[gmx-users] Using CPU with GPU

RJ rajiv at kaist.ac.kr
Sat Feb 11 03:08:15 CET 2017

Dear gmx users,Could you suggest me a correct md launch configuration. I am using an University Cluster and would like use :  Nodes 3 (3 * 20) has 60 MPI processes. NVIDIA Tesla K20Xm: ( 2 GPUs ). Kindly suggest the optimal way to get fast md run. I tried as the following bash script but ends with errors:------------------------------------------------------- #!/bin/bash #PBS -A super_star2 #PBS -q checkpt #PBS -l nodes=1:ppn=20:gpus=2 #PBS -l walltime=12:00:00 #PBS -V #PBS -j oe #PBS -N lyzo  # mdrun_d is the MPI version of mdrun.   export EXEC=mdrun_mpi #export WORKDIR=$PBS_O_WORKDIR export NPROCS=`wc -l $PBS_NODEFILE |gawk '//{print $1}'` export DIR=/work/rj/work_file cd $DIR mpirun -machinefile $PBS_NODEFILE -np $NPROCS `which $EXEC` -nb gpu -deffnm bact----------------------------------------------------------------------------------------------------------------------------PBS has allocated the following nodes:qb136qb140qb182A total of 60 processors on 3 nodes allocated--------------------------------------------------------------------------------------------------------Number of hardware threads detected (20) does not match the number reported by OpenMP (1).Consider setting the launch configuration manually!Reading file bact.tpr, VERSION 5.0.7 (single precision)Changing nstlist from 10 to 40, rlist from 1.4 to 1.472Using 60 MPI processesUsing 1 OpenMP thread per MPI process2 GPUs detected on host qb136:  #0: NVIDIA Tesla K20Xm, compute cap.: 3.5, ECC: yes, stat: compatible  #1: NVIDIA Tesla K20Xm, compute cap.: 3.5, ECC: yes, stat: compatible2 GPUs auto-selected for this run.Mapping of GPUs to the 20 PP ranks in this node: #0, #1----------------------------------------------------------------------------------------------------------------------------------------------------------------Program mdrun_mpi, VERSION 5.0.7Source code file: /project/fchen14/gromacs-5.0.7/src/gromacs/gmxlib/gmx_detect_hardware.c, line: 388Fatal error:Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node.mdrun_mpi was started with 20 PP MPI processes per node, but only 2 GPUs were detected.For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors-------------------------------------------------------

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