[gmx-developers] mpi and thread command line options

[Alexey Shvetsov]

Roland Schulz писал 2012-07-11 10:47:
> On Wed, Jul 11, 2012 at 2:33 AM, Alexey Shvetsov
> <alexxy at omrb.pnpi.spb.ru> wrote:
>> Hi!
>>
>> mvpich2/mvapich (as well as its derviations like platform
>> mpi,pc-mpi,intel-mpi) also will behave differently. So user can get
>> cryptic message about launching mpd, in case of launching mdrun -np
>> directly
> Not quite. mpich2 requires for MPI_Comm_spawn to work that the
> application is run with mpirun/mpiexec. See
> 
> http://lists.mcs.anl.gov/pipermail/mpich-discuss/2012-June/012638.html
> for the details. We would need to detect that and don't try to spawn
> in that case (and run in serial with a warning).
> Thus mpich2 would require: mpirun mdrun -np x. Of course that isn't
> more convenient than mpirun -np x mdrun. The only advantage would be
> that as with tmpi "mpirun mdrun" would automatically use as many 
> cores
> as are available and are useful for the system, whereas without spawn
> the user needs to decides the number of cores and we can't have any
> automatic mechanism helping the user.
>
> Roland

Ok. But how this will work with batch systems that automaticaly send 
number of processes to mpiexec, effective launch command will be

$ mpiexec mdrun_mpi $mdrunargs



>
>>
>> Roland Schulz писал 2012-07-11 05:09:
>>> On Tue, Jul 10, 2012 at 8:09 PM, Szilárd Páll
>>> <szilard.pall at cbr.su.se> wrote:
>>>> On Tue, Jul 10, 2012 at 11:15 PM, Berk Hess <hess at kth.se> wrote:
>>>>> Hi,
>>>>>
>>>>> We are working on the final part of the 4.6 release, which is
>>>>> making the MPI
>>>>> and OpenMP thread setup automated, fully checked and user 
>>>>> friendly.
>>>>> We have to decide on the naming of the options.
>>>>> Roland has an implementation of mpi spawn ready. This would allow
>>>>> to do
>>>>> mdrun -np #processes instead of using mpirun (at least with
>>>>> openmpi).
>>>>
>>>> Would this feature add anything but the convenience of being able 
>>>> to
>>>> run without mpirun on a single node? Without MPI spawning working
>>>> reliably in most cases (or with the ability to detect with a high
>>>> certainty when it does not), enabling an -np mdrun option would 
>>>> just
>>>> lead to confusion when mdrun exits with cryptic MPI error due to 
>>>> not
>>>> being able to spawn.
>>> The idea was to make mdrun behave the same whether it is compiled
>>> with
>>> real MPI or tMPI. Thus also only support a single node. But MPICH 
>>> is
>>> behaving quite stupid and they also don't seem to care. And only
>>> supporting it for OpenMPI is probably also more confusing then
>>> helpful
>>> (then tmpi+OpenMPI would behave the same but MPICH/MVAPICH would
>>> behave different). So you are probably right that it is better to 
>>> not
>>> add spawn at all.
>>>
>>>> Therefore, I'd be OK with a new *hidden* -np option that only 
>>>> works
>>>> in
>>>> single-node case, but not with a non-hidden one advertised in the
>>>> documentation/wiki.
>>> As a hidden option it would only help for testing. But I don't 
>>> think
>>> it is worth adding it for just that.
>>>
>>> Roland
>>
>> --
>> Best Regards,
>> Alexey 'Alexxy' Shvetsov
>> Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
>> Gatchina, Russia
>> Department of Molecular and Radiation Biophysics
>> Gentoo Team Ru
>> Gentoo Linux Dev
>> mailto:alexxyum at gmail.com
>> mailto:alexxy at gentoo.org
>> mailto:alexxy at omrb.pnpi.spb.ru
>> --
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>>
>>
>
>
>
> --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> 865-241-1537, ORNL PO BOX 2008 MS6309

-- 
Best Regards,
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, 
Gatchina, Russia
Department of Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux Dev
mailto:alexxyum at gmail.com
mailto:alexxy at gentoo.org
mailto:alexxy at omrb.pnpi.spb.ru