Hi ALL, I am trying to simulate a membrane protein system using CHARMM36 FF on GROAMCS4.5.5 on a parallel cluster running on MPI. The system consists of arounf 1,17,000 atoms. The job runs fine on 5 nodes (5X12=120 cores) using mpirun and gives proper output. But whenever I try to submit it on more than 5 nodes, the job gets killed with the following error:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- starting mdrun 'Protein' 50000000 steps, 100000.0 ps. NOTE: Turning on dynamic load balancing Fatal error in MPI_Sendrecv: Other MPI error Fatal error in MPI_Sendrecv: Other MPI error Fatal error in MPI_Sendrecv: Other MPI error ===================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 256 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES ===================================================================================== [proxy:0:0@cn034] HYD_pmcd_pmip_control_cmd_cb (./pm/pmiserv/pmip_cb.c:906): assert (!closed) failed [proxy:0:0@cn034] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:77): callback returned error status [proxy:0:0@cn034] main (./pm/pmiserv/pmip.c:214): demux engine error waiting for event . . . ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Why is this happening? Is it related to DD and PME? How to solve it? Any suggestion is welcome. Sorry for re-posting. Thanks and regards, Anirban
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