[gmx-users] mpirun problem

Szilárd Páll pall.szilard at gmail.com
Tue Nov 20 14:15:29 CET 2018


the most likely issue is that your GROMACS installation is not configured
for the correct architecture; e.g. if the compute or login node that the
cmake configure/compilation was done on is newer than the one that's
running on, mdrun will try to issue instructions that are not supported by
the CPU (e.g. an AVX512 introduced on the Skylake architecture on an older
CPU that only supports AVX2).


On Tue, Nov 20, 2018 at 6:34 AM Prabir Khatua <prabir07chem at gmail.com>

> Dear all,
> I am getting a problem with mpirun while I am trying to run the simulation
> using Gromacs.2018.4. However, it seems to work perfectly fine with the
> lower version of gromacs. The following is the error that I am receiving
> after the run:
> mpirun noticed that process rank 0 with PID 23603 on node c475 exited on
> signal 4 (Illegal instruction)
> I have used the following line for the make command.
> /home/prabir/SOFTWARE/CMAKE/cmake-3.11.4/bin/cmake ..
> -DGMX_GPU=off
> After the installation using above make command followed by make and make
> install, I can see the gmx_mpi executable in two directories i.e.,
> /home/prabir/SOFTWARE/GROMACS/CPU/SINGLE/gromacs-2018.4/bin and
> /home/prabir/SOFTWARE/GROMACS/CPU/SINGLE/gromacs-2018.4/build/bin.
> I am a bit confused which executable to be used. I am using the executable
> that is present in
> /home/prabir/SOFTWARE/GROMACS/CPU/SINGLE/gromacs-2018.4/bin. I am wondering
> whether the problem is arising due to the wrong path although I tried both
> the one and result remain the same.  It would be helpful, if someone helps
> me in fixing the problem.
> Thanks
> Prabir
> *Prabir Khatua*
> *Postdoctoral Research Associate*
> *Department of Chemistry & Biochemistry*
> *University of Oklahoma*
> *Norman, Oklahoma 73019*
> *U. S. A.*
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