Hi Szilard, Thank you for your reply. I rectified as you said. For trial purpose i took 8 nodes or 16 nodes... (-np 8) to text whether it is running or not. I gave the following command to run remd *mpirun -np 8 gmx_mpi_d mdrun -v -multi 8 -replex 1000 -deffnm remd* After giving the command it is giving following error Program: gmx mdrun, version 2018.4 Source file: src/gromacs/utility/futil.cpp (line 514) MPI rank: 0 (out of 32)
File input/output error: remd0.tpr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I am not able to understand why it is coming On Thu 25 Jul, 2019, 2:31 PM Szilárd Páll, <pall.szil...@gmail.com> wrote: > 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.bra...@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 > > -- > > 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? 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.