[Bioclusters] Operating system choice.

Chris Smith bioclusters@bioinformatics.org
Wed, 12 Nov 2003 10:30:39 -0800


On the linux side, LSF is dependent on kernel version and glibc version,
not the distribution version and type. In our readme files you'll see us
refer to specific versions of distributions, but that's more an
indication of what our QA department has actively tested on. I've run
LSF on many different combinations of kernel/glibc. We also don't use
rpm, so not worries there. :-)

We don't support FreeBSD. I've tried running in the linux compatibility
layer, but since we pull a lot of information out of /proc, this didn't
work too well (our lim wouldn't run, which basically means the machine
can't be in the cluster). I will say that the last time I tried this was
with a FreeBSD 4.0 machine, and I haven't tried since, so if anybody
knows any different, I'd like to know. 

Another point with FreeBSD (from your management's perspective), is that
we don't support it officially, so this could have an impact on the
decision. 

Hope this helps.

-- Chris

On Wed, 2003-11-12 at 10:00, David Robillard wrote:
> Good evening everyone,
> 
> I'm in the process of building a compute farm and my main concern is with the Operating System choice.
> 
> As a unix systems admin, I'm not a big fan of Red Hat linux products (or anything RPM based for that matter), because of dependency problems inherent to RPM. I would prefer to go with Debian GNU/Linux or with FreeBSD. Unfortunately, my Upper Management team thinks Linux and Red Hat are identical.
> 
> I thus face two barriers:
> 
> a) The OS needs to be compatible with Platform LSF and Veritas NetBackup client.
> 
> b) I need proper arguments to demonstrate to Upper Management why we should NOT use Red Hat. 
> 
> Therefore, 
> 
> Does anyone have experience with LSF/NetBackup on Debian or FreeBSD?
> 
> Could someone help me put together a "sales pitch" for either Debian or FreeBSD? Otherwise, the OS choice will be a business choice and not a technical/systems administration choice. Hence I'll be "stuck" with it...
> 
> Here are some details or the environment:
> 
> -I have 5+ years experience running Solaris, Debian, FreeBSD and Red Hat machines.
> -This compute farm will be running on x86 architecture, the Intel Xeon CPU.
> -Gigabit ethernet will be used for interconnect, nothing fancy here.
> -Master node will be connected to a SAN and will be backed-up by Veritas NetBackup.
> -Compute nodes will boot via PXE/Etherboot (undecided yet) and mount their kernel via NFS. A local drive will be there for swap.
> -The applications running on this compute farm are in-house algorithms which don't use MPI nor PVM.
> 
> Thanks for your help,
> 
> David
> 
> --
> David Robillard
> UNIX systems administrator
> david.robillard@galileogenomics.com
> +1 514 270 3991 x285
> Galileo Genomics
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