[Wien] MPI
Luis Ogando
lcodacal at gmail.com
Fri Feb 22 14:46:29 CET 2013
" 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. "
Me too !! :)
Thank you again ! I am aware of your valuable advices !
All the best,
Luis Ogando
2013/2/22 Laurence Marks <L-marks at northwestern.edu>
> 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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>>>> Wien at zeus.theochem.**tuwien.ac.at <Wien at zeus.theochem.tuwien.ac.at>>
>>>> http://zeus.theochem.tuwien.**ac.at/mailman/listinfo/wien<http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien>
>>>>
>>>>
>>>>
>>>>
>>>>
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>>>>
>>>>
>>> --
>>> Peter Blaha
>>> Inst.Materials Chemistry
>>> TU Vienna
>>> Getreidemarkt 9
>>> A-1060 Vienna
>>> Austria
>>> +43-1-5880115671
>>> ______________________________**_________________
>>> Wien mailing list
>>> Wien at zeus.theochem.tuwien.ac.**at <Wien at zeus.theochem.tuwien.ac.at>
>>> http://zeus.theochem.tuwien.**ac.at/mailman/listinfo/wien<http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien>
>>>
>>
>>
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