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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