[gmx-developers] mpi and thread command line options

Alexey Shvetsov alexxy at omrb.pnpi.spb.ru
Wed Jul 11 08:33:09 CEST 2012


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 

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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