[Bioclusters] Sequest on Linux

Botka, Christopher Christopher.Botka at joslin.harvard.edu
Wed Aug 17 12:10:56 EDT 2005


Thanks for all the info.  From what I have heard, the win2k server head
node is still a requirement.  What interconnect do you guys have on your
bladecenter?  I was at the Bauer Center at Harvard prior to coming here
and we had about 200 Intel IBM Blades and other than the 40GB IDE drive
failures on the early ones (lots of them failed), I liked the blades a
lot.  We have Dell 1Us and are still trying to decide what to use GigE
CU, GigF Fiber, or HBA->SAN.  If I can get away with GbitE Copper, I'd
be thrilled.  Do you figure PVM is causing the network bandwidth usage
for you guys?  How many CPUs/job on average?

Do you guys have any network attached storage?  I am planning to NAS
attached as much as I can and hopefully just have OS/scratch on the
nodes.  I'm still hopeful that in the middle to long term to be able to
integrate the Sequest nodes with LSF.  I've done some work with MPI and
LSF.  The only problem is that in a hi-use cluster LSF grabs a CPU at a
time and hold them until the total number of requested CPUs become
available.  This can tie up a CPU for quite a while as it waits for
others to get free.  I have not had any experience with PVM and a
scheduler, though I can't imagine it's too much different.

Thanks again for your time.


-----Original Message-----
bioclusters-bounces+christopher.botka=joslin.harvard.edu at bioinformatics.
[mailto:bioclusters-bounces+christopher.botka=joslin.harvard.edu at bioinfo
rmatics.org] On Behalf Of Brodie, Kent
Sent: Tuesday, August 16, 2005 11:44 AM
To: Clustering, compute farming & distributed computing in life science
Subject: RE: [Bioclusters] Sequest on Linux


As Simon introduced, we're running Sequest on Linux.   The installation
happens to be Suse 8; that's what was chosen because that provided the
best powerpc support at that time.   Ultimately, we'll likely switch the
nodes to RedHat later this year to match up with out other Linux
servers.   For Sequest, the particular flavor does not matter too much.
The head node of our Sequest environment is a Windows 2000 Server.  That
was a requirement from what I know.  (The JS20/Sequest install here
pre-dated my arrival...).

>From what I have seen, there's not really all that much I/O required to
make the Sequest animal work.   Most of the bandwidth needs are really
going to be on the network side, I believe.  That's where our JS20
bladecenter excels, because of the common network backplane.   The
chunks of data being analyzed are really nothing more than bits of

The Sequest head node basically blasts stuff to the remote worker nodes
via RSH/etc.   The raw files (FASTA and so on) used for comparative
analysis are all copied to the worker nodes "ahead of time", and the
data file chunks being analyzed just really aren't that large.    In out
environment, the JS20's have two little 40-GB 2.5" internal SCSI drives
on the blades.    The primary drive only has 3G used (operating system,
apps, sequest), and the secondary drive only has 1.6G used (raw data
files).  I do not suspect you're going to notice huge Sequest time
differences based on the drives.....   (I could be wrong?).   

For backups, we really don't care much, since each worker node is more
or less a clone of the other.   A dead node is easily replicated.   We
do keep weekly backups of the first node "just in case".

For integration, my understanding is that A Sequest-installed series of
systems can co-exist with other job scheduler environments on the same
cluster.    As I mentioned earlier, RSH playes a huge part in keeping
Sequest talking.    The technical communication between the nodes just
really isn't that complicated, and my assumption is something like
LSF/SGE/PBS/etc could peacefully co-exist.

If you have further scientific-like queries, Simon will tackle those,
and I'll be happy to address any other sysadmin-like questions you may

--Kent C. Brodie, MS
  Department of Physiology
  Human & Molecular Genetics Center
  Medical College of Wisconsin

> -----Original Message-----
> From: bioclusters-bounces+brodie=mcw.edu at bioinformatics.org
> [mailto:bioclusters-bounces+brodie=mcw.edu at bioinformatics.org] On
> Of Botka, Christopher
> Sent: Monday, August 15, 2005 11:46 PM
> To: bioclusters at bioinformatics.org
> Subject: [Bioclusters] Sequest on Linux
> Is anyone out there running Sequest on Linux for MS analysis?  We are
> the process of setting up a modest sized cluster to run Sequest and
> be interested in sharing info and experiences with anyone out there
> might be doing the same.
> Some issues:
>    1. I/O requirements - what's the minimum thruput needed to run
> We are gong to test both SATA and FC drives with multiple types of
> interconnects, as well as local SCSI drives.
>    2. Integration of the Thermo queuing system with other job
> systems (LSF/SGE etc) - Can Sequest be integrated into a general
> cluster?
>    3. Middle to long term storage requirements and back up strategies.
> Thanks,
> Chris
> botka at joslin.harvard.edu
> _______________________________________________
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