Dear Justin: The scripts I used is as follow: ## Set job parameters ## Job Name #BSUB -J OpenMPI
## Queue Name #BSUB -q medium_priority ## Output and Input Errors #BSUB -o job%J.out #BSUB -e job%J.err ## Specify walltime in HH:MM #BSUB -W 60:00 ## 16 Processors per Host #BSUB -R "span[ptile=16]" ## Requesting for 32 cores #BSUB -n 140 # Need to make our own machinefile MACHINEFILE=mymacs.$LSB_JOBID for i in `echo $LSB_HOSTS` do echo $i done > $MACHINEFILE ## load module enviroement module load openmpi-1.6.5-intel-v12.1.5 module load intel-12.1.5 ## Run mpi program cd /gpfs/home/hzhang020/REMD/remdrun/scratch /usr/local/RH6_apps/openmpi-1.6.5-intel-v12.1.5/bin/mpirun --bind-to-core --report-bindings -np 140 -machinefile $MACHINEFILE /usr/local/RH6_apps/gromacs-4.6.2-double-intel/bin/mdrun_mpi_d -s prefix_.tpr -multi 140 -replex 3000 There was not obvious error information, just have the output file size is always 0. After long time, I kill it myself. NOTE: The load imbalance in PME FFT and solve is 384%. For optimal PME load balancing PME grid_x (1728) and grid_y (1728) should be divisible by #PME_nodes_x (2) and PME grid_y (1728) and grid_z (1728) should be divisible by #PME_nodes_y (1) NOTE: The load imbalance in PME FFT and solve is 384%. For optimal PME load balancing PME grid_x (1728) and grid_y (1728) should be divisible by #PME_nodes_x (2) and PME grid_y (1728) and grid_z (1728) should be divisible by #PME_nodes_y (1) -------------------------------------------------------------------------- WARNING: A process refused to die! Host: comp094 PID: 6751 This process may still be running and/or consuming resources. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpirun noticed that process rank 273 with PID 30914 on node comp122 exited on signal 9 (Killed). -------------------------------------------------------------------------- ________________________________________ 发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> 代表 Justin Lemkul <jalem...@vt.edu> 发送时间: 2014年5月22日 10:57 收件人: gmx-us...@gromacs.org 主题: Re: [gmx-users] about exchange replica with replicas 140 On 5/21/14, 10:53 PM, #ZHANG HAIPING# wrote: > Dear gromacs user: > > I have encounter a problem when used HPC(high performance computer) to run > replica exchange. I find that when I used replica over 128, it will not work, > while under 128 , it is ok, even when I used cores much more than 128(several > cores for one replica). The version I used is gromacs-4.6.2-double-intel. > Hope for you help. > You need to provide more information. Specifically, what commands are you issuing? What does "will not work" mean? Is there a specific error you are getting? -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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. -- 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.