Time to build GenBank on a SunFire server

Michael Black mbblack at cstone.net
Thu Feb 12 15:21:31 EST 2004

Thanks Steve,

That was my gut feeling, but not having experience with GCG on a Sun, I
wasn't really sure what to expect.

Normally (even in the past on our old SGI) I do GenBank full release builds
manually (albeit building portions simultaneously), and just script
maintenance releases.  SRS indexing is always the last thing I do - it has
never crashed on me, but is slow.

We just seem to be getting terrible IO lag with this machine, and I think we
need to get someone from Sun down here to take a look at it.  Admittedly, we
did buy just about the worst SCSI card Sun sells for the SunFire series, but
even that seems like it couldn't account for the IO performance we are

Thanks for your comments.


Michael B. Black
Univ. of Virginia
mblack at virginia.edu

On 2/12/04 2:38 PM, in article 20040212134522.E57673-100000 at bio.fsu.edu,
"Steve Thompson" <stevet at bio.fsu.edu> wrote:

> Hi Michael -
> Yes, that's an insane build time on your SunFire server.  I can't compare
> it to another Sun, and I don't really keep track of my exact build times,
> and I don't do the whole process from a script, rather I do bits and
> pieces in between my other chores, but I regularly build all of GenBank
> (including tags!) here on a Dell PowerEdge 6650 (4 x 1.6GHz Pentium 4
> cpu's and 8GB RAM) with a RAID 5 setup of ~600GB.  Including downloading
> the whole thing from NCBI, I always get the entire process done in less
> than one workday!  Now building the LookUp SRS indices are another matter;
> that took about a week last time, and it ALWAYS causes a couple of core
> dumps, in spite of following GCG's suggestions regarding how many sections
> to split stuff up into.  Regardless, LookUp works afterwards.  Go figure.
>                            Cheers - Steve
>                                               Steven M. Thompson
>                               A C T G         stevet at bio.fsu.edu
>                                 \-/   http://bio.fsu.edu/~stevet/cv.html
>                                 /\
>                                /--|          FSU CSIT / BioInfo 4U
>                               /---/
>                               |--/    Florida State University School of
>                               \-/        Computational Science &
>                                /\           Information Technology
>                               /--\            1st floor DIRAC 150G
>                               |---\           Tallahassee, Florida
>                                \---\          32306-4120
>                                 \--|          850-644-4490
>                                  \-/
>                                  /\           2538 Winnwood Circle
>                                 /--\          Valdosta, Georgia
>                                /---|          31601-7953
>                                |--/           229-249-9751
> ---

More information about the Info-gcg mailing list

Send comments to us at biosci-help [At] net.bio.net