[gmx-users] TestBed in MPI not working
Justin A. Lemkul
jalemkul at vt.edu
Tue May 12 02:07:20 CEST 2009
Justin A. Lemkul wrote:
> Jones de Andrade wrote:
>> 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 line.
>> 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?
> Ah, sorry for the mis-read :) There is a simple fix that you can apply
> to the gmxtest.pl script:
> % diff gmxtest.pl gmxtest_orig.pl
> < system("$grompp -maxwarn 10 $ndx > grompp.out 2>&1");
> > system("$grompp -maxwarn 10 $ndx $par > grompp.out 2>&1");
>> 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,
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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