Bernhard Bandow wrote:
Dear users and developers of gromacs,
following the installation of gromacs 4.0.3 the tests show some
inconsistencies.
The software was compiled with Intel 11.0.069 compiler using mvapich2
Further options in configure were:
--enable-fortran
--enable-mpi
--with-fft=mkl
--enable-shared
The system gromacs is intended to run on uses mpiexec to initiate
message passing. So gmxtest.pl was modified at line 31 to:
$mdprefix = "mpiexec -np $parallel"
The output in mdrun.out starts with
-- NNODES=4, MYRANK=2, HOSTNAME=h01001
NNODES=4, MYRANK=0, HOSTNAME=h01001
NODEID=0 argc=1
NNODES=4, MYRANK=1, HOSTNAME=h01001
NODEID=1 argc=1
NNODES=4, MYRANK=3, HOSTNAME=h01001
NODEID=3 argc=1
NODEID=2 argc=1
:-) G R O M A C S (-:
...it seems to be a parallel run indeed.
Nontheless grompp.out of the corresponding run contains the lines:
-------------------------------------------------------
Program grompp, VERSION 4.0.3
Source code file: statutil.c, line: 727
Invalid command line argument:
-np
-------------------------------------------------------
which is related to line 159 of gmxtest.pl.
Are there any comments to the usage and position of the -np argument
under these circumstances in order to have more than an educated guess
for that?
-np for grompp is outdated. just remove it.
Best regards
Bernhard Bandow
--
---------------------------------------------------------------------
Dr. Bernhard Bandow Phone: +49 511 762 794727
Leibniz Universitaet Hannover FAX: +49 511 762 3003
RRZN / HLRN Email: ban...@rrzn.uni-hannover.de
Schlosswender Str. 5
D-30159 Hannover http://www.rrzn.uni-hannover.de/
Germany http://www.hlrn.de/
---------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
