Recently I have installed gromacs on the master node of my newly installed cluster. As the major requirement of the gromacs is GCC, OpenMPI and gmx_mpi, after compiling everything on the master node, I am able to use the software using GPU. But when I switch to compute node using "ssh", and run the gmx_mpi command, I get an error saying:
gmx_mpigmx_mpi: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by gmx_mpi)gmx_mpi: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by gmx_mpi)gmx_mpi: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /state/partition1/packages/gromacs/gromacs-2020.6_plumed-2.8/bin/../lib64/libgromacs_mpi.so.5)gmx_mpi: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /state/partition1/packages/gromacs/gromacs-2020.6_plumed-2.8/bin/../lib64/libgromacs_mpi.so.5)gmx_mpi: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /state/partition1/packages/gromacs/gromacs-2020.6_plumed-2.8/bin/../lib64/libgromacs_mpi.so.5)gmx_mpi: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.11' not found (required by /state/partition1/packages/gromacs/gromacs-2020.6_plumed-2.8/bin/../lib64/libgromacs_mpi.so.5)gmx_mpi: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /state/partition1/packages/gromacs/gromacs-2020.6_plumed-2.8/bin/../lib64/libgromacs_mpi.so.5)gmx_mpi: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /state/partition1/packages/gromacs/plumed-2.8_install/lib/libplumedKernel.so)gmx_mpi: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /state/partition1/packages/gromacs/plumed-2.8_install/lib/libplumedKernel.so)gmx_mpi: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /state/partition1/packages/gromacs/plumed-2.8_install/lib/libplumedKernel.so)
I understand that the issue is coming because of the linking issue of GCC between master and compute nodes.
The path of gcc on my master node is:
which gcc/usr/local/bin/gcc
The path of gcc on compute node is:
which gcc/usr/bin/gcc
I have been trying to link the GCC but unfortunately, I am not able to do that. Any suggestion on how to do this will really mean a lot. Thanks