[Bioclusters] cluster or SMP

Joe Landman landman at scalableinformatics.com
Tue Sep 4 13:10:49 EDT 2007

Chris Dagdigian wrote:
> Diskless clusters are generally a bad idea for any system that will be
> running life science informatics workflows. In general terms (without

Agreed with caveats.

> knowing your specific applications) it is generally a rule that most
> life science codes are performance bound by memory and disk access I/O

Yes and yes.

> limitations. If you build a diskless cluster and do lots of assemblies
> on genomes that are larger than what can fit in memory your cluster is
> going to be bogged down while nodes wait on network I/O requests.

If you can provide a 100 MB/s link to IO locally, and a 1000 MB/s link
to IO remotely, the latter is likely to be faster, irrespective of the
disk stateful/stateless nature.

> You can always tell a HPC vendor who knows nothing about life science
> because they try to sell you (a) MPI-optimized "beowulf" systems or (b)

Er... need to be careful here, MPI-HMMer, mpiBLAST, mpiClustalW and
other MPI codes do have some latency sensitivity, more scalability
limitations due to design issues in their work scheduler, but they also
need to schedule IO.  Infiniband (SDR) is not a bad technology (nor is
10GbE, though that is not cost effective yet, getting there, but not yet).

> diskless systems, both of which are totally (in most cases)
> inappropriate technology choices for our styles of work.

... sometimes ... .  I am seeing a higher proportion of systems that are
also doing MD and additional latency sensitive stuff.  That said, IB and
others really don't make sense below a certain size unless your code is
latency sensitive by design.  And this does happen, though less
frequently in informatics than other areas.  The aforementioned mpi
codes are examples of some that are going this route.

We are seeing ~60x with mpiHMMer on 64 cores, before we use hardware
acceleration.  If we run in an "overcommitted manner" (many more cores
per IB port) we see this impact.  If we run over pure gigabit, the
scalability is lower, though most folks won't care about 50x vs 60x.

> I think you are on to something with the SMP idea. You should research
> how many CPUs and how much memory you can pack into a single chassis
> along with a good performing storage subsystem.

[not a commercial, just info]

We have built desktop units that have 4-8 cores, 32 GB ram, and >1TB
disk with 500+ MB/s bandwidth for customers running research apps (CFD,
bio, chem, ...) .  With the soon to be available Barcelona, we will be
able to pack 16 cores, 64 GB ram and a fast IO subsystem in a single
system image deskside (SMP).

We are seeing *lots* of interest in these systems, including people
wanting to build clusters out of them.

Having used a dual and then a quad core unit as a desktop for a while, I
can tell you it is quite nice when you have enough ram and IO capability.

> My $.02 of course !

Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman at scalableinformatics.com
web  : http://www.scalableinformatics.com
phone: +1 734 786 8423
fax  : +1 866 888 3112
cell : +1 734 612 4615

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