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 <jalem...@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 <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> >> <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 >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/searchbefore >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> 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 <http://vt.edu/> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@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-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> 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@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
md.log
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