[yt-users] Trying to use 16 CPUs via a python notebook

[Nathan Goldbaum]

Hi Rick,

You need to launch the notebook in parallel using an MPI parallel IPython
cluster.  In addition, you will need to configure the notebook to hook into
IPython's built-in parallelism.

I've uploaded a notebook that uses parallel IPython here:

http://nbviewer.ipython.org/gist/ngoldbaum/32ca07cf4f5b3dd06add

Note that all the yt operations aren't really important, but the first few
cells where I check to make sure IPython's parallelism works and that MPI
parllelism is working are quite important.

Note also that you will need to launch the IPython cluster separately from
the notebook server using the "ipcluster" command.

If you want to learn more about parallel IPython, I'd encourage you to take
a look at Min Ranger-Kelley's tutorial from scipy 2014:
http://pyvideo.org/video/2738/interactive-parallel-computing-with-ipython-part

All that said, it does add a significant amount of semantic overhead to use
the IPython notebook in parallel.  It's generally much more straightforward
to work with yt in parallel using regular python scripts.

Hope that helps,

Nathan

On Wed, Jan 14, 2015 at 6:49 PM, Rick Sarmento <rsarment at asu.edu> wrote:

> Hello,
>
> I’m pretty new to yt… I’m trying to speed things up significantly since I
> have rather large RAMSES datasets (running 3Mpc sims with 2^9^3 particles).
> I’m using STAMPEDE at TACC, https://vis.tacc.utexas.edu/# , to startup a
> notebook on their visualization nodes (each has 16 cores). I’m trying to use
>
> import yt
> yt.enable_parallelism()
> ds = yt.load("./output_00011/info_00011.txt”)
>
> and then
>
> # Looking through the "z" axis... Plot temp weighted by density
> p = yt.ProjectionPlot(ds, "z", "temperature", weight_field="density")
> p.annotate_title(z)
> p.show()
>
> but I only see one python process via top … and NO speedup. What do I need
> to do to take advantage of the 16 cores?
>
> *Cheers!*
>
> *Rick Sarmento*
> SESE Astronomy/Astrophysics Grad Student
> rsarment at asu.edu
>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20150116/43f1a1f6/attachment.html>