[gmx-users] MVAPICH2 mdrun problem for SD and MD, GROMACS 4.0.5

[Daniel Adriano Silva M]

Mark,

Thank you!!! It was non directly MPI, since I tried the fresh
installation with intel and gcc but none worked, then i realized that
my compilation of FFTW could be the problem (compiled with icc 11),
then I recompiled FFTW with gcc and linking to this new fftw3.2.2 I
recompiled gromacs booth with gcc and intel, booth compilations seems
to work. Do you think that it could be any problem at mix gcc-fftw and
intel mdrun??? I will continue the tests with the new gmx-tests and
other TPRs.

Thanks
Daniel

2009/10/30 Mark Abraham <Mark.Abraham at anu.edu.au>:
> Daniel Adriano Silva M wrote:
>>
>> Mark,
>>
>> I will test, but please tell me: do you think MPI linking problem
>> could lead to problems with some dynamics and not with others as
>> happens to me? and also note that all my test where made with mvapich2
>> (even that with one core). Please justin, what do you think about?
>
> For example, observing symptoms from buffer overruns can be sensitive to the
> actual calculation being run because it can depend how the actual memory
> gets laid out and used. So here, that might translate to the kind of system
> being simulated, and the number of cores used. Such an overrun might be
> present in the code all the time, or only exists after a linking mismatch,
> or similar.
>
> Mark
>
>> Thanks
>> Daniel
>>
>> 2009/10/30 Mark Abraham <Mark.Abraham at anu.edu.au>:
>>>
>>> Daniel Adriano Silva M wrote:
>>>>
>>>> Dear Gromacs users,
>>>>
>>>> I am experimenting the next problem on an infiniband-cluster (8
>>>> intel-cores per node, GROMACS compiled with icc 11.1, all run through
>>>> mvapich2):
>>>>
>>>> I have a molecule (protein 498aa, solvated or in vacuum I get the same
>>>> problem at any box shape), when I try to SD minimize it with
>>>> mvapich2-mdrun, it minimizes well with 1, 2 or 3 cores and reaches
>>>> convergence in around 1000steps, however any further combination (4,5,
>>>> ...n cores) makes it to immediately stop (less than 20 steps) with:
>>>>
>>>> "Steepest Descents converged to machine precision...".
>>>>
>>>> Further if I take "the 1 core minimized structure" and try to make a
>>>> solvated-pr dynamics(2fs, MD, NTP, etc.) it also works with 1
>>>> processor, but with more cores it begins immediately to bring LINCS
>>>> warnings: and dies:
>>>>
>>>> "Too many LINCS warnings" or "Water molecule starting at atom 16221
>>>> can not be settled"
>>>>
>>>> For a "long time" I had made another md simulations on this cluster
>>>> with the same mdps and other proteic systems, and I only see this
>>>> behavior with this particular protein, of course  before send this
>>>> mail I re-tested previuos-working tprs.
>>>> Finally, the most suspicious is that I have another very similar
>>>> 8-core box (with the same processors) but with gromacs gcc compiled,
>>>> and it actually runs very well the same problematic molecule (even the
>>>> same tpr) with mpi and 8-cores.
>>>> What do you think??? Please, if you have some tpr to test something send
>>>> it.
>>>
>>> I'd guess you're having some problem with (dynamic) linking of the MPI
>>> library. Perhaps the version of some library has changed since recently,
>>> etc. I'd suggest compiling two fresh copies of GROMACS with either icc
>>> and
>>> gcc on the troublesome machine and seeing what happens with them.
>>>
>>> Mark
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