Specifications

For this series of tests, each application used the dual processor option available to
each binary distribution (”-a 2” for BLAST and “--cpu 2” for HMMER). The BLAST tests
used the query file supplied by the benchmark, cherry_tomato.fsa, and the blastn,
blastx, and tblastx programs, and conducted searches against the formatted databases
using Expectation Values ranging from 1.0e-10 to 1.0e-30. The HMMER tests calibrated
the supplied globin.hmm profile search statistics using hmmcalibrate and fixed
random sequence lengths of 400, 2000, and 8000; the tests also searched the nr
sequence database using the supplied globin.hmm profile.
Networking Throughput
To minimize bottlenecks and ensure maximum data throughput, Xserve G5 features
a high-performance I/O architecture optimized for server tasks.
The following results are based on benchmark testing performed in January 2004
by Apple in a laboratory setting using publicly available software. These server
configurations were tested:
• Apple Xserve G5. Dual 2GHz PowerPC G5, 1GB of PC3200 SDRAM, three 250GB
Apple Drive Modules, dual Gigabit Ethernet, and Mac OS X Server v10.3.2.
• IBM eServer x325. Dual Opteron 246 (2GHz), 1GB of PC2700 SDRAM, two 36GB
Ultra320 SCSI drives, dual Gigabit Ethernet, and Red Hat Linux Enterprise 3
(AMD 64-bit version).
• IBM eServer x335. Dual 3.2GHz Xeon, 1GB of PC2100 SDRAM, two 36GB Ultra320 SCSI
drives, dual Gigabit Ethernet, and Red Hat Linux 9.0 (unless otherwise indicated).
For each system, Apple installed the operating system on one drive and used the
other drive or drives to create a data volume. On the Xserve G5, the two remaining
drives were configured as a single volume using RAID 0. The Xeon- and Opteron-based
systems used 15,000-rpm drives.
9
Technology Overview
Xserve G5
Bioinformatics Benchmark System (BBSv3): Dual Processor Details
PowerPC G5
Dual 2.3GHz
Intel Xeon
Dual 3.4GHz
AMD Opteron
Dual 250 (2.4GHz)
Elapsed time in minutes—shorter bars are better
0
15
30
45
60
75
90
105
12 0
13 5
15 0
blastn blastn-nt blastx tblastx hmmer-
no-nr-1
hmmer-
no-nr-2
hmmer-
no-nr-3
hmmer-
with-nr
Testing conducted by Apple in January 2005 using preproduction Xserve G5 systems. All systems were configured with
4GB of RAM. Test results based on the Bioinformatics Benchmark System (BBSv3) at http://www.scalableinformatics.com/
metadot/index.pl?iid=2190 using Jan 1, 2005 FASTA databases and NCBI BLAST version 2.2.10 available from
ftp://ftp.ncbi.nlm.nih.gov/blast/executables and HMMER version 2.3.2 available from http://hmmer.wustl.edu.