[gmx-users] problem running gromacs job
Sonia Martinez
sonia at cti.csic.es
Mon Oct 6 15:54:14 CEST 2008
Dear Sirs,
We are trying to use Gromacs software at a academic and research centre in Madrid, Spain.
For this purpose, we downloaded gromacs-3.3.3.tar.gz from your webpage and compiled it as follows:
CC="/opt/intel/cce/10.0.023/bin/icc" CFLAGS="-O2
-L/opt/intel/mkl/9.1/lib/em64t -I/opt/intel/mkl/9.1/include"
MPILIBS="-L/opt/mpich-ch_p4-icc-large-1.2.7/lib/" ./configure
--with-fft=mkl --enable-mpi --enable-double --disable-threads
--prefix=/opt/gromacs-3.3.3 --disable-nice
Bellow you can find the way we submitted the job an the error we obtained.
In order to dismiss a MPI problem we have also used MPICH and LAM.
I look forward to your help with this problem.
Yours faithfully,
Sonia Martinez
Dra. Sonia Martínez Hedo
Química Computacional
ALTRAN / CTI-CSIC
[dbasabe at trueno34 gromacs]$ /opt/mpich-ch_p4-icc-large-1.2.7/bin/mpirun
-machinefile machines -np 2 /opt/gromacs-3.3.3/bin/mdrun_d -np 2 -s
1HYG-pt.tpr -o 1HYG-pt.trr -c 1HYG-pt.gro -e 1HYG-pt.edr -x 1HYG-pt.xtc
-v
NNODES=2, MYRANK=0,
HOSTNAME=trueno34.csic.es
NNODES=2, MYRANK=1,
HOSTNAME=trueno34.csic.es
NODEID=0
argc=14
:-) G R O M A C S
(-:
Giving Russians Opium May Alter Current Situation
:-) VERSION 3.3.3 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and
others.
Copyright (c) 1991-2000, University of Groningen, The
Netherlands.
Copyright (c) 2001-2008, The GROMACS development
team,
check out http://www.gromacs.org for more
information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) /opt/gromacs-3.3.3/bin/mdrun_d (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-s 1HYG-pt.tpr Input Generic run input: tpr tpb tpa xml
-o 1HYG-pt.trr Output Full precision trajectory: trr trj
-x 1HYG-pt.xtc Output, Opt! Compressed trajectory (portable xdr
format)
-c 1HYG-pt.gro Output Generic structure: gro g96 pdb
xml
-e 1HYG-pt.edr Output Generic energy: edr
ene
-g md.log Output Log
file
-dgdl dgdl.xvg Output, Opt. xvgr/xmgr
file
-field field.xvg Output, Opt. xvgr/xmgr
file
-table table.xvg Input, Opt. xvgr/xmgr
file
-tablep tablep.xvg Input, Opt. xvgr/xmgr
file
-rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro
g96 pdb
-tpi tpi.xvg Output, Opt. xvgr/xmgr
file
-ei sam.edi Input, Opt. ED sampling
input
-eo sam.edo Output, Opt. ED sampling
output
-j wham.gct Input, Opt. General coupling
stuff
-jo bam.gct Output, Opt. General coupling
stuff
-ffout gct.xvg Output, Opt. xvgr/xmgr
file
-devout deviatie.xvg Output, Opt. xvgr/xmgr
file
-runav runaver.xvg Output, Opt. xvgr/xmgr
file
-pi pull.ppa Input, Opt. Pull
parameters
-po pullout.ppa Output, Opt. Pull
parameters
-pd pull.pdo Output, Opt. Pull data
output
-pn pull.ndx Input, Opt. Index file
-mtx nm.mtx Output, Opt. Hessian matrix
-dn dipole.ndx Output, Opt. Index file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line
options
-nice int 19 Set the nicelevel
-deffnm string Set the default filename for all file
options
-[no]xvgr bool yes Add specific codes (legends etc.) in the
output
xvg files for the xmgrace program
-np int 2 Number of nodes, must be the same as used
for
grompp
-nt int 1 Number of threads to start on each node
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]sepdvdl bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-[no]multi bool no Do multiple simulations in parallel (only
with
-np > 1)
-replex int 0 Attempt replica exchange every # steps
-reseed int -1 Seed for replica exchange, -1 is generate a
seed
-[no]glas bool no Do glass simulation with special long range
corrections
-[no]ionize bool no Do a simulation including the effect of an
X-Ray
bombardment on your system
Getting Loaded...
Reading file 1HYG-pt.tpr, VERSION 3.3.3 (double precision)
NODEID=1 argc=14
Loaded with Money
Back Off! I just backed up 1HYG-pt.edr to ./#1HYG-pt.edr.1#
WARNING: This run will generate roughly 2871 Mb of data
WARNING: This run will generate roughly 2871 Mb of data
starting mdrun 'Protein in water'
7000000 steps, 14000.0 ps.
p0_1381: p4_error: interrupt SIGSEGV: 11
Killed by signal 2.
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