Molcas Forum

apfaulkn

Member

Registered: 2023-08-06

Posts: 2

[SOLVED] Molcas 8.6 in Parallel with OpenMPI 1.8.4 (GCC 4.8.2)

Molcas 8.6 was purchased for me by my PI 10 days ago. I have been trying to install the program to run in parallel on a Linux HPC cluster ever since then and it has not worked. I followed the instructions given in the email carefully and each time I initiate the install.sh script, all installations fail (86_serial, 86_parallel, etc...). The prebuilt version of the software does not seem to run in parallel even with the correct RUNBINARY variable (though it does seem to work in serial); here is an example of what the .log files say when I submit the job with a script that should call for the use of a parallel run:

                                   only a single process is used
                       available to each process: 32 GB of memory, 1 thread?
                                            pid: 190147

The result of running install.sh yields the same error in the same place for all installations:

cd src/alaska && /usr/bin/gmake
gmake[1]: Entering directory `/usr/local/usrapps/castellanogrp/molcas/src/alaska'
/usr/local/apps/openmpi/1.8.4-gcc4.8.2/bin/mpifort -o ../../bin/alaska.exe -pthread -I/usr/local/apps/openmpi/1.8.4-gcc4.8.2/lib -L/usr/local/lsf/8.3/linux2.6-glibc2.3-x86_64/lib -Wl,-rpath -Wl,/usr/local/lsf/8.3/linux2.6-glibc2.3-x86_64/lib -Wl,-rpath -Wl,/usr/local/apps/openmpi/1.8.4-gcc4.8.2/lib -Wl,--enable-new-dtags -L/usr/local/apps/openmpi/1.8.4-gcc4.8.2/lib -lmpi_usempi -lmpi_mpifh -lmpi -static-libgfortran main.o -Wl,--start-group -L../../lib -lalaska -L../../lib -lalaska_util -lamfi_util -laniso_util -lblas_m_util -lcasvb_util -lccsd_util -lccsort_util -lcct3_util -lcholesky_util -ldft_util -ldga_util -ldkh_old_util -ldkh_util -lembedding_util -lespf_util -lfaiemp_util -lfim_util -lfmm_util -lfock_util -lga2_util -lga_util -lgateway_util -lgrid_it_util -lgrid_util -lguessorb_util -lhyper_util -linput_util -lintegral_util -lio2_util -lio_util -lkriging_util -llapack_m_util -llibmsym_util -llinalg_util -llocalisation_util -lloprop_util -llucia_util -lmisc_util -lmknemo_util -lmma_util -lmolcas_ci_util -lmsym_util -lnq_util -loneint_util -lpcm_util -lpeekpoke_util -lppint_util -lproperty_util -lquadpack_util -lquater_util -lrestart_util -lri_util -lrunfile_util -lrys_util -lslapaf_util -lsort_util -lsystem_util -ltransform_util -lxml_util -lModules  -Wl,--end-group -Wl,--start-group /opt/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_gf_ilp64.a /opt/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_sequential.a /opt/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lm -ldl
/usr/bin/ld: cannot find -lgfortran
/usr/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
gmake[1]: *** [../../bin/alaska.exe] Error 1
gmake[1]: Leaving directory `/usr/local/usrapps/castellanogrp/molcas/src/alaska'
make: *** [src/alaska] Error 2

I have read the installation guide so many times and searched high and low for answers on the forum and other websites. I would really appreciate guidance on what could be causing this issue, as myself and those who work at the HPC center at my university are stumped for answers. I really do not want to waste my PI's money, as only running the program in serial is not feasible for the systems we study. Any help would be very much appreciated!!! I figured I would try asking the forum before I contact the developers directly.

Last edited by apfaulkn (2023-09-21 16:11:32)

valera

Administrator

Registered: 2015-11-03

Posts: 124

Re: [SOLVED] Molcas 8.6 in Parallel with OpenMPI 1.8.4 (GCC 4.8.2)

Compilation with static library has some advantages and some performance gain.
However, if the static library libgfortran.a is not available for your system, it is possible to remove -static-libgfortran from LDFLAGS in cfg/gnu.comp