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-requ...@gromacs.org.