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

[Daniel Adriano Silva M]

Mark,

Then I will try with other versions, check gmx-tests and not mix
compilers, thank you much by your help. Last question, I am afraid to
ask, but I have some simulations that were ran with this setup,
energy, temp, and pressure looks good on all, and it ran by pretty
long time (several ns) without any apparent errors, do you think that
there could be any way to check if these md-sims results are actually
wrong?

Thanks
Daniel

2009/10/30 Mark Abraham <Mark.Abraham at anu.edu.au>:
> Daniel Adriano Silva M wrote:
>>
>> 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.
>
> There have been known issues with linking and some versions of Intel
> compilers under various conditions with stuff in general and GROMACS in
> particular. I've never cared to understand why. Not mixing compilers is
> usually a good idea if there are problems.
>
> Mark
>
>> 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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