On 7/17/14, 1:51 AM, DeBaJiT DeY wrote:
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= 2 ; 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)
Hard to say without any actual information from Gromacs. Can you tell us:
1. Does the EM work on CPU?
2. Do other systems run on the GPU?
3. Can you post your .log file?
-Justin
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
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