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 ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.