[gmx-users] MPI_Recv invalid count and system explodes for large but not small parallelization on power6 but not opterons

Roland Schulz roland at utk.edu
Wed Mar 4 05:07:12 CET 2009


depending on your system size and th interconnect this might be OK.

Thus you need to give us more information. E.g.: how many atoms, how many
ns/day, what interconnect, PME?.

Also the messages at the end of the md.log might tell you some advices to
improve performance.


On Tue, Mar 3, 2009 at 10:48 PM, <chris.neale at utoronto.ca> wrote:

> Thanks Mark,
> your information is always useful. In this case, the page that you
> reference appears to be empty. All I see is "There is currently no text in
> this page, you can search for this page title in other pages or edit this
> page."
> Thanks also for your consideration of the massive scaling issue.
> Chris.
> chris.neale at utoronto.ca wrote:
>> Hello,
>> I am currently testing a large system on a power6 cluster. I have compiled
>> gromacs 4.0.4 successfully, and it appears to be working fine for <64
>> "cores" (sic, see later). First, I notice that it runs at approximately 1/2
>> the speed that it obtains on some older opterons, which is unfortunate but
>> acceptable. Second, I run into some strange issues when I have a greater
>> number of cores. Since there are 32 cores per node with simultaneous
>> multithreading this yields 64 tasks inside one box, and I realize that these
>> problems could be MPI related.
>> Some background:
>> This test system is stable for > 100ns on an opteron so I am quite
>> confident that I do not have a problem with my topology or starting
>> structure.
>> Compilation was successful with -O2 only when I modified the ./configure
>> file as follows, otherwise I got a stray ')' and a linking error:
>> [cneale at tcs-f11n05]$ diff configure.000 configure
>> 5052a5053
>>> ac_cv_f77_libs="-L/scratch/cneale/exe/fftw-3.1.2_aix/exec/lib -lxlf90
>>> -L/usr/lpp/xlf/lib -lxlopt -lxlf -lxlomp_ser -lpthreads -lm -lc"
> Rather than modify configure, I suggest you use a customized command
> line, such as the one described here
> http://wiki.gromacs.org/index.php/GROMACS_on_BlueGene. The output
> config.log will have a record of what you did, too.
> Sorry I can't help with the massive scaling issue.
> Mark
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