<div>Hi Justin,</div>
<div> </div>
<div>Now I am able to get the output but the error is still coming.</div>
<div> </div>
<div>I am attaching .log file and error file with this email. This might help.</div>
<div> </div>
<div>Thanks for helping all of us.</div>
<div> </div>
<div>Regards</div>
<div> </div>
<div>Shivkumar <br><br></div>
<div class="gmail_quote">On Thu, Dec 10, 2009 at 7:31 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br><br>shivkumar bale wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi Justin,
<div class="im"><br> Thanks for replying.<br> 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.<br>
<br></div></blockquote><br>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.<br>
<br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Regards<br> Shivkumar
<div class="im"><br><br>On Thu, Dec 10, 2009 at 6:59 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br><br><br> shivkumar bale wrote:<br><br> Hi Justin,<br> Sorry about the email. I just made a mistake while posting.<br> First of all, Thanks for replying.<br> I tried the suggestions you gave like I changed the pbc from<br>
full to xyz, removed -Dflex term and also changed the fourier<br> grid spacing but still I am getting the same error. I am<br> attaching the error message with this email. Have a look at it.<br> If you need any more information let me know.<br>
<br><br> Have a look at the .log file produced by mdrun, if there is one.<br> Otherwise, this really sounds more like a job for your sysadmin,<br> since there is no Gromacs-related output that you have shown thus<br>
far to indicate that this is a Gromacs problem.<br><br> -Justin<br><br> Thanks for your help.<br> Regards<br> Shivkumar<br><br><br> On Tue, Dec 8, 2009 at 5:53 AM, Justin A. Lemkul<br> <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
</div>
<div>
<div></div>
<div class="h5"> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br><br><br> You haven't addressed any of the comments or questions I<br>
posted earlier:<br><br> <a href="http://lists.gromacs.org/pipermail/gmx-users/2009-December/047294.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2009-December/047294.html</a><br>
<br> When asking for free help, demonstrate that you're willing to<br> take<br> the advice you're given, and if that fails, state what problems<br> remain. Otherwise, it seems like you're ignoring viable<br>
suggestions.<br><br> For the sake of being explicit: your .mdp file is wrong, and the<br> dynamics are likely spurious. Solve these issues (which I have<br> described for you!) before moving to a more peripherally-related<br>
solution. Also check the .log file; as I said before, Gromacs<br> rarely exits without offering its own error messages about what's<br> going wrong. There is nothing in this output that immediately<br>
suggests your PME spacing is remotely at fault, but other<br> parameters<br> in your .mdp file are clearly wrong.<br><br> -Justin<br><br> shivkumar bale wrote:<br><br> Hi Gromacs Users,<br>
<br> The error:<br><br> mpispawn.c:303 Unexpected exit status<br><br> Child exited abnormally!<br> Killing remote processes...DONE<br><br> Following is the link which might help:<br>
<br> <a href="http://www.ece.unm.edu/~etanner/MPI.html" target="_blank">http://www.ece.unm.edu/~etanner/MPI.html</a><br> <<a href="http://www.ece.unm.edu/~etanner/MPI.html" target="_blank">http://www.ece.unm.edu/%7Eetanner/MPI.html</a><br>
<<a href="http://www.ece.unm.edu/~etanner/MPI.html" target="_blank">http://www.ece.unm.edu/~etanner/MPI.html</a>><br> <<a href="http://www.ece.unm.edu/~etanner/MPI.html" target="_blank">http://www.ece.unm.edu/~etanner/MPI.html</a>>><br>
<br><br><br> I think the above error is because of the PME<br> calculations and<br> changing the grid spacing might work. But I dont know how to<br> change the grid spacing. Do you have any idea regarding<br>
that? Or<br> if you think the error is due to some other reason let me<br> know.<br><br> I am attaching the .mdp file with this email.<br><br> Thanks for the help.<br><br>
Regards<br><br> Shivkumar<br><br><br> -- ========================================<br><br> Justin A. Lemkul<br> Ph.D. Candidate<br> ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br> Department of Biochemistry<br> Virginia Tech<br> Blacksburg, VA<br></div></div> jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> <<a href="http://vt.edu/" target="_blank">http://vt.edu/</a>> <<a href="http://vt.edu/" target="_blank">http://vt.edu/</a>> | (540)
<div class="im"><br> 231-9080<br><br> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br> ========================================<br>
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<div class="h5"><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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