Changeset 27158

Timestamp:

07/11/22 11:53:24 (3 years ago)

Author:

jdquinn

Message:

CHG: Fixes for distributable using Solid Earth capabilities; cleanup

Location:

issm/trunk-jpl

Files:

• etc/environment.sh (modified) (2 diffs)
• externalpackages/dakota/install-6.2-mac.sh (modified) (3 diffs)
• externalpackages/gmt/configs/6/static/linux/cmake/ConfigUser.static.cmake (modified) (2 diffs)
• externalpackages/gmt/configs/6/static/mac/cmake/ConfigUser.static.cmake (modified) (2 diffs)
• m4/issm_options.m4 (modified) (1 diff)
• packagers/linux/package-issm-linux-binaries-matlab.sh (modified) (1 diff)
• packagers/linux/package-issm-linux-binaries-python-2.sh (modified) (1 diff)
• packagers/linux/package-issm-linux-binaries-python-3.sh (modified) (1 diff)
• packagers/mac/package-issm-mac-binaries-matlab.sh (modified) (2 diffs)
• packagers/mac/package-issm-mac-binaries-python-2.sh (modified) (2 diffs)
• packagers/mac/package-issm-mac-binaries-python-3.sh (modified) (2 diffs)
• src/m/coordsystems/gmtmaskparallel.m (modified) (1 diff)
• src/m/mesh/planet/gmsh/gmshplanet.m (modified) (1 diff)
• src/m/modules/CoordTransform.m (modified) (1 diff)

issm/trunk-jpl/etc/environment.sh

@@ -299 +299 @@
 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
@@ -497 +506 @@
 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
-
 SQLITE_ROOT="${ISSM_EXT_DIR}/sqlite/install"
 if [ -d "${SQLITE_ROOT}" ]; then

issm/trunk-jpl/externalpackages/dakota/install-6.2-mac.sh

@@ -11 +11 @@
 ## Environment
 #
+
+# Check for Python 2, required by Dakota
+#
+PYTHON_EXECUTABLE=$(which python2) || echo "Error: This version of Dakota requires Python 2"
 
 # Find libgfortran so that we do not have to hardcode it.
@@ -57 +61 @@
 cp configs/${VER}/mac/cmake/InstallDarwinDylibs.cmake ${DAK_SRC}/cmake
 
-#check for python 2, required by dakota
-PYTHONEXECUTIONPATH=$(which python2) || echo WARNING dakota will not compile without python2
-
 # Configure
 cd ${DAK_BUILD}
@@ -70 +71 @@
         -DCMAKE_Fortran_COMPILER=${MPI_HOME}/bin/mpif77 \
         -DCMAKE_Fortran_FLAGS="-fallow-argument-mismatch" \
-        -DPYTHON_EXECUTABLE=$PYTHONEXECUTIONPATH \
+        -DPYTHON_EXECUTABLE=${PYTHON_EXECUTABLE} \
         -DBoost_NO_BOOST_CMAKE=TRUE \
         -DHAVE_ACRO=OFF \

issm/trunk-jpl/externalpackages/gmt/configs/6/static/linux/cmake/ConfigUser.static.cmake

@@ -58 +58 @@
 # 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 +112 @@
 
 # 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]:

issm/trunk-jpl/externalpackages/gmt/configs/6/static/mac/cmake/ConfigUser.static.cmake

@@ -58 +58 @@
 # 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 +112 @@
 
 # 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]:

issm/trunk-jpl/m4/issm_options.m4

@@ -196 +196 @@
                         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"
                 ;;
                 *)

issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-matlab.sh

@@ -112 +112 @@
 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

issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-python-2.sh

@@ -105 +105 @@
 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

issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-python-3.sh

@@ -105 +105 @@
 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

issm/trunk-jpl/packagers/mac/package-issm-mac-binaries-matlab.sh

@@ -109 +109 @@
 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 +126 @@
 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

issm/trunk-jpl/packagers/mac/package-issm-mac-binaries-python-2.sh

@@ -101 +101 @@
 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 +118 @@
 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

issm/trunk-jpl/packagers/mac/package-issm-mac-binaries-python-3.sh

@@ -101 +101 @@
 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 +118 @@
 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

issm/trunk-jpl/src/m/coordsystems/gmtmaskparallel.m

@@ -4 +4 @@
 %   Usage:
 %      mask.ocean = gmtmaskparallel(md.mesh.lat,md.mesh.long,8);
+%
+%   TODO:
+%   - Remove hardcoded paths and instead find paths dynamically
 %
 

issm/trunk-jpl/src/m/mesh/planet/gmsh/gmshplanet.m

@@ -23 +23 @@
                 % need to do a bit more to find the Gmsh executable
                 [filepath,name,ext]=fileparts(which('gmsh.'));
-                setenv('PATH',[filepath ':' getenv('PATH')])
+                setenv('PATH',[filepath ':' getenv('PATH')]);
                 [s,r]=system(['gmsh -info 2>&1 | command grep ''Version'' | sed -e ''s/Version[[:blank:]]*:[[:blank:]]//'' | cut -d ''.'' -f1']);
                 if s~=0,

issm/trunk-jpl/src/m/modules/CoordTransform.m

@@ -34 +34 @@
 % the 'PROJ_LIB' environment variable so that the PROJ binary can find the 
 % assets it needs
-if isdir('share/proj')
+if isdir(what('share/proj').path)
         setenv('PROJ_LIB', what('share/proj').path);
 end