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.
************
gmxtest.pl
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
161c161
< system("$grompp -maxwarn 10 $ndx > grompp.out 2>&1");
---
> system("$grompp -maxwarn 10 $ndx $par > grompp.out 2>&1");
-Justin
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,
Jones
--
========================================
Justin A. Lemkul
Ph.D. Candidate
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
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
