[gmx-users] remd error

[Szilárd Páll]

This is an MPI / job scheduler error: you are requesting 2 nodes with
20 processes per node (=40 total), but starting 80 ranks.
--
Szilárd

On Thu, Jul 18, 2019 at 8:33 AM Bratin Kumar Das
<177cy500.bratin at nitk.edu.in> wrote:
>
> Hi,
>    I am running remd simulation in gromacs-2016.5. After generating the
> multiple .tpr file in each directory by the following command
> *for i in {0..7}; do cd equil$i; gmx grompp -f equil${i}.mdp -c em.gro -p
> topol.top -o remd$i.tpr -maxwarn 1; cd ..; done*
> I run *mpirun -np 80 gmx_mpi mdrun -s remd.tpr -multi 8 -replex 1000
> -reseed 175320 -deffnm remd_equil*
> It is giving the following error....
> There are not enough slots available in the system to satisfy the 40 slots
> that were requested by the application:
>   gmx_mpi
>
> Either request fewer slots for your application, or make more slots
> available
> for use.
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> There are not enough slots available in the system to satisfy the 40 slots
> that were requested by the application:
>   gmx_mpi
>
> Either request fewer slots for your application, or make more slots
> available
> for use.
> --------------------------------------------------------------------------
> I am not understanding the error. Any suggestion will be highly
> appriciated. The mdp file and the qsub.sh file is attached below
>
> qsub.sh.......................................
> #! /bin/bash
> #PBS -V
> #PBS -l nodes=2:ppn=20
> #PBS -l walltime=48:00:00
> #PBS -N mdrun-serial
> #PBS -j oe
> #PBS -o output.log
> #PBS -e error.log
> #cd /home/bratin/Downloads/GROMACS/Gromacs_fibril
> cd $PBS_O_WORKDIR
> module load openmpi3.0.0
> module load gromacs-2016.5
> NP='cat $PBS_NODEFILE | wc -1'
> # mpirun --machinefile $PBS_PBS_NODEFILE -np $NP 'which gmx_mpi' mdrun -v
> -s nvt.tpr -deffnm nvt
> #/apps/gromacs-2016.5/bin/mpirun -np 8 gmx_mpi mdrun -v -s remd.tpr -multi
> 8 -replex 1000 -deffnm remd_out
> for i in {0..7}; do cd equil$i; gmx grompp -f equil${i}.mdp -c em.gro -r
> em.gro -p topol.top -o remd$i.tpr -maxwarn 1; cd ..; done
>
> for i in {0..7}; do cd equil${i}; mpirun -np 40 gmx_mpi mdrun -v -s
> remd.tpr -multi 8 -replex 1000 -deffnm remd$i_out ; cd ..; done
> --
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