Time to build GenBank on a SunFire server

Michael Black mbblack at cstone.net
Thu Feb 12 12:47:43 EST 2004

Hello all,

I have a question about GCG performance on a Sunfire v480 server,
specifically, time to build genbank.  Last month, it took nearly 22.5 days
to build GenBnak 139.0, and that is just insane.

First, the machine specs:

SunFire v480 - 2x900Mhz UltraSparc III CPUs, 10GB RAM
SCSI controllor (SunSwift PCI) - 33Mhz, 32bit, 20MBps
RAID - CI Design, ultraSCSI2, 12x10,000rpm 74GB disks, RAID 5 (with one hot
swap) configuration.

As a test, we've tried building just plant+primate+rodent divisions of
GenBank 139.0, on the RAID and on one of the Sun's internal disks (which is
FibreChannel).  That build, which is about 10.7GB of data, takes about
137min (on average) to build on the RAID, and about 36min (average) on the
internal disk.  This is just running "genbanktogcg" with dbindexing on, and
the flat files on the same device as the GCG build.

For comparison, doing the same test build on a dual 800Mhz PIII RedHat box
(RAID is similar size, but might be 7200rpm disks, I'm not sure) - local
disk took about 38min average, and the RAID about 40min average.

Prior to getting the Sun, we were running GCG on a 4x180Mhz CPU SGI Origin
200 with 512MB RAM, and with the same CI Design RAID hung off it.  The last
GenBank build on that machine was release 137, which took about 8 to 9 days
to complete.

I fell something is drastically wrong with our SunFire!

If anyone else running GCG on a Sun, and locally maintaining GenBank, has
any insights on these speeds, I'd appreciate hearing from you.

TIA, Michael Black
Univ. of Virginia
mblack at virginia.edu

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