[IPython-dev] SciPy Sprint summary

Satrajit Ghosh satra@mit....
Sun Jul 18 13:01:03 CDT 2010


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>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>
>>>> wrote:
>>>>
>>>>> On Sat, Jul 17, 2010 at 6:23 AM, Satrajit Ghosh<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> 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>
>>>>>>> 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>
>>>>>>>>> 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
>>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> IPython-dev mailing list
>>>>>>>> IPython-dev@scipy.org
>>>>>>>> http://mail.scipy.org/mailman/listinfo/ipython-dev
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
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>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Brian E. Granger, Ph.D.
>>>>> Assistant Professor of Physics
>>>>> Cal Poly State University, San Luis Obispo
>>>>> bgranger@calpoly.edu
>>>>> ellisonbg@gmail.com
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>
>
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