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

David Mathog mathog at caltech.edu
Mon Feb 3 09:31:41 PST 2020

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.


David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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