Hi, First, make sure you can run a normal single-replica simulation with MPI on this machine, so that you know you have the mechanics right. Follow the cluster's documentation for setting up the scripts and calling MPI. I suspect your problem starts here, perhaps with having a suitable working directory to which to write your output files.
Next, be aware that locality is very important for the cores that participate in a single simulation. It's not enough to choose five cores per replica and deduce that 28 nodes can give enough total cores. Each replica should be assigned cores within the same node (or lose lots of performance), so you will have to do some arithmetic to choose how many replicas per node are suitable to fit all of the cores of those replicas within a node. The best choice for the number of replicas will depend on the number of cores per node. Mark On Sun., 9 Feb. 2020, 10:39 Mohammad Madani, <mohammad.mad...@uconn.edu> wrote: > Dear all users > I want to run a REMD simulation on the stampede2 cluster. > I have 376 replicas. when I run the simulation on 28 nodes and 1880 mpi > task ( 5core per replica) I get the error. > > [proxy:0:0...@c403-004.stampede2.tacc.utexas.edu] HYDU_create_process > (../../utils/launch/launch.c:825): execvp error on file traj.trr (No such > file or directory) > > I do not know what is the problem. > > Could you please help me? > > this is my bash script file: > #!/bin/bash > #SBATCH -J myjob > #SBATCH -o myjob.%j.out > #SBATCH -e myjob.%j.err > > #SBATCH --mail-user=mohammad.mad...@uconn.edu > #SBATCH --mail-type=ALL > #SBATCH -A TG-MCB180008 > > #SBATCH -p normal > #SBATCH -N 28 > #SBATCH -n 1880 > #SBATCH -t 48:00:00 > > module load gromacs/2019.4 > > module load intel/18.0.2 > > module load impi/18.0.2 > module mvapich2/2.3.1 > ibrun /opt/apps/intel18/impi/18.0.2/gromacs/2019.4/bin/mdrun_mpi -s -o > traj.trr -c nvt.gro -e ener.edr -g md.log -replex 500 -multidir equil0 > equil1 ..... equil375 > > Many thanks > > > [image: Mailtrack] > < > https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&; > > > Sender > notified by > Mailtrack > < > https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&; > > > 02/09/20, > 04:38:01 AM > -- > 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.
