[IPython-dev] SciPy Sprint summary

Justin Riley justin.t.riley@gmail....
Sun Jul 18 13:20:28 CDT 2010


Hi Satra,

 > i think it will be good to at least put the queue to
 > be used as a user option. most of the time installations of torque or
 > sge have multiple queues.

Agreed, this would be useful. I'll try to hack it in later tonight 
unless you get to it first ;)

~Justin


On 07/18/2010 02:01 PM, Satrajit Ghosh wrote:
> hi justin,
>
> this is fantastic. i think it will be good to at least put the queue to
> be used as a user option. most of the time installations of torque or
> sge have multiple queues.
>
> cheers,
>
> satra
>
>
> On Sun, Jul 18, 2010 at 1:02 PM, Justin Riley <justin.t.riley@gmail.com
> <mailto:justin.t.riley@gmail.com>> wrote:
>
>     Forgot to mention, in my fork PBS now automatically generates a
>     launch script as well if one is not specified. So, assuming you have
>     either SGE or Torque/PBS working it *should* be as simple as:
>
>     $ ipcluster sge -n 4
>
>     or
>
>     $ ipcluster pbs -n 4
>
>     You can of course still pass the --sge-script/--pbs-script options
>     but the user is no longer required to create a launch script themselves.
>
>     ~Justin
>
>
>     On 07/18/2010 12:58 PM, Justin Riley wrote:
>
>         Turns out that torque/pbs also support job arrays. I've updated my
>         0.10.1-sge branch with PBS job array support. Works well with torque
>         2.4.6. Also tested SGE support against 6.2u3.
>
>         Since the code is extremely similar between PBS/SGE I decided to
>         update
>         the BatchEngineSet base class to handle the core job array
>         logic. Given
>         that PBS/SGE are the only subclasses I figured this was OK. If not,
>         should be easy to break it out again.
>
>         ~Justin
>
>         On 07/18/2010 03:43 AM, Justin Riley wrote:
>
>             Hi Satra/Brian,
>
>             I modified your code to use the job array feature of SGE.
>             I've also made
>             it so that users don't need to specify --sge-script if they
>             don't need a
>             custom SGE launch script. My guess is that most users will
>             choose not to
>             specify --sge-script first and resort to using --sge-script
>             when the
>             generated launch script no longer meets their needs. More
>             details in the
>             git log here:
>
>             http://github.com/jtriley/ipython/tree/0.10.1-sge
>
>             Also, I need to test this, but I believe this code will fail
>             if the
>             folder containing the furl file is not NFS-mounted on the
>             SGE cluster.
>             Another option besides requiring NFS is to scp the furl file
>             to each
>             host as is done in the ssh mode of ipcluster, however, this
>             would
>             require password-less ssh to be configured properly (maybe
>             not so bad).
>             Another option is to dump the generated furl file into the
>             job script
>             itself. This has the advantage of only needing SGE installed but
>             certainly doesn't seem like the safest practice. Any
>             thoughts on how to
>             approach this?
>
>             Let me know what you think.
>
>             ~Justin
>
>             On 07/18/2010 12:05 AM, Brian Granger wrote:
>
>                 Is the array jobs feature what you want?
>
>                 http://wikis.sun.com/display/gridengine62u6/Submitting+Jobs
>
>                 Brian
>
>                 On Sat, Jul 17, 2010 at 9:00 PM, Brian
>                 Granger<ellisonbg@gmail.com <mailto:ellisonbg@gmail.com>>
>                 wrote:
>
>                     On Sat, Jul 17, 2010 at 6:23 AM, Satrajit
>                     Ghosh<satra@mit.edu <mailto:satra@mit.edu>> wrote:
>
>                         hi ,
>
>                         i've pushed my changes to:
>
>                         http://github.com/satra/ipython/tree/0.10.1-sge
>
>                         notes:
>
>                         1. it starts cleanly. i can connect and execute
>                         things. when i kill
>                         using
>                         ctrl-c, the messages appear to indicate that
>                         everything shut down
>                         well.
>                         however, the sge ipengine jobs are still running.
>
>
>                     What version of Python and Twisted are you running?
>
>                         2. the pbs option appears to require mpi to be
>                         present. i don't
>                         think one
>                         can launch multiple engines using pbs without
>                         mpi or without the
>                         workaround
>                         i've applied to the sge engine. basically it
>                         submits an sge job for
>                         each
>                         engine that i want to run. i would love to know
>                         if a single job can
>                         launch
>                         multiple engines on a sge/pbs cluster without mpi.
>
>
>                     I think you are right that pbs needs to use
>                     mpirun/mpiexec to start
>                     multiple engines using a single PBS job. I am not
>                     that familiar with
>                     SGE, can you start mulitple processes without mpi
>                     and with just a
>                     single SGE job? If so, let's try to get that working.
>
>                     Cheers,
>
>                     Brian
>
>                         cheers,
>
>                         satra
>
>                         On Thu, Jul 15, 2010 at 8:55 PM, Satrajit
>                         Ghosh<satra@mit.edu <mailto:satra@mit.edu>> wrote:
>
>
>                             hi justin,
>
>                             i hope to test it out tonight. from what
>                             fernando and i discussed,
>                             this
>                             should be relatively straightforward. once
>                             i'm done i'll push it to
>                             my fork
>                             of ipython and announce it here for others
>                             to test.
>
>                             cheers,
>
>                             satra
>
>
>                             On Thu, Jul 15, 2010 at 4:33 PM, Justin
>                             Riley<justin.t.riley@gmail.com
>                             <mailto:justin.t.riley@gmail.com>>
>                             wrote:
>
>
>                                 This is great news. Right now
>                                 StarCluster just takes advantage of
>                                 password-less ssh already being
>                                 installed and runs:
>
>                                 $ ipcluster ssh --clusterfile
>                                 /path/to/cluster_file.py
>
>                                 This works fine for now, however, having
>                                 SGE support would allow
>                                 ipcluster's load to be accounted for by
>                                 the queue.
>
>                                 Is Satra on the list? I have experience
>                                 with SGE and could help
>                                 with the
>                                 code if needed. I can also help test
>                                 this functionality.
>
>                                 ~Justin
>
>                                 On 07/15/2010 03:34 PM, Fernando Perez
>                                 wrote:
>
>                                     On Thu, Jul 15, 2010 at 10:34 AM, Brian
>                                     Granger<ellisonbg@gmail.com
>                                     <mailto:ellisonbg@gmail.com>>
>                                     wrote:
>
>                                         Thanks for the post. You should
>                                         also know that it looks like
>                                         someone
>                                         is going to add native SGE
>                                         support to ipcluster for 0.10.1.
>
>
>                                     Yes, Satra and I went over this last
>                                     night in detail (thanks to
>                                     Brian
>                                     for the pointers), and he said he
>                                     might actually already have some
>                                     code for it. I suspect we'll get
>                                     this in soon.
>
>                                     Cheers,
>
>                                     f
>
>
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>
>
>                     --
>                     Brian E. Granger, Ph.D.
>                     Assistant Professor of Physics
>                     Cal Poly State University, San Luis Obispo
>                     bgranger@calpoly.edu <mailto:bgranger@calpoly.edu>
>                     ellisonbg@gmail.com <mailto:ellisonbg@gmail.com>
>
>
>
>
>
>
>
>



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