Re: [AMBER] Best Linux Choice

From: Jason Swails <>
Date: Fri, 20 May 2016 14:04:59 -0400

I've played with way too many Linux distros in my time:

- Ubuntu (and its variants, Xubuntu, Lubuntu, and Kubuntu)
- Debian (from which Ubuntu is derived, but is more stable and has a slower
release schedule)
- Fedora (like Ubuntu)
- CentOS/RHEL (is to Fedora what Debian is to Ubuntu, loosely speaking)
- Mandriva
- OpenSUSE
- Gentoo

On my workstation, I love Gentoo. Nothing else even compares.

For clusters, I've usually seen centers run either CentOS/RHEL or Debian
(the slower-updating, more stable variants of Fedora and Ubuntu). They are
chosen specifically for this advertised stability, but that comes at a cost
-- you can't rely on the package manager to maintain a proper, up-to-date
scientific computing stack. You often have to install all of your own
libraries and programs from source and deploy them somewhere with a
sophisticated environment management system (think "module load <program>"
at supercomputers).

Most of the advice given here comes from people very familiar and
passionate about their workstation environment (myself included), but
scaling that up to a cluster is completely different. Ross actually works
at a supercomputing center (SDSC), and probably has the most direct
experience with actual dedicated clusters (although even he does a lot more
research than administering clusters). I'll just point out a few comments:

- Maintaining a cluster is a demanding job. Supercomputer centers have
teams of people managing them. This is not something you want to do as a
side-project with your primary role being researcher.
- A good workstation environment does not necessarily translate into a good
cluster environment (and vice versa) -- in fact, I despise having my
workstation be CentOS or Debian and would probably pull my hair out
administering a Gentoo cluster (but maybe not -- I've never administered a
cluster before)

So my advice here is the following:

- If you have to maintain the cluster, first try really really hard to get
it maintained by dedicated experts. Failing that, try harder. Failing
that, pick the distro you think you could get the most help with from local
experts/enthusiasts (including yourself)
- If some expert is maintaining it, let them choose ;)

All the best,

On Fri, May 20, 2016 at 9:03 AM, Robert Molt <> wrote:

> Good morning in the USA, good afternoon in Europe...
> I have to choose a flavor of Linux for a new cluster my research group
> is building, intending to run Amber with GPU execution (among other
> things). I am not used to making system admin-style choices and am
> soliciting advice.
> I am sure Amber can be properly compiled on many forms of Linux, with
> varying ease. I cannot get RedHat, unfortunately. Some of the free forms
> of Linux suffer from a lack of stability (constant updates). Do Amber
> veterans have strong opinions about a "best" overall choice in
> Linux-style to go with for computers intended to compile Amber? I am
> only experienced in RedHat, Ubuntu, and Mint but am happy to adapt to
> any flavor.
> --
> Dr. Robert Molt Jr.
> _______________________________________________
> AMBER mailing list

Jason M. Swails
AMBER mailing list
Received on Fri May 20 2016 - 11:30:03 PDT
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