[Bioclusters] Clusters

Saharinen Juha bioclusters@bioinformatics.org
Sat, 05 Jun 2004 18:57:33 +0300


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Hi Michael,

yes I'm aware the results could have been somewhat different if using =
some other compilers than GCC etc. (I actually tried hmmer with the G5 / =
IBM compiler, but it did not compile right away, and I did not bother =
trying to find out why, maybe just some small thing? With GCC there were =
no problems). But since this compilation optimization could have been =
endless (different comppiles, different optimizations, Altive, MMX, SSEs =
etc.), I thought not to do any of those (except the Altivec just form =
comparison, trying to find out why we did not see the same performance =
from G5 and Opterons). If someone is interested to try out those =
different compilers and optimizations, I would be nice to hear.

Note also that we actually had the G5 tower model, not the Xserve rack =
server. Its been said that there are some performance increasement with =
Xserve compared to tower, but personally I'm skeptical whether it would =
be that concreate, since in our tests the gap to Opterons was quite big?


(I did not know MSI makes the IBM servers, but the MSI K1-1000 does =
definately look very familiar....)

Juha

-----Original Message-----
From:	Michael Hanulec [mailto:hanulec@hanulec.com]
Sent:	Sat 5.6.2004 5:23
To:	bioclusters@bioinformatics.org
Cc:=09
Subject:	RE: [Bioclusters] Clusters


Juha these are some very good tests that I wish I could perform myself,
but I have no access to Apple G5 hardware.

> We had high hopes for Apple G5 after reading the blast/hmmer etc.
> comparisons on Apple www-pages. Apple kind borrowed us a dual-G5 2 GHz
> with 2 GB RAM and fast disks box. We ran different blasts and hmmer
> searches, both with binaries we compiled (gcc) and precompiled from
> Apple's ftp ("AG-blast") and hmmer www-page (which to best of our
> understanding are the same Apple refers in their ads). In addition we
> ran some statistical genetics apps (merlin and pseudomarker). We were =
in
> contact with Apple (actually a very knowledgeable tech guy form =
Apple!,
> but they couldn't really explain the differences we observed).

I'd be interested what would of happend if the binaries were compiled =
with
the IBM XL C/C++ and Fortran compilers:

http://www.absoft.com/Products/Compilers/C_C%2B%2B/XLC/XLC.html
http://www.absoft.com/Products/Compilers/Fortran/Macintosh/XLF/xlf.html

Unfortunately not all version of GCC are created equal.  I doubt the
opimization quality of the code produced by the OS X and x86-64 versions
is equal.

> The Opterons were IBMs e325 boxes with SCSI RAID-1 disks. Concerning
> blast & hmmer types of runs, we thought this could be explained by =
disk
> access speed (G5 had SATA drive), therefore we also mounted the blast =
/
> hmmer dbs over NFS (1 GBit Ethernet) on the Opterons, but this really
> did not change anything (1st runs were slower than from internal SCSI
> disks, but we produced the numbers as averages from runs 2-4). Both =
CPUs
> were in full use in G5s and Opterons, memory was not limiting factor =
(ie
> swapping etc. did not occur) and power-saving features etc. were
> switched off. The only type of app Altivec-enhanced G5 performed =
better
> than Opterons was "AGBlast" with wordsize 40 (but not with typical
> smaller word size). (Note also that there have been discussions about
> whether the performance increase in the "AGBlast" is from AltiVec or
> just from other non-platform specific optimization of the original =
NCBI
> blast code; the same optimizations are available for Intel/AMDs, but =
we
> did not try those). In addition, all non-AltiVec optimized apps
> performed slower than Opterons (no code optimizations were done in any
> tests, except with the AltiVec).

[ Just in case not everyone knows this MSI makes this Opteron server for
IBM.  The model is called the K1-1000.  ]

Again.. the use of commerical compilers to run these test would be
interesting also.  Currently there are a choice of three commerical =
AMD64
compilers: Absoft, PGI and PathScale.

-mike
--
hanulec@hanulec.com		cell: 858.518.2647 && 516.410.4478
https://secure.hanulec.com	      EFnet irc && aol im: hanulec
_______________________________________________
Bioclusters maillist  -  Bioclusters@bioinformatics.org
https://bioinformatics.org/mailman/listinfo/bioclusters



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