GROMACS Installation Problem in The Grid Computer

User discussions
1

GROMACS version: 2021.2
GROMACS modification: No

Hello all,

I am new to GROMACS. I wanted to install it on a grid computer servers supported by the government and I’ve done step by step instructions in the following link (The language of the instructions is in Turkish but you may find the commands similar so you may understand the installation pathway): https://docs.truba.gov.tr/how-to-guides/GROMACS/gromacs_install_TRUBA.html#hamsi-gromacs-install

In brief, I’ve installed GROMACS via GNU Compiler and OpenMPI on our cluster. After the installation, I didn’t get any response in my terminal when I typed “gmx_mpi”. I felt like I somehow solved it by sourcing GROMACS via “source /truba/home/username/bin/bin/GMXRC” command. But then, I’ve also encountered another problem typing the same command in my terminal, which is as follows:

gmx_mpi: /lib64/libstdc++.so.6: version CXXABI_1.3.9' not found (required by gmx_mpi) gmx_mpi: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20’ not found (required by /truba/home/username/bin/lib64/libgromacs_mpi.so.6)
gmx_mpi: /lib64/libstdc++.so.6: version CXXABI_1.3.8' not found (required by /truba/home/username/bin/lib64/libgromacs_mpi.so.6) gmx_mpi: /lib64/libstdc++.so.6: version GLIBCXX_3.4.22’ not found (required by /truba/home/username/bin/lib64/libgromacs_mpi.so.6)
gmx_mpi: /lib64/libstdc++.so.6: version CXXABI_1.3.9' not found (required by /truba/home/username/bin/lib64/libgromacs_mpi.so.6) gmx_mpi: /lib64/libstdc++.so.6: version CXXABI_1.3.11’ not found (required by /truba/home/username/bin/lib64/libgromacs_mpi.so.6)
gmx_mpi: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21’ not found (required by /truba/home/username/bin/lib64/libgromacs_mpi.so.6)

Any ideas? I am not sure if I did the right thing by sourcing the GMXRC file. Actually I can successfully use GROMACS in my own computer but I got confused when I try to work with our grid computer.

Are there any missing library files that I need to install? Any help would be appreciated because I need to perform MD simulation on our cluster ASAP :)

2

Any ideas? I am not sure if I did the right thing by sourcing the GMXRC file. Actually I can successfully use GROMACS in my own computer but I got confused when I try to work with our grid computer.

You did the right thing with GMXRC, no worries here.

It seems that you need to load the same (or some of) modules that you used when compiling the code. Probably, module load centos7.9/comp/gcc/7 would be enough.

3

Thank you for your respond, it worked and I got rid of above-mentioned warnings but still I’m unable to run gmx since I faced another problem with the following command:

“gmx_mpi pdb2gmx -f 1mh1.pdb -o 1mh1-p.gro -water spce -inter -ignh”

“Illegal instruction (core dumped)”

I tried to figure this out and made some search on the web but couldn’t get any proper solution.

4

This likely indicates that the compute nodes support different SIMD instruction set than the one you compiled for.

The guide you linked to explicitly says to use -DGMX_SIMD=AVX_512. If that does not work, I suggest trying -DGMX_SIMD=AVX2_256.

5

Thank you for your response, helped me a lot!