Hi Carlos,

I previously used Galaxy with a GridEngine cluster. Having GridEngine is no 
more complex than having SLURM.

R.E. you other email, recording cluster usage for labs' galaxy jobs, that 
requires the 'running jobs as real user' setup...


There are caveats with that setup r.e. file permissions / privacy of data 
between groups. In our situation everything has to be kept private, so to 
ensure jobs run as a real cluster user we have a complex setup using Galaxy 
pulsar as well as SLURM. Some notes on that in a GitHub issue here:




-----Original Message-----
From: Carlos Lijeron [mailto:clije...@hunter.cuny.edu]
Sent: Tuesday, May 05, 2015 11:18 AM
To: David Trudgian; Peter Cock
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Galaxy on CentOS?


We are in our final configuration stage and tomorrow we have a conversation 
with Silicon Mechanics business integration team to discuss the workload 
manager, and other details about the data center backbone speed.

As per your suggestion I inquired about using SLURM instead of SGI, but I 
havenĀ¹t been able to make a good case as to why this is.  My only support is 
your email / suggestion and your existing experience with an HPC, Bright and 

My inexperience with this type of setups and lack of personnel at our 
institution makes me rely 100% of everyone's feedback in this group

Thank you David and anyone else in the group for your contributions and 

Attached is the diagram of our future implementation.  Another concern that I 
have is that our sequencer will be located 0.5 miles from the HPC, but there is 
a 10 Gpbs point to point connection between the 2 buildings.
I wanted to find a way to calculate / predict the average amount of traffic 
that will go from the sequencer to the HPC so we can allocate specific 
bandwidth for our use and leave the rest to other users.


On 5/5/15, 10:24 AM, "David Trudgian" <david.trudg...@utsouthwestern.edu>

>Our Galaxy is running on RedHat 6.6 on our cluster - which is basically
>identical to CentOS 6.6. Per Peter's email we haven't had any big
>issues with Galaxy on CentOS 6.x.
>You are likely to want to use the postgresql packages from
>www.postrgresql.org, not the out-of-date versions that come with the
>distribution. I also installed an up-to-date python 2.7.x for Galaxy
>using pyenv but this shouldn't be necessary - Galaxy should work fine
>on python 2.6. In my case I did it to have a standard setup with other
>apps that do need python 2.7.
>Which workload manager will your cluster manager be configured to use?
>-----Original Message-----
>From: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] On
>Behalf Of Peter Cock
>Sent: Tuesday, May 05, 2015 3:13 AM
>To: Carlos Lijeron
>Cc: galaxy-dev@lists.galaxyproject.org
>Subject: Re: [galaxy-dev] Galaxy on CentOS?
>Hi Carlos,
>We're running Galaxy on CentOS 6.6, so that in itself shouldn't be a
>problem. Most of the effort was sorting out shared storage with the
>cluster, which in our case is managed with SGE (fairly commonly used
>with Galaxy).
>In reply to your thread last month David Trudgian said he was using
>Bright Cluster Manager:


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