[gmx-users] mpispawn.c:303 Unexpected exit status
shivkumar bale
kumarbale at gmail.com
Sat Dec 12 04:43:35 CET 2009
Hi Justin,
Now I am able to get the output but the error is still coming.
I am attaching .log file and error file with this email. This might help.
Thanks for helping all of us.
Regards
Shivkumar
On Thu, Dec 10, 2009 at 7:31 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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 <jalemkul at vt.edu<mailto:
>> jalemkul at 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
>> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at 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>
>> <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
>>
>> ========================================
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
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>> 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
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>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
> --
> ========================================
>
> 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.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-request at gromacs.org.
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>
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