[gmx-users] Regarding segmentation fault in GPU_gromacs 4.6.1

DeBaJiT DeY d25debajit at gmail.com
Thu Jul 17 07:51:19 CEST 2014


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*:
#SBATCH --job-name=GRMCS-GPU
#SBATCH --nodes=1
#SBATCH --gres=gpu:1
#SBATCH --nodelist=coe3
#SBATCH -e slurm.err



export PATH=/opt/cuda-5.0/bin:$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
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)


Debajit Dey

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