[gmx-users] TestBed in MPI not working

Jones de Andrade johannesrs at gmail.com
Tue May 12 01:59:11 CEST 2009

Hi Justin

This has been discussed several times on the list.  The -np flag is no
> longer necessary with grompp.  You don't get an mdrun.out because the .tpr
> file is likely never created, since grompp fails.

Yes, I know that and that is what I would have expected. But what I'm
running is the gmxtest.pl script. Even using the 4.0.4 version, it explicit
states that I must use "-np N" to make parallel works on its own command

Usage: ./gmxtest.pl [ -np N ] [-verbose ] [ -double ] [ simple | complex |
kernel | pdb2gmx | all ]
   or: ./gmxtest.pl clean | refclean | dist

I would expect that the script would use it only for mdrun and not for
grompp, but it seems to try to use on both. What becomes really strange it
the testbed really works. So, gmxtest.pl has a bug on 4.0.4? Or how should I
really tell gmxtest.pl to test in a growing number of cores?

>  Version 3.3.3 on the other hand already failed in so many different places
>> that I'm really thinking IF I'll make it available in the new cluster. :P
> What messages are you getting from 3.3.3?  I thought you said the 3.3.x
> series worked fine.

I'll login for those and try to get any reproducible error here. ;) As soon
as I have these, I post back in this thread.

Thanks a lot again,

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