Hi Justin.<br><br>Thanks a lot for that. It helped, but enough yet. :( Just made 4.0.4 tests reach the same "range of errors" that I'm getting with 3.3.3. :P<br><br>Using openMPI, it just complains that it can't find orted. That would mean that the paths are not in there, BUT they are. :P If I just try to run orted from the command line without any arguments:<br>
<br>*****************<br><i>gmxtest404 196% orted<br>[palpatine:28366] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 125<br>--------------------------------------------------------------------------<br>
It looks like orte_init failed for some reason; your parallel process is<br>likely to abort. There are many reasons that a parallel process can<br>fail during orte_init; some of which are due to configuration or<br>environment problems. This failure appears to be an internal failure;<br>
here's some additional information (which may only be relevant to an<br>Open MPI developer):<br><br> orte_ess_base_select failed<br> --> Returned value Not found (-13) instead of ORTE_SUCCESS<br>--------------------------------------------------------------------------<br>
[palpatine:28366] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file orted/orted_main.c at line 323<br></i>*****************<br><br>So, the shell IS finding the file. But when I do it not from the script anymore (I was already thinking in something on the "it-else-end" stack), all mpi tests fail with the following message on mdrun.out file:<br>
<br>**********************<br><i>orted: Command not found.<br>--------------------------------------------------------------------------<br>A daemon (pid 27972) died unexpectedly with status 1 while attempting<br>to launch so we are aborting.<br>
<br>There may be more information reported by the environment (see above).<br><br>This may be because the daemon was unable to find all the needed shared<br>libraries on the remote node. You may set your LD_LIBRARY_PATH to have the<br>
location of the shared libraries on the remote nodes and this will<br>automatically be forwarded to the remote nodes.<br>--------------------------------------------------------------------------<br>--------------------------------------------------------------------------<br>
mpirun noticed that the job aborted, but has no info as to the process<br>that caused that situation.<br>--------------------------------------------------------------------------<br>mpirun: clean termination accomplished<br>
</i>**********************<br><br>What is going on? Next thing I think about doing is to execute a full command line from one of the tests directly, to see that it works... :( :P<br><br>Now I'm absolutelly lost. Any ideas, please?<br>
<br>Thanks a lot,<br><br>Jones<br><br><div class="gmail_quote">On Mon, May 11, 2009 at 9:07 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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div></div><div class="h5"><br>
<br>
Justin A. Lemkul wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
Jones de Andrade wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Justin<br>
<br>
This has been discussed several times on the list. The -np flag is<br>
no longer necessary with grompp. You don't get an mdrun.out because<br>
the .tpr file is likely never created, since grompp fails.<br>
<br>
<br>
Yes, I know that and that is what I would have expected. But what I'm running is the gmxtest.pl script. Even using the 4.0.4 version, it explicit states that I must use "-np N" to make parallel works on its own command line.<br>
<br>
************<br>
gmxtest.pl<br>
Usage: ./gmxtest.pl [ -np N ] [-verbose ] [ -double ] [ simple | complex | kernel | pdb2gmx | all ]<br>
or: ./gmxtest.pl clean | refclean | dist<br>
************<br>
<br>
I would expect that the script would use it only for mdrun and not for grompp, but it seems to try to use on both. What becomes really strange it the testbed really works. So, gmxtest.pl has a bug on 4.0.4? Or how should I really tell gmxtest.pl to test in a growing number of cores?<br>
<br>
</blockquote>
<br>
Ah, sorry for the mis-read :) There is a simple fix that you can apply to the gmxtest.pl script:<br>
<br>
% diff gmxtest.pl gmxtest_orig.pl<br>
161c161<br>
< system("$grompp -maxwarn 10 $ndx > grompp.out 2>&1");<br>
---<br>
> system("$grompp -maxwarn 10 $ndx $par > grompp.out 2>&1");<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
Version 3.3.3 on the other hand already failed in so many<br>
different places that I'm really thinking IF I'll make it<br>
available in the new cluster. :P<br>
<br>
<br>
What messages are you getting from 3.3.3? I thought you said the<br>
3.3.x series worked fine.<br>
<br>
<br>
I'll login for those and try to get any reproducible error here. ;) As soon as I have these, I post back in this thread.<br>
<br>
Thanks a lot again,<br>
<br>
Jones<br>
</blockquote>
<br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<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>
<br>
========================================<br></div></div><div><div></div><div class="h5">
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