[gmx-users] REMD-error

Bratin Kumar Das 177cy500.bratin at nitk.edu.in
Wed Sep 4 12:48:04 CEST 2019


Thank you for your email sir.

On Wed, Sep 4, 2019 at 2:42 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> On Wed, 4 Sep 2019 at 10:47, Bratin Kumar Das <177cy500.bratin at 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.abraham at 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.bratin at 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.
> > > > --
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