Index: /issm/trunk-jpl/externalpackages/boost/install-1.7-linux-valgrind.sh =================================================================== --- /issm/trunk-jpl/externalpackages/boost/install-1.7-linux-valgrind.sh (revision 27426) +++ /issm/trunk-jpl/externalpackages/boost/install-1.7-linux-valgrind.sh (revision 27427) @@ -10,5 +10,5 @@ # Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz" +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz" # Unpack source @@ -23,6 +23,6 @@ rm -rf boost_${VER} -# Copy customized source and config files to 'src' directory -cp ./configs/1.73/boost/math/tools/user.hpp ./src/boost/math/tools/ +# Copy customized source and configuration files to 'src' directory +cp ./configs/1.73/boost/math/tools/user.hpp ./src/boost/math/tools # Configure Index: /issm/trunk-jpl/externalpackages/boost/install-1.7-mac-valgrind.sh =================================================================== --- /issm/trunk-jpl/externalpackages/boost/install-1.7-mac-valgrind.sh (revision 27427) +++ /issm/trunk-jpl/externalpackages/boost/install-1.7-mac-valgrind.sh (revision 27427) @@ -0,0 +1,66 @@ +#!/bin/bash +#set -eu # Do not `run set -eu` because it causes some targets to fail + + +## Constants +# +VER="1_73_0" + +PREFIX="${ISSM_DIR}/externalpackages/boost/install" # Set to location where external package should be installed + +## Environment +# +export LDFLAGS="-Wl,-headerpad_max_install_names" + +# Download source +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz" + +# Unpack source +tar -zxvf boost_${VER}.tar.gz + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Move source into 'src' directory +mv boost_${VER}/* src +rm -rf boost_${VER} + +# Copy customized source and configuration files to 'src' directory +cp ./configs/1.73/boost/math/tools/user.hpp ./src/boost/math/tools + +# Configure +cd src +./bootstrap.sh \ + --prefix=${PREFIX} \ + --with-python=python2.7 + +# Modify project config to enable MPI +printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam + +# Compile and install +./b2 install link=shared runtime-link=shared + +# Set install_name for all shared libraries +# +# NOTE: The install_name_tool prints an error message on some installations, +# but this is not a shell error, and it does not seem to affect the +# Boost libraries called by ISSM. For now, we are simply redirecting the +# error to null. +# +# TODO: +# - Modify the source to apply absolute paths to the library ids so that +# patching it after the fact with install_name_tool is not necessary. +# +cd ${PREFIX}/lib +for name in *.dylib; do + 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-jpl/jenkins/pine_island-mac-full-valgrind =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac-full-valgrind (revision 27426) +++ /issm/trunk-jpl/jenkins/pine_island-mac-full-valgrind (revision 27427) @@ -46,9 +46,10 @@ petsc install-3.16-mac.sh gsl install.sh - boost install-1.7-mac.sh + boost install-1.7-mac-valgrind.sh dakota install-6.2-mac.sh curl install-7-mac.sh netcdf install-4.7-parallel.sh proj install-6.sh + sqlite install.sh gdal install-3-python.sh gshhg install.sh Index: /issm/trunk-jpl/jenkins/ross-debian_linux-full-valgrind =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-full-valgrind (revision 27426) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-full-valgrind (revision 27427) @@ -51,4 +51,5 @@ netcdf install-4.7-parallel.sh proj install-6.sh + sqlite install.sh gdal install-3-python.sh gshhg install.sh Index: /issm/trunk-jpl/src/m/classes/toolkits.py =================================================================== --- /issm/trunk-jpl/src/m/classes/toolkits.py (revision 27426) +++ /issm/trunk-jpl/src/m/classes/toolkits.py (revision 27427) @@ -8,15 +8,14 @@ class toolkits(object): - ''' - TOOLKITS class definition + """TOOLKITS class definition - Usage: - self = toolkits() - ''' + Usage: + self = toolkits() + """ def __init__(self): #{{{ - #default toolkits + # Default toolkits if IssmConfig('_HAVE_PETSC_')[0]: - #MUMPS is the default toolkits + # MUMPS is the default toolkits if IssmConfig('_HAVE_MUMPS_')[0]: self.DefaultAnalysis = mumpsoptions() @@ -31,8 +30,8 @@ raise IOError("ToolkitsFile error: need at least Mumps or Gsl to define issm solver type") - #Use same solver for Recovery mode + # Use same solver for Recovery mode self.RecoveryAnalysis = self.DefaultAnalysis - #The other properties are dynamic + # The other properties are dynamic #}}} @@ -50,9 +49,9 @@ # md.toolkits = addoptions(md.toolkits, 'StressbalanceAnalysis') - #Create dynamic property if property does not exist yet + # Create dynamic property if property does not exist yet if not hasattr(self, analysis): setattr(self, analysis, None) - #Add toolkits options to analysis + # Add toolkits options to analysis if len(args) == 1: setattr(self, analysis, args[0]) @@ -62,5 +61,5 @@ def checkconsistency(self, md, solution, analyses): #{{{ - # TODO + # TODO: # - Implement something closer to a switch as in # src/m/classes/toolkits.m? @@ -74,17 +73,14 @@ def ToolkitsFile(self, filename): #{{{ - ''' - TOOLKITSFILE - build toolkits file + """TOOLKITSFILE - build toolkits file - Build a Petsc compatible options file, from the toolkits model - field + return options string. - This file will also be used when the toolkit used is 'issm' instead - of 'petsc'.s + Build a PETSc compatible options file, from the toolkits model field + return options string. + This file will also be used when the toolkit used is 'issm' instead of 'petsc'. - Usage: - ToolkitsFile(toolkits, filename) - ''' + Usage: + ToolkitsFile(toolkits, filename) + """ - #open file for writing + # Open file for writing try: fid = open(filename, 'w') @@ -92,21 +88,21 @@ raise IOError("ToolkitsFile error: could not open {}' for writing due to".format(filename), e) - #write header + # Write header fid.write("%s%s%s\n" % ('%Toolkits options file: ', filename, ' written from Python toolkits array')) - #start writing options + # Start writing options for analysis in list(vars(self).keys()): options = getattr(self, analysis) - #first write analysis: - fid.write("\n+{}\n".format(analysis)) #append a + to recognize it's an analysis enum - #now, write options + # First write analysis + fid.write("\n+{}\n".format(analysis)) # Append a + to recognize it's an analysis enum + # Now, write options for optionname, optionvalue in list(options.items()): if not optionvalue: - #this option has only one argument + # This option has only one argument fid.write("-{}\n".format(optionname)) else: - #option with value. value can be string or scalar + # Option with value. Value can be string or scalar. if isinstance(optionvalue, (bool, int, float)): fid.write("-{} {}\n".format(optionname, optionvalue))