Hello, I am trying to simulate a peptide-membrane system on GPU using gromacs 4.6.1 . However whenever I invoke the mdrun command I get an error as *srun: error: coe3: task 0: Segmentation fault (core dumped)*. Can anybody please suggest me what might be the problem?
*Script file used to submit the job*: #!/bin/bash #SBATCH --job-name=GRMCS-GPU #SBATCH --nodes=1 #SBATCH --gres=gpu:1 #SBATCH --nodelist=coe3 #SBATCH -e slurm.err #SBATCH -v #cd $SLURM_SUBMIT_DIR echo "CWD:" $SLURM_SUBMIT_DIR echo "NODELIST:" $SLURM_JOB_NODELIST export PATH=/opt/cuda-5.0/bin:$PATH export LD_LIBRARY_PATH=/opt/cuda-5.0/lib64:/opt/cuda-5.0/lib:$LD_LIBRARY_PATH srun -N1 -s /opt/apps/gromacs_GPU/bin/mdrun_mpi -deffnm EM *.mdp file for energy minimization*: title = EM of B2AR-POPC system ; Title of the miniization run ; Parameters describing the details of the Energy Minimization protocol define = ; Define any restrain ("-DPOSRES" OR "-DSTRONG_POSRES" OR leave blank if there is no restrain) integrator = steep ; EM Algorithm (steep = steepest descent; cg = conjugate gradiant; l-bfgs = Low-memory Broyden-Fletcher-Goldfarb-Shanno quasi-Newtonian minimizer) emtol = 100.0 ; Minimization is stopped when the maximum force on an atom is less than the given value (kJ/mol/nm) emstep = 0.01 ; Initial step size (nm) nsteps = 20000 ; Maximum number of (energy minimization) steps to be performed ; Parameters describing neighbors searching and details about interaction calculations nstlist = 1 ; Neighbor list update frequency (after every given number of steps) ns_type = grid ; Neighbor list search method (simple, grid) rlist = 1.2 ; Neighbor list search cut-off (nm) coulombtype = PME ; Long range electrostatic interactions treatment (cut-off, Ewald, PME) rcoulomb = 1.2 ; Short-range electrostatic cut-off (nm) rvdw = 1.2 ; Short-range van der Waals cut-off (nm) pbc = xyz ; Direction in which to use Perodic Boundary Conditions (xyz, xy, no) Thanks, Debajit Dey -- 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.