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.
Yep. Even the 4.0.4 version of gmxtest.pl as linked from here
http://wiki.gromacs.org/index.php/test_set is not actually functional
with GROMACS-4.0.4.
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?
See http://wiki.gromacs.org/index.php/grompp#Parallel_calculations.
There is no correct usage of grompp -np.
Mark
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