Hello everyone,
I am having trouble installing FreeFEM + PETSc on a HPC cluster. Precisely, the installation seems OK at first glance, and everything runs smoothly when I run the codes on one node; however, when I try to run on multiple nodes, the code just stops randomly, similarly to a previously problem report.
First, I tried the installation with the following modules:
module load git/2.39.1
module load intel/2022.1.2
module load openmpi/5.0.3
With this, the installation is successful, but the program stops without a message on multiple nodes.
Then, as suggested in a previous post, I tried to switch to the only intel MPI version which was the following: module load impi/2021.5.1
.
Then, the PETSc compilation was successful, while the compilation FreeFEM failed with the following message:
mv -f $depbase.Tpo $depbase.Po
depbase=`echo ../lglib/lg.tab.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
mpicxx -DHAVE_CONFIG_H -I. -I../.. -DPARALLELE -I./../fflib -I./../Graphics -I./../femlib -I./../bamglib/ -I"/sw/pkgs/arc/intel/2022.1.2/mpi/2021.5.1/include" -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker -Xlinker -rpath -Xlinker -Xlinker --enable-new-dtags -I/home/andrasz/FFinstall/petsc/arch-FreeFem/include/suitesparse -I/home/andrasz/FFinstall/petsc/arch-FreeFem/include -I./../../3rdparty/include/BemTool/ -I./../../3rdparty/boost/include -I../../plugin/mpi -DPARALLELE -DHAVE_ZLIB -g -DNDEBUG -O3 -mmmx -mavx2 -mavx -msse4.2 -msse2 -msse -std=gnu++14 -DBAMG_LONG_LONG -DNCHECKPTR -fPIC -MT ../lglib/lg.tab.o -MD -MP -MF $depbase.Tpo -c -o ../lglib/lg.tab.o ../lglib/lg.tab.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo compositeFESpace.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
mpicxx -DHAVE_CONFIG_H -I. -I../.. -DPARALLELE -I./../fflib -I./../Graphics -I./../femlib -I./../bamglib/ -I"/sw/pkgs/arc/intel/2022.1.2/mpi/2021.5.1/include" -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker -Xlinker -rpath -Xlinker -Xlinker --enable-new-dtags -I/home/andrasz/FFinstall/petsc/arch-FreeFem/include/suitesparse -I/home/andrasz/FFinstall/petsc/arch-FreeFem/include -I./../../3rdparty/include/BemTool/ -I./../../3rdparty/boost/include -I../../plugin/mpi -DPARALLELE -DHAVE_ZLIB -g -DNDEBUG -O3 -mmmx -mavx2 -mavx -msse4.2 -msse2 -msse -std=gnu++14 -DBAMG_LONG_LONG -DNCHECKPTR -fPIC -MT compositeFESpace.o -MD -MP -MF $depbase.Tpo -c -o compositeFESpace.o compositeFESpace.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo parallelempi.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
mpicxx -DHAVE_CONFIG_H -I. -I../.. -DPARALLELE -I./../fflib -I./../Graphics -I./../femlib -I./../bamglib/ -I"/sw/pkgs/arc/intel/2022.1.2/mpi/2021.5.1/include" -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker -Xlinker -rpath -Xlinker -Xlinker --enable-new-dtags -I/home/andrasz/FFinstall/petsc/arch-FreeFem/include/suitesparse -I/home/andrasz/FFinstall/petsc/arch-FreeFem/include -I./../../3rdparty/include/BemTool/ -I./../../3rdparty/boost/include -I../../plugin/mpi -DPARALLELE -DHAVE_ZLIB -g -DNDEBUG -O3 -mmmx -mavx2 -mavx -msse4.2 -msse2 -msse -std=gnu++14 -DBAMG_LONG_LONG -DNCHECKPTR -fPIC -MT parallelempi.o -MD -MP -MF $depbase.Tpo -c -o parallelempi.o parallelempi.cpp &&\
mv -f $depbase.Tpo $depbase.Po
g++: error: unrecognized command line option ‘-rpath’
make[3]: *** [Makefile:710: ffapi.o] Error 1
make[3]: *** Waiting for unfinished jobs....
g++: error: unrecognized command line option ‘-rpath’
g++: error: unrecognized command line option ‘-rpath’
g++: error: unrecognized command line option ‘-rpath’
g++: error: unrecognized command line option ‘-rpath’
make[3]: *** [Makefile:710: ../lglib/mymain.o] Error 1
make[3]: *** [Makefile:710: ../lglib/lg.tab.o] Error 1
make[3]: *** [Makefile:710: parallelempi.o] Error 1
make[3]: *** [Makefile:710: compositeFESpace.o] Error 1
make[3]: Leaving directory '/home/andrasz/FFinstall/FreeFem-sources/src/mpi'
make[2]: *** [Makefile:554: all-recursive] Error 1
make[2]: Leaving directory '/home/andrasz/FFinstall/FreeFem-sources/src'
make[1]: *** [Makefile:896: all-recursive] Error 1
make[1]: Leaving directory '/home/andrasz/FFinstall/FreeFem-sources'
I attach the config.logs of both cases. Any help with finding the issue is much appreciated.
config_intel_openmpi.zip (643.0 KB)
config_intel_intelmpi.zip (631.5 KB)