Can't run GROMACS on supercomputer cluster

User discussions
1

GROMACS version: 2020.2
GROMACS modification: No
I try to run my simulation on a supercomputer

This is my script

#!/bin/bash -l
#SBATCH -J faza_heksagonalna_trzy_warstwy_symulacja

#SBATCH -N 12 -n 288

###SBATCH --ntasks-per-node=1

#SBATCH -p plgrid-long

#SBATCH -A plgmgdghex

#SBATCH -t 168:00:00

#SBATCH --no-requeue

#SBATCH --mail-type=END

#SBATCH --mail-user=********@doctoral.uj.edu.pl

module load plgrid/tools/openmpi/1.10.1-gcc-5.2.0
module load plgrid/apps/gromacs/2020.2

mpirun -np 288 gmx_mpi mdrun -v -deffnm eq1  &> hex.log

I have a problem, because my simulation don’t want to run. In my log file I see

gmx_mpi: /net/software/local/software/GCC/5.2.0/lib64/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /net/software/local/gromacs/2020.2/bin/../lib64/libgromacs_mpi.so.5)
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
gmx_mpi: /net/software/local/software/GCC/5.2.0/lib64/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by /net/software/local/gromacs/2020.2/bin/../lib64/libgromacs_mpi.so.5)
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[40623,1],240]
  Exit code:    1
--------------------------------------------------------------------------
~

So I think the problem is probably with that
I load these modules from my clusters
module load plgrid/tools/openmpi/1.10.1-gcc-5.2.0
and
module load plgrid/apps/gromacs/2020.2

The second load gromacs, but the first gcc compiler? I think that I choose the wrong gcc compiler, but which I should use, how to know that? I can choose

plgrid/tools/openmpi/1.6.5-gcc-4.9.2
plgrid/tools/openmpi/1.6.5-pgi-15.7
plgrid/tools/openmpi/1.6.5-intel-15.0.2
plgrid/tools/openmpi/1.8.4-gcc-4.9.2
plgrid/tools/openmpi/1.8.4-intel-15.0.2
plgrid/tools/openmpi/1.8.8-intel-18.0.0
plgrid/tools/openmpi/1.10.1-gcc-4.9.2
plgrid/tools/openmpi/1.10.1-gcc-5.2.0
plgrid/tools/openmpi/1.10.1-gcc-5.3.0-i8
plgrid/tools/openmpi/1.10.1-pgi-15.7
plgrid/tools/openmpi/1.10.1-intel-16.0.0-i8
plgrid/tools/openmpi/1.10.1-intel-16.0.1
plgrid/tools/openmpi/1.10.3-intel-18.0.0
plgrid/tools/openmpi/2.0.1-gcc-4.9.2
plgrid/tools/openmpi/2.0.1-intel-15.0.2
plgrid/tools/openmpi/2.0.1-intel-17.0.0
plgrid/tools/openmpi/2.0.2-gcc-4.9.2
plgrid/tools/openmpi/2.1.1-gcc-6.4.0
plgrid/tools/openmpi/2.1.1-intel-15.0.2
plgrid/tools/openmpi/2.1.1-intel-17.0.4
plgrid/tools/openmpi/1.10.1-gcc-4.9.2
plgrid/tools/openmpi/1.10.1-gcc-5.2.0
plgrid/tools/openmpi/1.10.1-gcc-5.3.0-i8
plgrid/tools/openmpi/1.10.1-pgi-15.7
plgrid/tools/openmpi/1.10.1-intel-16.0.0-i8
plgrid/tools/openmpi/1.10.1-intel-16.0.1
plgrid/tools/openmpi/1.10.3-intel-18.0.0
plgrid/tools/openmpi/2.0.1-gcc-4.9.2
plgrid/tools/openmpi/2.0.1-intel-15.0.2
plgrid/tools/openmpi/2.0.1-intel-17.0.0
plgrid/tools/openmpi/2.0.2-gcc-4.9.2
plgrid/tools/openmpi/2.1.1-gcc-6.4.0
plgrid/tools/openmpi/2.1.1-intel-15.0.2
plgrid/tools/openmpi/2.1.1-intel-17.0.4
plgrid/tools/openmpi/2.1.2-intel-17.0.5
plgrid/tools/openmpi/3.0.0-gcc-4.9.2
plgrid/tools/openmpi/3.0.0-intel-18.0.0
plgrid/tools/openmpi/3.1.3-pgi-19.1
plgrid/tools/openmpi/3.1.4-gcc-4.8.5
plgrid/tools/openmpi/4.0-gcc-10.1.0 (cg)
plgrid/tools/openmpi/4.0-intel-19.1.1 (cg)
plgrid/tools/openmpi/4.0.1-gcc-9.1.0
plgrid/tools/openmpi/4.0.1-intel-18.0.0
plgrid/tools/openmpi/4.0.3-gcc-9.3.0 (cg)
plgrid/tools/openmpi/4.0.3-intel-19.1.1 (cg,D)

Which is right and I should load?

2

This is a question better addressed to your system administrator, who can tell you specifically how GROMACS was compiled and what its dependencies are.

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