[Beowulf] package management on Debian/Ubuntu (wasn't cluster os)

Tim Cutts tjrc at sanger.ac.uk
Fri May 20 04:28:58 PDT 2016

Yes and no.  My rule of thumb has always been to use the packaged version of a software package unless there's a very good reason not to.

We maintain a local package repository as well (using debarchiver), so if we need to make a custom version of a Debian/Ubuntu package, we generally make the change to the debian source package, build it with a new localised version number, and then upload it to our local repository.   For example, our local version of the blcr stuff:

12:24:13 tjrc at farm3-head2:~$ apt-cache policy blcr-dkms


  Installed: 0.8.5-2.1~sanger2

  Candidate: 0.8.5-2.1~sanger2

  Version table:

 *** 0.8.5-2.1~sanger2 0

        500 http://debian.internal.sanger.ac.uk/debian-sanger/ precise/main amd64 Packages

        100 /var/lib/dpkg/status

     0.8.2-15ubuntu2.1 0

        500 http://www.mirrorservice.org/sites/archive.ubuntu.com/ubuntu/ precise-updates/universe amd64 Packages

     0.8.2-15ubuntu2 0

        500 http://www.mirrorservice.org/sites/archive.ubuntu.com/ubuntu/ precise/universe amd64 Packages

12:24:54 tjrc at farm3-head2:~$

There are other cases where we just build from source separately (generally if it's something which has to work across multiple Linux versions, and therefore sits in our /software NFS filesystem).  We do this for our centrally supported R distributions, for example.



From: Jonathan Aquilina <jaquilina at eagleeyet.net<mailto:jaquilina at eagleeyet.net>>
Date: Friday, 20 May 2016 at 11:34
To: Tim Cutts <tjrc at sanger.ac.uk<mailto:tjrc at sanger.ac.uk>>
Cc: Christopher Samuel <samuel at unimelb.edu.au<mailto:samuel at unimelb.edu.au>>, Beowulf <beowulf at beowulf.org<mailto:beowulf at beowulf.org>>
Subject: Re: [Beowulf] cluster os

Going a bit off track from upgrades here.  In a cluster environment with debian do you spend a fair bit of time compiling anything from source?

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