[Bio-linux-dev] scheduler on Bio-Linux

Tim Booth tbooth at ceh.ac.uk
Tue Feb 17 14:03:01 EST 2015


Hi Jimmy,

So if you do:

$ sudo apt-get install gridengine-master torque-server slurm-llnl

In just a few seconds you'll have all three!

But this is not much use.  The problem is that all need to be properly
configured for your computing environment and as people's set-ups and
requirements are different I can't provide a single generic
configuration - you have to read up on your chosen job scheduler and set
it up for your own needs.

If you try to use one of the above and run into problems please do post
questions on the bio-linux users list (not this bio-linux-dev list)
because I know that several Bio-Linux users work on clusters and may be
able to help out.

Cheers,

TIM

On Tue, 2015-02-17 at 14:13 +0000, Jimmy Griffin wrote:
> Yes, something like SGE, Torque, or Slurm?
> 
> 
> On Tue, Feb 17, 2015, 7:00 AM null
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>            2. Re: Scheduler included into BioLinux 7+ (Tim Booth)
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>         Message: 1
>         Date: Tue, 17 Feb 2015 00:01:16 -0500
>         From: Jimmy Griffin <jimmy.g.griffin at gmail.com>
>         To: bio-linux-dev at nebclists.nerc.ac.uk
>         Subject: [Bio-linux-dev] Scheduler included into BioLinux 7+
>         Message-ID:
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>         <CAFRHGrie3yqSDXqZ6k_vK=xtAD0a1cN_8Wcgjc=HBH5eOp2zYg at mail.gmail.com>
>         Content-Type: text/plain; charset="iso-8859-1"
>         
>         Hello,
>         
>         Would there be any chance a scheduler be included into the
>         current or
>         future releases of Bio-Linux?
>         
>         --
>         Jimmy Griffin
>         
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>         Message: 2
>         Date: Tue, 17 Feb 2015 09:11:12 +0000
>         From: Tim Booth <tbooth at ceh.ac.uk>
>         To: Bio-Linux technical discussion
>                 <bio-linux-dev at nebclists.nerc.ac.uk>
>         Subject: Re: [Bio-linux-dev] Scheduler included into BioLinux
>         7+
>         Message-ID:
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>         <1424164272.12415.44.camel at wllt1771.nerc-wallingford.ac.uk>
>         Content-Type: text/plain; charset="UTF-8"
>         
>         Hi Jimmy,
>         
>         I'm not exactly sure what you mean by "a scheduler".  Do you
>         mean
>         something like SLURM or Condor?
>         
>         Cheers,
>         
>         TIM
>         
>         On Tue, 2015-02-17 at 05:01 +0000, Jimmy Griffin wrote:
>         > Hello,
>         >
>         >
>         > Would there be any chance a scheduler be included into the
>         current or
>         > future releases of Bio-Linux?
>         >
>         >
>         > --
>         > Jimmy Griffin
>         >
>         > The information contained in this email may be confidential
>         and/or
>         > legally
>         > privileged. It has been sent for the sole use of the
>         intended
>         > recipient(s).
>         > If the reader of this message is not an intended recipient,
>         you are
>         > hereby
>         > notified that any unauthorized review, use, disclosure,
>         > dissemination,
>         > distribution, or copying of this communication, or any of
>         its content,
>         > is
>         > strictly prohibited. If you have received this communication
>         in
>         > error,
>         > please contact the sender by reply email and destroy all
>         copies of
>         > the
>         > original message. Thank you.
>         >
>         >
>         
>         --
>         Tim Booth <tbooth at ceh.ac.uk>
>         NERC Environmental Bioinformatics Centre
>         
>         Centre for Ecology and Hydrology
>         Maclean Bldg, Benson Lane
>         Crowmarsh Gifford
>         Wallingford, England
>         OX10 8BB
>         
>         http://environmentalomics.org/bio-linux
>         +44 1491 69 2297
>         
>         
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>         End of Bio-Linux-dev Digest, Vol 46, Issue 4
>         ********************************************

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297




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