[Beowulf] Gentoo in the HPC environment

Jonathan Aquilina jaquilina at eagleeyet.net
Sat Jun 28 07:54:34 PDT 2014

Rapidly changing distros is mentioned in the response. What would classify
a rapidly changing distro. Take ubuntu is there six month release cycle
quick enough and even then they still wont have the latest versions of

New versions of software are being released daily and please correct if im
wrong but most distros do not release anything newer shortly there after
it coming out.

> On 06/25/2014 09:51 AM, Gavin W. Burris wrote:
>> 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/
> Unfortunately, the reality of the HPC code market is that, quite often,
> the OS required by the application for support is often at odds with
> what you describe above.  More often than not, commercial and closed
> source applications are built and qualified (for support and guarantee
> of functionality) against several very specific OS and library versions.
>   It is rare, in my experience with this, that any of these are
> up-to-date versions of Red Hat or Red Hat derived distributions.
> This is not to say that one should go with another distribution or not,
> there are valid engineering and support choices either way.
> But this said, given the often incompatible, and quite often
> non-solvable problems of providing a common supported platform for
> everything to run on, one unsupported platform is as good as the other,
> with the caveat that one needs to pay attention to the ease of
> management as well as other things.
> This is why stateless machines, booting an instance with a particular OS
> for a particular job, is a *far* more reasonable and workable approach
> than laying down one OS and demanding that applications conform to it.
> There is a bit more freedom when you have source, and can rebuild, but
> for commercial and closed source apps, if you want support from the
> vendors, you need to adhere to their requirements.
> Which means one of a few options
> 1) stateless as I had mentioned:  NFS or iSCSI like OS PXE booted on
> bare metal.  This is the best of the lot, as it gets very easy to create
> a dedicated stateless load for a particular application, providing
> everything the application needs to run at bare metal speed, without
> requiring a hard lock of a system to an OS.
> 2) VM based:  Just like stateless, but running as a VM atop a JEOS.
> This is the cloud model.  Almost bare metal speed, and a loss of access
> to things like IB and other fast PCIe cut-through technologies.  But
> this is what Amazon, et al provide.  You can build this yourself with
> OpenStack.  Works great for less latency sensitive apps, and you can
> have each VM be whatever the application needs to run supported.
> 3) Docker/Container based:  Sort of a cross between stateless and VM
> based, it provides direct hardware access, and you can set up
> effectively independent and completely supportable containers to run on
> each system, independent of the OS requirements of the job.  See
> http://www.docker.com/whatisdocker/
>> 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.
> You won't get vendor support for CentOS.  And CentOS cannot be "shipped"
> by a commercial entity anymore in a for profit manner, for any reason.
> See  http://www.centos.org/legal/trademarks/#unacceptable-uses .  They
> aimed this (obviously) at Oracle and OEL, but it presents, shall we say,
> some interesting collateral damage.
> If you want a Red Hat based distro in a commercial sense, you are
> currently limited to, not surprisingly, Red Hat.  Sure, you might use
> https://www.scientificlinux.org/ which is a rebuild + added bits -
> copyrighted bits.
> We switched our systems to Debian after we saw this.  We've been quite
> unhappy with some of the horrible broken-ness we've seen in the init
> system with {Red Hat|CentOS} 6.x for a while, and that legal change plus
> some nasty unfixable dracut stuff pushed us to better vistas.
>> 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
> Err ... no.  The center of mass of the market has moved on to the faster
> changing distributions.  We opted for Debian over Ubuntu due to
> silliness in the Ubuntu kernel bits that made adding our patches hard.
> Much easier with a sane system.  Its very ... very ... hard to fix all
> the breakage when we make changes to CentOS/Red Hat.  You might say
> "don't change", but since part of our value is inherent in the changes,
> well ...
> As I've been saying for more than a decade, the application OS
> requirements are a detail of the job.  Tools like kvm and docker let us
> get away from having a massive impedance mismatch between application
> requirements and node software environment requirements.
> Having fought the supported OS battles for decades (jeez ... since the
> 80s!), and having the scars to prove it, I personally prefer the
> simpler/better/lower friction route.  No more square pegs in round holes.
> --
> Joseph Landman, Ph.D
> Founder and CEO
> Scalable Informatics, Inc.
> email: landman at scalableinformatics.com
> web  : http://scalableinformatics.com
> twtr : @scalableinfo
> phone: +1 734 786 8423 x121
> cell : +1 734 612 4615
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