[gmx-users] remd error

[Bratin Kumar Das]

Thank you

On Mon 29 Jul, 2019, 6:45 PM Justin Lemkul, <jalemkul at vt.edu> wrote:

>
>
> On 7/29/19 7:55 AM, Bratin Kumar Das wrote:
> > 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
>
> The error means the input file (remd0.tpr) does not exist in the working
> directory.
>
> -Justin
>
> >
> > On Thu 25 Jul, 2019, 2:31 PM Szilárd Páll, <pall.szilard at 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.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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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
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>
> Virginia Tech Department of Biochemistry
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