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Re: Advice on using parallel as a batch queue system


From: Ole Tange
Subject: Re: Advice on using parallel as a batch queue system
Date: Wed, 9 Jan 2013 10:56:49 +0100

On Tue, Jan 8, 2013 at 6:22 PM, Tong, Lianheng <address@hidden> wrote:

> This is my first post and I am very pleased to have discovered gnu parallel 
> about a month ago. It had saved me a lot hassle while running a lot of serial 
> simulation jobs. So a big thanks to the developers :-)

I am happy it helped you. If you like GNU Parallel:

* Post the intro videos on Reddit/Diaspora*/forums/blogs/
  Identi.ca/Google+/Twitter/Facebook/Linkedin/mailing lists
* Get the merchandise https://www.gnu.org/s/parallel/merchandise.html
* Give a demo at your local user group/team/colleagues
* Request or write a review for your favourite blog or magazine
* Request or build a package for your favourite distribution (if it is
not already there)
* Invite me for your next conference (Contact http://ole.tange.dk)

If you use GNU Parallel for research:

* Please cite GNU Parallel in you publications (use --bibtex)

If GNU Parallel saves you money:

* (Have your company) donate to FSF https://my.fsf.org/donate/

> I have however encountered some problems when trying to use parallel as a 
> batch queue,
:
> So it seems that jobs are only run AFTER job-slots number (in this case 4) of 
> jobs have been submitted. If I have only sent 3 jobs to the queue, then none 
> of the jobs are executed until I send the SIGTERM to parallel to terminate 
> the queue.

>From 'man parallel':

  There are a two small issues when using GNU parallel as queue
system/batch manager:

  * You will get a warning if you do not submit JobSlots jobs within
the first second. E.g. if you have 8 cores and use -j+2 you have to
submit 10 jobs. These can be dummy jobs (e.g. echo foo). You can also
simply ignore the warning.

  * Jobs will be run immediately, but output from jobs will only be
printed when JobSlots more jobs has been started. E.g. if you have 10
jobslots then the output from the first completed job will only be
printed when job 11 is started.

It seems the warning is not working any more. But the essence is that
if you have 4 JobSlots, then you have to submit 4 jobs before they
start. After that you can submit one at a time.

After the first 4 jobs have completed, output of every job is delayed
by 4 jobs (unless you use --ungroup), but the job is run immediately.

There are 2 ways from here:

* Help re-phrasing the text in the man-page, so it is more clear what
is going on.

* Submit a patch that fixes the bug (without breaking/slowing down the
rest). Since this is a bug that:
    - does not affect me
    - does not seem critical
    - has a work-around
    - I do not get paid to fix
  then I am unlikely to spend time fixing it, but I will look
favourably at a patch that fixes it.

Hope that clears up the situation.


/Ole



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