAL([ADJOINTHORIZ], [test x$HAVE_ADJOINTHORIZ = xyes])
-
AC_MSG_RESULT($HAVE_ADJOINTHORIZ)
-
+dnl }}}
+dnl with-Age{{{
+AC_ARG_WITH([Age],
+ AS_HELP_STRING([--with-Age = YES], [compile with Age capabilities (default is yes)]),
+ [AGE=$withval],[AGE=yes])
+AC_MSG_CHECKING(for Age capability compilation)
+
+HAVE_AGE=no
+if test "x$AGE" = "xyes"; then
+ HAVE_AGE=yes
+ AC_DEFINE([_HAVE_AGE_],[1],[with Age capability])
+fi
+AM_CONDITIONAL([AGE], [test x$HAVE_AGE = xyes])
+AC_MSG_RESULT($HAVE_AGE)
dnl }}}
dnl with-Balancethickness2{{{
-
AC_ARG_WITH([Balancethickness2],
-
AS_HELP_STRING([--with-Balancethickness2 = YES], [compile with Balancethickness2 capabilities (default is yes)]),
-
[BALANCETHICKNESS2=$withval],[BALANCETHICKNESS2=yes])
-
AC_MSG_CHECKING(for Balancethickness2 capability compilation)
-
HAVE_BALANCETHICKNESS2=no
-
if test "x$BALANCETHICKNESS2" = "xyes"; then
-
HAVE_BALANCETHICKNESS2=yes
-
AC_DEFINE([_HAVE_BALANCETHICKNESS2_],[1],[with Balancethickness2 capability])
-
-fi
-
+fi
AM_CONDITIONAL([BALANCETHICKNESS2], [test x$HAVE_BALANCETHICKNESS2 = xyes])
-
AC_MSG_RESULT($HAVE_BALANCETHICKNESS2)
-
dnl }}}
dnl with-Balancethickness{{{
-
AC_ARG_WITH([Balancethickness],
-
AS_HELP_STRING([--with-Balancethickness = YES], [compile with Balancethickness capabilities (default is yes)]),
-
[BALANCETHICKNESS=$withval],[BALANCETHICKNESS=yes])
-
AC_MSG_CHECKING(for Balancethickness capability compilation)
-
HAVE_BALANCETHICKNESS=no
-
if test "x$BALANCETHICKNESS" = "xyes"; then
-
HAVE_BALANCETHICKNESS=yes
-
AC_DEFINE([_HAVE_BALANCETHICKNESS_],[1],[with Balancethickness capability])
-
-fi
-
+fi
AM_CONDITIONAL([BALANCETHICKNESS], [test x$HAVE_BALANCETHICKNESS = xyes])
-
AC_MSG_RESULT($HAVE_BALANCETHICKNESS)
-
dnl }}}
dnl with-BalancethicknessSoft{{{
-
AC_ARG_WITH([BalancethicknessSoft],
-
AS_HELP_STRING([--with-BalancethicknessSoft = YES], [compile with BalancethicknessSoft capabilities (default is yes)]),
-
[BALANCETHICKNESSSOFT=$withval],[BALANCETHICKNESSSOFT=yes])
-
AC_MSG_CHECKING(for BalancethicknessSoft capability compilation)
-
HAVE_BALANCETHICKNESSSOFT=no
-
if test "x$BALANCETHICKNESSSOFT" = "xyes"; then
-
HAVE_BALANCETHICKNESSSOFT=yes
-
AC_DEFINE([_HAVE_BALANCETHICKNESSSOFT_],[1],[with BalancethicknessSoft capability])
-
-fi
-
+fi
AM_CONDITIONAL([BALANCETHICKNESSSOFT], [test x$HAVE_BALANCETHICKNESSSOFT = xyes])
-
AC_MSG_RESULT($HAVE_BALANCETHICKNESSSOFT)
-
dnl }}}
dnl with-Balancevelocity{{{
-
AC_ARG_WITH([Balancevelocity],
-
AS_HELP_STRING([--with-Balancevelocity = YES], [compile with Balancevelocity capabilities (default is yes)]),
-
[BALANCEVELOCITY=$withval],[BALANCEVELOCITY=yes])
-
AC_MSG_CHECKING(for Balancevelocity capability compilation)
-
HAVE_BALANCEVELOCITY=no
-
if test "x$BALANCEVELOCITY" = "xyes"; then
-
HAVE_BALANCEVELOCITY=yes
-
AC_DEFINE([_HAVE_BALANCEVELOCITY_],[1],[with Balancevelocity capability])
-
-fi
-
+fi
AM_CONDITIONAL([BALANCEVELOCITY], [test x$HAVE_BALANCEVELOCITY = xyes])
-
AC_MSG_RESULT($HAVE_BALANCEVELOCITY)
-
dnl }}}
dnl with-DamageEvolution{{{
-
AC_ARG_WITH([DamageEvolution],
-
AS_HELP_STRING([--with-DamageEvolution = YES], [compile with DamageEvolution capabilities (default is yes)]),
-
[DAMAGEEVOLUTION=$withval],[DAMAGEEVOLUTION=yes])
-
AC_MSG_CHECKING(for DamageEvolution capability compilation)
-
HAVE_DAMAGEEVOLUTION=no
-
if test "x$DAMAGEEVOLUTION" = "xyes"; then
-
HAVE_DAMAGEEVOLUTION=yes
-
AC_DEFINE([_HAVE_DAMAGEEVOLUTION_],[1],[with DamageEvolution capability])
-
-fi
-
+fi
AM_CONDITIONAL([DAMAGEEVOLUTION], [test x$HAVE_DAMAGEEVOLUTION = xyes])
-
AC_MSG_RESULT($HAVE_DAMAGEEVOLUTION)
-
dnl }}}
dnl with-DepthAverage{{{
-
AC_ARG_WITH([DepthAverage],
-
AS_HELP_STRING([--with-DepthAverage = YES], [compile with DepthAverage capabilities (default is yes)]),
-
[DEPTHAVERAGE=$withval],[DEPTHAVERAGE=yes])
-
AC_MSG_CHECKING(for DepthAverage capability compilation)
-
HAVE_DEPTHAVERAGE=no
-
if test "x$DEPTHAVERAGE" = "xyes"; then
-
HAVE_DEPTHAVERAGE=yes
-
AC_DEFINE([_HAVE_DEPTHAVERAGE_],[1],[with DepthAverage capability])
-
-fi
-
+fi
AM_CONDITIONAL([DEPTHAVERAGE], [test x$HAVE_DEPTHAVERAGE = xyes])
-
AC_MSG_RESULT($HAVE_DEPTHAVERAGE)
-
dnl }}}
dnl with-Enthalpy{{{
-
AC_ARG_WITH([Enthalpy],
-
AS_HELP_STRING([--with-Enthalpy = YES], [compile with Enthalpy capabilities (default is yes)]),
-
[ENTHALPY=$withval],[ENTHALPY=yes])
-
AC_MSG_CHECKING(for Enthalpy capability compilation)
-
HAVE_ENTHALPY=no
-
if test "x$ENTHALPY" = "xyes"; then
-
HAVE_ENTHALPY=yes
-
AC_DEFINE([_HAVE_ENTHALPY_],[1],[with Enthalpy capability])
-
-fi
-
+fi
AM_CONDITIONAL([ENTHALPY], [test x$HAVE_ENTHALPY = xyes])
-
AC_MSG_RESULT($HAVE_ENTHALPY)
-
dnl }}}
dnl with-Esa{{{
-
AC_ARG_WITH([Esa],
-
AS_HELP_STRING([--with-Esa = YES], [compile with Esa capabilities (default is yes)]),
-
[ESA=$withval],[ESA=yes])
-
AC_MSG_CHECKING(for Esa capability compilation)
-
HAVE_ESA=no
-
if test "x$ESA" = "xyes"; then
-
HAVE_ESA=yes
-
AC_DEFINE([_HAVE_ESA_],[1],[with Esa capability])
-
-fi
-
+fi
AM_CONDITIONAL([ESA], [test x$HAVE_ESA = xyes])
-
AC_MSG_RESULT($HAVE_ESA)
-
dnl }}}
dnl with-Extrapolation{{{
-
AC_ARG_WITH([Extrapolation],
-
AS_HELP_STRING([--with-Extrapolation = YES], [compile with Extrapolation capabilities (default is yes)]),
-
[EXTRAPOLATION=$withval],[EXTRAPOLATION=yes])
-
AC_MSG_CHECKING(for Extrapolation capability compilation)
-
HAVE_EXTRAPOLATION=no
-
if test "x$EXTRAPOLATION" = "xyes"; then
-
HAVE_EXTRAPOLATION=yes
-
AC_DEFINE([_HAVE_EXTRAPOLATION_],[1],[with Extrapolation capability])
-
-fi
-
+fi
AM_CONDITIONAL([EXTRAPOLATION], [test x$HAVE_EXTRAPOLATION = xyes])
-
AC_MSG_RESULT($HAVE_EXTRAPOLATION)
-
dnl }}}
dnl with-ExtrudeFromBase{{{
-
AC_ARG_WITH([ExtrudeFromBase],
-
AS_HELP_STRING([--with-ExtrudeFromBase = YES], [compile with ExtrudeFromBase capabilities (default is yes)]),
-
[EXTRUDEFROMBASE=$withval],[EXTRUDEFROMBASE=yes])
-
AC_MSG_CHECKING(for ExtrudeFromBase capability compilation)
-
HAVE_EXTRUDEFROMBASE=no
-
if test "x$EXTRUDEFROMBASE" = "xyes"; then
-
HAVE_EXTRUDEFROMBASE=yes
-
AC_DEFINE([_HAVE_EXTRUDEFROMBASE_],[1],[with ExtrudeFromBase capability])
-
-fi
-
+fi
AM_CONDITIONAL([EXTRUDEFROMBASE], [test x$HAVE_EXTRUDEFROMBASE = xyes])
-
AC_MSG_RESULT($HAVE_EXTRUDEFROMBASE)
-
dnl }}}
dnl with-ExtrudeFromTop{{{
-
AC_ARG_WITH([ExtrudeFromTop],
-
AS_HELP_STRING([--with-ExtrudeFromTop = YES], [compile with ExtrudeFromTop capabilities (default is yes)]),
-
[EXTRUDEFROMTOP=$withval],[EXTRUDEFROMTOP=yes])
-
AC_MSG_CHECKING(for ExtrudeFromTop capability compilation)
-
HAVE_EXTRUDEFROMTOP=no
-
if test "x$EXTRUDEFROMTOP" = "xyes"; then
-
HAVE_EXTRUDEFROMTOP=yes
-
AC_DEFINE([_HAVE_EXTRUDEFROMTOP_],[1],[with ExtrudeFromTop capability])
-
-fi
-
+fi
AM_CONDITIONAL([EXTRUDEFROMTOP], [test x$HAVE_EXTRUDEFROMTOP = xyes])
-
AC_MSG_RESULT($HAVE_EXTRUDEFROMTOP)
-
dnl }}}
dnl with-FreeSurfaceBase{{{
-
AC_ARG_WITH([FreeSurfaceBase],
-
AS_HELP_STRING([--with-FreeSurfaceBase = YES], [compile with FreeSurfaceBase capabilities (default is yes)]),
-
[FREESURFACEBASE=$withval],[FREESURFACEBASE=yes])
-
AC_MSG_CHECKING(for FreeSurfaceBase capability compilation)
-
HAVE_FREESURFACEBASE=no
-
if test "x$FREESURFACEBASE" = "xyes"; then
-
HAVE_FREESURFACEBASE=yes
-
AC_DEFINE([_HAVE_FREESURFACEBASE_],[1],[with FreeSurfaceBase capability])
-
-fi
-
+fi
AM_CONDITIONAL([FREESURFACEBASE], [test x$HAVE_FREESURFACEBASE = xyes])
-
AC_MSG_RESULT($HAVE_FREESURFACEBASE)
-
dnl }}}
dnl with-FreeSurfaceTop{{{
-
AC_ARG_WITH([FreeSurfaceTop],
-
AS_HELP_STRING([--with-FreeSurfaceTop = YES], [compile with FreeSurfaceTop capabilities (default is yes)]),
-
[FREESURFACETOP=$withval],[FREESURFACETOP=yes])
-
AC_MSG_CHECKING(for FreeSurfaceTop capability compilation)
-
HAVE_FREESURFACETOP=no
-
if test "x$FREESURFACETOP" = "xyes"; then
-
HAVE_FREESURFACETOP=yes
-
AC_DEFINE([_HAVE_FREESURFACETOP_],[1],[with FreeSurfaceTop capability])
-
-fi
-
+fi
AM_CONDITIONAL([FREESURFACETOP], [test x$HAVE_FREESURFACETOP = xyes])
-
AC_MSG_RESULT($HAVE_FREESURFACETOP)
-
dnl }}}
dnl with-GLheightadvection{{{
-
AC_ARG_WITH([GLheightadvection],
-
AS_HELP_STRING([--with-GLheightadvection = YES], [compile with GLheightadvection capabilities (default is yes)]),
-
[GLHEIGHTADVECTION=$withval],[GLHEIGHTADVECTION=yes])
-
AC_MSG_CHECKING(for GLheightadvection capability compilation)
-
HAVE_GLHEIGHTADVECTION=no
-
if test "x$GLHEIGHTADVECTION" = "xyes"; then
-
HAVE_GLHEIGHTADVECTION=yes
-
AC_DEFINE([_HAVE_GLHEIGHTADVECTION_],[1],[with GLheightadvection capability])
-
-fi
-
+fi
AM_CONDITIONAL([GLHEIGHTADVECTION], [test x$HAVE_GLHEIGHTADVECTION = xyes])
-
AC_MSG_RESULT($HAVE_GLHEIGHTADVECTION)
-
dnl }}}
dnl with-HydrologyDCEfficient{{{
-
AC_ARG_WITH([HydrologyDCEfficient],
-
AS_HELP_STRING([--with-HydrologyDCEfficient = YES], [compile with HydrologyDCEfficient capabilities (default is yes)]),
-
[HYDROLOGYDCEFFICIENT=$withval],[HYDROLOGYDCEFFICIENT=yes])
-
AC_MSG_CHECKING(for HydrologyDCEfficient capability compilation)
-
HAVE_HYDROLOGYDCEFFICIENT=no
-
if test "x$HYDROLOGYDCEFFICIENT" = "xyes"; then
-
HAVE_HYDROLOGYDCEFFICIENT=yes
-
AC_DEFINE([_HAVE_HYDROLOGYDCEFFICIENT_],[1],[with HydrologyDCEfficient capability])
-
-fi
-
+fi
AM_CONDITIONAL([HYDROLOGYDCEFFICIENT], [test x$HAVE_HYDROLOGYDCEFFICIENT = xyes])
-
AC_MSG_RESULT($HAVE_HYDROLOGYDCEFFICIENT)
-
dnl }}}
dnl with-HydrologyDCInefficient{{{
-
AC_ARG_WITH([HydrologyDCInefficient],
-
AS_HELP_STRING([--with-HydrologyDCInefficient = YES], [compile with HydrologyDCInefficient capabilities (default is yes)]),
-
[HYDROLOGYDCINEFFICIENT=$withval],[HYDROLOGYDCINEFFICIENT=yes])
-
AC_MSG_CHECKING(for HydrologyDCInefficient capability compilation)
-
HAVE_HYDROLOGYDCINEFFICIENT=no
-
if test "x$HYDROLOGYDCINEFFICIENT" = "xyes"; then
-
HAVE_HYDROLOGYDCINEFFICIENT=yes
-
AC_DEFINE([_HAVE_HYDROLOGYDCINEFFICIENT_],[1],[with HydrologyDCInefficient capability])
-
-fi
-
+fi
AM_CONDITIONAL([HYDROLOGYDCINEFFICIENT], [test x$HAVE_HYDROLOGYDCINEFFICIENT = xyes])
-
AC_MSG_RESULT($HAVE_HYDROLOGYDCINEFFICIENT)
-
dnl }}}
dnl with-HydrologyGlaDS{{{
-
AC_ARG_WITH([HydrologyGlaDS],
-
AS_HELP_STRING([--with-HydrologyGlaDS = YES], [compile with HydrologyGlaDS capabilities (default is yes)]),
-
[HYDROLOGYGLADS=$withval],[HYDROLOGYGLADS=yes])
-
AC_MSG_CHECKING(for HydrologyGlaDS capability compilation)
-
HAVE_HYDROLOGYGLADS=no
-
if test "x$HYDROLOGYGLADS" = "xyes"; then
-
HAVE_HYDROLOGYGLADS=yes
-
AC_DEFINE([_HAVE_HYDROLOGYGLADS_],[1],[with HydrologyGlaDS capability])
-
-fi
-
+fi
AM_CONDITIONAL([HYDROLOGYGLADS], [test x$HAVE_HYDROLOGYGLADS = xyes])
-
AC_MSG_RESULT($HAVE_HYDROLOGYGLADS)
-
dnl }}}
dnl with-HydrologyPism{{{
-
AC_ARG_WITH([HydrologyPism],
-
AS_HELP_STRING([--with-HydrologyPism = YES], [compile with HydrologyPism capabilities (default is yes)]),
-
[HYDROLOGYPISM=$withval],[HYDROLOGYPISM=yes])
-
AC_MSG_CHECKING(for HydrologyPism capability compilation)
-
HAVE_HYDROLOGYPISM=no
-
if test "x$HYDROLOGYPISM" = "xyes"; then
-
HAVE_HYDROLOGYPISM=yes
-
AC_DEFINE([_HAVE_HYDROLOGYPISM_],[1],[with HydrologyPism capability])
-
-fi
-
+fi
AM_CONDITIONAL([HYDROLOGYPISM], [test x$HAVE_HYDROLOGYPISM = xyes])
-
AC_MSG_RESULT($HAVE_HYDROLOGYPISM)
-
dnl }}}
dnl with-HydrologyShakti{{{
-
AC_ARG_WITH([HydrologyShakti],
-
AS_HELP_STRING([--with-HydrologyShakti = YES], [compile with HydrologyShakti capabilities (default is yes)]),
-
[HYDROLOGYSHAKTI=$withval],[HYDROLOGYSHAKTI=yes])
-
AC_MSG_CHECKING(for HydrologyShakti capability compilation)
-
HAVE_HYDROLOGYSHAKTI=no
-
if test "x$HYDROLOGYSHAKTI" = "xyes"; then
-
HAVE_HYDROLOGYSHAKTI=yes
-
AC_DEFINE([_HAVE_HYDROLOGYSHAKTI_],[1],[with HydrologyShakti capability])
-
-fi
-
+fi
AM_CONDITIONAL([HYDROLOGYSHAKTI], [test x$HAVE_HYDROLOGYSHAKTI = xyes])
-
AC_MSG_RESULT($HAVE_HYDROLOGYSHAKTI)
-
dnl }}}
dnl with-HydrologyShreve{{{
-
AC_ARG_WITH([HydrologyShreve],
-
AS_HELP_STRING([--with-HydrologyShreve = YES], [compile with HydrologyShreve capabilities (default is yes)]),
-
[HYDROLOGYSHREVE=$withval],[HYDROLOGYSHREVE=yes])
-
AC_MSG_CHECKING(for HydrologyShreve capability compilation)
-
HAVE_HYDROLOGYSHREVE=no
-
if test "x$HYDROLOGYSHREVE" = "xyes"; then
-
HAVE_HYDROLOGYSHREVE=yes
-
AC_DEFINE([_HAVE_HYDROLOGYSHREVE_],[1],[with HydrologyShreve capability])
-
-fi
-
+fi
AM_CONDITIONAL([HYDROLOGYSHREVE], [test x$HAVE_HYDROLOGYSHREVE = xyes])
-
AC_MSG_RESULT($HAVE_HYDROLOGYSHREVE)
-
dnl }}}
dnl with-L2ProjectionBase{{{
-
AC_ARG_WITH([L2ProjectionBase],
-
AS_HELP_STRING([--with-L2ProjectionBase = YES], [compile with L2ProjectionBase capabilities (default is yes)]),
-
[L2PROJECTIONBASE=$withval],[L2PROJECTIONBASE=yes])
-
AC_MSG_CHECKING(for L2ProjectionBase capability compilation)
-
HAVE_L2PROJECTIONBASE=no
-
if test "x$L2PROJECTIONBASE" = "xyes"; then
-
HAVE_L2PROJECTIONBASE=yes
-
AC_DEFINE([_HAVE_L2PROJECTIONBASE_],[1],[with L2ProjectionBase capability])
-
-fi
-
+fi
AM_CONDITIONAL([L2PROJECTIONBASE], [test x$HAVE_L2PROJECTIONBASE = xyes])
-
AC_MSG_RESULT($HAVE_L2PROJECTIONBASE)
-
dnl }}}
dnl with-L2ProjectionEPL{{{
-
AC_ARG_WITH([L2ProjectionEPL],
-
AS_HELP_STRING([--with-L2ProjectionEPL = YES], [compile with L2ProjectionEPL capabilities (default is yes)]),
-
[L2PROJECTIONEPL=$withval],[L2PROJECTIONEPL=yes])
-
AC_MSG_CHECKING(for L2ProjectionEPL capability compilation)
-
HAVE_L2PROJECTIONEPL=no
-
if test "x$L2PROJECTIONEPL" = "xyes"; then
-
HAVE_L2PROJECTIONEPL=yes
-
AC_DEFINE([_HAVE_L2PROJECTIONEPL_],[1],[with L2ProjectionEPL capability])
-
-fi
-
+fi
AM_CONDITIONAL([L2PROJECTIONEPL], [test x$HAVE_L2PROJECTIONEPL = xyes])
-
AC_MSG_RESULT($HAVE_L2PROJECTIONEPL)
-
dnl }}}
dnl with-Levelset{{{
-
AC_ARG_WITH([Levelset],
-
AS_HELP_STRING([--with-Levelset = YES], [compile with Levelset capabilities (default is yes)]),
-
[LEVELSET=$withval],[LEVELSET=yes])
-
AC_MSG_CHECKING(for Levelset capability compilation)
-
HAVE_LEVELSET=no
-
if test "x$LEVELSET" = "xyes"; then
-
HAVE_LEVELSET=yes
-
AC_DEFINE([_HAVE_LEVELSET_],[1],[with Levelset capability])
-
-fi
-
+fi
AM_CONDITIONAL([LEVELSET], [test x$HAVE_LEVELSET = xyes])
-
AC_MSG_RESULT($HAVE_LEVELSET)
-
dnl }}}
dnl with-Love{{{
-
AC_ARG_WITH([Love],
-
AS_HELP_STRING([--with-Love = YES], [compile with Love capabilities (default is yes)]),
-
[LOVE=$withval],[LOVE=yes])
-
AC_MSG_CHECKING(for Love capability compilation)
-
HAVE_LOVE=no
-
if test "x$LOVE" = "xyes"; then
-
HAVE_LOVE=yes
-
AC_DEFINE([_HAVE_LOVE_],[1],[with Love capability])
-
-fi
-
+fi
AM_CONDITIONAL([LOVE], [test x$HAVE_LOVE = xyes])
-
AC_MSG_RESULT($HAVE_LOVE)
-
dnl }}}
dnl with-Masstransport{{{
-
AC_ARG_WITH([Masstransport],
-
AS_HELP_STRING([--with-Masstransport = YES], [compile with Masstransport capabilities (default is yes)]),
-
[MASSTRANSPORT=$withval],[MASSTRANSPORT=yes])
-
AC_MSG_CHECKING(for Masstransport capability compilation)
-
HAVE_MASSTRANSPORT=no
-
if test "x$MASSTRANSPORT" = "xyes"; then
-
HAVE_MASSTRANSPORT=yes
-
AC_DEFINE([_HAVE_MASSTRANSPORT_],[1],[with Masstransport capability])
-
-fi
-
+fi
AM_CONDITIONAL([MASSTRANSPORT], [test x$HAVE_MASSTRANSPORT = xyes])
-
AC_MSG_RESULT($HAVE_MASSTRANSPORT)
-
dnl }}}
dnl with-Melting{{{
-
AC_ARG_WITH([Melting],
-
AS_HELP_STRING([--with-Melting = YES], [compile with Melting capabilities (default is yes)]),
-
[MELTING=$withval],[MELTING=yes])
-
AC_MSG_CHECKING(for Melting capability compilation)
-
HAVE_MELTING=no
-
if test "x$MELTING" = "xyes"; then
-
HAVE_MELTING=yes
-
AC_DEFINE([_HAVE_MELTING_],[1],[with Melting capability])
-
-fi
-
+fi
AM_CONDITIONAL([MELTING], [test x$HAVE_MELTING = xyes])
-
AC_MSG_RESULT($HAVE_MELTING)
-
dnl }}}
dnl with-Oceantransport{{{
-
AC_ARG_WITH([Oceantransport],
-
AS_HELP_STRING([--with-Oceantransport = YES], [compile with Oceantransport capabilities (default is yes)]),
-
[OCEANTRANSPORT=$withval],[OCEANTRANSPORT=yes])
-
AC_MSG_CHECKING(for Oceantransport capability compilation)
-
HAVE_OCEANTRANSPORT=no
-
if test "x$OCEANTRANSPORT" = "xyes"; then
-
HAVE_OCEANTRANSPORT=yes
-
AC_DEFINE([_HAVE_OCEANTRANSPORT_],[1],[with Oceantransport capability])
-
-fi
-
+fi
AM_CONDITIONAL([OCEANTRANSPORT], [test x$HAVE_OCEANTRANSPORT = xyes])
-
AC_MSG_RESULT($HAVE_OCEANTRANSPORT)
-
dnl }}}
dnl with-Recovery{{{
-
AC_ARG_WITH([Recovery],
-
AS_HELP_STRING([--with-Recovery = YES], [compile with Recovery capabilities (default is yes)]),
-
[RECOVERY=$withval],[RECOVERY=yes])
-
AC_MSG_CHECKING(for Recovery capability compilation)
-
HAVE_RECOVERY=no
-
if test "x$RECOVERY" = "xyes"; then
-
HAVE_RECOVERY=yes
-
AC_DEFINE([_HAVE_RECOVERY_],[1],[with Recovery capability])
-
-fi
-
+fi
AM_CONDITIONAL([RECOVERY], [test x$HAVE_RECOVERY = xyes])
-
AC_MSG_RESULT($HAVE_RECOVERY)
-
dnl }}}
dnl with-Sampling{{{
-
AC_ARG_WITH([Sampling],
-
AS_HELP_STRING([--with-Sampling = YES], [compile with Sampling capabilities (default is yes)]),
-
[SAMPLING=$withval],[SAMPLING=yes])
-
AC_MSG_CHECKING(for Sampling capability compilation)
-
HAVE_SAMPLING=no
-
if test "x$SAMPLING" = "xyes"; then
-
HAVE_SAMPLING=yes
-
AC_DEFINE([_HAVE_SAMPLING_],[1],[with Sampling capability])
-
-fi
-
+fi
AM_CONDITIONAL([SAMPLING], [test x$HAVE_SAMPLING = xyes])
-
AC_MSG_RESULT($HAVE_SAMPLING)
-
dnl }}}
dnl with-Sealevelchange{{{
-
AC_ARG_WITH([Sealevelchange],
-
AS_HELP_STRING([--with-Sealevelchange = YES], [compile with Sealevelchange capabilities (default is yes)]),
-
[SEALEVELCHANGE=$withval],[SEALEVELCHANGE=yes])
-
AC_MSG_CHECKING(for Sealevelchange capability compilation)
-
HAVE_SEALEVELCHANGE=no
-
if test "x$SEALEVELCHANGE" = "xyes"; then
-
HAVE_SEALEVELCHANGE=yes
-
AC_DEFINE([_HAVE_SEALEVELCHANGE_],[1],[with Sealevelchange capability])
-
-fi
-
+fi
AM_CONDITIONAL([SEALEVELCHANGE], [test x$HAVE_SEALEVELCHANGE = xyes])
-
AC_MSG_RESULT($HAVE_SEALEVELCHANGE)
-
dnl }}}
dnl with-Smb{{{
-
AC_ARG_WITH([Smb],
-
AS_HELP_STRING([--with-Smb = YES], [compile with Smb capabilities (default is yes)]),
-
[SMB=$withval],[SMB=yes])
-
AC_MSG_CHECKING(for Smb capability compilation)
-
HAVE_SMB=no
-
if test "x$SMB" = "xyes"; then
-
HAVE_SMB=yes
-
AC_DEFINE([_HAVE_SMB_],[1],[with Smb capability])
-
-fi
-
+fi
AM_CONDITIONAL([SMB], [test x$HAVE_SMB = xyes])
-
AC_MSG_RESULT($HAVE_SMB)
-
dnl }}}
dnl with-Smooth{{{
-
AC_ARG_WITH([Smooth],
-
AS_HELP_STRING([--with-Smooth = YES], [compile with Smooth capabilities (default is yes)]),
-
[SMOOTH=$withval],[SMOOTH=yes])
-
AC_MSG_CHECKING(for Smooth capability compilation)
-
HAVE_SMOOTH=no
-
if test "x$SMOOTH" = "xyes"; then
-
HAVE_SMOOTH=yes
-
AC_DEFINE([_HAVE_SMOOTH_],[1],[with Smooth capability])
-
-fi
-
+fi
AM_CONDITIONAL([SMOOTH], [test x$HAVE_SMOOTH = xyes])
-
AC_MSG_RESULT($HAVE_SMOOTH)
-
dnl }}}
dnl with-Stressbalance{{{
-
AC_ARG_WITH([Stressbalance],
-
AS_HELP_STRING([--with-Stressbalance = YES], [compile with Stressbalance capabilities (default is yes)]),
-
[STRESSBALANCE=$withval],[STRESSBALANCE=yes])
-
AC_MSG_CHECKING(for Stressbalance capability compilation)
-
HAVE_STRESSBALANCE=no
-
if test "x$STRESSBALANCE" = "xyes"; then
-
HAVE_STRESSBALANCE=yes
-
AC_DEFINE([_HAVE_STRESSBALANCE_],[1],[with Stressbalance capability])
-
-fi
-
+fi
AM_CONDITIONAL([STRESSBALANCE], [test x$HAVE_STRESSBALANCE = xyes])
-
AC_MSG_RESULT($HAVE_STRESSBALANCE)
-
dnl }}}
dnl with-StressbalanceSIA{{{
-
AC_ARG_WITH([StressbalanceSIA],
-
AS_HELP_STRING([--with-StressbalanceSIA = YES], [compile with StressbalanceSIA capabilities (default is yes)]),
-
[STRESSBALANCESIA=$withval],[STRESSBALANCESIA=yes])
-
AC_MSG_CHECKING(for StressbalanceSIA capability compilation)
-
HAVE_STRESSBALANCESIA=no
-
if test "x$STRESSBALANCESIA" = "xyes"; then
-
HAVE_STRESSBALANCESIA=yes
-
AC_DEFINE([_HAVE_STRESSBALANCESIA_],[1],[with StressbalanceSIA capability])
-
-fi
-
+fi
AM_CONDITIONAL([STRESSBALANCESIA], [test x$HAVE_STRESSBALANCESIA = xyes])
-
AC_MSG_RESULT($HAVE_STRESSBALANCESIA)
-
dnl }}}
dnl with-StressbalanceVertical{{{
-
AC_ARG_WITH([StressbalanceVertical],
-
AS_HELP_STRING([--with-StressbalanceVertical = YES], [compile with StressbalanceVertical capabilities (default is yes)]),
-
[STRESSBALANCEVERTICAL=$withval],[STRESSBALANCEVERTICAL=yes])
-
AC_MSG_CHECKING(for StressbalanceVertical capability compilation)
-
HAVE_STRESSBALANCEVERTICAL=no
-
if test "x$STRESSBALANCEVERTICAL" = "xyes"; then
-
HAVE_STRESSBALANCEVERTICAL=yes
-
AC_DEFINE([_HAVE_STRESSBALANCEVERTICAL_],[1],[with StressbalanceVertical capability])
-
-fi
-
+fi
AM_CONDITIONAL([STRESSBALANCEVERTICAL], [test x$HAVE_STRESSBALANCEVERTICAL = xyes])
-
AC_MSG_RESULT($HAVE_STRESSBALANCEVERTICAL)
-
dnl }}}
dnl with-Thermal{{{
-
AC_ARG_WITH([Thermal],
-
AS_HELP_STRING([--with-Thermal = YES], [compile with Thermal capabilities (default is yes)]),
-
[THERMAL=$withval],[THERMAL=yes])
-
AC_MSG_CHECKING(for Thermal capability compilation)
-
HAVE_THERMAL=no
-
if test "x$THERMAL" = "xyes"; then
-
HAVE_THERMAL=yes
-
AC_DEFINE([_HAVE_THERMAL_],[1],[with Thermal capability])
-
-fi
-
+fi
AM_CONDITIONAL([THERMAL], [test x$HAVE_THERMAL = xyes])
-
AC_MSG_RESULT($HAVE_THERMAL)
-
dnl }}}
dnl with-UzawaPressure{{{
-
AC_ARG_WITH([UzawaPressure],
-
AS_HELP_STRING([--with-UzawaPressure = YES], [compile with UzawaPressure capabilities (default is yes)]),
-
[UZAWAPRESSURE=$withval],[UZAWAPRESSURE=yes])
-
AC_MSG_CHECKING(for UzawaPressure capability compilation)
-
HAVE_UZAWAPRESSURE=no
-
if test "x$UZAWAPRESSURE" = "xyes"; then
-
HAVE_UZAWAPRESSURE=yes
-
AC_DEFINE([_HAVE_UZAWAPRESSURE_],[1],[with UzawaPressure capability])
-
-fi
-
+fi
AM_CONDITIONAL([UZAWAPRESSURE], [test x$HAVE_UZAWAPRESSURE = xyes])
-
AC_MSG_RESULT($HAVE_UZAWAPRESSURE)
-
dnl }}}
Index: /issm/trunk/m4/issm_options.m4
===================================================================
--- /issm/trunk/m4/issm_options.m4 (revision 27231)
+++ /issm/trunk/m4/issm_options.m4 (revision 27232)
@@ -196,4 +196,8 @@
IS_MAC=yes
AC_DEFINE([_MAC_], [1], [is macOS])
+ dnl When standard Dakota installation has been updated to new
+ dnl version, remove the following
+ export CFLAGS="-Wno-deprecated-register -Wno-return-type"
+ export CXXFLAGS="-Wno-deprecated-register -Wno-return-type"
;;
*)
@@ -644,4 +648,5 @@
dnl TODO:
dnl - Should we also be checking if HAVE_BOOST before adding boost libs?
+ dnl - Clean up the following conditionals
dnl
case "${host_os}" in
@@ -668,5 +673,38 @@
elif test "${DAKOTA_VERSION}" == "6.1" || test "${DAKOTA_VERSION}" == "6.2"; then
if test "${BOOST_VERSION_MAJOR}" == "1"; then
- DAKOTAFLAGS="-DHAVE_CONFIG_H -DHAVE_CONFIG_H -DDISABLE_DAKOTA_CONFIG_H -DBOOST_DISABLE_ASSERTS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DHAVE_ADAPTIVE_SAMPLING -DHAVE_ESM -DHAVE_QUESO -DHAVE_QUESO_GPMSA -DHAVE_CONMIN -DHAVE_DDACE -DHAVE_DREAM -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_NOMAD -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
+ DAKOTAFLAGS="-DHAVE_CONFIG_H -DDISABLE_DAKOTA_CONFIG_H -DBOOST_DISABLE_ASSERTS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DHAVE_ADAPTIVE_SAMPLING -DHAVE_ESM -DHAVE_QUESO -DHAVE_QUESO_GPMSA -DHAVE_CONMIN -DHAVE_DDACE -DHAVE_DREAM -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_NOMAD -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
+ DAKOTALIB="-L${DAKOTA_ROOT}/lib -ldakota_src -ldakota_src_fortran -lnidr -lteuchos -lpecos -lpecos_src -llhs -llhs_mods -llhs_mod -ldfftpack -lsparsegrid -lsurfpack -lsurfpack -lsurfpack_fortran -lqueso -lconmin -lddace -ldream -lfsudace -lhopspack -lncsuopt -lcport -lnomad -loptpp -lpsuade -lamplsolver"
+ DAKOTALIB+=" -L${BOOST_ROOT}/lib -lboost_filesystem -lboost_program_options -lboost_regex -lboost_serialization -lboost_system"
+ DAKOTALIB+=" ${BLASLAPACKLIB}"
+ fi
+ AC_DEFINE([DISABLE_DAKOTA_CONFIG_H], [1], [enabling DAKOTA_CONFIG_H])
+ AC_DEFINE([DAKOTA_HAVE_MPI], [1], [enabling Dakota with MPI])
+ elif test "${DAKOTA_VERSION}" == "6.11"; then
+ if test "${BOOST_VERSION_MAJOR}" == "1"; then
+ if test "${BOOST_VERSION_MINOR}" == "55"; then
+ DAKOTAFLAGS="-DDISABLE_DAKOTA_CONFIG_H -DBOOST_MULTI_INDEX_DISABLE_SERIALIZATION -DDAKOTA_PLUGIN -DBOOST_DISABLE_ASSERTS -DDAKOTA_HAVE_BOOST_FS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DDAKOTA_UTILIB -DHAVE_ADAPTIVE_SAMPLING -DHAVE_CONMIN -DDAKOTA_DDACE -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
+ DAKOTALIB="-L${DAKOTA_ROOT}/lib -ldakota_src -ldream -lfsudace -lddace -lnomad -lpecos_src -llhs -llhs_mods -loptpp -lsurfpack -lconmin -ldakota_src_fortran -llhs_mod -lncsuopt -lsurfpack_fortran -lteuchos -lamplsolver -lcport -ldfftpack -lfsudace -lhopspack -lnidr -lpecos -lpsuade -lsparsegrid -L$BOOST_ROOT/lib -lboost_serialization -lboost_signals -lboost_regex -lboost_filesystem -lboost_system ${BLASLAPACKLIB}"
+ elif test "${BOOST_VERSION_MINOR}" == "72"; then
+ DAKOTAFLAGS="-DHAVE_CONFIG_H -DDISABLE_DAKOTA_CONFIG_H -DBOOST_DISABLE_ASSERTS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DHAVE_ADAPTIVE_SAMPLING -DHAVE_ESM -DHAVE_CONMIN -DHAVE_DDACE -DHAVE_DREAM -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_NOMAD -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
+ DAKOTALIB="-L${DAKOTA_ROOT}/lib -ldakota_src -ldakota_src_fortran -lnidr -lteuchosremainder -lteuchosnumerics -lteuchoscomm -lteuchosparameterlist -lteuchosparser -lteuchoscore -lpecos_util -lpecos_src -llhs -llhs_mods -llhs_mod -ldfftpack -lsparsegrid -lsurfpack -lsurfpack -lsurfpack_fortran -lapproxnn -lconmin -lddace -ldream -lfsudace -lhopspack -lncsuopt -lcport -lnomad -loptpp -lpsuade -lamplsolver -L${BOOST_ROOT}/lib -lboost_filesystem -lboost_program_options -lboost_regex -lboost_serialization -lboost_system ${BLASLAPACKLIB}"
+ fi
+ fi
+ AC_DEFINE([DISABLE_DAKOTA_CONFIG_H], [1], [enabling DAKOTA_CONFIG_H])
+ AC_DEFINE([DAKOTA_HAVE_MPI], [1], [enabling Dakota with MPI])
+ else
+ AC_MSG_ERROR([Dakota version not found or version (${DAKOTA_VERSION}) not supported!]);
+ fi
+ ;;
+ *linux*)
+ if test "${DAKOTA_VERSION}" == "5.1" || test "${DAKOTA_VERSION}" == "5.2"; then
+ DAKOTALIB="-L${DAKOTA_ROOT}/lib -ldakota -lteuchos -lpecos -llhs -lsparsegrid -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -loptpp -lpsuade -lncsuopt -lcolin -linterfaces -lmomh -lscolib -lpebbl -ltinyxml -lutilib -l3po -lhopspack -lnidr -lamplsolver -lboost_signals -lboost_regex -lboost_filesystem -lboost_system -ldl"
+ elif test "${DAKOTA_VERSION}" == "5.3" || test "${DAKOTA_VERSION}" == "5.3.1"; then
+ DAKOTAFLAGS="-DDISABLE_DAKOTA_CONFIG_H -DBOOST_MULTI_INDEX_DISABLE_SERIALIZATION -DDAKOTA_PLUGIN -DBOOST_DISABLE_ASSERTS -DDAKOTA_HAVE_BOOST_FS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DDAKOTA_COLINY -DDAKOTA_UTILIB -DHAVE_ADAPTIVE_SAMPLING -DHAVE_CONMIN -DDAKOTA_DDACE -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_JEGA -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
+ DAKOTALIB="-L${DAKOTA_ROOT}/lib -L${BOOST_ROOT}/lib -ldakota_src -lpecos_src -lscolib -ljega_fe -llhs -lpebbl -lcolin -linterfaces -lmods -lmoga -loptpp -lsampling -lsoga -lsurfpack -lutilib -lconmin -ldakota_src_fortran -lmod -lncsuopt -lsurfpack_fortran -lteuchos -l3po -lamplsolver -lanalyzer -lbose -lcport -ldace -ldfftpack -leutils -lfsudace -lhopspack -ljega -lnidr -lpecos -lpsuade -lrandom -ltinyxml -lutilities -lsparsegrid -lboost_signals -lboost_regex -lboost_filesystem -lboost_system"
+ AC_DEFINE([DISABLE_DAKOTA_CONFIG_H], [1], [enabling DAKOTA_CONFIG_H])
+ AC_DEFINE([DAKOTA_HAVE_MPI], [1], [enabling Dakota with MPI])
+ elif test "${DAKOTA_VERSION}" == "6.1" || test "${DAKOTA_VERSION}" == "6.2"; then
+ if test "${BOOST_VERSION_MAJOR}" == "1"; then
+ DAKOTAFLAGS="-DHAVE_CONFIG_H -DDISABLE_DAKOTA_CONFIG_H -DBOOST_DISABLE_ASSERTS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DHAVE_ADAPTIVE_SAMPLING -DHAVE_ESM -DHAVE_QUESO -DHAVE_QUESO_GPMSA -DHAVE_CONMIN -DHAVE_DDACE -DHAVE_DREAM -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_NOMAD -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
DAKOTALIB="-L${DAKOTA_ROOT}/lib -ldakota_src -ldakota_src_fortran -lnidr -lteuchos -lpecos -lpecos_src -llhs -llhs_mods -llhs_mod -ldfftpack -lsparsegrid -lsurfpack -lsurfpack -lsurfpack_fortran -lqueso -lconmin -lddace -ldream -lfsudace -lhopspack -lncsuopt -lcport -lnomad -loptpp -lpsuade -lamplsolver"
DAKOTALIB+=" -L${BOOST_ROOT}/lib -lboost_filesystem -lboost_program_options -lboost_regex -lboost_serialization -lboost_system"
@@ -691,37 +729,4 @@
fi
;;
- *linux*)
- if test "${DAKOTA_VERSION}" == "5.1" || test "${DAKOTA_VERSION}" == "5.2"; then
- DAKOTALIB="-L${DAKOTA_ROOT}/lib -ldakota -lteuchos -lpecos -llhs -lsparsegrid -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -loptpp -lpsuade -lncsuopt -lcolin -linterfaces -lmomh -lscolib -lpebbl -ltinyxml -lutilib -l3po -lhopspack -lnidr -lamplsolver -lboost_signals -lboost_regex -lboost_filesystem -lboost_system -ldl"
- elif test "${DAKOTA_VERSION}" == "5.3" || test "${DAKOTA_VERSION}" == "5.3.1"; then
- DAKOTAFLAGS="-DDISABLE_DAKOTA_CONFIG_H -DBOOST_MULTI_INDEX_DISABLE_SERIALIZATION -DDAKOTA_PLUGIN -DBOOST_DISABLE_ASSERTS -DDAKOTA_HAVE_BOOST_FS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DDAKOTA_COLINY -DDAKOTA_UTILIB -DHAVE_ADAPTIVE_SAMPLING -DHAVE_CONMIN -DDAKOTA_DDACE -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_JEGA -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
- DAKOTALIB="-L${DAKOTA_ROOT}/lib -L${BOOST_ROOT}/lib -ldakota_src -lpecos_src -lscolib -ljega_fe -llhs -lpebbl -lcolin -linterfaces -lmods -lmoga -loptpp -lsampling -lsoga -lsurfpack -lutilib -lconmin -ldakota_src_fortran -lmod -lncsuopt -lsurfpack_fortran -lteuchos -l3po -lamplsolver -lanalyzer -lbose -lcport -ldace -ldfftpack -leutils -lfsudace -lhopspack -ljega -lnidr -lpecos -lpsuade -lrandom -ltinyxml -lutilities -lsparsegrid -lboost_signals -lboost_regex -lboost_filesystem -lboost_system"
- AC_DEFINE([DISABLE_DAKOTA_CONFIG_H], [1], [enabling DAKOTA_CONFIG_H])
- AC_DEFINE([DAKOTA_HAVE_MPI], [1], [enabling Dakota with MPI])
- elif test "${DAKOTA_VERSION}" == "6.1" || test "${DAKOTA_VERSION}" == "6.2"; then
- if test "${BOOST_VERSION_MAJOR}" == "1"; then
- DAKOTAFLAGS="-DHAVE_CONFIG_H -DHAVE_CONFIG_H -DDISABLE_DAKOTA_CONFIG_H -DBOOST_DISABLE_ASSERTS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DHAVE_ADAPTIVE_SAMPLING -DHAVE_ESM -DHAVE_QUESO -DHAVE_QUESO_GPMSA -DHAVE_CONMIN -DHAVE_DDACE -DHAVE_DREAM -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_NOMAD -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
- DAKOTALIB="-L${DAKOTA_ROOT}/lib -ldakota_src -ldakota_src_fortran -lnidr -lteuchos -lpecos -lpecos_src -llhs -llhs_mods -llhs_mod -ldfftpack -lsparsegrid -lsurfpack -lsurfpack -lsurfpack_fortran -lqueso -lconmin -lddace -ldream -lfsudace -lhopspack -lncsuopt -lcport -lnomad -loptpp -lpsuade -lamplsolver"
- DAKOTALIB+=" -L${BOOST_ROOT}/lib -lboost_filesystem -lboost_program_options -lboost_regex -lboost_serialization -lboost_system"
- DAKOTALIB+=" ${BLASLAPACKLIB}"
- fi
- AC_DEFINE([DISABLE_DAKOTA_CONFIG_H], [1], [enabling DAKOTA_CONFIG_H])
- AC_DEFINE([DAKOTA_HAVE_MPI], [1], [enabling Dakota with MPI])
- elif test "${DAKOTA_VERSION}" == "6.11"; then
- if test "${BOOST_VERSION_MAJOR}" == "1"; then
- if test "${BOOST_VERSION_MINOR}" == "55"; then
- DAKOTAFLAGS="-DDISABLE_DAKOTA_CONFIG_H -DBOOST_MULTI_INDEX_DISABLE_SERIALIZATION -DDAKOTA_PLUGIN -DBOOST_DISABLE_ASSERTS -DDAKOTA_HAVE_BOOST_FS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DDAKOTA_UTILIB -DHAVE_ADAPTIVE_SAMPLING -DHAVE_CONMIN -DDAKOTA_DDACE -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
- DAKOTALIB="-L${DAKOTA_ROOT}/lib -ldakota_src -ldream -lfsudace -lddace -lnomad -lpecos_src -llhs -llhs_mods -loptpp -lsurfpack -lconmin -ldakota_src_fortran -llhs_mod -lncsuopt -lsurfpack_fortran -lteuchos -lamplsolver -lcport -ldfftpack -lfsudace -lhopspack -lnidr -lpecos -lpsuade -lsparsegrid -L$BOOST_ROOT/lib -lboost_serialization -lboost_signals -lboost_regex -lboost_filesystem -lboost_system ${BLASLAPACKLIB}"
- elif test "${BOOST_VERSION_MINOR}" == "72"; then
- DAKOTAFLAGS="-DHAVE_CONFIG_H -DHAVE_CONFIG_H -DDISABLE_DAKOTA_CONFIG_H -DBOOST_DISABLE_ASSERTS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DHAVE_ADAPTIVE_SAMPLING -DHAVE_ESM -DHAVE_CONMIN -DHAVE_DDACE -DHAVE_DREAM -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_NOMAD -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
- DAKOTALIB="-L${DAKOTA_ROOT}/lib -ldakota_src -ldakota_src_fortran -lnidr -lteuchosremainder -lteuchosnumerics -lteuchoscomm -lteuchosparameterlist -lteuchosparser -lteuchoscore -lpecos_util -lpecos_src -llhs -llhs_mods -llhs_mod -ldfftpack -lsparsegrid -lsurfpack -lsurfpack -lsurfpack_fortran -lapproxnn -lconmin -lddace -ldream -lfsudace -lhopspack -lncsuopt -lcport -lnomad -loptpp -lpsuade -lamplsolver -L${BOOST_ROOT}/lib -lboost_filesystem -lboost_program_options -lboost_regex -lboost_serialization -lboost_system ${BLASLAPACKLIB}"
- fi
- fi
- AC_DEFINE([DISABLE_DAKOTA_CONFIG_H], [1], [enabling DAKOTA_CONFIG_H])
- AC_DEFINE([DAKOTA_HAVE_MPI], [1], [enabling Dakota with MPI])
- else
- AC_MSG_ERROR([Dakota version not found or version (${DAKOTA_VERSION}) not supported!]);
- fi
- ;;
esac
@@ -826,8 +831,10 @@
elif ls ${PYTHON_ROOT}/lib/libpython${PYTHON_VERSION}m.* 1> /dev/null 2>&1; then
PYTHONLIB="-L${PYTHON_ROOT}/lib -lpython${PYTHON_VERSION}m"
+ elif ls ${PYTHON_ROOT}/lib/libpython${PYTHON_VERSION}.* 1> /dev/null 2>&1; then
+ PYTHONLIB="-L${PYTHON_ROOT}/lib -lpython${PYTHON_VERSION}"
elif ls ${PYTHON_ROOT}/lib64/libpython${PYTHON_VERSION}m.* 1> /dev/null 2>&1; then
PYTHONLIB="-L${PYTHON_ROOT}/lib64 -lpython${PYTHON_VERSION}m"
- elif ls ${PYTHON_ROOT}/lib/libpython${PYTHON_VERSION}.* 1> /dev/null 2>&1; then
- PYTHONLIB="-L${PYTHON_ROOT}/lib -lpython${PYTHON_VERSION}"
+ elif ls ${PYTHON_ROOT}/lib64/libpython${PYTHON_VERSION}.* 1> /dev/null 2>&1; then
+ PYTHONLIB="-L${PYTHON_ROOT}/lib64 -lpython${PYTHON_VERSION}"
else
AC_MSG_ERROR([libpython not found! Please locate this file and contact ISSM developers via forum or email.]);
@@ -2748,5 +2755,5 @@
AS_HELP_STRING([--with-cxxoptflags=CXXOPTFLAGS], [C++ optimization flags (i.e. --with-cxxoptflags="-march=opteron -O3 -std=c++11"]),
[CXXOPTFLAGS=${withval}],
- [CXXOPTFLAGS="-g -O2 -fPIC -std=c++11"]
+ [CXXOPTFLAGS="-g -O2 -fPIC -std=c++11 -D_DO_NOT_LOAD_GLOBALS_"]
)
AC_SUBST([CXXOPTFLAGS])
Index: /issm/trunk/packagers/linux/complete-issm-linux-binaries-matlab.sh
===================================================================
--- /issm/trunk/packagers/linux/complete-issm-linux-binaries-matlab.sh (revision 27231)
+++ /issm/trunk/packagers/linux/complete-issm-linux-binaries-matlab.sh (revision 27232)
@@ -6,5 +6,5 @@
#
# Normally, we would put this directly into the project configuration under
-# 'Build' -> 'Excute shell', but becasue it is a bit more involved, it is a
+# 'Build' -> 'Execute shell', but because it is a bit more involved, it is a
# good idea to version it.
#
Index: /issm/trunk/packagers/linux/complete-issm-linux-binaries-python-2.sh
===================================================================
--- /issm/trunk/packagers/linux/complete-issm-linux-binaries-python-2.sh (revision 27231)
+++ /issm/trunk/packagers/linux/complete-issm-linux-binaries-python-2.sh (revision 27232)
@@ -6,5 +6,5 @@
#
# Normally, we would put this directly into the project configuration under
-# 'Build' -> 'Excute shell', but becasue it is a bit more involved, it is a
+# 'Build' -> 'Execute shell', but because it is a bit more involved, it is a
# good idea to version it.
#
Index: /issm/trunk/packagers/linux/complete-issm-linux-binaries-python-3.sh
===================================================================
--- /issm/trunk/packagers/linux/complete-issm-linux-binaries-python-3.sh (revision 27231)
+++ /issm/trunk/packagers/linux/complete-issm-linux-binaries-python-3.sh (revision 27232)
@@ -6,5 +6,5 @@
#
# Normally, we would put this directly into the project configuration under
-# 'Build' -> 'Excute shell', but becasue it is a bit more involved, it is a
+# 'Build' -> 'Execute shell', but because it is a bit more involved, it is a
# good idea to version it.
#
Index: /issm/trunk/packagers/linux/package-issm-linux-binaries-matlab.sh
===================================================================
--- /issm/trunk/packagers/linux/package-issm-linux-binaries-matlab.sh (revision 27231)
+++ /issm/trunk/packagers/linux/package-issm-linux-binaries-matlab.sh (revision 27232)
@@ -112,4 +112,22 @@
cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST} 2> /dev/null
+echo "Moving GSHHG assets to share/"
+if [ -d ${ISSM_DIR}/externalpackages/gmt/install/share/coast ]; then
+ mkdir ${ISSM_DIR}/share 2> /dev/null
+ cp -R ${ISSM_DIR}/externalpackages/gmt/install/share/coast ${ISSM_DIR}/share
+else
+ echo "GSHHG not found"
+ exit 1
+fi
+
+echo "Moving PROJ assets to share/"
+if [ -d ${ISSM_DIR}/externalpackages/proj/install/share/proj ]; then
+ mkdir ${ISSM_DIR}/share 2> /dev/null
+ cp -R ${ISSM_DIR}/externalpackages/proj/install/share/proj ${ISSM_DIR}/share
+else
+ echo "PROJ not found"
+ exit 1
+fi
+
# Run tests
if [ ${skip_tests} -eq 0 ]; then
@@ -119,8 +137,8 @@
# Run tests, redirecting output to logfile and suppressing output to console
- ${MATLAB_PATH}/bin/matlab -nojvm -nosplash -nojvm -r "try, addpath ${ISSM_DIR}/bin ${ISSM_DIR}/lib; runme(${MATLAB_NROPTIONS}); exit; catch me,fprintf('%s',getReport(me)); exit; end" &> matlab.log
+ ${MATLAB_PATH}/bin/matlab -nojvm -nosplash -nojvm -r "try, addpath ${ISSM_DIR}/bin ${ISSM_DIR}/lib ${ISSM_DIR}/share; runme(${MATLAB_NROPTIONS}); exit; catch me,fprintf('%s',getReport(me)); exit; end" &> matlab.log
# Check that MATLAB did not exit in error
- matlabExitedInError=`grep -E "Activation cannot proceed|Error in matlab_run|Illegal use of reserved keyword" matlab.log | wc -l`
+ matlabExitedInError=`grep -c -E "Activation cannot proceed|Error in matlab_run|Illegal use of reserved keyword|Invalid MEX-file" matlab.log`
if [ ${matlabExitedInError} -ne 0 ]; then
@@ -136,8 +154,10 @@
# Check that all tests passed
- numTestsFailed=`cat matlab.log | grep -c -e "FAILED|ERROR"`
+ sed -i "/FAILED TO establish the default connection to the WindowServer/d" matlab.log # First, need to remove WindowServer error message
+ numTestsFailed=`grep -c -E "FAILED|ERROR" matlab.log`
if [ ${numTestsFailed} -ne 0 ]; then
echo "One or more tests FAILED"
+ cat matlab.log
exit 1
else
@@ -152,5 +172,5 @@
svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package)
echo "Copying assets to package: ${PKG}"
-cp -rf bin examples lib scripts test ${PKG}
+cp -rf bin examples lib scripts share test ${PKG}
mkdir ${PKG}/execution
echo "Cleaning up unneeded/unwanted files"
Index: /issm/trunk/packagers/linux/package-issm-linux-binaries-python-2.sh
===================================================================
--- /issm/trunk/packagers/linux/package-issm-linux-binaries-python-2.sh (revision 27231)
+++ /issm/trunk/packagers/linux/package-issm-linux-binaries-python-2.sh (revision 27232)
@@ -105,4 +105,21 @@
cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST} 2> /dev/null
+echo "Moving GSHHG assets to share/"
+if [ -d ${ISSM_DIR}/externalpackages/gmt/install/share/coast ]; then
+ mkdir ${ISSM_DIR}/share 2> /dev/null
+ cp -R ${ISSM_DIR}/externalpackages/gmt/install/share/coast ${ISSM_DIR}/share
+else
+ echo "GSHHG not found"
+ exit 1
+fi
+
+echo "Moving PROJ assets to share/"
+if [ -d ${ISSM_DIR}/externalpackages/proj/install/share/proj ]; then
+ mkdir ${ISSM_DIR}/share 2> /dev/null
+ cp -R ${ISSM_DIR}/externalpackages/proj/install/share/proj ${ISSM_DIR}/share
+else
+ echo "PROJ not found"
+ exit 1
+fi
# Run tests
@@ -122,5 +139,5 @@
# Check that Python did not exit in error
pythonExitCode=`echo $?`
- pythonExitedInError=`grep -E "Error|Standard exception|Traceback|bad interpreter" python.log | wc -l`
+ pythonExitedInError=`grep -c -E "Error|Standard exception|Traceback|bad interpreter" python.log`
if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then
@@ -136,8 +153,10 @@
# Check that all tests passed
- numTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"`
+ sed -i "/FAILED TO establish the default connection to the WindowServer/d" python.log # First, need to remove WindowServer error message
+ numTestsFailed=`grep -c -E "FAILED|ERROR" python.log`
if [[ ${numTestsFailed} -ne 0 ]]; then
echo "One or more tests FAILED"
+ cat python.log
exit 1
else
@@ -152,5 +171,5 @@
svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package)
echo "Copying assets to package: ${PKG}"
-cp -rf bin examples lib scripts test ${PKG}
+cp -rf bin examples lib scripts share test ${PKG}
mkdir ${PKG}/execution
${ISSM_DIR}/scripts/py_to_pyc.sh ${PKG}/bin # Compile Python source files
Index: /issm/trunk/packagers/linux/package-issm-linux-binaries-python-3.sh
===================================================================
--- /issm/trunk/packagers/linux/package-issm-linux-binaries-python-3.sh (revision 27231)
+++ /issm/trunk/packagers/linux/package-issm-linux-binaries-python-3.sh (revision 27232)
@@ -105,4 +105,21 @@
cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST} 2> /dev/null
+echo "Moving GSHHG assets to share/"
+if [ -d ${ISSM_DIR}/externalpackages/gmt/install/share/coast ]; then
+ mkdir ${ISSM_DIR}/share 2> /dev/null
+ cp -R ${ISSM_DIR}/externalpackages/gmt/install/share/coast ${ISSM_DIR}/share
+else
+ echo "GSHHG not found"
+ exit 1
+fi
+
+echo "Moving PROJ assets to share/"
+if [ -d ${ISSM_DIR}/externalpackages/proj/install/share/proj ]; then
+ mkdir ${ISSM_DIR}/share 2> /dev/null
+ cp -R ${ISSM_DIR}/externalpackages/proj/install/share/proj ${ISSM_DIR}/share
+else
+ echo "PROJ not found"
+ exit 1
+fi
# Run tests
@@ -125,5 +142,5 @@
# Check that Python did not exit in error
pythonExitCode=`echo $?`
- pythonExitedInError=`grep -E "Error|Standard exception|Traceback|bad interpreter" python.log | wc -l`
+ pythonExitedInError=`grep -c -E "Error|Standard exception|Traceback|bad interpreter" python.log`
if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then
@@ -139,8 +156,10 @@
# Check that all tests passed
- numTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"`
+ sed -i "/FAILED TO establish the default connection to the WindowServer/d" python.log # First, need to remove WindowServer error message
+ numTestsFailed=`grep -c -E "FAILED|ERROR" python.log`
if [[ ${numTestsFailed} -ne 0 ]]; then
echo "One or more tests FAILED"
+ cat python.log
exit 1
else
@@ -155,5 +174,5 @@
svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package)
echo "Copying assets to package: ${PKG}"
-cp -rf bin examples lib scripts test ${PKG}
+cp -rf bin examples lib scripts share test ${PKG}
mkdir ${PKG}/execution
${ISSM_DIR}/scripts/py_to_pyc.sh ${PKG}/bin # Compile Python source files
Index: /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-matlab.sh
===================================================================
--- /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-matlab.sh (revision 27231)
+++ /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-matlab.sh (revision 27232)
@@ -138,4 +138,6 @@
echo "Removing lock file from repository for signed packages"
svn update \
+ --trust-server-cert \
+ --non-interactive \
--username ${ISSM_BINARIES_REPO_USER} \
--password ${ISSM_BINARIES_REPO_PASS} \
@@ -156,4 +158,6 @@
# If lock file exists, a signing build is still in process by JPL Cybersecurity
svn update \
+ --trust-server-cert \
+ --non-interactive \
--username ${ISSM_BINARIES_REPO_USER} \
--password ${ISSM_BINARIES_REPO_PASS} \
@@ -214,4 +218,6 @@
sleep ${SIGNING_CHECK_PERIOD}
svn update \
+ --trust-server-cert \
+ --non-interactive \
--username ${ISSM_BINARIES_REPO_USER} \
--password ${ISSM_BINARIES_REPO_PASS} \
@@ -221,4 +227,6 @@
# Retrieve notarization lock file
svn update \
+ --trust-server-cert \
+ --non-interactive \
--username ${ISSM_BINARIES_REPO_USER} \
--password ${ISSM_BINARIES_REPO_PASS} \
Index: /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-python-2.sh
===================================================================
--- /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-python-2.sh (revision 27231)
+++ /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-python-2.sh (revision 27232)
@@ -138,4 +138,6 @@
echo "Removing lock file from repository for signed packages"
svn update \
+ --trust-server-cert \
+ --non-interactive \
--username ${ISSM_BINARIES_REPO_USER} \
--password ${ISSM_BINARIES_REPO_PASS} \
@@ -156,4 +158,6 @@
# If lock file exists, a signing build is still in process by JPL Cybersecurity
svn update \
+ --trust-server-cert \
+ --non-interactive \
--username ${ISSM_BINARIES_REPO_USER} \
--password ${ISSM_BINARIES_REPO_PASS} \
@@ -214,4 +218,6 @@
sleep ${SIGNING_CHECK_PERIOD}
svn update \
+ --trust-server-cert \
+ --non-interactive \
--username ${ISSM_BINARIES_REPO_USER} \
--password ${ISSM_BINARIES_REPO_PASS} \
@@ -221,4 +227,6 @@
# Retrieve notarization lock file
svn update \
+ --trust-server-cert \
+ --non-interactive \
--username ${ISSM_BINARIES_REPO_USER} \
--password ${ISSM_BINARIES_REPO_PASS} \
Index: /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-python-3.sh
===================================================================
--- /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-python-3.sh (revision 27231)
+++ /issm/trunk/packagers/mac/commit_for_signing-issm-mac-binaries-python-3.sh (revision 27232)
@@ -138,4 +138,6 @@
echo "Removing lock file from repository for signed packages"
svn update \
+ --trust-server-cert \
+ --non-interactive \
--username ${ISSM_BINARIES_REPO_USER} \
--password ${ISSM_BINARIES_REPO_PASS} \
@@ -156,4 +158,6 @@
# If lock file exists, a signing build is still in process by JPL Cybersecurity
svn update \
+ --trust-server-cert \
+ --non-interactive \
--username ${ISSM_BINARIES_REPO_USER} \
--password ${ISSM_BINARIES_REPO_PASS} \
@@ -214,4 +218,6 @@
sleep ${SIGNING_CHECK_PERIOD}
svn update \
+ --trust-server-cert \
+ --non-interactive \
--username ${ISSM_BINARIES_REPO_USER} \
--password ${ISSM_BINARIES_REPO_PASS} \
@@ -221,4 +227,6 @@
# Retrieve notarization lock file
svn update \
+ --trust-server-cert \
+ --non-interactive \
--username ${ISSM_BINARIES_REPO_USER} \
--password ${ISSM_BINARIES_REPO_PASS} \
Index: /issm/trunk/packagers/mac/complete-issm-mac-binaries-matlab.sh
===================================================================
--- /issm/trunk/packagers/mac/complete-issm-mac-binaries-matlab.sh (revision 27231)
+++ /issm/trunk/packagers/mac/complete-issm-mac-binaries-matlab.sh (revision 27232)
@@ -6,5 +6,5 @@
#
# Normally, we would put this directly into the project configuration under
-# 'Build' -> 'Excute shell', but becasue it is a bit more involved, it is a
+# 'Build' -> 'Execute shell', but because it is a bit more involved, it is a
# good idea to version it.
#
@@ -33,10 +33,11 @@
# Debugging:
# - Relies on a very tight handshake with project on remote JPL Cybersecurity
-# Jenkins server. Debugging may be perfomed locally by running,
+# Jenkins server. Debugging may be performed locally by running,
#
# packagers/mac/sign-issm-mac-binaries-matlab.sh
#
-# with "ISSM_BINARIES_USER" and "ISSM_BINARIES_PASS" hardcoded to Apple
-# Developer credentials.
+# with "AD_IDENTITY", "AD_USERNAME", and "ASC_PROVIDER" hardcoded to Apple
+# Developer credentials (make sure to also set keychain password in
+# "ALTOOL_PASSWORD").
# - Removing stdout/stderr redirections to null device (> /dev/null 2>&1) can
# help debug potential SVN issues.
Index: /issm/trunk/packagers/mac/complete-issm-mac-binaries-python-2.sh
===================================================================
--- /issm/trunk/packagers/mac/complete-issm-mac-binaries-python-2.sh (revision 27231)
+++ /issm/trunk/packagers/mac/complete-issm-mac-binaries-python-2.sh (revision 27232)
@@ -6,5 +6,5 @@
#
# Normally, we would put this directly into the project configuration under
-# 'Build' -> 'Excute shell', but becasue it is a bit more involved, it is a
+# 'Build' -> 'Execute shell', but because it is a bit more involved, it is a
# good idea to version it.
#
@@ -33,10 +33,11 @@
# Debugging:
# - Relies on a very tight handshake with project on remote JPL Cybersecurity
-# Jenkins server. Debugging may be perfomed locally by running,
+# Jenkins server. Debugging may be performed locally by running,
#
# packagers/mac/sign-issm-mac-binaries-python-2.sh
#
-# with "ISSM_BINARIES_USER" and "ISSM_BINARIES_PASS" hardcoded to Apple
-# Developer credentials.
+# with "AD_IDENTITY", "AD_USERNAME", and "ASC_PROVIDER" hardcoded to Apple
+# Developer credentials (make sure to also set keychain password in
+# "ALTOOL_PASSWORD").
# - Removing stdout/stderr redirections to null device (> /dev/null 2>&1) can
# help debug potential SVN issues.
Index: /issm/trunk/packagers/mac/complete-issm-mac-binaries-python-3.sh
===================================================================
--- /issm/trunk/packagers/mac/complete-issm-mac-binaries-python-3.sh (revision 27231)
+++ /issm/trunk/packagers/mac/complete-issm-mac-binaries-python-3.sh (revision 27232)
@@ -6,5 +6,5 @@
#
# Normally, we would put this directly into the project configuration under
-# 'Build' -> 'Excute shell', but becasue it is a bit more involved, it is a
+# 'Build' -> 'Execute shell', but because it is a bit more involved, it is a
# good idea to version it.
#
@@ -33,10 +33,11 @@
# Debugging:
# - Relies on a very tight handshake with project on remote JPL Cybersecurity
-# Jenkins server. Debugging may be perfomed locally by running,
+# Jenkins server. Debugging may be performed locally by running,
#
# packagers/mac/sign-issm-mac-binaries-python-3.sh
#
-# with "ISSM_BINARIES_USER" and "ISSM_BINARIES_PASS" hardcoded to Apple
-# Developer credentials.
+# with "AD_IDENTITY", "AD_USERNAME", and "ASC_PROVIDER" hardcoded to Apple
+# Developer credentials (make sure to also set keychain password in
+# "ALTOOL_PASSWORD").
# - Removing stdout/stderr redirections to null device (> /dev/null 2>&1) can
# help debug potential SVN issues.
Index: /issm/trunk/packagers/mac/package-issm-mac-binaries-matlab.sh
===================================================================
--- /issm/trunk/packagers/mac/package-issm-mac-binaries-matlab.sh (revision 27231)
+++ /issm/trunk/packagers/mac/package-issm-mac-binaries-matlab.sh (revision 27232)
@@ -109,4 +109,12 @@
fi
+echo "Moving Gmsh binaries to bin/"
+if [ -f ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh ]; then
+ cp ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh .
+else
+ echo "Gmsh not found"
+ exit 1
+fi
+
echo "Moving GMT binaries to bin/"
if [ -f ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt-config ]; then
@@ -118,9 +126,19 @@
fi
-echo "Moving Gmsh binaries to bin/"
-if [ -f ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh ]; then
- cp ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh .
+echo "Moving GSHHG assets to share/"
+if [ -d ${ISSM_DIR}/externalpackages/gmt/install/share/coast ]; then
+ mkdir ${ISSM_DIR}/share 2> /dev/null
+ cp -R ${ISSM_DIR}/externalpackages/gmt/install/share/coast ${ISSM_DIR}/share
else
- echo "Gmsh not found"
+ echo "GSHHG not found"
+ exit 1
+fi
+
+echo "Moving PROJ assets to share/"
+if [ -d ${ISSM_DIR}/externalpackages/proj/install/share/proj ]; then
+ mkdir ${ISSM_DIR}/share 2> /dev/null
+ cp -R ${ISSM_DIR}/externalpackages/proj/install/share/proj ${ISSM_DIR}/share
+else
+ echo "PROJ not found"
exit 1
fi
@@ -133,8 +151,8 @@
# Run tests, redirecting output to logfile and suppressing output to console
- ${MATLAB_PATH}/bin/matlab -nojvm -nosplash -nojvm -r "try, addpath ${ISSM_DIR}/bin ${ISSM_DIR}/lib; runme(${MATLAB_NROPTIONS}); exit; catch me,fprintf('%s',getReport(me)); exit; end" &> matlab.log
+ ${MATLAB_PATH}/bin/matlab -nojvm -nosplash -nojvm -r "try, addpath ${ISSM_DIR}/bin ${ISSM_DIR}/lib ${ISSM_DIR}/share; runme(${MATLAB_NROPTIONS}); exit; catch me,fprintf('%s',getReport(me)); exit; end" &> matlab.log
# Check that MATLAB did not exit in error
- matlabExitedInError=`grep -E "Activation cannot proceed|Error in matlab_run|Illegal use of reserved keyword" matlab.log | wc -l`
+ matlabExitedInError=`grep -c -E "Activation cannot proceed|Error in matlab_run|Illegal use of reserved keyword" matlab.log`
if [ ${matlabExitedInError} -ne 0 ]; then
@@ -150,8 +168,10 @@
# Check that all tests passed
- numTestsFailed=`cat matlab.log | grep -c -e "FAILED|ERROR"`
+ sed -i '' "/FAILED TO establish the default connection to the WindowServer/d" matlab.log # First, need to remove WindowServer error message
+ numTestsFailed=`grep -c -E "FAILED|ERROR" matlab.log`
if [ ${numTestsFailed} -ne 0 ]; then
echo "One or more tests FAILED"
+ cat matlab.log
exit 1
else
@@ -166,5 +186,5 @@
svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package)
echo "Copying assets to package: ${PKG}"
-cp -rf bin examples lib scripts test ${PKG}
+cp -rf bin examples lib scripts share test ${PKG}
mkdir ${PKG}/execution
cp packagers/mac/issm-executable_entitlements.plist ${PKG}/bin/entitlements.plist
Index: /issm/trunk/packagers/mac/package-issm-mac-binaries-python-2.sh
===================================================================
--- /issm/trunk/packagers/mac/package-issm-mac-binaries-python-2.sh (revision 27231)
+++ /issm/trunk/packagers/mac/package-issm-mac-binaries-python-2.sh (revision 27232)
@@ -101,4 +101,12 @@
fi
+echo "Moving Gmsh binaries to bin/"
+if [ -f ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh ]; then
+ cp ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh .
+else
+ echo "Gmsh not found"
+ exit 1
+fi
+
echo "Moving GMT binaries to bin/"
if [ -f ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt-config ]; then
@@ -110,9 +118,19 @@
fi
-echo "Moving Gmsh binaries to bin/"
-if [ -f ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh ]; then
- cp ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh .
+echo "Moving GSHHG assets to share/"
+if [ -d ${ISSM_DIR}/externalpackages/gmt/install/share/coast ]; then
+ mkdir ${ISSM_DIR}/share 2> /dev/null
+ cp -R ${ISSM_DIR}/externalpackages/gmt/install/share/coast ${ISSM_DIR}/share
else
- echo "Gmsh not found"
+ echo "GSHHG not found"
+ exit 1
+fi
+
+echo "Moving PROJ assets to share/"
+if [ -d ${ISSM_DIR}/externalpackages/proj/install/share/proj ]; then
+ mkdir ${ISSM_DIR}/share 2> /dev/null
+ cp -R ${ISSM_DIR}/externalpackages/proj/install/share/proj ${ISSM_DIR}/share
+else
+ echo "PROJ not found"
exit 1
fi
@@ -134,5 +152,5 @@
# Check that Python did not exit in error
pythonExitCode=`echo $?`
- pythonExitedInError=`grep -E "Error|Standard exception|Traceback|bad interpreter" python.log | wc -l`
+ pythonExitedInError=`grep -c -E "Error|Standard exception|Traceback|bad interpreter" python.log`
if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then
@@ -148,8 +166,10 @@
# Check that all tests passed
- numTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"`
+ sed -i '' "/FAILED TO establish the default connection to the WindowServer/d" python.log # First, need to remove WindowServer error message
+ numTestsFailed=`grep -c -E "FAILED|ERROR" python.log`
if [ ${numTestsFailed} -ne 0 ]; then
echo "One or more tests FAILED"
+ cat python.log
exit 1
else
@@ -164,5 +184,5 @@
svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package)
echo "Copying assets to package: ${PKG}"
-cp -rf bin examples lib scripts test ${PKG}
+cp -rf bin examples lib scripts share test ${PKG}
mkdir ${PKG}/execution
cp packagers/mac/issm-executable_entitlements.plist ${PKG}/bin/entitlements.plist
Index: /issm/trunk/packagers/mac/package-issm-mac-binaries-python-3.sh
===================================================================
--- /issm/trunk/packagers/mac/package-issm-mac-binaries-python-3.sh (revision 27231)
+++ /issm/trunk/packagers/mac/package-issm-mac-binaries-python-3.sh (revision 27232)
@@ -101,4 +101,12 @@
fi
+echo "Moving Gmsh binaries to bin/"
+if [ -f ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh ]; then
+ cp ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh .
+else
+ echo "Gmsh not found"
+ exit 1
+fi
+
echo "Moving GMT binaries to bin/"
if [ -f ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt-config ]; then
@@ -110,9 +118,19 @@
fi
-echo "Moving Gmsh binaries to bin/"
-if [ -f ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh ]; then
- cp ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh .
-else
- echo "Gmsh not found"
+echo "Moving GSHHG assets to share/"
+if [ -d ${ISSM_DIR}/externalpackages/gmt/install/share/coast ]; then
+ mkdir ${ISSM_DIR}/share 2> /dev/null
+ cp -R ${ISSM_DIR}/externalpackages/gmt/install/share/coast ${ISSM_DIR}/share
+else
+ echo "GSHHG not found"
+ exit 1
+fi
+
+echo "Moving PROJ assets to share/"
+if [ -d ${ISSM_DIR}/externalpackages/proj/install/share/proj ]; then
+ mkdir ${ISSM_DIR}/share 2> /dev/null
+ cp -R ${ISSM_DIR}/externalpackages/proj/install/share/proj ${ISSM_DIR}/share
+else
+ echo "PROJ not found"
exit 1
fi
@@ -137,5 +155,5 @@
# Check that Python did not exit in error
pythonExitCode=`echo $?`
- pythonExitedInError=`grep -E "Error|Standard exception|Traceback|bad interpreter" python.log | wc -l`
+ pythonExitedInError=`grep -c -E "Error|Standard exception|Traceback|bad interpreter" python.log`
if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then
@@ -151,8 +169,10 @@
# Check that all tests passed
- numTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"`
+ sed -i '' "/FAILED TO establish the default connection to the WindowServer/d" python.log # First, need to remove WindowServer error message
+ numTestsFailed=`grep -c -E "FAILED|ERROR" python.log`
if [ ${numTestsFailed} -ne 0 ]; then
echo "One or more tests FAILED"
+ cat python.log
exit 1
else
@@ -167,5 +187,5 @@
svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package)
echo "Copying assets to package: ${PKG}"
-cp -rf bin examples lib scripts test ${PKG}
+cp -rf bin examples lib scripts share test ${PKG}
mkdir ${PKG}/execution
cp packagers/mac/issm-executable_entitlements.plist ${PKG}/bin/entitlements.plist
Index: /issm/trunk/packagers/mac/sign-issm-mac-binaries-matlab.sh
===================================================================
--- /issm/trunk/packagers/mac/sign-issm-mac-binaries-matlab.sh (revision 27231)
+++ /issm/trunk/packagers/mac/sign-issm-mac-binaries-matlab.sh (revision 27232)
@@ -45,5 +45,5 @@
# the 'Bindings' section under a 'Username and password (separated)' binding
# (requires 'Credentials Binding Plugin').
-# - For local debugging, the aformentioned credentials can be hardcoded into
+# - For local debugging, the aforementioned credentials can be hardcoded into
# the 'USERNAME' and 'PASSWORD' constants below.
################################################################################
@@ -109,5 +109,5 @@
# # Check out copy of repository for unsigned packages
-# echo "Checking out copy of respository for unsigned packages"
+# echo "Checking out copy of repository for unsigned packages"
# svn checkout \
# --trust-server-cert \
@@ -160,10 +160,10 @@
# Sleep until notarization request response is received
-echo "Waiting for notarizaion request response"
+echo "Waiting for notarization request response"
while [[ ! -f ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} || ! -z $(find ${NOTARIZATION_LOGFILE_PATH} -empty -name ${NOTARIZATION_LOGFILE}) ]]; do
sleep 30
done
-echo "Notarizaion request response received"
+echo "Notarization request response received"
# Check if UUID exists in response
@@ -249,5 +249,5 @@
# Check out copy of repository for signed packages
-echo "Checking out copy of respository for signed packages"
+echo "Checking out copy of repository for signed packages"
SVN_ATTEMPT=0
SVN_SUCCESS=0
@@ -271,5 +271,5 @@
if [ ${SVN_SUCCESS} -eq 0 ]; then
- echo "Checkout of respository for signed packages failed"
+ echo "Checkout of repository for signed packages failed"
exit 1
fi
@@ -308,5 +308,5 @@
if [ ${SVN_SUCCESS} -eq 0 ]; then
- echo "Commit to respository for signed packages failed"
+ echo "Commit to repository for signed packages failed"
exit 1
fi
@@ -331,5 +331,5 @@
if [ ${SVN_SUCCESS} -eq 0 ]; then
- echo "Commit to respository for signed packages failed"
+ echo "Commit to repository for signed packages failed"
exit 1
fi
Index: /issm/trunk/packagers/mac/sign-issm-mac-binaries-python-2.sh
===================================================================
--- /issm/trunk/packagers/mac/sign-issm-mac-binaries-python-2.sh (revision 27231)
+++ /issm/trunk/packagers/mac/sign-issm-mac-binaries-python-2.sh (revision 27232)
@@ -45,5 +45,5 @@
# the 'Bindings' section under a 'Username and password (separated)' binding
# (requires 'Credentials Binding Plugin').
-# - For local debugging, the aformentioned credentials can be hardcoded into
+# - For local debugging, the aforementioned credentials can be hardcoded into
# the 'USERNAME' and 'PASSWORD' constants below.
################################################################################
@@ -109,5 +109,5 @@
# # Check out copy of repository for unsigned packages
-# echo "Checking out copy of respository for unsigned packages"
+# echo "Checking out copy of repository for unsigned packages"
# svn checkout \
# --trust-server-cert \
@@ -170,10 +170,10 @@
# Sleep until notarization request response is received
-echo "Waiting for notarizaion request response"
+echo "Waiting for notarization request response"
while [[ ! -f ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} || ! -z $(find ${NOTARIZATION_LOGFILE_PATH} -empty -name ${NOTARIZATION_LOGFILE}) ]]; do
sleep 30
done
-echo "Notarizaion request response received"
+echo "Notarization request response received"
# Check if UUID exists in response
@@ -259,5 +259,5 @@
# Check out copy of repository for signed packages
-echo "Checking out copy of respository for signed packages"
+echo "Checking out copy of repository for signed packages"
SVN_ATTEMPT=0
SVN_SUCCESS=0
@@ -281,5 +281,5 @@
if [ ${SVN_SUCCESS} -eq 0 ]; then
- echo "Checkout of respository for signed packages failed"
+ echo "Checkout of repository for signed packages failed"
exit 1
fi
@@ -318,5 +318,5 @@
if [ ${SVN_SUCCESS} -eq 0 ]; then
- echo "Commit to respository for signed packages failed"
+ echo "Commit to repository for signed packages failed"
exit 1
fi
@@ -341,5 +341,5 @@
if [ ${SVN_SUCCESS} -eq 0 ]; then
- echo "Commit to respository for signed packages failed"
+ echo "Commit to repository for signed packages failed"
exit 1
fi
Index: /issm/trunk/packagers/mac/sign-issm-mac-binaries-python-3.sh
===================================================================
--- /issm/trunk/packagers/mac/sign-issm-mac-binaries-python-3.sh (revision 27231)
+++ /issm/trunk/packagers/mac/sign-issm-mac-binaries-python-3.sh (revision 27232)
@@ -45,5 +45,5 @@
# the 'Bindings' section under a 'Username and password (separated)' binding
# (requires 'Credentials Binding Plugin').
-# - For local debugging, the aformentioned credentials can be hardcoded into
+# - For local debugging, the aforementioned credentials can be hardcoded into
# the 'USERNAME' and 'PASSWORD' constants below.
################################################################################
@@ -109,5 +109,5 @@
# # Check out copy of repository for unsigned packages
-# echo "Checking out copy of respository for unsigned packages"
+# echo "Checking out copy of repository for unsigned packages"
# svn checkout \
# --trust-server-cert \
@@ -170,10 +170,10 @@
# Sleep until notarization request response is received
-echo "Waiting for notarizaion request response"
+echo "Waiting for notarization request response"
while [[ ! -f ${NOTARIZATION_LOGFILE_PATH}/${NOTARIZATION_LOGFILE} || ! -z $(find ${NOTARIZATION_LOGFILE_PATH} -empty -name ${NOTARIZATION_LOGFILE}) ]]; do
sleep 30
done
-echo "Notarizaion request response received"
+echo "Notarization request response received"
# Check if UUID exists in response
@@ -259,5 +259,5 @@
# Check out copy of repository for signed packages
-echo "Checking out copy of respository for signed packages"
+echo "Checking out copy of repository for signed packages"
SVN_ATTEMPT=0
SVN_SUCCESS=0
@@ -281,5 +281,5 @@
if [ ${SVN_SUCCESS} -eq 0 ]; then
- echo "Checkout of respository for signed packages failed"
+ echo "Checkout of repository for signed packages failed"
exit 1
fi
@@ -318,5 +318,5 @@
if [ ${SVN_SUCCESS} -eq 0 ]; then
- echo "Commit to respository for signed packages failed"
+ echo "Commit to repository for signed packages failed"
exit 1
fi
@@ -341,5 +341,5 @@
if [ ${SVN_SUCCESS} -eq 0 ]; then
- echo "Commit to respository for signed packages failed"
+ echo "Commit to repository for signed packages failed"
exit 1
fi
Index: /issm/trunk/packagers/mac/test-issm-mac-binaries-matlab.sh
===================================================================
--- /issm/trunk/packagers/mac/test-issm-mac-binaries-matlab.sh (revision 27231)
+++ /issm/trunk/packagers/mac/test-issm-mac-binaries-matlab.sh (revision 27232)
@@ -34,5 +34,5 @@
# Check that MATLAB did not exit in error
matlabExitCode=`echo $?`
-matlabExitedInError=`grep -E "Activation cannot proceed|license|Error|Warning: Name is nonexistent or not a directory" matlab.log | wc -l`
+matlabExitedInError=`grep -c -E "Activation cannot proceed|license|Error|Warning: Name is nonexistent or not a directory" matlab.log`
if [[ ${matlabExitCode} -ne 0 || ${matlabExitedInError} -ne 0 ]]; then
@@ -45,8 +45,9 @@
# Check that all tests passed
-numTestsFailed=`cat matlab.log | grep -c -e "FAILED|ERROR"`
+numTestsFailed=`grep -c -E "FAILED|ERROR" matlab.log`
if [[ ${numTestsFailed} -ne 0 ]]; then
echo "One or more tests FAILED"
+ cat matlab.log
exit 1
else
Index: /issm/trunk/packagers/mac/test-issm-mac-binaries-python-2.sh
===================================================================
--- /issm/trunk/packagers/mac/test-issm-mac-binaries-python-2.sh (revision 27231)
+++ /issm/trunk/packagers/mac/test-issm-mac-binaries-python-2.sh (revision 27232)
@@ -34,5 +34,5 @@
# Check that Python did not exit in error
pythonExitCode=`echo $?`
-pythonExitedInError=`grep -E "runme.py: error" python.log | wc -l`
+pythonExitedInError=`grep -c -E "runme.py: error" python.log`
if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then
@@ -44,8 +44,9 @@
# Check that all tests passed
-numTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"`
+numTestsFailed=`grep -c -E "FAILED|ERROR" python.log`
if [[ ${numTestsFailed} -ne 0 ]]; then
echo "One or more tests FAILED"
+ cat python.log
exit 1
else
Index: /issm/trunk/packagers/mac/test-issm-mac-binaries-python-3.sh
===================================================================
--- /issm/trunk/packagers/mac/test-issm-mac-binaries-python-3.sh (revision 27231)
+++ /issm/trunk/packagers/mac/test-issm-mac-binaries-python-3.sh (revision 27232)
@@ -34,5 +34,5 @@
# Check that Python did not exit in error
pythonExitCode=`echo $?`
-pythonExitedInError=`grep -E "runme.py: error" python.log | wc -l`
+pythonExitedInError=`grep -c -E "runme.py: error" python.log`
if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then
@@ -44,8 +44,9 @@
# Check that all tests passed
-numTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"`
+numTestsFailed=`grep -c -E "FAILED|ERROR" python.log`
if [[ ${numTestsFailed} -ne 0 ]]; then
echo "One or more tests FAILED"
+ cat python.log
exit 1
else
Index: /issm/trunk/packagers/mac/transfer-issm-mac-binaries.sh
===================================================================
--- /issm/trunk/packagers/mac/transfer-issm-mac-binaries.sh (revision 27231)
+++ /issm/trunk/packagers/mac/transfer-issm-mac-binaries.sh (revision 27232)
@@ -76,4 +76,6 @@
# Retrieve signed and notarized package
svn update \
+ --trust-server-cert \
+ --non-interactive \
--username ${ISSM_BINARIES_REPO_USER} \
--password ${ISSM_BINARIES_REPO_PASS} \
Index: /issm/trunk/src/c/Makefile.am
===================================================================
--- /issm/trunk/src/c/Makefile.am (revision 27231)
+++ /issm/trunk/src/c/Makefile.am (revision 27232)
@@ -346,5 +346,6 @@
./classes/Inputs/ControlInput.cpp \
./classes/Inputs/TransientInput.cpp \
- ./classes/Inputs/ArrayInput.cpp
+ ./classes/Inputs/ArrayInput.cpp \
+ ./classes/Inputs/IntArrayInput.cpp
#}}}
# ADJOINTMPI/MeDiPack sources {{{
@@ -400,5 +401,5 @@
endif
#}}}
-#GSL sources {{{
+# GSL sources {{{
if GSL
issm_sources += ./toolkits/gsl/DenseGslSolve.cpp
@@ -419,4 +420,7 @@
if ADJOINTHORIZ
issm_sources += ./analyses/AdjointHorizAnalysis.cpp
+endif
+if AGE
+issm_sources += ./analyses/AgeAnalysis.cpp
endif
if BALANCETHICKNESS
@@ -530,11 +534,5 @@
issm_sources += \
./cores/love_core.cpp \
- ./analyses/LoveAnalysis.cpp \
- ./modules/FourierLoveCorex/FourierLoveCorex.cpp \
- ./modules/FourierLoveCorex/lnb_param.f90 \
- ./modules/FourierLoveCorex/model.f90 \
- ./modules/FourierLoveCorex/util.f90 \
- ./modules/FourierLoveCorex/lovenb_sub.f90 \
- ./modules/FourierLoveCorex/love_numbers.f90
+ ./analyses/LoveAnalysis.cpp
endif
endif
@@ -831,5 +829,5 @@
# External packages
-LDADD += $(CHACOLIB) $(DAKOTALIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(NEOPZLIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(MPLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(BLACSLIB) $(HDF5LIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(AMPILIB) $(ADJOINTMPILIB) $(ADOLCLIB) $(MPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJLIB) $(ESMFLIB) $(OSLIBS)
+LDADD += $(SEMICLIB) $(M1QN3LIB) $(CHACOLIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(NEOPZLIB) $(TAOLIB) $(PLAPACKLIB) $(MPLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(BLACSLIB) $(HDF5LIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(SCOTCHLIB) $(MKLLIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(AMPILIB) $(ADJOINTMPILIB) $(ADOLCLIB) $(MPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJLIB) $(ESMFLIB) $(OSLIBS)
if FORTRAN
@@ -842,4 +840,5 @@
issm_slc_SOURCES = main/issm_slc.cpp
issm_slc_CXXFLAGS= $(CXXFLAGS) $(CXXOPTFLAGS)
+issm_slc_LDADD = $(DAKOTALIB) $(LDADD)
if OCEAN
@@ -859,5 +858,5 @@
issm_dakota_SOURCES = main/issm_dakota.cpp
issm_dakota_CXXFLAGS= $(CXXFLAGS) $(CXXOPTFLAGS) $(COPTFLAGS)
-issm_dakota_LDADD= $(LDADD)
+issm_dakota_LDADD = $(DAKOTALIB) $(LDADD)
bin_PROGRAMS += issm_post
issm_post_SOURCES = main/issm_post.cpp
Index: /issm/trunk/src/c/analyses/AdjointHorizAnalysis.cpp
===================================================================
--- /issm/trunk/src/c/analyses/AdjointHorizAnalysis.cpp (revision 27231)
+++ /issm/trunk/src/c/analyses/AdjointHorizAnalysis.cpp (revision 27232)
@@ -3362,5 +3362,5 @@
element->AddInput(AdjointpEnum,lambdap,element->PressureInterpolation());
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(vdoflist);
xDelete(pdoflist);
@@ -3414,5 +3414,5 @@
element->AddInput(AdjointyEnum,lambday,element->GetElementType());
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(values);
xDelete(lambdax);
@@ -3483,5 +3483,5 @@
element->AddInput(AdjointyEnum,lambday,element->GetElementType());
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(values);
xDelete(lambdax);
Index: /issm/trunk/src/c/analyses/AgeAnalysis.cpp
===================================================================
--- /issm/trunk/src/c/analyses/AgeAnalysis.cpp (revision 27232)
+++ /issm/trunk/src/c/analyses/AgeAnalysis.cpp (revision 27232)
@@ -0,0 +1,537 @@
+#include "./AgeAnalysis.h"
+#include "../toolkits/toolkits.h"
+#include "../classes/classes.h"
+#include "../shared/shared.h"
+#include "../modules/modules.h"
+
+/*Model processing*/
+void AgeAnalysis::CreateConstraints(Constraints* constraints,IoModel* iomodel){/*{{{*/
+
+ IoModelToConstraintsx(constraints,iomodel,"md.age.spcage",AgeAnalysisEnum,P1Enum);
+
+}/*}}}*/
+void AgeAnalysis::CreateLoads(Loads* loads, IoModel* iomodel){/*{{{*/
+
+ if(iomodel->domaintype==Domain2DhorizontalEnum) _error_("2d meshes not supported yet");
+
+}/*}}}*/
+void AgeAnalysis::CreateNodes(Nodes* nodes,IoModel* iomodel,bool isamr){/*{{{*/
+
+ int finiteelement = P1Enum;
+
+ if(iomodel->domaintype==Domain3DEnum) iomodel->FetchData(2,"md.mesh.vertexonbase","md.mesh.vertexonsurface");
+ ::CreateNodes(nodes,iomodel,AgeAnalysisEnum,finiteelement);
+ iomodel->DeleteData(2,"md.mesh.vertexonbase","md.mesh.vertexonsurface");
+}/*}}}*/
+int AgeAnalysis::DofsPerNode(int** doflist,int domaintype,int approximation){/*{{{*/
+ return 1;
+}/*}}}*/
+void AgeAnalysis::UpdateElements(Elements* elements,Inputs* inputs,IoModel* iomodel,int analysis_counter,int analysis_type){/*{{{*/
+
+ /*Now, is the model 3d? otherwise, do nothing: */
+ if(iomodel->domaintype==Domain2DhorizontalEnum)return;
+
+ /*Update elements: */
+ int finiteelement = P1Enum;
+ int counter=0;
+ for(int i=0;inumberofelements;i++){
+ if(iomodel->my_elements[i]){
+ Element* element=(Element*)elements->GetObjectByOffset(counter);
+ element->Update(inputs,i,iomodel,analysis_counter,analysis_type,finiteelement);
+ counter++;
+ }
+ }
+
+ bool dakota_analysis, ismovingfront;
+ iomodel->FetchDataToInput(inputs,elements,"md.geometry.thickness",ThicknessEnum);
+ iomodel->FetchDataToInput(inputs,elements,"md.geometry.surface",SurfaceEnum);
+ iomodel->FetchDataToInput(inputs,elements,"md.geometry.base",BaseEnum);
+ iomodel->FetchDataToInput(inputs,elements,"md.mask.ice_levelset",MaskIceLevelsetEnum);
+ iomodel->FetchDataToInput(inputs,elements,"md.mask.ocean_levelset",MaskOceanLevelsetEnum);
+ if(iomodel->domaintype!=Domain2DhorizontalEnum){
+ iomodel->FetchDataToInput(inputs,elements,"md.mesh.vertexonbase",MeshVertexonbaseEnum);
+ iomodel->FetchDataToInput(inputs,elements,"md.mesh.vertexonsurface",MeshVertexonsurfaceEnum);
+ }
+ iomodel->FetchDataToInput(inputs,elements,"md.mesh.vertexonbase",MeshVertexonbaseEnum);
+ iomodel->FetchDataToInput(inputs,elements,"md.mesh.vertexonsurface",MeshVertexonsurfaceEnum);
+ iomodel->FetchDataToInput(inputs,elements,"md.initialization.age",AgeEnum);
+ iomodel->FetchDataToInput(inputs,elements,"md.initialization.vx",VxEnum);
+ iomodel->FetchDataToInput(inputs,elements,"md.initialization.vy",VyEnum);
+ iomodel->FetchDataToInput(inputs,elements,"md.initialization.vz",VzEnum);
+ InputUpdateFromConstantx(inputs,elements,0.,VxMeshEnum);
+ InputUpdateFromConstantx(inputs,elements,0.,VyMeshEnum);
+ InputUpdateFromConstantx(inputs,elements,0.,VzMeshEnum);
+}/*}}}*/
+void AgeAnalysis::UpdateParameters(Parameters* parameters,IoModel* iomodel,int solution_enum,int analysis_enum){/*{{{*/
+
+ int numoutputs;
+ char** requestedoutputs = NULL;
+
+ parameters->AddObject(iomodel->CopyConstantObject("md.age.stabilization",AgeStabilizationEnum));
+
+ iomodel->FindConstant(&requestedoutputs,&numoutputs,"md.age.requested_outputs");
+ parameters->AddObject(new IntParam(AgeNumRequestedOutputsEnum,numoutputs));
+ if(numoutputs)parameters->AddObject(new StringArrayParam(AgeRequestedOutputsEnum,requestedoutputs,numoutputs));
+ iomodel->DeleteData(&requestedoutputs,numoutputs,"md.age.requested_outputs");
+
+}/*}}}*/
+
+/*Finite Element Analysis*/
+void AgeAnalysis::Core(FemModel* femmodel){/*{{{*/
+ _error_("not implemented");
+}/*}}}*/
+void AgeAnalysis::PreCore(FemModel* femmodel){/*{{{*/
+ _error_("not implemented");
+}/*}}}*/
+ElementVector* AgeAnalysis::CreateDVector(Element* element){/*{{{*/
+ /*Default, return NULL*/
+ return NULL;
+}/*}}}*/
+ElementMatrix* AgeAnalysis::CreateJacobianMatrix(Element* element){/*{{{*/
+_error_("Not implemented");
+}/*}}}*/
+ElementMatrix* AgeAnalysis::CreateKMatrix(Element* element){/*{{{*/
+
+ _error_("STOP");
+ /* Check if ice in element */
+ if(!element->IsIceInElement()) return NULL;
+
+ /*compute all stiffness matrices for this element*/
+ ElementMatrix* Ke1=CreateKMatrixVolume(element);
+ ElementMatrix* Ke2=CreateKMatrixShelf(element);
+ ElementMatrix* Ke =new ElementMatrix(Ke1,Ke2);
+
+ /*clean-up and return*/
+ delete Ke1;
+ delete Ke2;
+ return Ke;
+}/*}}}*/
+ElementMatrix* AgeAnalysis::CreateKMatrixShelf(Element* element){/*{{{*/
+
+ /* Check if ice in element */
+ if(!element->IsIceInElement()) return NULL;
+
+ /*Initialize Element matrix and return if necessary*/
+ if(!element->IsOnBase() || !element->IsAllFloating()) return NULL;
+
+ IssmDouble dt,Jdet,D;
+ IssmDouble *xyz_list_base = NULL;
+
+ /*Get basal element*/
+ if(!element->IsOnBase() || !element->IsAllFloating()) return NULL;
+
+ /*Fetch number of nodes for this finite element*/
+ int numnodes = element->GetNumberOfNodes();
+
+ /*Initialize vectors*/
+ ElementMatrix* Ke = element->NewElementMatrix();
+ IssmDouble* basis = xNew(numnodes);
+
+ /*Retrieve all inputs and parameters*/
+ element->GetVerticesCoordinatesBase(&xyz_list_base);
+ element->FindParam(&dt,TimesteppingTimeStepEnum);
+ IssmDouble gravity = element->FindParam(ConstantsGEnum);
+ IssmDouble rho_water = element->FindParam(MaterialsRhoSeawaterEnum);
+ IssmDouble rho_ice = element->FindParam(MaterialsRhoIceEnum);
+ IssmDouble heatcapacity = element->FindParam(MaterialsHeatcapacityEnum);
+ IssmDouble mixed_layer_capacity= element->FindParam(MaterialsMixedLayerCapacityEnum);
+
+ /* Start looping on the number of gaussian points: */
+ Gauss* gauss=element->NewGaussBase(4);
+ while(gauss->next()){
+
+ element->JacobianDeterminantBase(&Jdet,xyz_list_base,gauss);
+ element->NodalFunctions(basis,gauss);
+
+ D=gauss->weight*Jdet*rho_water*mixed_layer_capacity/(heatcapacity*rho_ice);
+ if(reCast(dt)) D=dt*D;
+ for(int i=0;ivalues[i*numnodes+j] += D*basis[i]*basis[j];
+ }
+
+ /*Clean up and return*/
+ delete gauss;
+ xDelete(basis);
+ xDelete(xyz_list_base);
+ return Ke;
+}/*}}}*/
+ElementMatrix* AgeAnalysis::CreateKMatrixVolume(Element* element){/*{{{*/
+
+ /* Check if ice in element */
+ if(!element->IsIceInElement()) return NULL;
+
+ /*Intermediaries */
+ int stabilization;
+ IssmDouble Jdet,dt,u,v,w,um,vm,wm,vel;
+ IssmDouble h,hx,hy,hz,vx,vy,vz,D_scalar;
+ IssmDouble tau_parameter,diameter;
+ IssmDouble tau_parameter_anisotropic[2],tau_parameter_hor,tau_parameter_ver;
+ IssmDouble* xyz_list = NULL;
+
+ /*Fetch number of nodes and dof for this finite element*/
+ int numnodes = element->GetNumberOfNodes();
+
+ /*Initialize Element vector and other vectors*/
+ ElementMatrix* Ke = element->NewElementMatrix();
+ IssmDouble* basis = xNew(numnodes);
+ IssmDouble* dbasis = xNew(3*numnodes);
+ IssmDouble K[3][3];
+
+ /*Retrieve all inputs and parameters*/
+ element->GetVerticesCoordinates(&xyz_list);
+ element->FindParam(&dt,TimesteppingTimeStepEnum);
+ element->FindParam(&stabilization,AgeStabilizationEnum);
+ IssmDouble rho_water = element->FindParam(MaterialsRhoSeawaterEnum);
+ IssmDouble rho_ice = element->FindParam(MaterialsRhoIceEnum);
+ IssmDouble gravity = element->FindParam(ConstantsGEnum);
+ IssmDouble heatcapacity = element->FindParam(MaterialsHeatcapacityEnum);
+ IssmDouble thermalconductivity = 1.;
+ IssmDouble kappa = thermalconductivity/(rho_ice*heatcapacity);
+ Input* vx_input = element->GetInput(VxEnum); _assert_(vx_input);
+ Input* vy_input = element->GetInput(VyEnum); _assert_(vy_input);
+ Input* vz_input = element->GetInput(VzEnum); _assert_(vz_input);
+ Input* vxm_input = element->GetInput(VxMeshEnum); _assert_(vxm_input);
+ Input* vym_input = element->GetInput(VyMeshEnum); _assert_(vym_input);
+ Input* vzm_input = element->GetInput(VzMeshEnum); _assert_(vzm_input);
+
+ /* Start looping on the number of gaussian points: */
+ Gauss* gauss=element->NewGauss(4);
+ while(gauss->next()){
+
+ element->JacobianDeterminant(&Jdet,xyz_list,gauss);
+ element->NodalFunctions(basis,gauss);
+ element->NodalFunctionsDerivatives(dbasis,xyz_list,gauss);
+
+ D_scalar=gauss->weight*Jdet;
+ if(dt!=0.) D_scalar=D_scalar*dt;
+
+ /*Conduction: */
+ for(int i=0;ivalues[i*numnodes+j] += D_scalar*kappa*(
+ dbasis[0*numnodes+j]*dbasis[0*numnodes+i] + dbasis[1*numnodes+j]*dbasis[1*numnodes+i] + dbasis[2*numnodes+j]*dbasis[2*numnodes+i]
+ );
+ }
+ }
+
+ /*Advection: */
+ vx_input->GetInputValue(&u,gauss); vxm_input->GetInputValue(&um,gauss); vx=u-um;
+ vy_input->GetInputValue(&v,gauss); vym_input->GetInputValue(&vm,gauss); vy=v-vm;
+ vz_input->GetInputValue(&w,gauss); vzm_input->GetInputValue(&wm,gauss); vz=w-wm;
+ for(int i=0;ivalues[i*numnodes+j] += D_scalar*(
+ vx*dbasis[0*numnodes+j]*basis[i] + vy*dbasis[1*numnodes+j]*basis[i] +vz*dbasis[2*numnodes+j]*basis[i]
+ );
+ }
+ }
+
+ /*Transient: */
+ if(dt!=0.){
+ D_scalar=gauss->weight*Jdet;
+ for(int i=0;ivalues[i*numnodes+j] += D_scalar*basis[j]*basis[i];
+ D_scalar=D_scalar*dt;
+ }
+
+ /*Artifficial diffusivity*/
+ if(stabilization==1){
+ element->ElementSizes(&hx,&hy,&hz);
+ vel=sqrt(vx*vx + vy*vy + vz*vz)+1.e-14;
+ h=sqrt( pow(hx*vx/vel,2) + pow(hy*vy/vel,2) + pow(hz*vz/vel,2));
+ K[0][0]=h/(2.*vel)*fabs(vx*vx); K[0][1]=h/(2.*vel)*fabs(vx*vy); K[0][2]=h/(2.*vel)*fabs(vx*vz);
+ K[1][0]=h/(2.*vel)*fabs(vy*vx); K[1][1]=h/(2.*vel)*fabs(vy*vy); K[1][2]=h/(2.*vel)*fabs(vy*vz);
+ K[2][0]=h/(2.*vel)*fabs(vz*vx); K[2][1]=h/(2.*vel)*fabs(vz*vy); K[2][2]=h/(2.*vel)*fabs(vz*vz);
+ for(int i=0;i<3;i++) for(int j=0;j<3;j++) K[i][j] = D_scalar*K[i][j];
+
+ for(int i=0;ivalues[i*numnodes+j] += (
+ dbasis[0*numnodes+i] *(K[0][0]*dbasis[0*numnodes+j] + K[0][1]*dbasis[1*numnodes+j]+ K[0][2]*dbasis[2*numnodes+j]) +
+ dbasis[1*numnodes+i] *(K[1][0]*dbasis[0*numnodes+j] + K[1][1]*dbasis[1*numnodes+j]+ K[1][2]*dbasis[2*numnodes+j]) +
+ dbasis[2*numnodes+i] *(K[2][0]*dbasis[0*numnodes+j] + K[2][1]*dbasis[1*numnodes+j]+ K[2][2]*dbasis[2*numnodes+j])
+ );
+ }
+ }
+ }
+ else if(stabilization==2){
+ diameter=element->MinEdgeLength(xyz_list);
+ tau_parameter=element->StabilizationParameter(u-um,v-vm,w-wm,diameter,kappa);
+ for(int i=0;ivalues[i*numnodes+j]+=tau_parameter*D_scalar*
+ ((u-um)*dbasis[0*numnodes+i]+(v-vm)*dbasis[1*numnodes+i]+(w-wm)*dbasis[2*numnodes+i])*
+ ((u-um)*dbasis[0*numnodes+j]+(v-vm)*dbasis[1*numnodes+j]+(w-wm)*dbasis[2*numnodes+j]);
+ }
+ }
+ if(dt!=0.){
+ D_scalar=gauss->weight*Jdet;
+ for(int i=0;ivalues[i*numnodes+j]+=tau_parameter*D_scalar*basis[j]*((u-um)*dbasis[0*numnodes+i]+(v-vm)*dbasis[1*numnodes+i]+(w-wm)*dbasis[2*numnodes+i]);
+ }
+ }
+ }
+ }
+ /*anisotropic SUPG*/
+ else if(stabilization==3){
+ element->NodalFunctionsDerivatives(dbasis,xyz_list,gauss);
+ element->ElementSizes(&hx,&hy,&hz);
+ element->StabilizationParameterAnisotropic(&tau_parameter_anisotropic[0],u-um,v-vm,w-wm,hx,hy,hz,kappa);
+ tau_parameter_hor=tau_parameter_anisotropic[0];
+ tau_parameter_ver=tau_parameter_anisotropic[1];
+ for(int i=0;ivalues[i*numnodes+j]+=D_scalar*
+ (sqrt(tau_parameter_hor)*(u-um)*dbasis[0*numnodes+i]+sqrt(tau_parameter_hor)*(v-vm)*dbasis[1*numnodes+i]+sqrt(tau_parameter_ver)*(w-wm)*dbasis[2*numnodes+i])*
+ (sqrt(tau_parameter_hor)*(u-um)*dbasis[0*numnodes+j]+sqrt(tau_parameter_hor)*(v-vm)*dbasis[1*numnodes+j]+sqrt(tau_parameter_ver)*(w-wm)*dbasis[2*numnodes+j]);
+ }
+ }
+ }
+ }
+
+ /*Clean up and return*/
+ xDelete(xyz_list);
+ xDelete(basis);
+ xDelete(dbasis);
+ delete gauss;
+ return Ke;
+}/*}}}*/
+ElementVector* AgeAnalysis::CreatePVector(Element* element){/*{{{*/
+
+ _error_("STOP");
+
+ /* Check if ice in element */
+ if(!element->IsIceInElement()) return NULL;
+
+ /*compute all load vectors for this element*/
+ ElementVector* pe1=CreatePVectorVolume(element);
+ ElementVector* pe2=CreatePVectorSheet(element);
+ ElementVector* pe3=CreatePVectorShelf(element);
+ ElementVector* pe =new ElementVector(pe1,pe2,pe3);
+
+ /*clean-up and return*/
+ delete pe1;
+ delete pe2;
+ delete pe3;
+ return pe;
+}/*}}}*/
+ElementVector* AgeAnalysis::CreatePVectorSheet(Element* element){/*{{{*/
+
+ /* Check if ice in element */
+ if(!element->IsIceInElement()) return NULL;
+
+ /* Geothermal flux on ice sheet base and basal friction */
+ if(!element->IsOnBase() || element->IsAllFloating()) return NULL;
+
+ IssmDouble dt,Jdet,geothermalflux,vx,vy,vz;
+ IssmDouble alpha2,scalar,basalfriction,heatflux;
+ IssmDouble *xyz_list_base = NULL;
+
+ /*Fetch number of nodes for this finite element*/
+ int numnodes = element->GetNumberOfNodes();
+
+ /*Initialize vectors*/
+ ElementVector* pe = element->NewElementVector();
+ IssmDouble* basis = xNew(numnodes);
+
+ /*Retrieve all inputs and parameters*/
+ element->GetVerticesCoordinatesBase(&xyz_list_base);
+ element->FindParam(&dt,TimesteppingTimeStepEnum);
+ Input* vx_input = element->GetInput(VxEnum); _assert_(vx_input);
+ Input* vy_input = element->GetInput(VyEnum); _assert_(vy_input);
+ Input* vz_input = element->GetInput(VzEnum); _assert_(vz_input);
+ Input* geothermalflux_input = element->GetInput(BasalforcingsGeothermalfluxEnum); _assert_(geothermalflux_input);
+ IssmDouble rho_ice = element->FindParam(MaterialsRhoIceEnum);
+ IssmDouble heatcapacity = element->FindParam(MaterialsHeatcapacityEnum);
+
+ /*Build friction element, needed later: */
+ Friction* friction=new Friction(element,3);
+
+ /* Start looping on the number of gaussian points: */
+ Gauss* gauss = element->NewGaussBase(4);
+ while(gauss->next()){
+
+ element->JacobianDeterminantBase(&Jdet,xyz_list_base,gauss);
+ element->NodalFunctions(basis,gauss);
+
+ geothermalflux_input->GetInputValue(&geothermalflux,gauss);
+ friction->GetAlpha2(&alpha2,gauss);
+ vx_input->GetInputValue(&vx,gauss);
+ vy_input->GetInputValue(&vy,gauss);
+ vz_input->GetInputValue(&vz,gauss);
+ vz = 0.;//FIXME
+ basalfriction = alpha2*(vx*vx + vy*vy + vz*vz);
+ heatflux = (basalfriction+geothermalflux)/(rho_ice*heatcapacity);
+
+ scalar = gauss->weight*Jdet*heatflux;
+ if(dt!=0.) scalar=dt*scalar;
+
+ for(int i=0;ivalues[i]+=scalar*basis[i];
+ }
+
+ /*Clean up and return*/
+ delete gauss;
+ delete friction;
+ xDelete(basis);
+ xDelete(xyz_list_base);
+ return pe;
+}/*}}}*/
+ElementVector* AgeAnalysis::CreatePVectorShelf(Element* element){/*{{{*/
+
+ /* Check if ice in element */
+ if(!element->IsIceInElement()) return NULL;
+
+ IssmDouble t_pmp,dt,Jdet,scalar_ocean,pressure;
+ IssmDouble *xyz_list_base = NULL;
+
+ /*Get basal element*/
+ if(!element->IsOnBase() || !element->IsAllFloating()) return NULL;
+
+ /*Fetch number of nodes for this finite element*/
+ int numnodes = element->GetNumberOfNodes();
+
+ /*Initialize vectors*/
+ ElementVector* pe = element->NewElementVector();
+ IssmDouble* basis = xNew(numnodes);
+
+ /*Retrieve all inputs and parameters*/
+ element->GetVerticesCoordinatesBase(&xyz_list_base);
+ element->FindParam(&dt,TimesteppingTimeStepEnum);
+ Input* pressure_input=element->GetInput(PressureEnum); _assert_(pressure_input);
+ IssmDouble gravity = element->FindParam(ConstantsGEnum);
+ IssmDouble rho_water = element->FindParam(MaterialsRhoSeawaterEnum);
+ IssmDouble rho_ice = element->FindParam(MaterialsRhoIceEnum);
+ IssmDouble heatcapacity = element->FindParam(MaterialsHeatcapacityEnum);
+ IssmDouble mixed_layer_capacity= element->FindParam(MaterialsMixedLayerCapacityEnum);
+
+ /* Start looping on the number of gaussian points: */
+ Gauss* gauss=element->NewGaussBase(4);
+ while(gauss->next()){
+
+ element->JacobianDeterminantBase(&Jdet,xyz_list_base,gauss);
+ element->NodalFunctions(basis,gauss);
+
+ pressure_input->GetInputValue(&pressure,gauss);
+ t_pmp=element->TMeltingPoint(pressure);
+
+ scalar_ocean=gauss->weight*Jdet*rho_water*mixed_layer_capacity*(t_pmp)/(heatcapacity*rho_ice);
+ if(reCast(dt)) scalar_ocean=dt*scalar_ocean;
+
+ for(int i=0;ivalues[i]+=scalar_ocean*basis[i];
+ }
+
+ /*Clean up and return*/
+ delete gauss;
+ xDelete(basis);
+ xDelete(xyz_list_base);
+ return pe;
+}/*}}}*/
+ElementVector* AgeAnalysis::CreatePVectorVolume(Element* element){/*{{{*/
+
+ /* Check if ice in element */
+ if(!element->IsIceInElement()) return NULL;
+
+ /*Intermediaries*/
+ int stabilization;
+ IssmDouble Jdet,phi,dt;
+ IssmDouble temperature;
+ IssmDouble tau_parameter,diameter,hx,hy,hz;
+ IssmDouble tau_parameter_anisotropic[2],tau_parameter_hor,tau_parameter_ver;
+ IssmDouble u,v,w;
+ IssmDouble scalar_def,scalar_transient;
+ IssmDouble* xyz_list = NULL;
+
+ /*Fetch number of nodes and dof for this finite element*/
+ int numnodes = element->GetNumberOfNodes();
+
+ /*Initialize Element vector*/
+ ElementVector* pe = element->NewElementVector();
+ IssmDouble* basis = xNew(numnodes);
+ IssmDouble* dbasis = xNew(3*numnodes);
+
+ /*Retrieve all inputs and parameters*/
+ element->GetVerticesCoordinates(&xyz_list);
+ IssmDouble rho_ice = element->FindParam(MaterialsRhoIceEnum);
+ IssmDouble heatcapacity = element->FindParam(MaterialsHeatcapacityEnum);
+ IssmDouble thermalconductivity = 1.;
+ IssmDouble kappa = thermalconductivity/(rho_ice*heatcapacity);
+ element->FindParam(&dt,TimesteppingTimeStepEnum);
+ element->FindParam(&stabilization,AgeStabilizationEnum);
+ Input* vx_input=element->GetInput(VxEnum); _assert_(vx_input);
+ Input* vy_input=element->GetInput(VyEnum); _assert_(vy_input);
+ Input* vz_input=element->GetInput(VzEnum); _assert_(vz_input);
+ Input* temperature_input = NULL;
+ if(reCast(dt)){temperature_input = element->GetInput(TemperatureEnum); _assert_(temperature_input);}
+
+ /* Start looping on the number of gaussian points: */
+ Gauss* gauss=element->NewGauss(4);
+ while(gauss->next()){
+
+ element->JacobianDeterminant(&Jdet,xyz_list,gauss);
+ element->NodalFunctions(basis,gauss);
+ element->ViscousHeating(&phi,xyz_list,gauss,vx_input,vy_input,vz_input);
+
+ scalar_def=phi/(rho_ice*heatcapacity)*Jdet*gauss->weight;
+ if(reCast(dt)) scalar_def=scalar_def*dt;
+
+ for(int i=0;ivalues[i]+=scalar_def*basis[i];
+
+ /* Build transient now */
+ if(reCast(dt)){
+ temperature_input->GetInputValue(&temperature, gauss);
+ scalar_transient=temperature*Jdet*gauss->weight;
+ for(int i=0;ivalues[i]+=scalar_transient*basis[i];
+ }
+
+ if(stabilization==2){
+ element->NodalFunctionsDerivatives(dbasis,xyz_list,gauss);
+ diameter=element->MinEdgeLength(xyz_list);
+ vx_input->GetInputValue(&u,gauss);
+ vy_input->GetInputValue(&v,gauss);
+ vz_input->GetInputValue(&w,gauss);
+
+ tau_parameter=element->StabilizationParameter(u,v,w,diameter,kappa);
+
+ for(int i=0;ivalues[i]+=tau_parameter*scalar_def*(u*dbasis[0*numnodes+i]+v*dbasis[1*numnodes+i]+w*dbasis[2*numnodes+i]);
+ if(reCast(dt)){
+ for(int i=0;ivalues[i]+=tau_parameter*scalar_transient*(u*dbasis[0*numnodes+i]+v*dbasis[1*numnodes+i]+w*dbasis[2*numnodes+i]);
+ }
+ }
+ /* anisotropic SUPG */
+ else if(stabilization==3){
+ element->NodalFunctionsDerivatives(dbasis,xyz_list,gauss);
+ element->ElementSizes(&hx,&hy,&hz);
+ vx_input->GetInputValue(&u,gauss);
+ vy_input->GetInputValue(&v,gauss);
+ vz_input->GetInputValue(&w,gauss);
+ element->StabilizationParameterAnisotropic(&tau_parameter_anisotropic[0],u,v,w,hx,hy,hz,kappa);
+ tau_parameter_hor=tau_parameter_anisotropic[0];
+ tau_parameter_ver=tau_parameter_anisotropic[1];
+
+ for(int i=0;ivalues[i]+=scalar_def*(tau_parameter_hor*u*dbasis[0*numnodes+i]+tau_parameter_hor*v*dbasis[1*numnodes+i]+tau_parameter_ver*w*dbasis[2*numnodes+i]);
+ }
+ }
+
+ /*Clean up and return*/
+ xDelete(basis);
+ xDelete(dbasis);
+ xDelete(xyz_list);
+ delete gauss;
+ return pe;
+
+}/*}}}*/
+void AgeAnalysis::GetSolutionFromInputs(Vector* solution,Element* element){/*{{{*/
+ element->GetSolutionFromInputsOneDof(solution,AgeEnum);
+}/*}}}*/
+void AgeAnalysis::GradientJ(Vector* gradient,Element* element,int control_type,int control_interp,int control_index){/*{{{*/
+ _error_("Not implemented yet");
+}/*}}}*/
+void AgeAnalysis::InputUpdateFromSolution(IssmDouble* solution,Element* element){/*{{{*/
+
+ element->InputUpdateFromSolutionOneDof(solution,AgeEnum);
+
+}/*}}}*/
+void AgeAnalysis::UpdateConstraints(FemModel* femmodel){/*{{{*/
+ SetActiveNodesLSMx(femmodel);
+
+ _error_("Should also automatically constrain surface/basal nodes where we have inflow");
+}/*}}}*/
Index: /issm/trunk/src/c/analyses/AgeAnalysis.h
===================================================================
--- /issm/trunk/src/c/analyses/AgeAnalysis.h (revision 27232)
+++ /issm/trunk/src/c/analyses/AgeAnalysis.h (revision 27232)
@@ -0,0 +1,39 @@
+/*! \file AgeAnalysis.h
+ * \brief: header file for generic external result object
+ */
+
+#ifndef _AGEANALYSIS_
+#define _AGEANALYSIS_
+
+/*Headers*/
+#include "./Analysis.h"
+
+class AgeAnalysis: public Analysis{
+
+ public:
+ /*Model processing*/
+ void CreateConstraints(Constraints* constraints,IoModel* iomodel);
+ void CreateLoads(Loads* loads, IoModel* iomodel);
+ void CreateNodes(Nodes* nodes,IoModel* iomodel,bool isamr=false);
+ int DofsPerNode(int** doflist,int domaintype,int approximation);
+ void UpdateElements(Elements* elements,Inputs* inputs,IoModel* iomodel,int analysis_counter,int analysis_type);
+ void UpdateParameters(Parameters* parameters,IoModel* iomodel,int solution_enum,int analysis_enum);
+
+ /*Finite element Analysis*/
+ void Core(FemModel* femmodel);
+ void PreCore(FemModel* femmodel);
+ ElementVector* CreateDVector(Element* element);
+ ElementMatrix* CreateJacobianMatrix(Element* element);
+ ElementMatrix* CreateKMatrix(Element* element);
+ ElementMatrix* CreateKMatrixShelf(Element* element);
+ ElementMatrix* CreateKMatrixVolume(Element* element);
+ ElementVector* CreatePVector(Element* element);
+ ElementVector* CreatePVectorSheet(Element* element);
+ ElementVector* CreatePVectorShelf(Element* element);
+ ElementVector* CreatePVectorVolume(Element* element);
+ void GetSolutionFromInputs(Vector* solution,Element* element);
+ void GradientJ(Vector* gradient,Element* element,int control_type,int control_interp,int control_index);
+ void InputUpdateFromSolution(IssmDouble* solution,Element* element);
+ void UpdateConstraints(FemModel* femmodel);
+};
+#endif
Index: /issm/trunk/src/c/analyses/DamageEvolutionAnalysis.cpp
===================================================================
--- /issm/trunk/src/c/analyses/DamageEvolutionAnalysis.cpp (revision 27231)
+++ /issm/trunk/src/c/analyses/DamageEvolutionAnalysis.cpp (revision 27232)
@@ -714,5 +714,5 @@
}
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(newdamage);
xDelete(doflist);
Index: /issm/trunk/src/c/analyses/EnthalpyAnalysis.cpp
===================================================================
--- /issm/trunk/src/c/analyses/EnthalpyAnalysis.cpp (revision 27231)
+++ /issm/trunk/src/c/analyses/EnthalpyAnalysis.cpp (revision 27232)
@@ -76,5 +76,5 @@
}
- /*Free ressources:*/
+ /*Free resources:*/
iomodel->DeleteData(spcvector,"md.thermal.spctemperature");
iomodel->DeleteData(spcvectorstatic,"md.thermal.spctemperature");
@@ -348,5 +348,5 @@
}
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(indices);
delete gauss;
@@ -1358,5 +1358,5 @@
}
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(indices);
xDelete(indicesup);
@@ -1432,5 +1432,5 @@
}
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(indices);
xDelete(indicesup);
@@ -1614,5 +1614,5 @@
}
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(values);
xDelete(pressure);
Index: /issm/trunk/src/c/analyses/EnumToAnalysis.cpp
===================================================================
--- /issm/trunk/src/c/analyses/EnumToAnalysis.cpp (revision 27231)
+++ /issm/trunk/src/c/analyses/EnumToAnalysis.cpp (revision 27232)
@@ -25,4 +25,7 @@
#ifdef _HAVE_ADJOINTHORIZ_
case AdjointHorizAnalysisEnum : return new AdjointHorizAnalysis();
+ #endif
+ #ifdef _HAVE_AGE_
+ case AgeAnalysisEnum : return new AgeAnalysis();
#endif
#ifdef _HAVE_BALANCETHICKNESS2_
Index: /issm/trunk/src/c/analyses/EsaAnalysis.cpp
===================================================================
--- /issm/trunk/src/c/analyses/EsaAnalysis.cpp (revision 27231)
+++ /issm/trunk/src/c/analyses/EsaAnalysis.cpp (revision 27232)
@@ -144,5 +144,5 @@
ISSM_MPI_Allgatherv(U_elastic_local, m, ISSM_MPI_DOUBLE, U_elastic, recvcounts, displs, ISSM_MPI_DOUBLE,IssmComm::GetComm());
ISSM_MPI_Allgatherv(H_elastic_local, m, ISSM_MPI_DOUBLE, H_elastic, recvcounts, displs, ISSM_MPI_DOUBLE,IssmComm::GetComm());
- /*free ressources: */
+ /*Free resources: */
xDelete(recvcounts);
xDelete(displs);
@@ -156,5 +156,5 @@
parameters->AddObject(new DoubleVecParam(EsaHElasticEnum,H_elastic,M));
- /*free ressources: */
+ /*Free resources: */
xDelete(love_h);
xDelete(love_l);
Index: /issm/trunk/src/c/analyses/FreeSurfaceBaseAnalysis.cpp
===================================================================
--- /issm/trunk/src/c/analyses/FreeSurfaceBaseAnalysis.cpp (revision 27231)
+++ /issm/trunk/src/c/analyses/FreeSurfaceBaseAnalysis.cpp (revision 27232)
@@ -42,5 +42,5 @@
}
- /*free ressources: */
+ /*Free resources: */
iomodel->DeleteData(vertex_pairing,"md.masstransport.vertex_pairing");
iomodel->DeleteData(nodeonbase,"md.mesh.vertexonbase");
Index: /issm/trunk/src/c/analyses/FreeSurfaceTopAnalysis.cpp
===================================================================
--- /issm/trunk/src/c/analyses/FreeSurfaceTopAnalysis.cpp (revision 27231)
+++ /issm/trunk/src/c/analyses/FreeSurfaceTopAnalysis.cpp (revision 27232)
@@ -42,5 +42,5 @@
}
- /*free ressources: */
+ /*Free resources: */
iomodel->DeleteData(vertex_pairing,"md.masstransport.vertex_pairing");
iomodel->DeleteData(nodeonsurface,"md.mesh.vertexonsurface");
Index: /issm/trunk/src/c/analyses/HydrologyDCEfficientAnalysis.cpp
===================================================================
--- /issm/trunk/src/c/analyses/HydrologyDCEfficientAnalysis.cpp (revision 27231)
+++ /issm/trunk/src/c/analyses/HydrologyDCEfficientAnalysis.cpp (revision 27232)
@@ -11,8 +11,13 @@
void HydrologyDCEfficientAnalysis::UpdateParameters(Parameters* parameters,IoModel* iomodel,int solution_enum,int analysis_enum){/*{{{*/
+ bool isefficientlayer;
int hydrology_model;
int eplflip_lock;
int eplthickcomp;
- bool isefficientlayer;
+ IssmDouble eplinitthick;
+ IssmDouble eplcolapsethick;
+ IssmDouble eplmaxthick;
+ IssmDouble eplcond;
+
/*retrieve some parameters: */
iomodel->FindConstant(&hydrology_model,"md.hydrology.model");
@@ -27,10 +32,20 @@
if(!isefficientlayer) return;
- /*If yes, initialize a flip flop counter*/
+ /*If yes, get the parameters*/
iomodel->FetchData(&eplflip_lock,"md.hydrology.eplflip_lock");
+ iomodel->FetchData(&eplthickcomp,"md.hydrology.epl_thick_comp");
+
parameters->AddObject(new IntParam(HydrologydcEplflipLockEnum,eplflip_lock));
-
- iomodel->FetchData(&eplthickcomp,"md.hydrology.epl_thick_comp");
parameters->AddObject(new IntParam(HydrologydcEplThickCompEnum,eplthickcomp));
+
+ iomodel->FetchData(&eplinitthick,"md.hydrology.epl_initial_thickness");
+ iomodel->FetchData(&eplcolapsethick,"md.hydrology.epl_colapse_thickness");
+ iomodel->FetchData(&eplmaxthick,"md.hydrology.epl_max_thickness");
+ iomodel->FetchData(&eplcond,"md.hydrology.epl_conductivity");
+ parameters->AddObject(new DoubleParam(HydrologydcEplInitialThicknessEnum,eplinitthick));
+ parameters->AddObject(new DoubleParam(HydrologydcEplColapseThicknessEnum,eplcolapsethick));
+ parameters->AddObject(new DoubleParam(HydrologydcEplMaxThicknessEnum,eplmaxthick));
+ parameters->AddObject(new DoubleParam(HydrologydcEplConductivityEnum,eplcond));
+
}/*}}}*/
void HydrologyDCEfficientAnalysis::UpdateElements(Elements* elements,Inputs* inputs,IoModel* iomodel,int analysis_counter,int analysis_type){/*{{{*/
@@ -419,5 +434,5 @@
element->AddBasalInput(EplHeadSubstepEnum,eplHeads,P1Enum);
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(eplHeads);
xDelete(doflist);
Index: /issm/trunk/src/c/analyses/HydrologyDCInefficientAnalysis.cpp
===================================================================
--- /issm/trunk/src/c/analyses/HydrologyDCInefficientAnalysis.cpp (revision 27231)
+++ /issm/trunk/src/c/analyses/HydrologyDCInefficientAnalysis.cpp (revision 27232)
@@ -23,8 +23,11 @@
int numoutputs;
bool isefficientlayer;
+ bool sliceadapt;
IssmDouble penalty_factor;
IssmDouble rel_tol;
IssmDouble leakagefactor;
IssmDouble sedimentlimit;
+ IssmDouble sed_poro;
+ IssmDouble sed_thick;
char** requestedoutputs = NULL;
@@ -43,4 +46,5 @@
iomodel->FetchData(&hydro_maxiter, "md.hydrology.max_iter" );
iomodel->FetchData(&hydroslices, "md.hydrology.steps_per_step");
+ iomodel->FetchData(&sliceadapt, "md.hydrology.step_adapt");
iomodel->FetchData(&averaging_method, "md.hydrology.averaging");
iomodel->FetchData(&isefficientlayer, "md.hydrology.isefficientlayer");
@@ -55,9 +59,16 @@
parameters->AddObject(new IntParam(HydrologydcMaxIterEnum,hydro_maxiter));
parameters->AddObject(new IntParam(HydrologyStepsPerStepEnum,hydroslices));
+ parameters->AddObject(new BoolParam(HydrologyStepAdaptEnum,sliceadapt));
parameters->AddObject(new IntParam(HydrologyAveragingEnum,averaging_method));
-
parameters->AddObject(new BoolParam(HydrologydcIsefficientlayerEnum,isefficientlayer));
parameters->AddObject(new DoubleParam(HydrologydcPenaltyFactorEnum,penalty_factor));
parameters->AddObject(new DoubleParam(HydrologydcRelTolEnum,rel_tol));
+
+ iomodel->FetchData(&sed_poro, "md.hydrology.sediment_porosity" );
+ iomodel->FetchData(&sed_thick, "md.hydrology.sediment_thickness" );
+
+ parameters->AddObject(new DoubleParam(HydrologydcSedimentPorosityEnum,sed_poro));
+ parameters->AddObject(new DoubleParam(HydrologydcSedimentThicknessEnum,sed_thick));
+
if(transfer_flag==1){
iomodel->FetchData(&leakagefactor,"md.hydrology.leakage_factor");
@@ -110,4 +121,6 @@
iomodel->FetchDataToInput(inputs,elements,"md.hydrology.sediment_transmitivity",HydrologydcSedimentTransmitivityEnum);
iomodel->FetchDataToInput(inputs,elements,"md.hydrology.mask_thawed_node",HydrologydcMaskThawedNodeEnum);
+
+
if(iomodel->domaintype!=Domain2DhorizontalEnum){
iomodel->FetchDataToInput(inputs,elements,"md.mesh.vertexonbase",MeshVertexonbaseEnum);
@@ -518,5 +531,5 @@
element->AddBasalInput(SedimentHeadResidualEnum,residual,P1Enum);
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(values);
xDelete(residual);
Index: /issm/trunk/src/c/analyses/HydrologyShaktiAnalysis.cpp
===================================================================
--- /issm/trunk/src/c/analyses/HydrologyShaktiAnalysis.cpp (revision 27231)
+++ /issm/trunk/src/c/analyses/HydrologyShaktiAnalysis.cpp (revision 27232)
@@ -242,5 +242,4 @@
element->NodalFunctions(basis,gauss);
- /***/
base_input->GetInputValue(&bed,gauss);
thickness_input->GetInputValue(&thickness,gauss);
@@ -288,6 +287,4 @@
IssmDouble PMPheat,dissipation,dpressure_water[2],dbed[2];
IssmDouble* xyz_list = NULL;
-// IssmDouble dgapxx; /***/
-// IssmDouble dgapyy; /***/
/*Fetch number of nodes and dof for this finite element*/
@@ -315,6 +312,4 @@
Input* br_input = element->GetInput(HydrologyBumpHeightEnum); _assert_(br_input);
Input* headold_input = element->GetInput(HydrologyHeadOldEnum); _assert_(headold_input);
-// Input* dgapxx_input = element->GetInput(HydrologyGapHeightXXEnum); /***/
-// Input* dgapyy_input = element->GetInput(HydrologyGapHeightYYEnum); /***/
/*Get conductivity from inputs*/
@@ -346,6 +341,4 @@
br_input->GetInputValue(&br,gauss);
headold_input->GetInputValue(&head_old,gauss);
-// dgapxx_input->GetInputValue(&dgapxx,gauss); /***/
-// dgapyy_input->GetInputValue(&dgapyy,gauss); /***/
/*Get ice A parameter*/
@@ -365,8 +358,4 @@
frictionheat=alpha2*(vx*vx+vy*vy);
- /* Take out frictional heat for large gap height */
- if(gap>br)
- frictionheat=0.;
-
/*Get water and ice pressures*/
IssmDouble pressure_ice = rho_ice*g*thickness; _assert_(pressure_ice>0.);
@@ -379,10 +368,8 @@
/*Compute change in sensible heat due to changes in pressure melting point*/
- dpressure_water[0] = rho_water*g*(dh[0] - dbed[0]);
+ dpressure_water[0] = rho_water*g*(dh[0] - dbed[0]);
dpressure_water[1] = rho_water*g*(dh[1] - dbed[1]);
- PMPheat=CT*CW*conductivity*rho_water*(dh[0]*dpressure_water[0]+dh[1]*dpressure_water[1]);
- PMPheat=0; /*** TEST no PMPheat***/
-
- meltrate = 1/latentheat*(G+frictionheat+rho_water*g*conductivity*(dh[0]*dh[0]+dh[1]*dh[1])-PMPheat);
+
+ meltrate = 1/latentheat*(G+frictionheat+rho_water*g*conductivity*(dh[0]*dh[0]+dh[1]*dh[1]));
for(int i=0;ivalues[i]+=Jdet*gauss->weight*
@@ -396,16 +383,4 @@
)*basis[i];
- /* Test with experimental diffusivity term*/
-// for(int i=0;ivalues[i]+=Jdet*gauss->weight*
- // (
- // meltrate*(1/rho_water-1/rho_ice)
- // +A*pow(fabs(pressure_ice - pressure_water),n-1)*(pressure_ice + rho_water*g*bed)*gap
- // +(n-1)*A*pow(fabs(pressure_ice - pressure_water),n-1)*(rho_water*g*head)*gap
- // -beta*sqrt(vx*vx+vy*vy)
- // +ieb
- // +storage*head_old/dt
- // +0.e-5*(dgapxx+dgapyy)
- // )*basis[i];
-
}
@@ -458,14 +433,4 @@
values[i]=solution[doflist[i]];
- /*overburden cap: make sure that p_water hrho_ice*thickness[i]/rho_water+bed[i]){
-// values[i] = rho_ice*thickness[i]/rho_water+bed[i];
-// }
-
- /*Make sure that negative pressure is not allowed*/
-// if(values[i]GetInput(HydrologyBumpSpacingEnum); _assert_(lr_input);
Input* br_input = element->GetInput(HydrologyBumpHeightEnum); _assert_(br_input);
- // Input* dgapxx_input = element->GetInput(HydrologyGapHeightXXEnum); /***/
- // Input* dgapyy_input = element->GetInput(HydrologyGapHeightYYEnum); /***/
/*Get conductivity from inputs*/
@@ -598,6 +559,4 @@
lr_input->GetInputValue(&lr,gauss);
br_input->GetInputValue(&br,gauss);
-// dgapxx_input->GetInputValue(&dgapxx,gauss); /***/
-// dgapyy_input->GetInputValue(&dgapyy,gauss); /***/
/*Get ice A parameter*/
@@ -617,8 +576,4 @@
frictionheat=alpha2*(vx*vx+vy*vy);
- /* Take out frictional heat for large gap height */
- if(gap>br)
- frictionheat=0.;
-
/*Get water and ice pressures*/
IssmDouble pressure_ice = rho_ice*g*thickness; _assert_(pressure_ice>0.);
@@ -629,9 +584,7 @@
dpressure_water[0] = rho_water*g*(dh[0] - dbed[0]);
dpressure_water[1] = rho_water*g*(dh[1] - dbed[1]);
- PMPheat=CT*CW*conductivity*rho_water*(dh[0]*dpressure_water[0]+dh[1]*dpressure_water[1]);
-PMPheat=0; /*** TEST no PMPheat***/
dissipation=rho_water*g*conductivity*(dh[0]*dh[0]+dh[1]*dh[1]);
- meltrate = 1/latentheat*(G+frictionheat+rho_water*g*conductivity*(dh[0]*dh[0]+dh[1]*dh[1])-PMPheat);
+ meltrate = 1/latentheat*(G+frictionheat+rho_water*g*conductivity*(dh[0]*dh[0]+dh[1]*dh[1]));
element->AddInput(DummyEnum,&meltrate,P0Enum);
@@ -647,12 +600,4 @@
));
- /* TEST with experimental gap height "diffusivity" for melting walls */
-// newgap += gauss->weight*Jdet*(gap+dt*(
- // meltrate/rho_ice
- // -A*pow(fabs(pressure_ice-pressure_water),n-1)*(pressure_ice-pressure_water)*lc
- // +beta*sqrt(vx*vx+vy*vy)
-// +0.e-5*(dgapxx+dgapyy))
- // );
-
totalweights +=gauss->weight*Jdet;
@@ -667,10 +612,8 @@
/*Divide by connectivity*/
newgap = newgap/totalweights;
- IssmDouble mingap = 1e-6;
+ IssmDouble mingap = 1e-3;
if(newgapthickness)
-// newgap = thickness;
+ /*Limit gap height*/
if(newgap>1)
newgap = 1;
Index: /issm/trunk/src/c/analyses/HydrologyShreveAnalysis.cpp
===================================================================
--- /issm/trunk/src/c/analyses/HydrologyShreveAnalysis.cpp (revision 27231)
+++ /issm/trunk/src/c/analyses/HydrologyShreveAnalysis.cpp (revision 27232)
@@ -320,5 +320,5 @@
element->AddInput(AccumulatedDeltaTwsEnum,deltawatercolumn,P1Enum);
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(oldwatercolumn);
xDelete(deltawatercolumn);
Index: /issm/trunk/src/c/analyses/LevelsetAnalysis.cpp
===================================================================
--- /issm/trunk/src/c/analyses/LevelsetAnalysis.cpp (revision 27231)
+++ /issm/trunk/src/c/analyses/LevelsetAnalysis.cpp (revision 27232)
@@ -114,6 +114,4 @@
break;
case CalvingParameterizationEnum:
- iomodel->FetchDataToInput(inputs,elements,"md.calving.stress_threshold_groundedice",CalvingStressThresholdGroundediceEnum);
- iomodel->FetchDataToInput(inputs,elements,"md.calving.stress_threshold_floatingice",CalvingStressThresholdFloatingiceEnum);
iomodel->FetchDataToInput(inputs,elements,"md.geometry.bed",BedEnum);
break;
@@ -221,10 +219,12 @@
break;
case CalvingParameterizationEnum:
+ parameters->AddObject(iomodel->CopyConstantObject("md.calving.use_param",CalvingUseParamEnum));
parameters->AddObject(iomodel->CopyConstantObject("md.calving.min_thickness",CalvingMinthicknessEnum));
- parameters->AddObject(iomodel->CopyConstantObject("md.calving.use_param",CalvingUseParamEnum));
- parameters->AddObject(iomodel->CopyConstantObject("md.calving.scale_theta",CalvingScaleThetaEnum));
- parameters->AddObject(iomodel->CopyConstantObject("md.calving.amp_alpha",CalvingAmpAlphaEnum));
- parameters->AddObject(iomodel->CopyConstantObject("md.calving.midp",CalvingMidpointEnum));
- parameters->AddObject(iomodel->CopyConstantObject("md.calving.nonlinearlaw",CalvingNonlinearLawEnum));
+ parameters->AddObject(iomodel->CopyConstantObject("md.calving.theta",CalvingThetaEnum));
+ parameters->AddObject(iomodel->CopyConstantObject("md.calving.alpha",CalvingAlphaEnum));
+ parameters->AddObject(iomodel->CopyConstantObject("md.calving.xoffset",CalvingXoffsetEnum));
+ parameters->AddObject(iomodel->CopyConstantObject("md.calving.yoffset",CalvingYoffsetEnum));
+ parameters->AddObject(iomodel->CopyConstantObject("md.calving.vel_lowerbound",CalvingVelLowerboundEnum));
+ parameters->AddObject(iomodel->CopyConstantObject("md.calving.vel_upperbound",CalvingVelUpperboundEnum));
break;
default:
@@ -891,5 +891,5 @@
}
- /*Free ressources:*/
+ /*Free resources:*/
delete vec_constraint_nodes;
Index: /issm/trunk/src/c/analyses/MasstransportAnalysis.cpp
===================================================================
--- /issm/trunk/src/c/analyses/MasstransportAnalysis.cpp (revision 27231)
+++ /issm/trunk/src/c/analyses/MasstransportAnalysis.cpp (revision 27232)
@@ -86,5 +86,5 @@
}
- /*free ressources: */
+ /*Free resources: */
iomodel->DeleteData(vertex_pairing,"md.masstransport.vertex_pairing");
iomodel->DeleteData(nodeonbase,"md.mesh.vertexonbase");
@@ -928,5 +928,5 @@
element->AddBasalInput(BaseEnum,newbase,P1Enum);
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(newthickness);
xDelete(newbase);
Index: /issm/trunk/src/c/analyses/OceantransportAnalysis.cpp
===================================================================
--- /issm/trunk/src/c/analyses/OceantransportAnalysis.cpp (revision 27231)
+++ /issm/trunk/src/c/analyses/OceantransportAnalysis.cpp (revision 27232)
@@ -147,5 +147,5 @@
solution->SetValues(numdof,doflist,values,INS_VAL);
- /*Free ressources:*/
+ /*Free resources:*/
delete gauss;
xDelete(doflist);
@@ -197,5 +197,5 @@
element->AddInput(StrEnum,&strmean,P0Enum);
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(bp);
xDelete(str);
Index: /issm/trunk/src/c/analyses/SamplingAnalysis.cpp
===================================================================
--- /issm/trunk/src/c/analyses/SamplingAnalysis.cpp (revision 27231)
+++ /issm/trunk/src/c/analyses/SamplingAnalysis.cpp (revision 27232)
@@ -289,5 +289,5 @@
element->AddInput(SampleEnum,newsample,element->GetElementType());
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(newsample);
xDelete(tau);
Index: /issm/trunk/src/c/analyses/SealevelchangeAnalysis.cpp
===================================================================
--- /issm/trunk/src/c/analyses/SealevelchangeAnalysis.cpp (revision 27231)
+++ /issm/trunk/src/c/analyses/SealevelchangeAnalysis.cpp (revision 27232)
@@ -17,4 +17,13 @@
void SealevelchangeAnalysis::CreateNodes(Nodes* nodes,IoModel* iomodel,bool isamr){/*{{{*/
::CreateNodes(nodes,iomodel,SealevelchangeAnalysisEnum,P1Enum);
+}/*}}}*/
+void SealevelchangeAnalysis::DeleteBarystaticContributionsParam(FemModel* femmodel){/*{{{*/
+ BarystaticContributions* barycontrib=NULL;
+ GenericParam* barycontribparam=NULL;
+
+ barycontribparam = xDynamicCast*>(femmodel->parameters->FindParamObject(BarystaticContributionsEnum));
+ barycontrib=barycontribparam->GetParameterValue();
+
+ delete barycontrib;
}/*}}}*/
int SealevelchangeAnalysis::DofsPerNode(int** doflist,int domaintype,int approximation){/*{{{*/
@@ -115,4 +124,7 @@
IssmDouble planetradius=0;
IssmDouble planetarea=0;
+ IssmDouble constant=0;
+ IssmDouble rho_earth;
+ int isgrd=0;
bool selfattraction=false;
bool elastic=false;
@@ -128,4 +140,6 @@
int numoutputs;
char** requestedoutputs = NULL;
+ int* recvcounts = NULL;
+ int* displs=NULL;
/*transition vectors: */
@@ -149,4 +163,5 @@
if(isexternal) parameters->AddObject(iomodel->CopyConstantObject("md.solidearth.external.nature",SolidearthExternalNatureEnum));
parameters->AddObject(iomodel->CopyConstantObject("md.solidearth.settings.runfrequency",SolidearthSettingsRunFrequencyEnum));
+ parameters->AddObject(iomodel->CopyConstantObject("md.solidearth.settings.degacc",SolidearthSettingsDegreeAccuracyEnum));
parameters->AddObject(iomodel->CopyConstantObject("md.solidearth.settings.reltol",SolidearthSettingsReltolEnum));
parameters->AddObject(iomodel->CopyConstantObject("md.solidearth.settings.abstol",SolidearthSettingsAbstolEnum));
@@ -172,7 +187,7 @@
parameters->AddObject(new DoubleParam(CumBslcHydroEnum,0.0));
parameters->AddObject(new DoubleParam(CumGmtslcEnum,0.0));
-
/*compute planet area and plug into parameters:*/
iomodel->FetchData(&planetradius,"md.solidearth.planetradius");
+ iomodel->FetchData(&rho_earth,"md.materials.earth_density");
planetarea=4*M_PI*planetradius*planetradius;
parameters->AddObject(new DoubleParam(SolidearthPlanetAreaEnum,planetarea));
@@ -236,5 +251,6 @@
parameters->FindParam(&grdmodel,GrdModelEnum);
- if(grdmodel==ElasticEnum){
+ parameters->FindParam(&isgrd,SolidearthSettingsGRDEnum);
+ if(grdmodel==ElasticEnum && isgrd){
/*Deal with elasticity {{{*/
iomodel->FetchData(&selfattraction,"md.solidearth.settings.selfattraction");
@@ -250,4 +266,7 @@
}
+ //default values
+ nt=1;
+ ntimesteps=1;
/*love numbers: */
if(viscous || elastic){
@@ -264,7 +283,7 @@
parameters->AddObject(new DoubleParam(SolidearthSettingsTimeAccEnum,timeacc));
- parameters->AddObject(new DoubleMatParam(LoadLoveHEnum,love_h,ndeg,precomputednt));
- parameters->AddObject(new DoubleMatParam(LoadLoveKEnum,love_k,ndeg,precomputednt));
- parameters->AddObject(new DoubleMatParam(LoadLoveLEnum,love_l,ndeg,precomputednt));
+ //parameters->AddObject(new DoubleMatParam(LoadLoveHEnum,love_h,ndeg,precomputednt));
+ //parameters->AddObject(new DoubleMatParam(LoadLoveKEnum,love_k,ndeg,precomputednt));
+ //parameters->AddObject(new DoubleMatParam(LoadLoveLEnum,love_l,ndeg,precomputednt));
if (rotation){
@@ -277,7 +296,7 @@
parameters->AddObject(new DoubleMatParam(LovePolarMotionTransferFunctionColinearEnum,love_pmtf_colinear,1,precomputednt));
parameters->AddObject(new DoubleMatParam(LovePolarMotionTransferFunctionOrthogonalEnum,love_pmtf_ortho,1,precomputednt));
- parameters->AddObject(new DoubleMatParam(TidalLoveHEnum,love_th,ndeg,precomputednt));
- parameters->AddObject(new DoubleMatParam(TidalLoveKEnum,love_tk,ndeg,precomputednt));
- parameters->AddObject(new DoubleMatParam(TidalLoveLEnum,love_tl,ndeg,precomputednt));
+ //parameters->AddObject(new DoubleMatParam(TidalLoveHEnum,love_th,ndeg,precomputednt));
+ //parameters->AddObject(new DoubleMatParam(TidalLoveKEnum,love_tk,ndeg,precomputednt));
+ //parameters->AddObject(new DoubleMatParam(TidalLoveLEnum,love_tl,ndeg,precomputednt));
}
@@ -308,15 +327,8 @@
}
}
- else {
- ntimesteps=1;
- nt=1;
- }
-
#ifdef _HAVE_AD_
- G_viscoelastic=xNew(M*ntimesteps,"t");
U_viscoelastic=xNew(M*ntimesteps,"t");
if(horiz)H_viscoelastic=xNew(M*ntimesteps,"t");
#else
- G_viscoelastic=xNew(M*ntimesteps);
U_viscoelastic=xNew(M*ntimesteps);
if(horiz)H_viscoelastic=xNew(M*ntimesteps);
@@ -324,99 +336,97 @@
}
if(selfattraction){
-#ifdef _HAVE_AD_
- G_gravi=xNew(M,"t");
-#else
- G_gravi=xNew(M);
-#endif
- }
-
- if(rotation) parameters->AddObject(iomodel->CopyConstantObject("md.solidearth.lovenumbers.tk2secular",TidalLoveK2SecularEnum));
- if(selfattraction){
-
/*compute combined legendre + love number (elastic green function):*/
m=DetermineLocalSize(M,IssmComm::GetComm());
GetOwnershipBoundariesFromRange(&lower_row,&upper_row,m,IssmComm::GetComm());
+#ifdef _HAVE_AD_
+ G_gravi=xNew(M,"t");
+ G_gravi_local=xNew(m,"t");
+ G_viscoelastic=xNew(M*ntimesteps,"t");
+ G_viscoelastic_local=xNew(m*ntimesteps,"t");
+#else
+ G_gravi=xNew(M);
+ G_gravi_local=xNew(m);
+ G_viscoelastic=xNew(M*ntimesteps);
+ G_viscoelastic_local=xNew(m*ntimesteps);
+#endif
}
if(viscous | elastic){
#ifdef _HAVE_AD_
- G_viscoelastic_local=xNew(m*ntimesteps,"t");
U_viscoelastic_local=xNew(m*ntimesteps,"t");
if(horiz)H_viscoelastic_local=xNew(m*ntimesteps,"t");
#else
- G_viscoelastic_local=xNew(m*ntimesteps);
U_viscoelastic_local=xNew(m*ntimesteps);
if(horiz)H_viscoelastic_local=xNew(m*ntimesteps);
#endif
}
- if(selfattraction){
-#ifdef _HAVE_AD_
- G_gravi_local=xNew(m,"t");
-#else
- G_gravi_local=xNew(m);
-#endif
- }
-
+
+ if(rotation) parameters->AddObject(iomodel->CopyConstantObject("md.solidearth.lovenumbers.tk2secular",TidalLoveK2SecularEnum));
+ constant=3/rho_earth/planetarea;
if(selfattraction){
for(int i=lower_row;i(i)*degacc * M_PI / 180.0;
- G_gravi_local[i-lower_row]= .5/sin(alpha/2.0);
- }
- }
- if(viscous | elastic){
- for(int i=lower_row;i(i)*degacc * M_PI / 180.0;
-
- for(int t=0;t(i)*degacc * M_PI / 180.0;
+
+ for(int t=0;t(IssmComm::GetSize());
- int* displs=xNew(IssmComm::GetSize());
+ recvcounts=xNew(IssmComm::GetSize());
+ displs=xNew(IssmComm::GetSize());
int rc;
int offset;
@@ -424,18 +434,15 @@
//deal with selfattraction first:
ISSM_MPI_Allgather(&m,1,ISSM_MPI_INT,recvcounts,1,ISSM_MPI_INT,IssmComm::GetComm());
-
/*displs: */
ISSM_MPI_Allgather(&lower_row,1,ISSM_MPI_INT,displs,1,ISSM_MPI_INT,IssmComm::GetComm());
-
/*All gather:*/
ISSM_MPI_Allgatherv(G_gravi_local, m, ISSM_MPI_DOUBLE, G_gravi, recvcounts, displs, ISSM_MPI_DOUBLE,IssmComm::GetComm());
+ rc=m*ntimesteps;
+ offset=lower_row*ntimesteps;
+ ISSM_MPI_Allgather(&rc,1,ISSM_MPI_INT,recvcounts,1,ISSM_MPI_INT,IssmComm::GetComm());
+ ISSM_MPI_Allgather(&offset,1,ISSM_MPI_INT,displs,1,ISSM_MPI_INT,IssmComm::GetComm());
+ ISSM_MPI_Allgatherv(G_viscoelastic_local, m*ntimesteps, ISSM_MPI_DOUBLE, G_viscoelastic, recvcounts, displs, ISSM_MPI_DOUBLE,IssmComm::GetComm());
if(elastic){
- rc=m*ntimesteps;
- offset=lower_row*ntimesteps;
- ISSM_MPI_Allgather(&rc,1,ISSM_MPI_INT,recvcounts,1,ISSM_MPI_INT,IssmComm::GetComm());
- ISSM_MPI_Allgather(&offset,1,ISSM_MPI_INT,displs,1,ISSM_MPI_INT,IssmComm::GetComm());
-
- ISSM_MPI_Allgatherv(G_viscoelastic_local, m*ntimesteps, ISSM_MPI_DOUBLE, G_viscoelastic, recvcounts, displs, ISSM_MPI_DOUBLE,IssmComm::GetComm());
ISSM_MPI_Allgatherv(U_viscoelastic_local, m*ntimesteps, ISSM_MPI_DOUBLE, U_viscoelastic, recvcounts, displs, ISSM_MPI_DOUBLE,IssmComm::GetComm());
if(horiz)ISSM_MPI_Allgatherv(H_viscoelastic_local, m*ntimesteps, ISSM_MPI_DOUBLE, H_viscoelastic, recvcounts, displs, ISSM_MPI_DOUBLE,IssmComm::GetComm());
@@ -448,7 +455,9 @@
/*Avoid singularity at 0: */
G_gravi[0]=G_gravi[1];
+ for(int t=0;t(M*nt,"t");
U_viscoelastic_interpolated=xNew(M*nt,"t");
- if(horiz)H_viscoelastic_interpolated=xNew(M*nt,"t");
+ if(horiz) H_viscoelastic_interpolated=xNew(M*nt,"t");
if(rotation){
Pmtf_col_interpolated=xNew(nt,"t");
@@ -475,5 +484,5 @@
G_viscoelastic_interpolated=xNew(M*nt);
U_viscoelastic_interpolated=xNew(M*nt);
- if(horiz)H_viscoelastic_interpolated=xNew(M*nt);
+ if(horiz) H_viscoelastic_interpolated=xNew(M*nt);
if(rotation){
Pmtf_col_interpolated=xNew(nt);
@@ -485,10 +494,8 @@
}
#endif
-
for(int t=0;t(M,"t");
#else
- G_viscoelastic_interpolated=G_viscoelastic;
- U_viscoelastic_interpolated=U_viscoelastic;
- if(horiz)H_viscoelastic_interpolated=H_viscoelastic;
+ G_viscoelastic_interpolated=xNew(M);
#endif
-
- if(rotation){ //if this cpu handles degree 2
+ xMemCpy(G_viscoelastic_interpolated,G_viscoelastic,M);
+
+ if(elastic){
#ifdef _HAVE_AD_
- Pmtf_col_interpolated=xNew(1,"t");
- Pmtf_ortho_interpolated=xNew(1,"t");
- Pmtf_z_interpolated=xNew(1,"t");
- Love_tk2_interpolated=xNew(1,"t");
- Love_th2_interpolated=xNew(1,"t");
- if (horiz) Love_tl2_interpolated=xNew(1,"t");
+ U_viscoelastic_interpolated=xNew(M,"t");
+ if (horiz) H_viscoelastic_interpolated=xNew(M,"t");
#else
- Pmtf_col_interpolated=xNew(1);
- Pmtf_ortho_interpolated=xNew(1);
- Pmtf_z_interpolated=xNew(1);
- Love_tk2_interpolated=xNew(1);
- Love_th2_interpolated=xNew(1);
- if (horiz) Love_tl2_interpolated=xNew(1);
+ U_viscoelastic_interpolated=xNew(M);
+ if (horiz) H_viscoelastic_interpolated=xNew(M);
#endif
-
- Pmtf_col_interpolated=love_pmtf_colinear;
- Pmtf_ortho_interpolated=love_pmtf_ortho;
- Pmtf_z_interpolated[0]=1.0+love_k[2];
- Love_tk2_interpolated[0]=love_tk[2];
- Love_th2_interpolated[0]=love_th[2];
- if (horiz) Love_tl2_interpolated[0]=love_tl[2];
+ xMemCpy(U_viscoelastic_interpolated,U_viscoelastic,M);
+ if (horiz) xMemCpy(H_viscoelastic_interpolated,H_viscoelastic,M);
+
+ if(rotation){ //if this cpu handles degree 2
+#ifdef _HAVE_AD_
+ Pmtf_col_interpolated=xNew(1,"t");
+ Pmtf_ortho_interpolated=xNew(1,"t");
+ Pmtf_z_interpolated=xNew(1,"t");
+ Love_tk2_interpolated=xNew(1,"t");
+ Love_th2_interpolated=xNew(1,"t");
+ if (horiz) Love_tl2_interpolated=xNew(1,"t");
+#else
+ Pmtf_col_interpolated=xNew(1);
+ Pmtf_ortho_interpolated=xNew(1);
+ Pmtf_z_interpolated=xNew(1);
+ Love_tk2_interpolated=xNew(1);
+ Love_th2_interpolated=xNew(1);
+ if (horiz) Love_tl2_interpolated=xNew(1);
+#endif
+
+ Pmtf_col_interpolated[0]=love_pmtf_colinear[0];
+ Pmtf_ortho_interpolated[0]=love_pmtf_ortho[0];
+ Pmtf_z_interpolated[0]=1.0+love_k[2];
+ Love_tk2_interpolated[0]=love_tk[2];
+ Love_th2_interpolated[0]=love_th[2];
+ if (horiz) Love_tl2_interpolated[0]=love_tl[2];
+ }
+
}
}
-
/*Save our precomputed tables into parameters*/
parameters->AddObject(new DoubleVecParam(SealevelchangeGSelfAttractionEnum,G_gravi,M));
+ parameters->AddObject(new DoubleVecParam(SealevelchangeGViscoElasticEnum,G_viscoelastic_interpolated,M*nt));
if(viscous || elastic){
- parameters->AddObject(new DoubleVecParam(SealevelchangeGViscoElasticEnum,G_viscoelastic_interpolated,M*nt));
parameters->AddObject(new DoubleVecParam(SealevelchangeUViscoElasticEnum,U_viscoelastic_interpolated,M*nt));
if(horiz)parameters->AddObject(new DoubleVecParam(SealevelchangeHViscoElasticEnum,H_viscoelastic_interpolated,M*nt));
@@ -582,9 +597,12 @@
}
}
-
/*free resources: */
xDelete(G_gravi);
xDelete(G_gravi_local);
+ xDelete(G_viscoelastic);
+ xDelete(G_viscoelastic_local);
+ xDelete(G_viscoelastic_interpolated);
if(elastic){
+ xDelete(love_timefreq);
xDelete(love_h);
xDelete(love_k);
@@ -593,16 +611,25 @@
xDelete(love_tk);
xDelete(love_tl);
- xDelete(G_viscoelastic);
- xDelete(G_viscoelastic_local);
+
+ xDelete(G_viscoelastic_interpolated);
xDelete(U_viscoelastic);
+ xDelete(U_viscoelastic_interpolated);
xDelete(U_viscoelastic_local);
+ xDelete(U_viscoelastic_interpolated);
if(horiz){
xDelete(H_viscoelastic);
+ xDelete(H_viscoelastic_interpolated);
xDelete(H_viscoelastic_local);
+ xDelete(H_viscoelastic_interpolated);
}
if(rotation){
xDelete(love_pmtf_colinear);
xDelete(love_pmtf_ortho);
-
+ xDelete(Pmtf_col_interpolated);
+ xDelete(Pmtf_ortho_interpolated);
+ xDelete(Pmtf_z_interpolated);
+ xDelete(Love_tk2_interpolated);
+ xDelete(Love_th2_interpolated);
+ if (horiz) xDelete(Love_tl2_interpolated);
}
}
@@ -632,4 +659,5 @@
iomodel->DeleteData(&requestedoutputs,numoutputs,"md.solidearth.requested_outputs");
/*}}}*/
+
}/*}}}*/
Index: /issm/trunk/src/c/analyses/SealevelchangeAnalysis.h
===================================================================
--- /issm/trunk/src/c/analyses/SealevelchangeAnalysis.h (revision 27231)
+++ /issm/trunk/src/c/analyses/SealevelchangeAnalysis.h (revision 27232)
@@ -16,4 +16,5 @@
void CreateLoads(Loads* loads, IoModel* iomodel);
void CreateNodes(Nodes* nodes,IoModel* iomodel,bool isamr=false);
+ static void DeleteBarystaticContributionsParam(FemModel* femmodel);
int DofsPerNode(int** doflist,int domaintype,int approximation);
void UpdateElements(Elements* elements,Inputs* inputs,IoModel* iomodel,int analysis_counter,int analysis_type);
Index: /issm/trunk/src/c/analyses/SmbAnalysis.cpp
===================================================================
--- /issm/trunk/src/c/analyses/SmbAnalysis.cpp (revision 27231)
+++ /issm/trunk/src/c/analyses/SmbAnalysis.cpp (revision 27232)
@@ -249,4 +249,5 @@
parameters->AddObject(iomodel->CopyConstantObject("md.smb.aIdx",SmbAIdxEnum));
parameters->AddObject(iomodel->CopyConstantObject("md.smb.eIdx",SmbEIdxEnum));
+ parameters->AddObject(iomodel->CopyConstantObject("md.smb.tcIdx",SmbTcIdxEnum));
parameters->AddObject(iomodel->CopyConstantObject("md.smb.swIdx",SmbSwIdxEnum));
parameters->AddObject(iomodel->CopyConstantObject("md.smb.denIdx",SmbDenIdxEnum));
Index: /issm/trunk/src/c/analyses/StressbalanceAnalysis.cpp
===================================================================
--- /issm/trunk/src/c/analyses/StressbalanceAnalysis.cpp (revision 27231)
+++ /issm/trunk/src/c/analyses/StressbalanceAnalysis.cpp (revision 27232)
@@ -502,5 +502,5 @@
}
- /*free ressources: */
+ /*Free resources: */
iomodel->DeleteData(penalties,"md.stressbalance.vertex_pairing");
@@ -1308,5 +1308,5 @@
solution->SetValues(numdof,doflist,values,INS_VAL);
- /*Free ressources:*/
+ /*Free resources:*/
delete gauss;
xDelete(values);
@@ -2143,5 +2143,5 @@
element->AddBasalInput(VelEnum,vel,element->GetElementType());
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(vel);
xDelete(vz);
@@ -2749,5 +2749,5 @@
element->AddBasalInput(VyBaseEnum,vy,element->GetElementType());
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(vel);
xDelete(vz);
@@ -3275,5 +3275,5 @@
}
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(vel);
xDelete(vx);
@@ -3343,5 +3343,5 @@
solution->SetValues(numdof,doflist,values,INS_VAL);
- /*Free ressources:*/
+ /*Free resources:*/
delete gauss;
xDelete(values);
@@ -3992,5 +3992,5 @@
element->AddInput(VelEnum,vel,element->GetElementType());
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(vel);
xDelete(vz);
@@ -6505,5 +6505,5 @@
if(pnumdof>0) solution->SetValues(pnumdof,pdoflist,pvalues,INS_VAL);
- /*Free ressources:*/
+ /*Free resources:*/
delete gauss;
xDelete(pdoflist);
@@ -6668,5 +6668,5 @@
if(dim==3) element->AddInput(VzEnum,vz,v_interp);
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(pressure);
xDelete(vel);
@@ -8566,5 +8566,5 @@
element->AddInput(PressureEnum,pressure,P1Enum);
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(pressure);
xDelete(vel);
@@ -8669,5 +8669,5 @@
element->AddInput(PressureEnum,pressure,P1Enum);
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(pressure);
xDelete(vel);
@@ -8760,5 +8760,5 @@
element->AddInput(PressureEnum,pressure,P1Enum);
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(surface);
xDelete(pressure);
Index: /issm/trunk/src/c/analyses/StressbalanceSIAAnalysis.cpp
===================================================================
--- /issm/trunk/src/c/analyses/StressbalanceSIAAnalysis.cpp (revision 27231)
+++ /issm/trunk/src/c/analyses/StressbalanceSIAAnalysis.cpp (revision 27232)
@@ -554,5 +554,5 @@
solution->SetValues(numdof,doflist,values,INS_VAL);
- /*Free ressources:*/
+ /*Free resources:*/
delete gauss;
xDelete(doflist);
@@ -630,5 +630,5 @@
element->AddInput(PressureEnum,pressure,P1Enum);
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(thickness);
xDelete(surface);
Index: /issm/trunk/src/c/analyses/StressbalanceVerticalAnalysis.cpp
===================================================================
--- /issm/trunk/src/c/analyses/StressbalanceVerticalAnalysis.cpp (revision 27231)
+++ /issm/trunk/src/c/analyses/StressbalanceVerticalAnalysis.cpp (revision 27232)
@@ -657,5 +657,5 @@
element->AddInput(VelEnum,vel,P1Enum);
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(surface);
xDelete(pressure);
Index: /issm/trunk/src/c/analyses/ThermalAnalysis.cpp
===================================================================
--- /issm/trunk/src/c/analyses/ThermalAnalysis.cpp (revision 27231)
+++ /issm/trunk/src/c/analyses/ThermalAnalysis.cpp (revision 27232)
@@ -65,5 +65,5 @@
}
- /*Free ressources:*/
+ /*Free resources:*/
iomodel->DeleteData(spcvector,"md.thermal.spctemperature");
iomodel->DeleteData(spcvectorstatic,"md.thermal.spctemperature");
@@ -839,5 +839,5 @@
}
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(values);
xDelete(surface);
Index: /issm/trunk/src/c/analyses/UzawaPressureAnalysis.cpp
===================================================================
--- /issm/trunk/src/c/analyses/UzawaPressureAnalysis.cpp (revision 27231)
+++ /issm/trunk/src/c/analyses/UzawaPressureAnalysis.cpp (revision 27232)
@@ -287,5 +287,5 @@
}
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(values);
xDelete(valueslambda);
Index: /issm/trunk/src/c/analyses/analyses.h
===================================================================
--- /issm/trunk/src/c/analyses/analyses.h (revision 27231)
+++ /issm/trunk/src/c/analyses/analyses.h (revision 27232)
@@ -11,4 +11,5 @@
#include "./AdjointBalancethickness2Analysis.h"
#include "./AdjointHorizAnalysis.h"
+#include "./AgeAnalysis.h"
#include "./BalancethicknessAnalysis.h"
#include "./Balancethickness2Analysis.h"
Index: /issm/trunk/src/c/classes/Cfdragcoeffabsgrad.cpp
===================================================================
--- /issm/trunk/src/c/classes/Cfdragcoeffabsgrad.cpp (revision 27231)
+++ /issm/trunk/src/c/classes/Cfdragcoeffabsgrad.cpp (revision 27232)
@@ -69,5 +69,13 @@
/*}}}*/
void Cfdragcoeffabsgrad::Marshall(MarshallHandle* marshallhandle){/*{{{*/
- _error_("not implemented yet!");
+
+ /*ok, marshall operations: */
+ int object_enum=CfdragcoeffabsgradEnum;
+ marshallhandle->call(object_enum);
+
+ marshallhandle->call(this->definitionenum);
+ marshallhandle->call(this->name);
+ marshallhandle->call(this->weights_enum);
+ marshallhandle->call(this->timepassedflag);
}
/*}}}*/
Index: /issm/trunk/src/c/classes/Dakota/IssmDirectApplicInterface.h
===================================================================
--- /issm/trunk/src/c/classes/Dakota/IssmDirectApplicInterface.h (revision 27231)
+++ /issm/trunk/src/c/classes/Dakota/IssmDirectApplicInterface.h (revision 27232)
@@ -118,5 +118,5 @@
}
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(variables);
for(i=0;i(variables);
for(i=0;iSetValues(numnodes,doflist,values,INS_VAL);
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(doflist);
xDelete(values);
@@ -4012,4 +4013,5 @@
int aIdx=0;
int eIdx=0;
+ int tcIdx=0;
int denIdx=0;
int dsnowIdx=0;
@@ -4096,4 +4098,5 @@
parameters->FindParam(&aIdx,SmbAIdxEnum);
parameters->FindParam(&eIdx,SmbEIdxEnum);
+ parameters->FindParam(&tcIdx,SmbTcIdxEnum);
parameters->FindParam(&denIdx,SmbDenIdxEnum);
parameters->FindParam(&swIdx,SmbSwIdxEnum);
@@ -4348,5 +4351,5 @@
}
/*Thermal profile computation:*/
- if(isthermal)thermo(&EC, &T, &ulw, re, dz, d, swf, dlw, Ta, V, eAir, pAir, eIdx, teValue, dulwrfValue, teThresh, W[0], smb_dt, m, Vz, Tz, thermo_scaling,rho_ice,this->Sid(),isconstrainsurfaceT,isdeltaLWup);
+ if(isthermal)thermo(&shf, &lhf, &EC, &T, &ulw, re, dz, d, swf, dlw, Ta, V, eAir, pAir, tcIdx, eIdx, teValue, dulwrfValue, teThresh, W[0], smb_dt, dzMin, m, Vz, Tz, thermo_scaling,rho_ice,this->Sid(),isconstrainsurfaceT,isdeltaLWup);
/*Change in thickness of top cell due to evaporation/condensation assuming same density as top cell.
@@ -4364,14 +4367,7 @@
if(isdensification)densification(&d,&dz, T, re, denIdx, aIdx, swIdx, adThresh, C, smb_dt, Tmean,rho_ice,m,this->Sid());
- /*Calculate upward longwave radiation flux [W m-2] not used in energy balance. Calculated for every
- * sub-time step in thermo equations*/
- //ulw = 5.67E-8 * pow(T[0],4.0) * teValue; // + deltatest here
-
/*Calculate net longwave [W m-2]*/
meanULW = meanULW + ulw*smb_dt/dt;
netLW = netLW + (dlw - ulw)*smb_dt/dt;
-
- /*Calculate turbulent heat fluxes [W m-2]*/
- if(isturbulentflux)turbulentFlux(&shf, &lhf, &dayEC, Ta, T[0], V, eAir, pAir, d[0], W[0], Vz, Tz,rho_ice,this->Sid());
/*Verbose some results in debug mode: {{{*/
Index: /issm/trunk/src/c/classes/Elements/Element.h
===================================================================
--- /issm/trunk/src/c/classes/Elements/Element.h (revision 27231)
+++ /issm/trunk/src/c/classes/Elements/Element.h (revision 27232)
@@ -404,5 +404,5 @@
virtual void SealevelchangeGeometrySubElementKernel(SealevelGeometry* slgeom)=0;
virtual void SealevelchangeShift(GrdLoads* loads, IssmDouble offset, SealevelGeometry* slgeom)=0;
- virtual void SealevelchangeGeometryInitial(IssmDouble* xxe, IssmDouble* yye, IssmDouble* zze, IssmDouble* areae)=0;
+ virtual void SealevelchangeGeometryInitial(IssmDouble* xxe, IssmDouble* yye, IssmDouble* zze, IssmDouble* areae, int* lids)=0;
virtual void SealevelchangeGeometryCentroidLoads(SealevelGeometry* slgeom, IssmDouble* xxe, IssmDouble* yye, IssmDouble* zze, IssmDouble* areae)=0;
virtual void SealevelchangeGeometrySubElementLoads(SealevelGeometry* slgeom, IssmDouble* areae)=0;
Index: /issm/trunk/src/c/classes/Elements/ElementHook.cpp
===================================================================
--- /issm/trunk/src/c/classes/Elements/ElementHook.cpp (revision 27231)
+++ /issm/trunk/src/c/classes/Elements/ElementHook.cpp (revision 27232)
@@ -120,5 +120,5 @@
if(this->hneighbors)this->hneighbors->Marshall(marshallhandle);
- /*Free ressources: */
+ /*Free resources: */
if(hnodesi_null) xDelete(hnodesi_null);
Index: /issm/trunk/src/c/classes/Elements/Penta.cpp
===================================================================
--- /issm/trunk/src/c/classes/Elements/Penta.cpp (revision 27231)
+++ /issm/trunk/src/c/classes/Elements/Penta.cpp (revision 27232)
@@ -2604,5 +2604,5 @@
this->AddInput(enum_type,values,this->element_type);
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(values);
xDelete(doflist);
@@ -2645,5 +2645,5 @@
}
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(doflist);
}
@@ -2699,5 +2699,5 @@
inputs->SetPentaInput(name,P1Enum,NUMVERTICES,lidlist,values);
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(doflist);
return;
@@ -2712,5 +2712,5 @@
inputs->SetPentaInput(name,P1Enum,NUMVERTICES,lidlist,values);
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(doflist);
return;
Index: /issm/trunk/src/c/classes/Elements/Penta.h
===================================================================
--- /issm/trunk/src/c/classes/Elements/Penta.h (revision 27231)
+++ /issm/trunk/src/c/classes/Elements/Penta.h (revision 27232)
@@ -227,5 +227,5 @@
void SealevelchangeGeometrySubElementKernel(SealevelGeometry* slgeom){_error_("not implemented yet");};
void SealevelchangeShift(GrdLoads* loads, IssmDouble offset, SealevelGeometry* slgeom){_error_("not implemented yet");};
- void SealevelchangeGeometryInitial(IssmDouble* xxe, IssmDouble* yye, IssmDouble* zze, IssmDouble* areae){_error_("not implemented yet");};
+ void SealevelchangeGeometryInitial(IssmDouble* xxe, IssmDouble* yye, IssmDouble* zze, IssmDouble* areae, int* lids){_error_("not implemented yet");};
void SealevelchangeGeometryCentroidLoads(SealevelGeometry* slgeom, IssmDouble* xxe, IssmDouble* yye, IssmDouble* zze, IssmDouble* areae){_error_("not implemented yet");};
void SealevelchangeGeometrySubElementLoads(SealevelGeometry* slgeom, IssmDouble* areae){_error_("not implemented yet");};
Index: /issm/trunk/src/c/classes/Elements/Seg.h
===================================================================
--- /issm/trunk/src/c/classes/Elements/Seg.h (revision 27231)
+++ /issm/trunk/src/c/classes/Elements/Seg.h (revision 27232)
@@ -180,5 +180,5 @@
void SealevelchangeGeometrySubElementKernel(SealevelGeometry* slgeom){_error_("not implemented yet");};
void SealevelchangeShift(GrdLoads* loads, IssmDouble offset, SealevelGeometry* slgeom){_error_("not implemented yet");};
- void SealevelchangeGeometryInitial(IssmDouble* xxe, IssmDouble* yye, IssmDouble* zze, IssmDouble* areae){_error_("not implemented yet");};
+ void SealevelchangeGeometryInitial(IssmDouble* xxe, IssmDouble* yye, IssmDouble* zze, IssmDouble* areae, int* lids){_error_("not implemented yet");};
void SealevelchangeGeometryCentroidLoads(SealevelGeometry* slgeom, IssmDouble* xxe, IssmDouble* yye, IssmDouble* zze, IssmDouble* areae){_error_("not implemented yet");};
void SealevelchangeGeometrySubElementLoads(SealevelGeometry* slgeom, IssmDouble* areae){_error_("not implemented yet");};
Index: /issm/trunk/src/c/classes/Elements/Tetra.cpp
===================================================================
--- /issm/trunk/src/c/classes/Elements/Tetra.cpp (revision 27231)
+++ /issm/trunk/src/c/classes/Elements/Tetra.cpp (revision 27232)
@@ -446,5 +446,5 @@
this->AddInput(enum_type,values,this->element_type);
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(values);
xDelete(doflist);
Index: /issm/trunk/src/c/classes/Elements/Tetra.h
===================================================================
--- /issm/trunk/src/c/classes/Elements/Tetra.h (revision 27231)
+++ /issm/trunk/src/c/classes/Elements/Tetra.h (revision 27232)
@@ -187,5 +187,5 @@
void SealevelchangeGeometrySubElementKernel(SealevelGeometry* slgeom){_error_("not implemented yet");};
void SealevelchangeShift(GrdLoads* loads, IssmDouble offset, SealevelGeometry* slgeom){_error_("not implemented yet");};
- void SealevelchangeGeometryInitial(IssmDouble* xxe, IssmDouble* yye, IssmDouble* zze, IssmDouble* areae){_error_("not implemented yet");};
+ void SealevelchangeGeometryInitial(IssmDouble* xxe, IssmDouble* yye, IssmDouble* zze, IssmDouble* areae, int* lids){_error_("not implemented yet");};
void SealevelchangeGeometryCentroidLoads(SealevelGeometry* slgeom, IssmDouble* xxe, IssmDouble* yye, IssmDouble* zze, IssmDouble* areae){_error_("not implemented yet");};
void SealevelchangeGeometrySubElementLoads(SealevelGeometry* slgeom, IssmDouble* areae){_error_("not implemented yet");};
Index: /issm/trunk/src/c/classes/Elements/Tria.cpp
===================================================================
--- /issm/trunk/src/c/classes/Elements/Tria.cpp (revision 27231)
+++ /issm/trunk/src/c/classes/Elements/Tria.cpp (revision 27232)
@@ -376,4 +376,5 @@
IssmDouble time;
IssmDouble coeff, indrate;
+ IssmDouble bed, bedrate = 1.0;
/*Retrieve all inputs and parameters we will need*/
@@ -382,4 +383,5 @@
parameters->FindParam(&indrate,CalvingTestIndependentRateEnum,time);
+ Input *bs_input = this->GetInput(BedEnum);_assert_(bs_input);
Input* vx_input = this->GetInput(VxEnum); _assert_(vx_input);
Input* vy_input = this->GetInput(VyEnum); _assert_(vy_input);
@@ -399,9 +401,12 @@
lsf_slopey_input->GetInputValue(&dphidy,&gauss);
+ bs_input->GetInputValue(&bed,&gauss);
+ bedrate = (bed>0)?0.0:1.0;
+
vel=sqrt(vx*vx + vy*vy) + 1e-14;
dphi=sqrt(dphidx*dphidx+dphidy*dphidy)+ 1e-14;
- calvingratex[iv]= coeff*vx + indrate*dphidx/dphi;
- calvingratey[iv]= coeff*vy + indrate*dphidy/dphi;
+ calvingratex[iv]= coeff*vx + bedrate*indrate*dphidx/dphi;
+ calvingratey[iv]= coeff*vy + bedrate*indrate*dphidy/dphi;
calvingrate[iv] = sqrt(calvingratex[iv]*calvingratex[iv] + calvingratey[iv]*calvingratey[iv]);
}
@@ -835,10 +840,10 @@
IssmDouble lambda1,lambda2,ex,ey,vx,vy,vel;
IssmDouble sigma_vm[NUMVERTICES];
- IssmDouble B,sigma_max,sigma_max_floating,sigma_max_grounded,n;
+ IssmDouble B, n;
IssmDouble epse_2,groundedice,bed,sealevel;
- IssmDouble arate, rho_ice, rho_water, thickness, paramX, Hab;
- int use_parameter=0;
- int nonlinear_law=0;
- IssmDouble theta, alpha, midp, gamma;
+ IssmDouble arate, rho_ice, rho_water, thickness;
+ int use_parameter=-1;
+ IssmDouble gamma, theta, alpha, xoffset, yoffset;
+ IssmDouble vel_lower, vel_upper, vrate, truncateVrate;
/* Get node coordinates and dof list: */
@@ -852,6 +857,4 @@
Input *bs_input = this->GetInput(BedEnum); _assert_(bs_input);
Input *H_input = this->GetInput(ThicknessEnum); _assert_(H_input);
- Input *smax_fl_input = this->GetInput(CalvingStressThresholdFloatingiceEnum); _assert_(smax_fl_input);
- Input *smax_gr_input = this->GetInput(CalvingStressThresholdGroundediceEnum); _assert_(smax_gr_input);
Input *n_input = this->GetInput(MaterialsRheologyNEnum); _assert_(n_input);
Input *sl_input = this->GetInput(SealevelEnum); _assert_(sl_input);
@@ -864,8 +867,10 @@
/* Use which parameter */
this->FindParam(&use_parameter, CalvingUseParamEnum);
- this->FindParam(&theta, CalvingScaleThetaEnum);
- this->FindParam(&alpha, CalvingAmpAlphaEnum);
- this->FindParam(&midp, CalvingMidpointEnum);
- this->FindParam(&nonlinear_law, CalvingNonlinearLawEnum);
+ this->FindParam(&theta, CalvingThetaEnum);
+ this->FindParam(&alpha, CalvingAlphaEnum);
+ this->FindParam(&xoffset, CalvingXoffsetEnum);
+ this->FindParam(&yoffset, CalvingYoffsetEnum);
+ this->FindParam(&vel_lower, CalvingVelLowerboundEnum);
+ this->FindParam(&vel_upper, CalvingVelUpperboundEnum);
/* Start looping on the number of vertices: */
@@ -882,9 +887,9 @@
bs_input->GetInputValue(&bed,gauss);
H_input->GetInputValue(&thickness,gauss);
- smax_fl_input->GetInputValue(&sigma_max_floating,gauss);
- smax_gr_input->GetInputValue(&sigma_max_grounded,gauss);
vel=sqrt(vx*vx+vy*vy)+1.e-14;
sl_input->GetInputValue(&sealevel,gauss);
arate_input->GetInputValue(&arate,gauss);
+ vrate = 1.0;
+ if (vel < vel_upper) vrate = vel / vel_upper;
/*Compute strain rate and viscosity: */
@@ -904,30 +909,30 @@
sigma_vm[iv] = sqrt(3.) * B * pow(epse_2,1./(2.*n));
- /*Tensile stress threshold*/
- if(groundedice<0)
- sigma_max = sigma_max_floating;
- else
- sigma_max = sigma_max_grounded;
-
switch (use_parameter) {
case 0:
- /* bed elevation */
- paramX = bed;
+ /* 0 Linear: f(x) = y_{o} + \alpha (x+x_{o}) */
+ gamma = yoffset = alpha * (bed+xoffset);
break;
case 1:
- /* Height above floatation */
- if (bed>sealevel) paramX = 0.0;
- else paramX = thickness - (rho_water/rho_ice) * (sealevel-bed);
+ /* 1 tanh: f(x)=y_{o}-\frac{\theta}{2}\tanh(\alpha(x+x_{o})) */
+ gamma = yoffset - 0.5*theta*tanh(alpha*(bed+xoffset));
break;
case 2:
- /* Thicknese */
- paramX = thickness;
+ /* 2 tanh(thicknes): f(x)=y_{o}-\frac{\theta}{2}\tanh(\alpha(x+x_{o})) */
+ gamma = yoffset - 0.5*theta*tanh(alpha*(-thickness+xoffset));
+ break;
+ case 3:
+ /* 3 tanh(normal vel): f(x)=y_{o}-\frac{\theta}{2}\tanh(\alpha(x+x_{o})) */
+ _error_("The normalized velocity is not supported yet!");
+ gamma = yoffset - 0.5*theta*tanh(alpha*(vel+xoffset));
break;
case 4:
- /* bed elevation+linear curve fitting */
- paramX = bed;
+ /* 4 tanh(truncated vel): f(x)=y_{o}-\frac{\theta}{2}\tanh(\alpha(x+x_{o})) */
+ truncateVrate = (min(vel_upper, max(vel_lower, vel))-vel_lower) / vel_upper;
+ gamma = 0.5*theta*(tanh(alpha*xoffset) - tanh(alpha*(truncateVrate+xoffset)));
break;
case -1:
- /* use nothing, just the arate*/
+ /* nothing, just the arate*/
+ gamma = 1;
break;
default:
@@ -935,32 +940,17 @@
}
- /* Compute the hyperbolic tangent function */
- if ((use_parameter>-0.5) & (use_parameter<3)) {
- gamma = 0.5*theta*(1.0-tanh((paramX+midp)/alpha))+(1.0-theta);
- if (gamma<0.0) gamma =0.0;
- }
- else if (use_parameter>=3) {
- gamma = alpha*paramX + theta;
- if (gamma > 1.0) gamma = 1.0;
- if (gamma < 0.0) gamma = 0.0;
- }
- else gamma = 1;
+ /* set upper and lower bounds */
+ if (gamma > 1.0) gamma = 1.0;
+ if (gamma < 0.0) gamma = 0.0;
+ if (bed >= sealevel) gamma = 0.0;
/*-------------------------------------------*/
- if (nonlinear_law) {
- /*This von Mises type has too strong positive feedback with vel included
- * calvingrate[iv] = (arate+sigma_vm[iv]*vel/sigma_max)*gamma;
- */
- Hab = thickness - (rho_water/rho_ice) * (sealevel-bed);
- if (Hab < 0.) Hab = 0.;
- if (bed > sealevel) Hab = 0.;
-
- calvingrate[iv] = (arate+Hab/sigma_max)*gamma;
- }
+ if (use_parameter < 3) {
+ calvingrate[iv] = arate*gamma*vrate;
+ }
else {
calvingrate[iv] = arate*gamma;
}
}
-
/*Add input*/
this->AddInput(CalvingCalvingrateEnum,&calvingrate[0],P1DGEnum);
@@ -2018,5 +2008,5 @@
else for(int i=0;iAddInput(enum_type,values,this->element_type);
- /*Free ressources:*/
+ /*Free resources:*/
xDelete(values);
xDelete(doflist);
@@ -6044,5 +6034,5 @@
pY->SetValues(gsize,indices,Y_values,ADD_VAL);
- /*free ressources:*/
+ /*Free resources:*/
xDelete(indices);
xDelete(U_values); xDelete(N_values); xDelete(E_values);
@@ -6206,5 +6196,5 @@
pEast->SetValues(gsize,indices,E_values,ADD_VAL);
- /*free ressources:*/
+ /*Free resources:*/
xDelete(indices);
xDelete(U_values); xDelete(N_values); xDelete(E_values);
@@ -6313,5 +6303,5 @@
}
- /*Free ressources: */
+ /*Free resources: */
xDelete(hes);
xDelete(times);
@@ -6320,5 +6310,5 @@
}
/*}}}*/
-void Tria::SealevelchangeGeometryInitial(IssmDouble* xxe, IssmDouble* yye, IssmDouble* zze, IssmDouble* areae){ /*{{{*/
+void Tria::SealevelchangeGeometryInitial(IssmDouble* xxe, IssmDouble* yye, IssmDouble* zze, IssmDouble* areae, int* lids){ /*{{{*/
/*Declarations:{{{*/
@@ -6342,21 +6332,7 @@
#ifdef _HAVE_RESTRICT_
- IssmDouble* __restrict__ G=NULL;
- IssmDouble* __restrict__ GU=NULL;
- IssmDouble* __restrict__ GN=NULL;
- IssmDouble* __restrict__ GE=NULL;
- IssmDouble* __restrict__ G_viscoelastic_precomputed=NULL;
IssmDouble* __restrict__ G_gravi_precomputed=NULL;
- IssmDouble* __restrict__ U_viscoelastic_precomputed=NULL;
- IssmDouble* __restrict__ H_viscoelastic_precomputed=NULL;
#else
- IssmDouble* G=NULL;
- IssmDouble* GU=NULL;
- IssmDouble* GN=NULL;
- IssmDouble* GE=NULL;
- IssmDouble* G_viscoelastic_precomputed=NULL;
IssmDouble* G_gravi_precomputed=NULL;
- IssmDouble* U_viscoelastic_precomputed=NULL;
- IssmDouble* H_viscoelastic_precomputed=NULL;
#endif
@@ -6364,4 +6340,5 @@
int index;
int M;
+ IssmDouble degacc;
IssmDouble doubleindex,lincoef;
@@ -6380,4 +6357,8 @@
/*Rotational:*/
#ifdef _HAVE_RESTRICT_
+ IssmDouble* __restrict__ Grot=NULL;
+ IssmDouble* __restrict__ GUrot=NULL;
+ IssmDouble* __restrict__ GNrot=NULL;
+ IssmDouble* __restrict__ GErot=NULL;
IssmDouble* __restrict__ tide_love_h = NULL;
IssmDouble* __restrict__ tide_love_k = NULL;
@@ -6386,9 +6367,11 @@
IssmDouble* __restrict__ LoveRotU = NULL;
IssmDouble* __restrict__ LoveRothoriz = NULL;
- IssmDouble* __restrict__ Grot = NULL;
- IssmDouble* __restrict__ GUrot = NULL;
- IssmDouble* __restrict__ GNrot = NULL;
- IssmDouble* __restrict__ GErot = NULL;
+ int* __restrict__ AplhaIndex = NULL;
+ int* __restrict__ AzimuthIndex = NULL;
#else
+ IssmDouble* Grot=NULL;
+ IssmDouble* GUrot=NULL;
+ IssmDouble* GNrot=NULL;
+ IssmDouble* GErot=NULL;
IssmDouble* tide_love_h = NULL;
IssmDouble* tide_love_k = NULL;
@@ -6397,8 +6380,6 @@
IssmDouble* LoveRotU = NULL;
IssmDouble* LoveRothoriz = NULL;
- IssmDouble* Grot = NULL;
- IssmDouble* GUrot = NULL;
- IssmDouble* GNrot = NULL;
- IssmDouble* GErot = NULL;
+ int* AlphaIndex = NULL;
+ int* AzimuthIndex = NULL;
#endif
@@ -6439,19 +6420,9 @@
/*Recover precomputed green function kernels:{{{*/
- DoubleVecParam* parameter = static_cast(this->parameters->FindParamObject(SealevelchangeGSelfAttractionEnum)); _assert_(parameter);
- parameter->GetParameterValueByPointer((IssmDouble**)&G_gravi_precomputed,&M);
-
+ parameters->FindParam(°acc,SolidearthSettingsDegreeAccuracyEnum);
+ M=reCast(180.0/degacc+1.);
+
+ DoubleVecParam* parameter;
if(computeelastic){
- parameter = static_cast(this->parameters->FindParamObject(SealevelchangeGViscoElasticEnum)); _assert_(parameter);
- parameter->GetParameterValueByPointer((IssmDouble**)&G_viscoelastic_precomputed,NULL);
-
- parameter = static_cast(this->parameters->FindParamObject(SealevelchangeUViscoElasticEnum)); _assert_(parameter);
- parameter->GetParameterValueByPointer((IssmDouble**)&U_viscoelastic_precomputed,NULL);
-
- if(horiz){
- parameter = static_cast(this->parameters->FindParamObject(SealevelchangeHViscoElasticEnum)); _assert_(parameter);
- parameter->GetParameterValueByPointer((IssmDouble**)&H_viscoelastic_precomputed,NULL);
- }
-
if(computerotation){
parameter = static_cast(this->parameters->FindParamObject(SealevelchangeTidalH2Enum)); _assert_(parameter);
@@ -6489,92 +6460,45 @@
}
- constant=3/rho_earth/planetarea;
-
- G=xNewZeroInit(3*nel*nt);
- if(computeelastic){
- GU=xNewZeroInit(3*nel*nt);
- if(horiz){
- GN=xNewZeroInit(3*nel*nt);
- GE=xNewZeroInit