shivkumar bale wrote:
Hi Justin,
Thanks for replying.
No .log file is produced. Can you elaborate what do you mean by ' this
really sounds more like a job for your sysadmin '. What should I exactly
do to rectify this error? I am new to super computers and gromacs.
If no output is produced, then there are plenty of potential problems - faulty
Gromacs installation, buggy MPI implementation (they are out there!), node
problems, etc. Whoever is in charge of the cluster (your system administrator)
may be able to probe system log files or run debug analysis to see what's wrong.
There's nothing more anyone here can likely provide.
-Justin
Regards
Shivkumar
On Thu, Dec 10, 2009 at 6:59 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
shivkumar bale wrote:
Hi Justin,
Sorry about the email. I just made a mistake while posting.
First of all, Thanks for replying.
I tried the suggestions you gave like I changed the pbc from
full to xyz, removed -Dflex term and also changed the fourier
grid spacing but still I am getting the same error. I am
attaching the error message with this email. Have a look at it.
If you need any more information let me know.
Have a look at the .log file produced by mdrun, if there is one.
Otherwise, this really sounds more like a job for your sysadmin,
since there is no Gromacs-related output that you have shown thus
far to indicate that this is a Gromacs problem.
-Justin
Thanks for your help.
Regards
Shivkumar
On Tue, Dec 8, 2009 at 5:53 AM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
You haven't addressed any of the comments or questions I
posted earlier:
http://lists.gromacs.org/pipermail/gmx-users/2009-December/047294.html
When asking for free help, demonstrate that you're willing to
take
the advice you're given, and if that fails, state what problems
remain. Otherwise, it seems like you're ignoring viable
suggestions.
For the sake of being explicit: your .mdp file is wrong, and the
dynamics are likely spurious. Solve these issues (which I have
described for you!) before moving to a more peripherally-related
solution. Also check the .log file; as I said before, Gromacs
rarely exits without offering its own error messages about what's
going wrong. There is nothing in this output that immediately
suggests your PME spacing is remotely at fault, but other
parameters
in your .mdp file are clearly wrong.
-Justin
shivkumar bale wrote:
Hi Gromacs Users,
The error:
mpispawn.c:303 Unexpected exit status
Child exited abnormally!
Killing remote processes...DONE
Following is the link which might help:
http://www.ece.unm.edu/~etanner/MPI.html
<http://www.ece.unm.edu/%7Eetanner/MPI.html
<http://www.ece.unm.edu/~etanner/MPI.html>
<http://www.ece.unm.edu/~etanner/MPI.html>>
I think the above error is because of the PME
calculations and
changing the grid spacing might work. But I dont know how to
change the grid spacing. Do you have any idea regarding
that? Or
if you think the error is due to some other reason let me
know.
I am attaching the .mdp file with this email.
Thanks for the help.
Regards
Shivkumar
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> <http://vt.edu/> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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