[gmx-users] Re : mdrun errors with gromacs 5.1 in parallel

[Mark Abraham]

Hi,

You need to build an MPI-enabled version of GROMACS, which will default to
being named gmx_mpi. Thus

/home/lipi/openmpi164/bin/mpirun -np 16
/app/setups/gromacs-5.1.1/build/bin/gmx_mpi mdrun -deffnm
step6.2_equilibration -rdd 1.8

Your run is starting 16 serial mdrun, which are then fighting over the same
checkpoint file.

Mark

On Thu, May 26, 2016 at 9:32 AM Antara mazumdar <antara.mazumdar at igib.in>
wrote:

> Dear Users,
>   I was trying to do equilibration of a mixed lipid vesicle using gromacs
> 5.1 in parallel using the below pasted pbs script :
>
>
> #!/bin/tcsh
> #PBS -l walltime=48:00:00
> #PBS -N VES_new_16
> #PBS -q workq
> #PBS -l select=1:ncpus=16:mpiprocs=16
> #PBS -V
>
> # Go to the directory from which you submitted the job
> cd $PBS_O_WORKDIR
>
> #export MPI_DEBUG=all
> #export MPI_IB_RAILS=2
> #export MPI_DSM_DISTRIBUTE=1
> #export MPI_VERBOSE=1
> #export MPI_BUFS_THRESHOLD=1
> #export MPI_BUFS_PER_PROC=1024
> #export OMP_NUM_THREADS=1
> #export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home1/gkpatra/gmp/lib
> module load intel-cluster-studio-2013
>
>
> setenv OMP_NUM_THREADS 1
> /home/lipi/openmpi164/bin/mpirun -np 16
> /app/setups/gromacs-5.1.1/build/bin/gmx mdrun mpi -deffnm
> step6.2_equilibration -rdd 1.8 > test.dat
>
> This is generating multiple output and checkpoint files while its trying to
> run :
>
>
>  #step6.2_equilibration.xtc.6#
>  #step6.2_equilibration_step4400.cpt.1#
>  #step6.2_equilibration.log.3#
> #step6.2_equilibration.log.5#
>  #step6.2_equilibration.log.4#
>  #step6.2_equilibration.log.2#
>  step6.2_equilibration_prev.cpt
>  #step6.2_equilibration.log.6#
> step6.2_equilibration.cpt
> #step6.2_equilibration.xtc.3#
>  #step6.2_equilibration.xtc.5#
> #step6.2_equilibration.xtc.7#
> step6.2_equilibration.xtc
>
> When i check the log file to see the errors , it is showing the following :
>
>       Step           Time         Lambda
>               0        0.00000        0.00000
>
>    Energies (kJ/mol)
>            Bond       G96Angle        LJ (SR)   Coulomb (SR)   Coul. recip.
>     1.18159e+05    3.78079e+04   -8.79894e+06   -1.10782e+06    4.70754e+05
> Flat-bottom posres      Potential    Kinetic En.   Total Energy
> Temperature
>     4.65013e+06   -4.62990e+06    2.25820e+02   -4.62968e+06    6.73923e-02
>  Pressure (bar)
>    -7.74545e+01
>
> DD  step 39 load imb.: force 22.2%
>
> Writing checkpoint, step 560 at Thu May 26 11:57:56 2016
>
>
>
> -------------------------------------------------------
> Program gmx mdrun, VERSION 5.1.1
> Source code file:
> /app/setups/gromacs-5.1.1/src/gromacs/gmxlib/checkpoint.cpp, line: 1670
>
> File input/output error:
> Cannot rename checkpoint file; maybe you are out of disk space?
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
>
> I am not able to find the solution for it. What could be causing this? I
> have not been able to find help from HPC support available to us.
>
>
>
> Kind Regards,
> Antara
>
> --
> Junior research fellow(project)
> Systems biology group
> CSIR-Institute of Genomics & Integrative Biology
> South Campus
> New Delhi -  110020
> M : +91-9717970040
> --
> --
> 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-request at gromacs.org.
>