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<DIV><FONT face=Arial size=2>Dear Sirs,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>We are trying to use Gromacs software at a academic
and research centre in Madrid, Spain.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial><FONT size=2>For this purpose, we downloaded </FONT><A
href="ftp://ftp.gromacs.org/pub/gromacs/gromacs-3.3.3.tar.gz"><STRONG><FONT
color=#0066cc size=2>gromacs-3.3.3.tar.gz</FONT></STRONG></A><FONT
size=2> from your webpage and compiled it as follows:</FONT></FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2><FONT face="Times New Roman"
size=3>CC="/opt/intel/cce/10.0.023/bin/icc"
CFLAGS="-O2<BR>-L/opt/intel/mkl/9.1/lib/em64t
-I/opt/intel/mkl/9.1/include"<BR>MPILIBS="-L/opt/mpich-ch_p4-icc-large-1.2.7/lib/"
./configure<BR>--with-fft=mkl --enable-mpi --enable-double
--disable-threads<BR>--prefix=/opt/gromacs-3.3.3
--disable-nice</FONT><BR></FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Bellow you can find the way we submitted the
job an the error we obtained.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>In order to dismiss a MPI problem we have also used
MPICH and LAM.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I look forward to your help with this
problem.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Yours faithfully,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Sonia Martinez</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>
<DIV><FONT face=Arial size=2>Dra. Sonia Martínez Hedo<BR>Química Computacional
<BR>ALTRAN / CTI-CSIC</FONT></DIV>
<DIV> </DIV>
<DIV> </DIV></FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV>[dbasabe@trueno34 gromacs]$
/opt/mpich-ch_p4-icc-large-1.2.7/bin/mpirun<BR>-machinefile machines -np 2
/opt/gromacs-3.3.3/bin/mdrun_d -np 2 -s<BR>1HYG-pt.tpr -o 1HYG-pt.trr -c
1HYG-pt.gro -e 1HYG-pt.edr -x
1HYG-pt.xtc<BR>-v
<BR>NNODES=2,
MYRANK=0,<BR>HOSTNAME=trueno34.csic.es
<BR>NNODES=2,
MYRANK=1,<BR>HOSTNAME=trueno34.csic.es
<BR>NODEID=0<BR>argc=14
<BR>
:-) G R O M A C
S<BR>(-:
<BR><BR>
Giving Russians Opium May Alter Current
Situation<BR><BR>
:-) VERSION 3.3.3 (-:<BR><BR><BR>
Written by David van der Spoel, Erik Lindahl, Berk Hess,
and<BR>others.<BR> Copyright (c) 1991-2000,
University of Groningen, The<BR>Netherlands.
<BR>
Copyright (c) 2001-2008, The GROMACS
development<BR>team,
<BR> check out
<A href="">http://www.gromacs.org</A> for
more<BR>information.
<BR><BR> This program is free
software; you can redistribute it
and/or<BR> modify it under
the terms of the GNU General Public License
<BR> as published by the Free
Software Foundation; either version
2<BR> of
the License, or (at your option) any later version.
<BR><BR> :-)
/opt/gromacs-3.3.3/bin/mdrun_d (double precision)
(-:<BR><BR>Option Filename
Type
Description<BR>------------------------------------------------------------<BR>
-s 1HYG-pt.tpr
Input Generic run input: tpr tpb tpa
xml<BR> -o 1HYG-pt.trr
Output Full precision trajectory: trr
trj<BR> -x 1HYG-pt.xtc Output, Opt! Compressed
trajectory (portable xdr<BR>format)<BR> -c
1HYG-pt.gro Output Generic structure:
gro g96 pdb<BR>xml <BR>
-e 1HYG-pt.edr
Output Generic energy:
edr<BR>ene
<BR> -g md.log
Output
Log<BR>file
<BR>-dgdl dgdl.xvg Output, Opt.
xvgr/xmgr<BR>file
<BR>-field field.xvg Output, Opt.
xvgr/xmgr<BR>file
<BR>-table table.xvg Input, Opt.
xvgr/xmgr<BR>file
<BR>-tablep tablep.xvg Input, Opt.
xvgr/xmgr<BR>file
<BR>-rerun rerun.xtc Input, Opt. Generic
trajectory: xtc trr trj gro<BR>g96
pdb<BR>-tpi tpi.xvg Output, Opt.
xvgr/xmgr<BR>file
<BR> -ei sam.edi Input,
Opt. ED
sampling<BR>input
<BR> -eo sam.edo Output,
Opt. ED
sampling<BR>output
<BR> -j wham.gct Input,
Opt. General
coupling<BR>stuff
<BR> -jo bam.gct Output,
Opt. General
coupling<BR>stuff
<BR>-ffout gct.xvg Output, Opt.
xvgr/xmgr<BR>file
<BR>-devout deviatie.xvg Output, Opt.
xvgr/xmgr<BR>file
<BR>-runav runaver.xvg Output, Opt.
xvgr/xmgr<BR>file
<BR> -pi pull.ppa Input,
Opt.
Pull<BR>parameters
<BR> -po pullout.ppa Output, Opt.
Pull<BR>parameters
<BR> -pd pull.pdo Output, Opt.
Pull
data<BR>output
<BR> -pn pull.ndx Input,
Opt. Index file<BR>-mtx
nm.mtx Output, Opt. Hessian matrix<BR> -dn
dipole.ndx Output, Opt. Index
file<BR><BR>Option Type
Value
Description<BR>------------------------------------------------------<BR>-[no]h
bool no Print help info and
quit<BR>-[no]X bool
no Use dialog box GUI to edit command
line<BR>options<BR>-nice
int 19 Set the
nicelevel<BR>-deffnm
string Set the default filename
for all file<BR>options<BR>-[no]xvgr bool
yes Add specific codes (legends etc.) in
the<BR>output<BR>
xvg files for the xmgrace
program<BR>-np
int 2 Number of nodes,
must be the same as
used<BR>for<BR>
grompp<BR>-nt
int 1 Number of threads to
start on each node<BR>-[no]v
bool yes Be loud and noisy<BR>-[no]compact
bool yes Write a compact log
file<BR>-[no]sepdvdl bool no Write
separate V and dVdl terms for
each<BR>
interaction type and node to the log file(s)<BR>-[no]multi
bool no Do multiple simulations in
parallel
(only<BR>with<BR>
-np > 1)<BR>-replex int
0 Attempt replica exchange every #
steps<BR>-reseed int
-1 Seed for replica exchange, -1 is generate
a<BR>seed<BR>-[no]glas bool
no Do glass simulation with special long
range<BR>
corrections<BR>-[no]ionize bool
no Do a simulation including the effect of
an<BR>X-Ray<BR>
bombardment on your system<BR><BR>Getting Loaded...<BR>Reading file 1HYG-pt.tpr,
VERSION 3.3.3 (double precision)<BR>NODEID=1 argc=14<BR>Loaded with
Money<BR><BR><BR>Back Off! I just backed up 1HYG-pt.edr to
./#1HYG-pt.edr.1#<BR><BR>WARNING: This run will generate roughly 2871 Mb of
data<BR><BR><BR>WARNING: This run will generate roughly 2871 Mb of
data<BR><BR>starting mdrun 'Protein in water'<BR>7000000 steps, 14000.0
ps.<BR><BR>p0_1381: p4_error: interrupt SIGSEGV: 11<BR>Killed by signal
2.<BR></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
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