[Bioclusters] more NCBI BLAST testing on opterons

Joseph Landman bioclusters@bioinformatics.org
Thu, 18 Sep 2003 11:20:01 -0400


  We have been doing more testing on Opterons.  This time a 246 unit. 
For the particular NCBI BLAST job we are using (blastx of 74 sequences
vs nr from July, will happily supply both the database and the test
scripts to anyone in exchange for their results and machine details),
the dual Opteron is showing an execution time with 2 threads giving the
best results, and the Xeon 3 GHz system showing best results with 4
threads (odd, HT must be working).

  What we are seeing is that comparing the best efforts of these two
platforms, using the binary suitable with gcc on both platforms, that
the 246 completes the run in 586 seconds, while the Xeon completes it in
1006 seconds.  These are wall clock seconds, as measured by the start
and end times of the script.

  Note:  We are trying to work with the Intel compiler as well to see if
it helps.  We are using sse2 on gcc, and m64 mode on the Opteron.

  We are also seeing some interesting affinity bits.  It looks like we
need a way to pin memories and CPUs together for scheduling for best
performance.  Has anyone successfully built the NCBI toolkit using the
ICC?  If so, would you be willing to share your linux.ncbi.mk file? 


Joseph Landman, Ph.D
Scalable Informatics LLC
email: landman@scalableinformatics.com
  web: http://scalableinformatics.com
phone: +1 734 612 4615