This is a multi-part message in MIME format. --Boundary_(ID_Om2WFfW00Wa+BZ7NGvVVmg) Content-type: text/plain; charset=Windows-1252 Content-transfer-encoding: quoted-printable 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 --Boundary_(ID_Om2WFfW00Wa+BZ7NGvVVmg) Content-type: application/ms-tnef; name=winmail.dat Content-transfer-encoding: base64 Content-disposition: attachment; filename=winmail.dat eJ8+IiIPAQaQCAAEAAAAAAABAAEAAQeQBgAIAAAA5AQAAAAAAADoAAEIgAcAGAAAAElQTS5NaWNy b3NvZnQgTWFpbC5Ob3RlADEIAQ2ABAACAAAAAgACAAEEgAEAGwAAAFJFOiBbQmlvY2x1c3RlcnNd IENsdXN0ZXJzAK0JAQWAAwAOAAAA1AcGAAUAEgA5ACEABgBYAQEggAMADgAAANQHBgAFABIAOQAh AAYAWAEBCYABACEAAAA3NDU0NTVGMDgyQkVFNTRDODM4QkVGMzNGNDVEMTZDNAA9BwEDkAYAJBEA ADcAAAADACYAAAAAAAMANgAAAAAAQAA5AEYuK9AVS8QBHgA9AAEAAAAFAAAAUkU6IAAAAAACAUcA 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