Dear Gromacs users, I am trying to run a script in HPC using 80 CPUs from 4 nodes each with 128gb of memory available. while running the below mdrun for energy minimisation process, I am getting memory allocation issue and the job is being halted. Is there any issue with the way I am utilizing OpenMP and MPI process in the code? What could be possible solutions.
Note while running the code in my workstation, I am not getting any error and the energy minimization is converging quite well. Part of the script given below: *export OMP_NUM_THREADS=4* *srun --ntasks-per-node=5 gmx_mpi mdrun $FLAGS -v -deffnm min_step000 -ntomp 4 >> mdrun.log 2>&1* Error in mdrun.log is as below: *Program gmx mdrun, VERSION 5.1.2* *Source code file: /home/alp514/source/corona2-build/gromacs-5.1.2/src/gromacs/utility/smalloc.c, line: 227* *Fatal error:* *Not enough memory. Failed to realloc 302664 bytes for *f, *f=19367240* *(called from file /home/alp514/source/corona2-build/gromacs-5.1.2/src/gromacs/domdec/domdec.cpp, line 1708)* *For more information and tips for troubleshooting, please check the GROMACS* *website at http://www.gromacs.org/Documentation/Errors <http://www.gromacs.org/Documentation/Errors>* *-------------------------------------------------------* *: Cannot allocate memory* *Halting parallel program gmx mdrun on rank 27 out of 80* *[cli_27]: aborting job:* *application called MPI_Abort(MPI_COMM_WORLD, 1) - process 27* *srun: error: sol-b410: task 27: Exited with exit code 1* *[sol-b411:mpi_rank_47][handle_cqe] Send desc error in msg to 27, wc_opcode=1* *srun: error: sol-b411: task 47: Exited with exit code 252* *[sol-b411:mpi_rank_47][handle_cqe] Msg from 27: wc.status=12, wc.wr_id=0x331ff40, wc.opcode=1, vbuf->phead->type=0 = MPIDI_CH3_PKT_EAGER_SEND* *[sol-b411:mpi_rank_47][handle_cqe] ../mvapich2-2.1/src/mpid/ch3/channels/mrail/src/gen2/ibv_channel_manager.c:587: [] Got completion with error 12, vendor code=0x81, dest rank=27* Thanks in advance, Hoping suggestions on the resolution. *Thanks and regards,* *Joydeep Munshi,* *Graduate Research Assistant,* *Mechanical Engineering and Mechanics,* *Lehigh University* -- 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.