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From: John Kitchin <jkitchin@andrew.cmu.edu>
To: Christoph Groth <christoph@grothesque.org>
Cc: "emacs-orgmode@gnu.org" <emacs-orgmode@gnu.org>
Subject: Re: babel and long-running computations
Date: Sun, 20 Apr 2014 09:29:33 -0400	[thread overview]
Message-ID: <CAJ51ETqAUdey5tuE62fAQ0hNPH+kD_0CfOYKmd_5tbpkk5p-ZA@mail.gmail.com> (raw)
In-Reply-To: <87lhv4ut1n.fsf@grothesque.org>

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You are describing what I see as a need to run processes asynchronously.

We use the Torque queue system for this. It takes care of scheduling and
running jobs on a cluster.

On Thu, Apr 17, 2014 at 6:52 AM, Christoph Groth

> Hi Julian,
> > Generally, org-babel is suited for long running computations.  Its
> > caching can help you avoid rerunning code chunks.  And long runtime does
> > not conflict with the idea of reproducible research, it just may be not
> > very comfortable for the user.
> I agree of course that it’s generally a good idea to structure the
> analysis in small logical steps and to save intermediate results.  Let
> me narrow down my question then: does org-babel support working with
> tasks that take several minutes to execute?  By this I mean (most
> important first):
> - Not freezing the editor during the execution of a task

You code-block should exit if a job is submitted, and record the job-id so
that you can check it later. Alternatively, you could do this in ipython
notebooks if you have python functions that return jobids.

> - Being able to execute multiple independent tasks in parallel

No problem. this is what queue systems were designed for.

> - Being able to interrupt a running task

you do this with the queue commands, e.g. qdel jobid

> - Being able to inspect the incomplete output of a running task

This is just checking the output files in the running jobs directories.

> I’d love to hear about any frameworks or workflows that fulfill these
> requirements.
> Cheers
> Christoph
> PS.
> I’m using ipython notebooks but I’m not happy with them because of the
> freezing problem and the complete lack of isolation of tasks within a
> single notebook (they live in a common mutable namespace).  I think a
> useful framework must be “functional” at the highest level for caching
> and dependencies to be useful.

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  parent reply	other threads:[~2014-04-20 13:29 UTC|newest]

Thread overview: 14+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2014-04-17  8:45 babel and long-running computations Christoph Groth
2014-04-17  9:47 ` Julian Gehring
2014-04-17 10:52   ` Christoph Groth
2014-04-17 12:06     ` Thorsten Jolitz
2014-04-17 12:45       ` Christoph Groth
2014-04-17 14:58         ` Waldemar Quevedo
2014-04-17 15:29         ` Eric Schulte
2014-04-17 16:29           ` Christoph Groth
2014-04-17 16:44             ` Nick Dokos
2014-04-17 15:33     ` Eric S Fraga
2014-04-20 13:29     ` John Kitchin [this message]
2014-04-18 13:20 ` John Kitchin
2014-04-19 21:49   ` Christoph Groth
2014-04-20 13:21     ` John Kitchin

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