[gmx-users] TestBed in MPI not working

Jones de Andrade johannesrs at gmail.com
Tue May 12 03:42:33 CEST 2009


Hi Justin.

Well, bothering again. Good and bad news.

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.

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?

Second, here comes the real bad news: Lots of erros.

Without MPI, in single precision, 4 complex and 16 kernel tests fail.

Without MPI, but in double precision, "just" the 16 kernel tests fail.

With MPI, in single precision, it fails on 1 simple, 9 complex and 16 kernel
tests!

And with MPI and double precision, 1 simple, 7 complex and 16 kernel tests
fails. :P

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.

I will look deeper into the erros above, and tell you later.

Thanks a lot,

Jones

On Mon, May 11, 2009 at 9:41 PM, Jones de Andrade <johannesrs at gmail.com>wrote:

> Hi Justin.
>
> 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
>
> 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:
>
> *****************
> *gmxtest404 196% orted
> [palpatine:28366] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file
> runtime/orte_init.c at line 125
> --------------------------------------------------------------------------
> It looks like orte_init failed for some reason; your parallel process is
> likely to abort.  There are many reasons that a parallel process can
> fail during orte_init; some of which are due to configuration or
> environment problems.  This failure appears to be an internal failure;
> here's some additional information (which may only be relevant to an
> Open MPI developer):
>
>   orte_ess_base_select failed
>   --> Returned value Not found (-13) instead of ORTE_SUCCESS
> --------------------------------------------------------------------------
> [palpatine:28366] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file
> orted/orted_main.c at line 323
> ******************
>
> 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:
>
> **********************
> *orted: Command not found.
> --------------------------------------------------------------------------
> A daemon (pid 27972) died unexpectedly with status 1 while attempting
> to launch so we are aborting.
>
> There may be more information reported by the environment (see above).
>
> This may be because the daemon was unable to find all the needed shared
> libraries on the remote node. You may set your LD_LIBRARY_PATH to have the
> location of the shared libraries on the remote nodes and this will
> automatically be forwarded to the remote nodes.
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> mpirun noticed that the job aborted, but has no info as to the process
> that caused that situation.
> --------------------------------------------------------------------------
> mpirun: clean termination accomplished
> ***********************
>
> 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
>
> Now I'm absolutelly lost. Any ideas, please?
>
> Thanks a lot,
>
> Jones
>
>
> On Mon, May 11, 2009 at 9:07 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> Justin A. Lemkul wrote:
>>
>>>
>>>
>>> Jones de Andrade wrote:
>>>
>>>> Hi Justin
>>>>
>>>>    This has been discussed several times on the list.  The -np flag is
>>>>    no longer necessary with grompp.  You don't get an mdrun.out because
>>>>    the .tpr file is likely never created, since grompp fails.
>>>>
>>>>
>>>> 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.
>>>>
>>>> ************
>>>> gmxtest.pl
>>>> Usage: ./gmxtest.pl [ -np N ] [-verbose ] [ -double ] [ simple | complex
>>>> | kernel | pdb2gmx | all ]
>>>>   or: ./gmxtest.pl clean | refclean | dist
>>>> ************
>>>>
>>>> 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?
>>>>
>>>>
>>>
>>> Ah, sorry for the mis-read :)  There is a simple fix that you can apply
>>> to the gmxtest.pl script:
>>>
>>> % diff gmxtest.pl gmxtest_orig.pl
>>> 161c161
>>> <         system("$grompp -maxwarn 10 $ndx > grompp.out 2>&1");
>>> ---
>>>  >         system("$grompp -maxwarn 10 $ndx $par > grompp.out 2>&1");
>>>
>>> -Justin
>>>
>>>
>>>>
>>>>        Version 3.3.3 on the other hand already failed in so many
>>>>        different places that I'm really thinking IF I'll make it
>>>>        available in the new cluster. :P
>>>>
>>>>
>>>>    What messages are you getting from 3.3.3?  I thought you said the
>>>>    3.3.x series worked fine.
>>>>
>>>>
>>>> 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.
>>>>
>>>> Thanks a lot again,
>>>>
>>>> Jones
>>>>
>>>
>>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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