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Re: HP compute nodes ; Is GNU parallel executing files in parallel?


From: Calvin Morrison
Subject: Re: HP compute nodes ; Is GNU parallel executing files in parallel?
Date: Wed, 28 Jun 2017 10:26:59 -0400

With regards to using a cluster,

It's possible you are being limited by the system administrator. If
you are using any type of queuing system it's possible there are
limitations in place. I would speak to them first for help. Also if
you are using a queue like Torque or similar, instead of using
parallel you could submit many jobs using their queue system instead
of trying to do the same thing in parallel

Calvin

On 27 June 2017 at 21:57, Ole Tange <address@hidden> wrote:
> On Tue, Jun 27, 2017 at 9:34 PM, Anukesh K A <address@hidden> wrote:
>
>> Hi,
>>
>> My name is Anukesh
>
> Hi Anukesh
>
> Thanks for your report.
>
> Unfortunately I have not been able to reproduce the behavior you see:
> Amongst other things I do not have access to
> /scratch/halstead/v/vmishra/DWN_FILE_NEW/*.
>
> Luckily there is a procedure that has proven to speed up finding a
> solution. This procedure is described in the section on Reporting Bugs
> in the man page:
>
> REPORTING BUGS
>
> Report bugs to <address@hidden> or
> https://savannah.gnu.org/bugs/?func=additem&group=parallel
>
> See a perfect bug report on
> https://lists.gnu.org/archive/html/bug-parallel/2015-01/msg00000.html
>
> Your bug report should always include:
>
> * The error message you get (if any).
>
> * The complete output of parallel --version. If you are not running
> the latest released version (see http://ftp.gnu.org/gnu/parallel/) you
> should specify why you believe the problem is not fixed in that
> version.
>
> * A minimal, complete, and verifiable example (See description on
> http://stackoverflow.com/help/mcve). It should be a complete example
> that others can run that shows the problem including all files needed
> to run the example. This should preferably be small and simple, so try
> to remove as many options as possible. A combination of yes, seq, cat,
> echo, and sleep can reproduce most errors. If your example requires
> large files, see if you can make them by something like seq 1000000 >
> file or yes | head -n 10000000 > file. If your example requires remote
> execution, see if you can use localhost - maybe using another login.
>
> * The output of your example. If your problem is not easily reproduced
> by others, the output might help them figure out the problem.
>
> * Whether you have watched the intro videos
> (http://www.youtube.com/playlist?list=PL284C9FF2488BC6D1), walked
> through the tutorial (man parallel_tutorial), and read the EXAMPLE
> section in the man page (man parallel - search for EXAMPLE:).
>
> If you suspect the error is dependent on your environment or
> distribution, please see if you can reproduce the error on one of
> these VirtualBox images:
> http://sourceforge.net/projects/virtualboximage/files/
> http://www.osboxes.org/virtualbox-images/
>
> Specifying the name of your distribution is not enough as you may have
> installed software that is not in the VirtualBox images.
>
> If you cannot reproduce the error on any of the VirtualBox images
> above, see if you can build a VirtualBox image on which you can
> reproduce the error. If not you should assume the debugging will be
> done through you. That will put more burden on you and it is extra
> important you give any information that help. In general the problem
> will be fixed faster and with less work for you if you can reproduce
> the error on a VirtualBox.
>
> ---
>
> Hope this will get you further.
>
>
> /Ole
>



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