anyone using FreeBSD? (Was: Re: [Bioclusters] Re: [Biodevelopers] Re: how are the Redhat product changes affecting existing and future plans?)

Thu, 6 Nov 2003 11:56:23 -0300

+----[ Dan Bolser <dmb@mrc-dunn.cam.ac.uk> (05.Nov.2003 19:09):
|
| Does anyone know of a publically maintained RPM directory
| which the community could synchronize against?
| 
| The redHat channel is not the only way I heard.

There are several RPM repositories. The main problem here is
if you trust what you're getting. And this not only applies to
security. Personally I like to build (compile) source
myself. Then I have full control of configure and build optimizations. 

| What hope FreeBSD?

This is also a question I'm asking myself. I'm a FreeBSD
user myself, and I see it as a perfect OS for this kind of
'synchronization' issues. 

Both the kernel and userland programs are easily compiled
from source. Binary packages also exist, but the majority of
FreeBSD users use binary packages built locally, just to
make it easier to distribute things between different
machines: you build apps in one, and distribute to all the
others.

And this is where the FreeBSD ports collection comes to
play. The collection has over 9000 ports, including all
major bioinformatics tools. Basically the ports system
provides a unified set of makefiles that are used to drive
the i) fetch, ii) extract, iii) patch (if necessary), iv)
configure, v) build and vi) install of software. Also, you
have port-specific makefiles that let you tweak build
options. So you get the best of both worlds: compilation
from source, with user specified options AND ease of use.

Source synchronization of kernel, userland and ports is
easily done using CVSup, although you can also use other
methods (anonymous CVS, CTM, etc)
<http://www.polstra.com/projects/freeware/CVSup/>

In fact, since I first installed FreeBSD from CDROM a few
years ago, I kept my system updated (through several
releases), just updating my sources, and rebuilding and
reinstalling everything.

The Gentoo Linux portage system is based on the FreeBSD
ports system, and as far as I know, it is intended to
provide similar features, although I've never used and don't
know how mature it is.

The main drawbacks I see for the adoption of FreeBSD are:
i) commercial software or software that is not open source.
Although FreeBSD can run linux binaries, executables are not
usually tested on FreeBSD, but on Linux, so it is expected
that issues may arise.
ii) a small installed base in the bio- or bio-clustering
communities (there is a significant installed-base in the
network and ISP/sysadmin business), and also there are
companies selling systems with FreeBSD installed. 
<http://www.freebsdsystems.com/>
<http://www.ironsystems.com/>

Any FreeBSD users willing to share clustering experiences
out there?

Fernan

| J.W. Bizzaro said:
| > (Added Biodevelopers to the thread.)
| >
| > There's a discussion about this on Slashdot, including mention of the  Fedora
| > project:
| >
| >    http://slashdot.org/article.pl?sid=03/11/03/1749259
| >
| > Cheers.
| > Jeff
| >
| > Chris Dagdigian wrote:
| >>
| >> Another item that has been on my mind recently...
| >>
| >> What are people doing about RedHat deciding to kill off their consumer  product
| >> line? Are people going to pay the freight for Redhat Enterprise  Linux or are
| >> people just going to use Suse/Debian/Gentoo etc.
| >>
| >> My needs are pretty simple but I'm having a hard time placing myself  into
| >> Redhat's current product plans.
| >>
| >> I need:
| >>
| >> 1. A stable OS with a product lifetime of at least 1 year (ideally 2+) 2.
| >> Product errata, updates and security patches for full lifespan 3. No OS or
| >> product phone/email support or SLA
| >>
| >> The RHL transition to Fedora Linux is fine but it sounds as if the OS is  going
| >> to change very fast (major updates 2-3 times per year). On the  plus side it is
| >> still free and the leaders seem committed to fast errata  and security updates.
| >> Still I can't see using this on a production  cluster due to the pace of change
| >> and the chance that I'd be left  without updates if I froze on a particular
| >> Fedora release.
| >>
| >> I can justify (maybe) the cost for the $125 product (Redhat WS) that  they are
| >> pitching towards compute clusters. The update services and  5-year product
| >> lifespan is worth paying for. The big question for me is  what do I have to pay
| >> _after_ the initial $125 purchase. I can't seem to  find any info on the Redhat
| >> website telling me how much I'll have to pay
| >>  for updates after my intial 1-year RedHat Network service runs out.
| >>
| >> This also leaves the question of what RHEL flavor to run on cluster head  nodes,
| >> fileservers and database machines. $349 for RH ES could be  justified for a
| >> critical node but damn what if I want to run that stuff  on Opteron or Itanium
| >> or a node with 4CPUs? The cost for RH AS (starting  at $1400) is not justifiable
| >> to me. Putting a 'cheap' RHEL flavor on a  head node and manually
| >> compiling/updating/supporting additional network  services built by hand from
| >> source or .srpms may be more of an
| >> operational headache than the cost savings justify.
| >>
| >> I'm torn right now between diving back into Gentoo/Debian or possibly  jumping
| >> on the Suse bandwagon given their existing support for Opteron  etc. Novell just
| >> bought Suse today so who knows what that is going to do.
| >>
| >> I'd be interested in knowing how current RHL users are planning the  transition
| >> and how future cluster buyers are changing their plans.  Personally I think I'm
| >> going to need to stay on top of RHEL for project  that demand it while also
| >> maintaining some sort of deep familiarity with  one or more alternatives.
| >>
| >> -Chris
| >>
| >>
| >>
| >>
| >>
| >>
| >> _______________________________________________
| >> Bioclusters maillist  -  Bioclusters@bioinformatics.org
| >> https://bioinformatics.org/mailman/listinfo/bioclusters
| >
| >
| > --
| > J.W. Bizzaro                                jeff@bioinformatics.org President,
| > Bioinformatics.Org       http://bioinformatics.org/~jeff "As we enjoy great
| > advantages from the inventions of others, we
| > should be glad of an opportunity to serve others by any invention
| > of ours; and this we should do freely and generously."
| >                     -- Benjamin Franklin
| > --
| >
| > _______________________________________________
| > Biodevelopers mailing list
| > Biodevelopers@bioinformatics.org
| > https://bioinformatics.org/mailman/listinfo/biodevelopers
| 
| 
| 
| _______________________________________________
| Bioclusters maillist  -  Bioclusters@bioinformatics.org
| https://bioinformatics.org/mailman/listinfo/bioclusters
| 
|
+----]

-- 
F e r n a n   A g u e r o
http://genoma.unsam.edu.ar/~fernan