[yt-users] Running YT in Parallel on Nautilus

Dave Semeraro semeraro at ncsa.illinois.edu
Fri Apr 8 11:39:20 PDT 2011


no problem. I requested NICS update their 1.7 to the latest stable version. 

----- Original Message -----
> 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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> >
> 
> 
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