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?
Under 4.0.x, grompp no longer needs the -np flag. Are you trying to run an
older (3.3.x) version of gmxtest.pl?
AFAIK, there is no test set directly related to Gromacs 4.0.3; the current test
set is for 4.0.4; I would suggest upgrading to Gromacs 4.0.4 and using the
appropriate test set.
-Justin
Best regards
Bernhard Bandow
--
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Dr. Bernhard Bandow Phone: +49 511 762 794727
Leibniz Universitaet Hannover FAX: +49 511 762 3003
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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