[Wien] MPI

[Laurence Marks]

Please be aware that the "-x LD_LIBRARY_PATH -x PATH" may be critical.

To explain (for others if needed), openmpi does not by default propogate
environmental variables, unless they have changed this recently. The
authors of the code argue that this is for security reasons, and I believe
openmpi has been designed to work with PBS and similar accounting systems
common on large clusters.

The "-x" propogates environmental variables, here the search path and
information on shared libraries. On some systems you might need more.

Unfortunately there is no robust way to propogate the environmental
variables set by ulimit with openmpi. This has been patched by including a
software setting for the relevant parameters which seems to work well
except sometimes for Mac's. In principle it could crash on some systems if
the sysadmin has set some restrictions.

N.B., make sure to use the right blacs version when linking, this changes
with the different flavors of mpi. I often forget to do this.

---------------------------
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu 1-847-491-3996
"Research is to see what everybody else has seen, and to think what nobody
else has thought"
Albert Szent-Gyorgi
 On Feb 22, 2013 7:01 AM, "Luis Ogando" <lcodacal at gmail.com> wrote:

>  Dear Prof. Blaha, Prof. Marks and Wien2k community,
>
>     I noticed that the "siteconfig_lapw" defines MPI_REMOTE as
>
>  setenv MPI_REMOTE "1"
>
>  even when one answers 0 to the correspondent question. I had previously
> changed it to 0, but I believe that I recompiled something after that and
> the value "1" was set again.
>    I am doing another test to check if this the origin of my problems with
> openmpi.
>    Unfortunately, I am not proficient in shell scripts, so I can not point
> the exact problem with the MPI_REMOTE setting (even if there is a real one).
>    Thank you one more time for the help,
>                                     Luis Ogando
>
>
>
>
>
> 2013/2/20 Peter Blaha <pblaha at theochem.tuwien.ac.at>
>
>> On an SMP machine make sure you have in $WIENROOT/parallel_options
>>
>> setenv USE_REMOTE 0
>> setenv MPI_REMOTE 0
>>
>> Am 20.02.2013 17:45, schrieb Luis Ogando:
>>
>>> Dear Prof. Marks,
>>>
>>>     Thank you very much for your prompt answer.
>>>     I am using openmpi, but I believe that I am facing some of the
>>> tricky issues you mentioned. I work in a SMP machine and the calculation
>>> starts fine. After some tens of iterations, MPI suddenly asks for a
>>> password and everything goes down to the drain.
>>>     I am using open mpi 1.6. Do you recommend any older version ??
>>>     All the best,
>>>                    Luis Ogando
>>>
>>>
>>>
>>>
>>> 2013/2/20 Laurence Marks <L-marks at northwestern.edu
>>>  <mailto:L-marks at northwestern.**edu <L-marks at northwestern.edu>>>
>>>
>>>
>>>     One that works.
>>>
>>>     Some versions of openmpi have problems although that is probably the
>>>     best option for the future. There are some tricky issues with openmpi
>>>     related to how your flavor of ssh works, there is no standard and
>>> some
>>>     do not propogate kill commands which means that they can leave
>>>     orphans.
>>>
>>>     An alternative is mvapich. In a benchmark that I did a few months ago
>>>     the Intel mpi was much better for AVX instructions, but that may have
>>>     changed.
>>>
>>>     Openmpi is easy to compile; mvapich can be a little trickier.
>>>
>>>     N.B., if you have fast connections, e.g. infiniband, they are more
>>>     than fast enough and I have never seen this as rate limiting with
>>>     Wien2k. With ethernet it matters.
>>>
>>>     On Wed, Feb 20, 2013 at 10:29 AM, Luis Ogando <lcodacal at gmail.com
>>>      <mailto:lcodacal at gmail.com>> wrote:
>>>      > Dear Wien2k community,
>>>      >
>>>      >    Is there any recommended flavor and version of an MPI compiler
>>>     to use
>>>      > with " Intel(R) Fortran Intel(R) 64 Compiler XE for applications
>>>     running on
>>>      > Intel(R) 64, Version 12.0.3.174 Build 20110309 " ?
>>>      >    All the best,
>>>      >                       Luis Ogando
>>>
>>>
>>>
>>>     --
>>>     Professor Laurence Marks
>>>     Department of Materials Science and Engineering
>>>     Northwestern University
>>>      www.numis.northwestern.edu <http://www.numis.**northwestern.edu<http://www.numis.northwestern.edu>
>>> >
>>>     1-847-491-3996 <tel:1-847-491-3996>
>>>
>>>     "Research is to see what everybody else has seen, and to think what
>>>     nobody else has thought"
>>>     Albert Szent-Gyorgi
>>>     ______________________________**_________________
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>>>
>>>
>>>
>>>
>>>
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>>>
>> --
>> Peter Blaha
>> Inst.Materials Chemistry
>> TU Vienna
>> Getreidemarkt 9
>> A-1060 Vienna
>> Austria
>> +43-1-5880115671
>>  ______________________________**_________________
>> Wien mailing list
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>>
>
>
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