[Beowulf] Gentoo in the HPC environment

Gavin W. Burris bug at wharton.upenn.edu
Mon Jun 30 06:22:27 PDT 2014

Hi, Jonathan.

If you have access to a RHEL or CentOS 6 system, you can see
all the running kernel options in one of these files:
/usr/src/kernels/`uname -r`/.config
/boot/config-`uname -r`

I get what your saying about optimization.  I understand Gentoo touts
the ability to recompile EVERYTHING with custom compiler options.  But,
like I've said, you are then in unsupported territory.  I am protective
of my time; I prefer not to double-check that fiddling with the build
environment does not break each individual piece of installed software.
I am also wary of over-optimizing and created subtle bugs / decelerating
codes!  :D  Give your users the latest Intel compiler for their
applications instead, since that is where the majority of your CPU time
is spent.

The following document has lots of good optimization info.  Much of what
is said here may be applicable to Linux, in-general.  I cannot overstate
the added value engineers at Red Hat are contributing here by testing
all of this as a whole.

That said, nothing is stopping you from rebuilding a CentOS kernel with
different options and sticking it in a local yum repo.  Also, you can do
a very minimal install; The default happens to be just that, default.
I'm looking at a not-so-minimal boot of CentOS 6, 113 MB memory used.


On Sat 06/28/14 03:38PM +0200, Jonathan Aquilina wrote:
> Correct me if I am wrong here, and apologies for the delay as this thread
> and discussion has really taken off.
> My arguments for gentoo is more along the lines of optimization of the
> source code for ones hardware.
> You mention CentOS and Red hat how optimized is the heart of the system
> for the hard ware its running on? How secure are they as an os? Reason I
> bring up these questions is that I feel that resource are wasted that
> could be used for more important things.
> Another thing that I like about gentoo is the hardened profiles as well as
> the extra security features that one can setup at the kernel level as
> well, but that is going off my point.
> I for instance currently even though nothing is running on it have a vps
> with 2gb of ram and with no websites or db on there yet just the servers
> ram wise i use about 62mb. I look at the low memory foot print as an
> advantage in the sense that the rest of the ram can be used for more
> important things.
> > Hi, Jonathan.
> >
> > I would make a strong argument against Gentoo.  I would recommend that
> > you choose Red Hat or its binary-compatible derivatives, like CentOS.
> >
> > At the end of the day, you need to ask yourself what you are trying to
> > accomplish.  In an HPC environment, that should be a customer-facing
> > service that is reliable and well supported.  You do not want to be
> > constantly patching, compiling or changing APIs out from underneath of
> > research code.  Enterprise Linux provides a stable base for HPC
> > application development with a very solid lifecycle.
> > https://access.redhat.com/site/support/policy/updates/errata/
> >
> > Being part of a larger community, running the same builds, has its
> > advantages.  You won't be the only person encountering a weird stability
> > or performance bug.  You also get vendor hardware support, which is
> > huge.
> >
> > I know the counter arguments here.  There is always going to be the
> > coder that wants Ubuntu and this-month's release of $LANGUAGE, like on
> > their vagrant box.  I have found the Software Collections to be a
> > fantastic solution to this demand.  You get the stability of an
> > enterprise OS, plus the latest language features for developers.  This,
> > along with environment modules, is win-win.
> > http://wiki.centos.org/AdditionalResources/Repositories/SCL
> >
> > Even if you are a one-man shop, ask yourself what you want to be doing.
> > Do you want to be a systems programmer, or do you want to be a
> > research application developer.  Your time is precious.  Choose wisely.
> >
> > Cheers.
> >
> >
> > On Tue 06/24/14 08:43AM +0200, Jonathan Aquilina wrote:
> >> Hey guys,
> >>
> >> I am just curious as I have recently switched to Gentoo for every day
> >> use
> >> due to its customizability and how everything is compiled for a
> >> particular
> >> system.  Has anyone used Gentoo in an HPC application?
> >>
> >> Regards,
> >> Jonathan
> >>
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> > --
> > Gavin W. Burris
> > Senior Project Leader for Research Computing
> > The Wharton School
> > University of Pennsylvania
> >

Gavin W. Burris
Senior Project Leader for Research Computing
The Wharton School
University of Pennsylvania

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