[gmx-developers] mpi and thread command line options

[Roland Schulz]

On Wed, Jul 11, 2012 at 7:19 AM, Alexey Shvetsov
<alexxy at omrb.pnpi.spb.ru> wrote:
> 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

The idea was to only do any spawn if mdrun_mpi is started in serial
(mpiexec -n 1). It was only meant to make mdrun_mpi behave the same as
tmpi mdrun for a single node. On clusters with batch system nothing
would have changed over the current situation.

Roland

>
>
>
>>
>>>
>>> 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
> --
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