Thank you for your email sir. On Wed, Sep 4, 2019 at 2:42 PM Mark Abraham <mark.j.abra...@gmail.com> wrote:
> Hi, > > On Wed, 4 Sep 2019 at 10:47, Bratin Kumar Das <177cy500.bra...@nitk.edu.in > > > wrote: > > > Respected Mark Abraham, > > The command-line and the job > > submission script is given below > > > > #!/bin/bash > > #SBATCH -n 130 # Number of cores > > > > Per the docs, this is a guide to sbatch about how many (MPI) tasks you want > to run. It's not a core request. > > #SBATCH -N 5 # no of nodes > > > > This requires a certain number of nodes. So to implement both your > instructions, MPI has to start 26 tasks per node. That would make sense if > you had nodes with a multiple 26 cores. My guess is that your nodes have a > multiple of 16 cores, based on the error message. MPI saw that you asked to > allocate more tasks on cores than available cores, and decided not to set a > number of OpenMP threads per MPI task, so that fell back on a default, > which produced 16, which GROMACS can see doesn't make sense. > > If you want to use -N and -n, then you need to make a choice that makes > sense for the number of cores per node. Easier might be to use -n 130 and > -c 2 to express what I assume is your intent to have 2 cores per MPI task. > Now slurm+MPI can pass that message along properly to OpenMP. > > Your other message about -ntomp can only have come from running gmx_mpi_d > -ntmpi, so just a typo we don't need to worry about further. > > Mark > > #SBATCH -t 0-20:00:00 # Runtime in D-HH:MM > > #SBATCH -p cpu # Partition to submit to > > #SBATCH -o hostname_%j.out # File to which STDOUT will be written > > #SBATCH -e hostname_%j.err # File to which STDERR will be written > > #loading gromacs > > module load gromacs/2018.4 > > #specifying work_dir > > WORKDIR=/home/chm_bratin/GMX_Projects/REMD/4wbu-REMD-inst-clust_1/stage-1 > > > > > > mpirun -np 130 gmx_mpi_d mdrun -v -s remd_nvt_next2.tpr -multidir equil0 > > equil1 equil2 equil3 equil4 equil5 equil6 equil7 equil8 equil9 equil10 > > equil11 equil12 equil13 equil14 equil15 equil16 equil17 equil18 equil19 > > equil20 equil21 equil22 equil23 equil24 equil25 equil26 equil27 equil28 > > equil29 equil30 equil31 equil32 equil33 equil34 equil35 equil36 equil37 > > equil38 equil39 equil40 equil41 equil42 equil43 equil44 equil45 equil46 > > equil47 equil48 equil49 equil50 equil51 equil52 equil53 equil54 equil55 > > equil56 equil57 equil58 equil59 equil60 equil61 equil62 equil63 equil64 > > -deffnm remd_nvt -cpi remd_nvt.cpt -append > > > > On Wed, Sep 4, 2019 at 2:13 PM Mark Abraham <mark.j.abra...@gmail.com> > > wrote: > > > > > Hi, > > > > > > We need to see your command line in order to have a chance of helping. > > > > > > Mark > > > > > > On Wed, 4 Sep 2019 at 05:46, Bratin Kumar Das < > > 177cy500.bra...@nitk.edu.in > > > > > > > wrote: > > > > > > > Dear all, > > > > I am running one REMD simulation with 65 replicas. I am > > using > > > > 130 cores for the simulation. I am getting the following error. > > > > > > > > Fatal error: > > > > Your choice of number of MPI ranks and amount of resources results in > > > using > > > > 16 > > > > OpenMP threads per rank, which is most likely inefficient. The > optimum > > is > > > > usually between 1 and 6 threads per rank. If you want to run with > this > > > > setup, > > > > specify the -ntomp option. But we suggest to change the number of MPI > > > > ranks. > > > > > > > > when I am using -ntomp option ...it is throwing another error > > > > > > > > Fatal error: > > > > Setting the number of thread-MPI ranks is only supported with > > thread-MPI > > > > and > > > > GROMACS was compiled without thread-MPI > > > > > > > > > > > > while GROMACS is compiled with threated-MPI... > > > > > > > > plerase help me in this regard. > > > > -- > > > > 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. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? 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