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module purge
module load intel/intelParallelStudio2019
module load library/xz/5.2.4
module load library/hdf5/5-1.10.5-intel
module load library/netcdf/netcdf-fortran/4.5.2-intel
module load library/netcdf/netcdf-cxx/4.3.1-intel
module load library/netcdf/netcdf-c/4.7.3-intel
module load mpi/mpich/3.3.2-intel
module list
Currently Loaded Modulefiles:
1) intel/intelParallelStudio2019 4) library/netcdf/netcdf-fortran/4.5.2-intel 7) mpi/mpich/3.3.2-intel
2) library/xz/5.2.4 5) library/netcdf/netcdf-cxx/4.3.1-intel
3) library/hdf5/5-1.10.5-intel 6) library/netcdf/netcdf-c/4.7.3-intel
cd /sw/Delft3D/62441/src/Delft3D_newversion/Delft3D_Source_62441/src.intel
sh autogen.sh 2>&1 | tee autogenLogs-intel.txt
./configure --prefix=/sw/Delft3D/62441intel 2>&1 | tee configureLogs-intel.txt
cd /sw/Delft3D/62441/src/Delft3D_newversion/Delft3D_Source_62441/src.intel/scripts_lgpl/linux
chmod +x *
cd /sw/Delft3D/62441/src/Delft3D_newversion/Delft3D_Source_62441/src.intel
#Perform FIX 1:
# You may skip FIX 2 as it is done and no longer needed:
#Perform FIX 3
make 2>&1 | tee makeLogs-intel.txt
make install 2>&1 | tee makeInstallLogs.txt
Some of the fixes:
==================
FIX 1:
=====
cd /sw/Delft3D/62441/src/Delft3D_newversion/Delft3D_Source_62441/src.intel
sh fixPTHread.sh
........Notes and Reference.........................
cat fixPTHread.sh
#Reference#https://lists.gnu.org/archive/html/emacs-devel/2019-05/msg00032.html
/bin/ld: //usr/lib64/libpthread.so.0: error adding symbols: DSO
missing from command line
collect2: error: ld returned 1 exit status
On Red Hat and Fedora I believe this is because of `-lrt`. I patch the
makefiles so '-lrt' becomes '-;rt -lpthread'. I do so (1) after
unpacking the tarball; and (2) after configure. It usually sidesteps
this error.
for file in $(find "$PWD" -iname 'Makefile')
do
echo "patching $file"
sed -e 's|-lrt|-lrt -lpthread|g' "$file" > "$file.fixed"
mv "$file.fixed" "$file"
touch -t 19700101000020912101610 "$file"
done
.................................
>>>>>>>>>>>>>>>>>>
FIX 2: Only needs to be done once.
======
mkdir /sw/intel/ps/2019up5/intelpython3/intel64/
ln -s /sw/intel/ps/2019up5/intelpython3/include/ /sw/intel/ps/2019up5/intelpython3/intel64/include
FIX 3: Manually compile two binaries. piece.f and concat.f
======
cd /sw/Delft3D/62441/src/Delft3D_newversion/Delft3D_Source_62441/src.intel/engines_gpl/waq/packages/waq_utils_f/src/interact
I had to do this manually:
/sw/Delft3D/62441/src/Delft3D_newversion/Delft3D_Source_62441/src.intel/libtool --tag=F77 --mode=compile mpif77 -DWITH_DELFTONLINE -I/sw/mpi/mpich/3.3.2-intel/include:-I/sw/library/netcdf/NetCDF-C/4.7.3-intel/include:-I/sw/library/netcdf/netcdf-cxx/4-4.3.1-intel/include:-I/sw/library/netcdf/NetCDF-Fortran/4.5.2-intel/include:-I/sw/library/hdf5/5-1.10.5-intel/include:-I/sw/library/xz/5.2.4/include -c -o piece.lo piece.f
/sw/Delft3D/62441/src/Delft3D_newversion/Delft3D_Source_62441/src.intel/libtool --tag=F77 --mode=compile mpif77 -DWITH_DELFTONLINE -I/sw/mpi/mpich/3.3.2-intel/include:-I/sw/library/netcdf/NetCDF-C/4.7.3-intel/include:-I/sw/library/netcdf/netcdf-cxx/4-4.3.1-intel/include:-I/sw/library/netcdf/NetCDF-Fortran/4.5.2-intel/include:-I/sw/library/hdf5/5-1.10.5-intel/include:-I/sw/library/xz/5.2.4/include -c -o concat.lo concat.f
mpif77 -DWITH_DELFTONLINE -I/sw/mpi/mpich/3.3.2-intel/include:-I/sw/library/netcdf/NetCDF-C/4.7.3-intel/include:-I/sw/library/netcdf/netcdf-cxx/4-4.3.1-intel/include:-I/sw/library/netcdf/NetCDF-Fortran/4.5.2-intel/include:-I/sw/library/hdf5/5-1.10.5-intel/include:-I/sw/library/xz/5.2.4/include -frecursive -c concat.f -fPIC -o
>>>>>>>>>>>>>>>>>>>>>>>
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