[gmx-users] remd error

[Justin Lemkul]

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
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Virginia Tech Department of Biochemistry
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