[gmx-users] Error when running pbs files using GROMACS on hpc cluster

[Anh Vo]

Hi everyone,

I have submitted pbs files to run GROMACS on a high performance computing
cluster, but I received error files showing these messages:



"...

 librdmacm: Warning: couldn\'t read ABI version.

 librdmacm: Warning: assuming: 4

 librdmacm: Fatal: unable to open /dev/infiniband/rdma_cm

 librdmacm: Fatal: unable to open /dev/infiniband/rdma_cm ..."


and


"--------------------------------------------------------------------------

mpirun noticed that process rank 28 with PID 0 on node shadow-
0119.hpc.msstate.edu exited on signal 11 (Segmentation fault).

--------------------------------------------------------------------------

40 total processes killed (some possibly by mpirun during cleanup)"


This error happened when I used mpirun to run my jobs on several nodes (10
nodes in this case). When I didn't use mpirun and run with only 1 node,
there is no error produced. The command I used are:


*"gmx grompp -f step7_production_01.mdp -c step6.6_equilibration.gro -n
index.ndx -p topol.top -o step7_1_01.tpr -maxwarn -1*
*mpirun -np 200 gmx_mpi mdrun -v -deffnm step7_1_01"*


Is that mpirun command correct? I'm not sure if those errors is relevant to
using mpirun.  I don't understand what the errors mean, or how should I fix
them?

Please help me with this problem. Thank you very much for sharing your time.


Best regards,

Anh Vo