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

[Antara mazumdar]

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
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