[yt-users] Running YT in Parallel on Nautilus

gso at physics.ucsd.edu gso at physics.ucsd.edu
Fri Apr 8 11:37:49 PDT 2011


Sorry I should have made it more clear, the install script I was referring
to is the YT 2.1 dev version, the one already installed on Nautilus is
1.7.

From
G.S.

>
> I believe YT is installed on nautilus globally. If you want to use YT on
> Nautilus you can get your environment set up by executing
> "module load yt" from the command line. mpi4py and all that should already
> be there.
>
> Dave Semeraro
>
> ----- Original Message -----
>> I guess this would be a sort of followup to Stephen's email of running
>> YT
>> on Kraken, here's what I figured out combined with what I got from the
>> system admin:
>>
>> Installing mpi4py can be a little more troublesome because there's no
>> mpicc wrapper, you'll have to edit the mpi.cfg file and put in:
>>
>> mpicc = gcc -lmpi
>> mpicxx = g++ -lmpi++ -lmpi
>>
>> then do:
>> python setup.py build --mpi=<your mpi section name in mpi.cfg>
>> python setup.py install
>>
>> (following http://mpi4py.scipy.org/docs/usrman/install.html)
>>
>> next you'll have to set these environment variables, I have it in a
>> .bashrc and source it every time I log into Nautilus.
>>
>> module swap mpt mpt/2.03
>> export MPI_SHARED_NEIGHBORHOOD=HOST
>>
>> Last but not least, the system admin told me SGI identified a bug so
>> that
>> mpi at least under python works for only up to 8 processors. I've
>> tried
>> 16 and failed, tried 8 and ran, so I believe their story.
>>
>> so under an interactive queue, you'll want to do something like:
>> mpiexec -np 8 python script.py --parallel
>> to run YT in parallel
>>
>> Hope this helps
>>
>> From
>> G.S.
>>
>> > Hi All,
>> >
>> > I've just updated the common install of yt on Kraken to 2.1, and
>> > added
>> > an install of the unstable branch. Both are full copies of yt that
>> > is
>> > kept on lustre in a non-volatile place. This means that it is
>> > accessible from both the login nodes and the compute nodes, but
>> > unlike
>> > most files on Lustre, will not be deleted automatically.
>> >
>> > If you wish to use yt 2.1, which will only see changes for bug
>> > fixes,
>> > please set your environment using these settings:
>> >
>> > YT_DEST => /lustre/scratch/proj/yt_common/2.1
>> > PATH => /lustre/scratch/proj/yt_common/2.1/bin/
>> > PYTHONPATH =>
>> > /lustre/scratch/proj/yt_common/2.1/lib/python2.7/site-packages/
>> > LD_LIBRARY_PATH => /lustre/scratch/proj/yt_common/2.1/lib/
>> >
>> > If you wish to use the unstable branch, which I'll update on Kraken
>> > when I remember to do it (or you can bug me if I haven't):
>> >
>> > YT_DEST => /lustre/scratch/proj/yt_common/unstable
>> > PATH => /lustre/scratch/proj/yt_common/unstable/bin/
>> > PYTHONPATH =>
>> > /lustre/scratch/proj/yt_common/unstable/lib/python2.7/site-packages/
>> > LD_LIBRARY_PATH => /lustre/scratch/proj/yt_common/unstable/lib/
>> >
>> > The older versions of yt at /lustre/scratch/proj/yt_common/2.0 and
>> > /lustre/scratch/proj/yt_common/trunk will be deleted within a week
>> > or
>> > so.
>> >
>> >
>> > --
>> > Stephen Skory
>> > s at skory.us
>> > http://stephenskory.com/
>> > 510.621.3687 (google voice)
>> > _______________________________________________
>> > yt-users mailing list
>> > yt-users at lists.spacepope.org
>> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >
>>
>>
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