[IPython-dev] SciPy Sprint summary
Justin Riley
justin.t.riley at gmail.com
Sun Jul 18 14:20:28 EDT 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 at gmail.com
> <mailto:justin.t.riley at 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 at gmail.com <mailto:ellisonbg at gmail.com>>
> wrote:
>
> On Sat, Jul 17, 2010 at 6:23 AM, Satrajit
> Ghosh<satra at mit.edu <mailto:satra at 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 at mit.edu <mailto:satra at 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 at gmail.com
> <mailto:justin.t.riley at 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 at gmail.com
> <mailto:ellisonbg at 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 at calpoly.edu <mailto:bgranger at calpoly.edu>
> ellisonbg at gmail.com <mailto:ellisonbg at gmail.com>
>
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