[gmx-users] problems with gmxtest.pl

[Justin A. Lemkul]

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
> 
> --
> ---------------------------------------------------------------------
>   Dr. Bernhard Bandow            Phone: +49 511  762 794727
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-- 
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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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