Ok, summary of errors begin here.<br><br>First, errors with MPI in double precision:<br><br>1 Simple Test:<br>bham: ns type Simple is not supported with domain decomposition, use particle decomposition: mdrun -pd<br><br>7 Complex Tests:<br>
acetonitrilRF: ns type Simple is not supported with domain decomposition, use particle decomposition: mdrun -pd<br>aminoacids: ns type Simple is not supported with domain decomposition, use particle decomposition: mdrun -pd<br>
argon: ns type Simple is not supported with domain decomposition, use particle decomposition: mdrun -pd<br>sw: ns type Simple is not supported with domain decomposition, use particle decomposition: mdrun -pd<br>tip4p: ns type Simple is not supported with domain decomposition, use particle decomposition: mdrun -pd<br>
urea: ns type Simple is not supported with domain decomposition, use particle decomposition: mdrun -pd<br>water: ns type Simple is not supported with domain decomposition, use particle decomposition: mdrun -pd<br><br>16 Kernel Tests: 0 computation time. Something gone REALLY bad on those... :(<br>
<br>Except for the kernel tests, (seems that) in all I'm getting that same error message (still looking at it). Are those expected to appear? And the kernel ones? Am I wrong, or that means compilation problems (specially because they appear in all tests, single and double precision, with and withou MPI).<br>
<br>Also getting error in serial in single precision in 4 complex tests. Those seems to have run, but yelded wrong results?<br><br>Does anybody has any clue, please? Shall I go straight to recompilation, despite there is no reason for failure here?<br>
<br>Thanks a lot!<br><br>Jones<br><br><div class="gmail_quote">On Mon, May 11, 2009 at 10:42 PM, Jones de Andrade <span dir="ltr"><<a href="mailto:johannesrs@gmail.com">johannesrs@gmail.com</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;">
Hi Justin.<br><br>Well, bothering again. Good and bad news.<br><br>The good news: I found a strange "work-around" for my problems here. For some reason, the perl script updates the path, environments and everything else when runs. So, the variables I placed on the script I was using where simply lost. Workaround here was, then, to just include those in the .tcshrc file and log again.<br>
<br>The problem is that it's not pratical. I'm trying a lot of different MPIs and libraries compilations, and having to edit that file, and or logou/login or source it, is not pratical at all. Is there any other way, so that the perl script will be happy with the variables it has when its called, instead of initializing all them again?<br>
<br>Second, here comes the real bad news: Lots of erros.<br><br>Without MPI, in single precision, 4 complex and 16 kernel tests fail.<br><br>Without MPI, but in double precision, "just" the 16 kernel tests fail.<br>
<br>With MPI, in single precision, it fails on 1 simple, 9 complex and 16 kernel tests!<br><br>And with MPI and double precision, 1 simple, 7 complex and 16 kernel tests fails. :P<br><br>Edit: Just received your message. Well, it seems that I've done a mistake on my script, but since at least part of the tests worked, it means that it's not the MPI that is, at least, missconfigured.<br>
<br>I will look deeper into the erros above, and tell you later.<br><br>Thanks a lot,<br><font color="#888888"><br>Jones</font><div><div></div><div class="h5"><br><br><div class="gmail_quote">On Mon, May 11, 2009 at 9:41 PM, Jones de Andrade <span dir="ltr"><<a href="mailto:johannesrs@gmail.com" target="_blank">johannesrs@gmail.com</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;">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><font color="#888888"><br>Jones</font><div><div></div><div><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" target="_blank">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><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>
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