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

Antara mazumdar antara.mazumdar at igib.in
Wed May 25 10:29:39 CEST 2016

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,

Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040

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