[Beowulf] First cluster in 20 years - questions about today

Jörg Saßmannshausen sassy-work at sassy.formativ.net
Thu Feb 6 14:05:55 PST 2020

Dear all,

my saying as well. See my previous message.

All the best


Am Montag, 3. Februar 2020, 09:31:41 GMT schrieb David Mathog:
> On 2020-02-02 19:25, beowulf-request at beowulf.org wrote:
> >> On Sat, 1 Feb 2020 22:21:09 -0500, you wrote:
> >> >Should I consider Solaris or illumos?
> >> 
> >> Unless you are absolutely sure the software you want to run works on
> >> Solaris, using Solaris/Illumos is likely asking for trouble.
> > 
> > I'm testing FreeBSD right now and will test *SunOS before commiting a
> > full
> > deployment.
> Stop wasting time on that - support for OS's other than linux for
> academically maintained scientific software is spotty at best.   The
> only one that even comes close is OS X, because a lot of academics have
> Macs, but it would be super expensive to build a cluster out of those.
> Moreover, many developers, in biology at least, have pretty much given
> up on portability and focus on providing docker images.  In those cases
> you may find that building from source (needed for maximum performance)
> on even common variants like CentOS can be difficult.
> > My initial 3 nodes are socket 940 Opteron based.
> Fine chip in its time, which is however long past.  Even a 5 year old
> Xeon will run rings around.  I say that having just thrown out the last
> of my Opterons and replaced them with 5 year old Xeons!
> A bit of research up front on memory and cpu requirments for the
> software you want to run should pay off performance wise in the final
> cluster. Some code demands a lot of memory but can barely make use of a
> second core while other software is exactly the other way around.  If
> the processing is split between different machines the speed and type of
> network connection will be an issue.  You need some handle on this
> before you start buying hardware because both "a lot of memory" and "a
> lot of cores" ups the cost.
> Consider also that you might want to run GPU versions of some programs.
> When that is available it can be a significant performance enhancement.
> Will each of your nodes be able to support a GPU?   Plan ahead as these
> often have quite large power requirements which may overload your supply
> circuits or overwhelm a room's A/C.
> Regards,
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
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