On 8/20/19 5:56 PM, Anh Vo wrote:
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.
None of those are GROMACS errors; they are coming from your system
indicating there are problems with the MPI library. Consult your sysadmins.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==
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