[gmx-users] mdrun terminated with errors with gromacs 5.1 in parallel

Mark Abraham mark.j.abraham at gmail.com
Wed May 25 12:04:45 CEST 2016


The command

/app/setups/gromacs-5.1.1/build/bin/gmx mdrun mpi

isn't what you used to start the simulation - it couldn't work. Please copy
and paste actual things, and do also check out the advice in the install
guide about how to get access to installed versions of GROMACS by source

Investigate that checkpoint file, e.g. ls -l. If you ran the first
simulation as root and now with your normal user, then things will not be
allowed... (don't use root for anything except make install).

For the second part, make sure your MPI system is working, e.g. by running
some other MPI test program. If there's a GROMACS problem, then you'll have
to look elsewhere in the output files to understand where it starts.


On Wed, May 25, 2016 at 10:30 AM Antara mazumdar <antara.mazumdar at igib.in>

> Dear Gromacs users,
>    I was trying to do equilibration of a mixed lipid vesicle using gromacs
> 5.1 in parallel.
> My pbs script file details for this is the following :
> /home/lipi/openmpi164/bin/mpirun -np 48
> /app/setups/gromacs-5.1.1/build/bin/gmx mdrun mpi -deffnm
> step6.2_equilibration -rdd 1.8 > test.dat
> However, the mdrun is terminated with the following two errors.
> *1)Cannot rename checkpoint file; maybe you are out of disk space?*
> i have checked the disk space, it still has terabytes of space left to be
> used. The folder where i am running it is hardly 45 MB.
> *2)mpirun noticed that process rank 10 with PID 62690 on node cn0013 exited
> on signal 11 (Segmentation fault).*
> Can anyone suggest me how to resolve it?
> Kind Regards,
> Antara
> --
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