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Try to handle OS where hdf5/netcdf can be installed to lib64 instead of lib #1163

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Merged
drroe merged 2 commits into from
Feb 20, 2026
Merged

Try to handle OS where hdf5/netcdf can be installed to lib64 instead of lib #1163

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8ef043c
Try to handle cases where lib64 may be present instead of lib
drroe Feb 20, 2026
314f9b8
Try to handle netcdf lib64 as well
drroe Feb 20, 2026
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32 changes: 24 additions & 8 deletions configure
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Original file line number Diff line number Diff line change
Expand Up @@ -127,6 +127,7 @@ REBUILDOPT='' # Can be set to --rebuild and passed to get_library.sh
BUILDTESTOPT='silent' # Set to blank to avoid asking about building libraries
INSTALL_DAT='install_dat' # Target for installing data directory
SPECIFIED_LIB_DIR='' # Specified library directory
LIBDIR='lib' # Set by SetLibDir() to lib or lib64
#CPPTRAJSRC='' # CPPTRAJ source directory
COMPERR='cpptrajcfg.compile.err'
COMPOUT='cpptrajcfg.compile.out'
Expand Down Expand Up @@ -425,6 +426,17 @@ WrnMsg() {
>&2 echo "Warning: $*"
}

#-------------------------------------------------------------------------------
# SetLibDir <prefix> <lib>
# Search for <prefix>/lib64/<lib> and set LIBDIR to lib64 if found.
SetLibDir() {
LIBDIR='lib'
checklibfile="$1/lib64/$2"
if [ -f "$checklibfile" ] ; then
LIBDIR='lib64'
fi
}

#-------------------------------------------------------------------------------
# Check for '--with' and '-no' library keys.
CheckLibraryKeys() {
Expand Down Expand Up @@ -686,17 +698,19 @@ EOF
nc_requires_hdf5_flags=0
lhdf5_hl='-lhdf5_hl'
lhdf5='-lhdf5'
SetLibDir "${LIB_HOME[$LHDF5]}" "libhdf5_hl.a"
if [ ! -z "${LIB_HOME[$LHDF5]}" ] ; then
if [ -f "${LIB_HOME[$LHDF5]}/lib/libhdf5_hl.a" ] ; then
lhdf5_hl=${LIB_HOME[$LHDF5]}/lib/libhdf5_hl.a
if [ -f "${LIB_HOME[$LHDF5]}/$LIBDIR/libhdf5_hl.a" ] ; then
lhdf5_hl=${LIB_HOME[$LHDF5]}/$LIBDIR/libhdf5_hl.a
fi
if [ -f "${LIB_HOME[$LHDF5]}/lib/libhdf5.a" ] ; then
lhdf5=${LIB_HOME[$LHDF5]}/lib/libhdf5.a
if [ -f "${LIB_HOME[$LHDF5]}/$LIBDIR/libhdf5.a" ] ; then
lhdf5=${LIB_HOME[$LHDF5]}/$LIBDIR/libhdf5.a
fi
fi
if [ "${LIB_STAT[$LNETCDF]}" = 'specified' ] ; then
export LD_LIBRARY_PATH="${LIB_HOME[$LNETCDF]}/lib:$LD_LIBRARY_PATH"
if [ ! -f "${LIB_HOME[$LNETCDF]}/lib/libnetcdf.so" -a -f "${LIB_HOME[$LNETCDF]}/lib/libnetcdf.a" ] ; then
SetLibDir "${LIB_HOME[$LNETCDF]}" "libnetcdf.a"
if [ ! -f "${LIB_HOME[$LNETCDF]}/$LIBDIR/libnetcdf.so" -a -f "${LIB_HOME[$LNETCDF]}/$LIBDIR/libnetcdf.a" ] ; then
#echo "DEBUG: Only static NetCDF library is present."
nc_requires_hdf5_flags=1
hdf5_flags="$lhdf5_hl $lhdf5 -ldl ${LIB_FLAG[$LZIP]}"
Expand Down Expand Up @@ -738,9 +752,10 @@ EOF
if [ $? -ne 0 ] ; then
if [ "${LIB_STAT[$LHDF5]}" = 'enabled' ] ; then
# See if there is already a version of HDF5 in CPPTRAJHOME
SetLibDir "$CPPTRAJHOME" "libhdf5_hl.a"
LIB_STAT[$LHDF5]='specified'
LIB_HOME[$LHDF5]=$CPPTRAJHOME
LIB_FLAG[$LHDF5]="$CPPTRAJHOME/lib/libhdf5_hl.a $CPPTRAJHOME/lib/${LIB_STTC[$LHDF5]} -ldl ${LIB_FLAG[$LZIP]}"
LIB_FLAG[$LHDF5]="$CPPTRAJHOME/$LIBDIR/libhdf5_hl.a $CPPTRAJHOME/$LIBDIR/${LIB_STTC[$LHDF5]} -ldl ${LIB_FLAG[$LZIP]}"
LIB_INCL[$LHDF5]="-I$CPPTRAJHOME/include"
TestProgram $BUILDTESTOPT " Checking for bundled HDF5" "$CXX" "$CXXFLAGS ${LIB_INCL[$LHDF5]}" testp.cpp "${LIB_FLAG[$LHDF5]}"
if [ $? -ne 0 ] ; then
Expand Down Expand Up @@ -784,11 +799,12 @@ EOF
rebuild_netcdf='--rebuild'
fi
if [ $check_netcdf -ne 0 -o "${LIB_MAKE[$LNETCDF]}" == 'yes' ] ; then
SetLibDir "$CPPTRAJHOME" "${LIB_STTC[$LNETCDF]}"
if [ "${LIB_STAT[$LNETCDF]}" = 'enabled' ] ; then
# See if there is already a version of NetCDF in CPPTRAJHOME
LIB_STAT[$LNETCDF]='specified'
LIB_HOME[$LNETCDF]=$CPPTRAJHOME
LIB_FLAG[$LNETCDF]=$CPPTRAJHOME/lib/${LIB_STTC[$LNETCDF]}
LIB_FLAG[$LNETCDF]=$CPPTRAJHOME/$LIBDIR/${LIB_STTC[$LNETCDF]}
LIB_INCL[$LNETCDF]="-I$CPPTRAJHOME/include"
if [ "${LIB_STAT[$LHDF5]}" != 'off' ] ; then
# Netcdf needs to know where hdf5 is
Expand All @@ -809,7 +825,7 @@ EOF
echo "Overriding MAKE_COMMAND with 'make -j1' to avoid NetCDF4/HDF5 race conditions."
fi
PREFIX=$CPPTRAJHOME CC=$CC CFLAGS=$CFLAGS LIBNAME='netcdf' MAKE_COMMAND='make -j1' \
CPPFLAGS=${LIB_INCL[$LHDF5]} LDFLAGS="-L$CPPTRAJHOME/lib" \
CPPFLAGS=${LIB_INCL[$LHDF5]} LDFLAGS="-L$CPPTRAJHOME/$LIBDIR" \
SRCDIR=$NETCDF_SRCDIR SRCTAR=$NETCDF_SRCTAR URL=$NETCDF_URL ./get_library.sh $rebuild_netcdf $NETCDF4_OPTS
netcdferr=$?
else
Expand Down