<br><br><div class="gmail_quote">On Mon, Sep 12, 2011 at 8:33 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="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div></div><div class="h5"><br>
<br>
lina wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
I am confused, why the job is running,<br>
<br>
but they did not write the .edr, .log .xtc ... files.<br>
<br>
Everything showed so normal, just not writing,<br>
<br>
when I used thread, all is fine, the writing is normal.<br>
<br>
just use mpi, I tried different nodes, still not work, now two hours later, still no writing, just running.<br>
<br>
Thanks for providing any clue for me to examine.<br>
<br>
<br>
</blockquote>
<br></div></div>
Sounds like your MPI implementation is broken or you haven't issued the command right. If you have a test command that you know should work, run that. Otherwise, it's impossible to know if the problem is with Gromacs or something external. If you compiled with threading support, but not MPI (in a separate binary) then MPI will not work on the thread-enabled executable.<br>
</blockquote><div><br>I suspected it's MPI issue, but couple of days ago it's fine, and the results was able to write.<br><br>I installed both MPI and thread but with different prefix to distinguish. <br><br>Thanks, <br>
</div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<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.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br><font color="#888888">
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br>
</font></blockquote></div><br><br clear="all"><br>-- <br>Best Regards,<br><br>lina<br><br><br>