"Best" machine for xtal computing?

Kay Diederichs dikay at sun2.ruf.uni-freiburg.de
Fri Feb 7 04:18:07 EST 1997


Yoram Puius (puius at aecom.yu.edu) wrote (edited):
: 
: We are looking to buy a number-cruncher for protein crystallography
: (i.e. very fast in running X-PLOR, TNT, XDS, etc.)  We have mostly
: SGIs as combination graphics/processing stations, but we're looking
: into a number cruncher described by SGI as an 
: 
: "Origin Server, 4XR1000, 180MHz, 1MB cache, 128MBmem, 2X2.2GB Sys Disk
: (2 Twr no skins) IRIX for 4CPUs"
: 
: I am assuming this means a machine with four R1000 CPUs, which are
: certainly faster than what we have around, although I don't know
: if X-PLOR has been optimized for the R10000 machines yet.  I am
: not counting on anyone out there parallelizing existing software,
: by the way.

The Origin server family replaces the Challenge server family. 
You might be able to buy Challenge/PowerChallenge still, but the price/
performance ratio is (much) better for the Origin family. They are very
expandable, up to supercomputer range.
Do not expect X-PLOR (current version) to run significantly faster
on SGI multiprocessor, as it doesn't parallelize well. Of course you can
run several X-PLOR jobs at the same time on a multiprocessor machine, and
that is probably the preferred mode, if your problem is tractable by that.
I/O is not an issue with X-PLOR, and probably not even with XDS.

: Do the "4XR1000" CPUs mean
: that we could run four X-PLOR jobs simultaneously (ignoring disk
: I/O problems)?  How does this compare with a Challenge Server?

see above.

I heard that the maximum clock rate of the R10000 might be pushed
up to 300Mhz within 1997, and performance scales almost linear with the
clock rate. There will very soon be a 2-processor R10000 'octane' workstation
replacing the 'Indigo2' line. Likewise, the 'O2' replaces the 'Indy' line.
So I'd say, don't buy (Power)Challenge/Indy/Indigo2, look at the new options!

The above reflects my understanding of current SGI computer lines,
which is worth just my 2 Pfennige!

Kay
-- 
Kay Diederichs  (dikay at ruf.uni-freiburg.de and Kay.Diederichs at uni-konstanz.de)
Universitaet Freiburg, Institut fuer Biophysik, Albertstr. 23 
D-79104 Freiburg, Germany   Tel. +49/(0)761/2035391 FAX +49/(0)761/2035016
and: Universitaet Konstanz, Fakultaet fuer Biologie, Postfach 5560, M656
D-78434 Konstanz, Germany   Tel. +49/(0)7531/884049 FAX +49/(0)7531/883183




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