[IPython-dev] SciPy Sprint summary

Justin Riley justin.t.riley@gmail....
Sun Jul 18 02:43:27 CDT 2010


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
>>>>>
>>>>> _______________________________________________
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>>>>> 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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