[Beowulf] Please help to setup Beowulf

Robert G. Brown rgb at phy.duke.edu
Tue Feb 17 06:34:24 PST 2009

On Tue, 17 Feb 2009, Mike Davis wrote:

> Geoff Jacobs wrote:
>> Why do you say this? Debian (5.0, what I checked just now) includes all
>> the basic Beowulf elements and even tosses in GROMACS pre-compiled for
>> OpenMPI. If it's what his people are used to there's no reason to switch.
> I don't know about RGB, but I would argue that you let your applications lead

rgb has given up distro wars for lent, sorry.  His bot thinks that
Debian is peachy, while running on Fedora, and feeling warm and fuzzy
towards Centos.  It thinks SuSE is Sexy, Mandriva is Magic, and even
manages to have great respect for those that just start from sources and
build the whole damn thing, automagically or not.

rgb is very, very slightly less enamored of "on-top-of" cluster linuces,
not because they aren't marvelous works of collective beauty but because
for many purposes the larger distros have engulfed them and simply
co-opted many of the packages they once provided as "extra".  Fedora 10
is up to some 15,000 prebuilt packages (including GROMACS as well), and
of course it is STILL far behind Debian (but EVERYTHING is behind Debian
in raw package count;-). Note well that he still loves them as well, but
thinks of them as sort of like kissing your sister, or perhaps your aunt
Katie -- the one that always gives you $100 for your birthday but who
likes to pinch your cheek and has a mustache.

It's worth it, barely, if you REALLY need the money.  And we all
remember when she did give us some very cool presents in Christmases

> you to OS choice because they are the whole point. If your apps won't  (or 
> won't readily ) run on your OS, you need a different OS.

With that said, I of course agree dead on with this statement.  However,
I just wanted (and continue to want) a concrete statement of just what
the cluster consists of and what he plans to do with it before messing
with the question.  We also need to identify whether or not we're
starting at the "This is called a `category 5 ethernet cable' and plugs
into this `RJ-45 Jack' that you can find on the back of your computer
case" level or if we're simply telling him how to install GROMACS (or
whatever) on a PoPC already set up on a network and getting him to where
he can start it on the command line.

> In my case I primarily run CentOS because it provides support for a number of 
> apps that are pre-built for RedHat and has the tools I need to build new 
> apps. I tried Ubuntu on a small cluster that I was helping a Quantum Chemist 
> setup and found nothing but frustration. Due to the slow internet connection 
> at his home, any update was painfully slow.The base install lacked compilers 
> but had oh so much multimedia support. I hoped that the install could be 
> customized in a manner similar to using kickstart (which I've been using 
> since 1995 or so), but I couldn't find that capability in the documentation.

Home installs are a PITA, no doubt.  Distros are now rather large, and
watching a multi-GB-through-DSL install is like watching an enterprising
yellowjacket try to down a triple-cream mocha enorme through its itty
bitty probiscis.  Come back later.  Much later.  And watch out for the
fat, buzzy yellowjacket when you do.

> All of his work and the various programs that interested him required fortran 
> which was still another update. After several evenings of searching and 
> trying to setup proxy servers for updates to nodes. I switched the entire 
> cluster (4 nodes) to CentOS and had his primary application (GAMESS) running 
> in a few minutes compiled for both serial and ddi sockets.
> In short, the applications are the whole point of a working cluster. If an OS 
> will not readily support the apps, you need a new OS.

Absolutely.  And as soon as we find out what he wants to do and what
he's trying to do it on, we'll figure out if he needs a new OS.  But he
probably CAN get by with Debian OR Centos OR Fedora OR Oscarocks OR SL
OR SuSE -- with only mildly differential work.  So we need to eventually
hear how skilled he is with any of the distros.  If he's never used
anything but Windows (installed by somebody else) then reinstalling to
ANY of them is going to be an uphill battle compared to (maybe) running
apt to get whatever.

And assuming he's in India, I have no idea what HIS bandwidth issues
are.  If he's someplace small and relatively poor with a very thin and
heavily shared pipe to the outside world, a reinstall to anything at all
might well entail waiting on that damn yellowjacket, or in his case
these orange-yellow paper wasps that like to come to water sources and
whose stings (I know from bitter experience) hurt like hell.  I'd hate
to see one hopped up on a double espresso and a whole lot of sugar...


> Mike
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Robert G. Brown	                       http://www.phy.duke.edu/~rgb/
Duke University Dept. of Physics, Box 90305
Durham, N.C. 27708-0305
Phone: 1-919-660-2567  Fax: 919-660-2525     email:rgb at phy.duke.edu

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