Time to build GenBank on a SunFire server

Karl-Heinz Glatting glatting at dkdz.de
Fri Feb 13 08:26:18 EST 2004

Hi Michael,

we use a Sunfire 880 to build GCG indices for GenBank and it takes 
something like a day
or so when doing a bit of parallelization. The disks are not local on 
this machine but on
a Linux fileserver. So I guess your problem has something to do with 
network connection
between the SUN and your fileserver.

best regards,


Karl-Heinz Glatting
Bioinformatics Service Group
Department of Molecular Biophysics
Deutsches Krebsforschungszentrum (DKFZ)
(German Cancer Research Center)
Heidelberg, Germany
E-Mail: glatting at dkfz-heidelberg.de

Michael Black wrote:

>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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