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