Dear Kay,
Of course we would like to try. We are still (!) working on converting our
facility (as I have discussed off and on with you) to more novel computers,
with more novel programs and a better setup.
Just yesterday I had decided that it would be good to follow your example to
use ifort, because it does make the code a lot faster. The addition you write
about is very welcome.
We are still running cns 1.1; would you recommend to upgrade to 1.2 first and
if so, how would we go about that? I have not seen any formal announcements for
2.2
Thanks,
Mark
Mark van der Woerd, PhD
Research Scientist
Dept. of Biochemistry and Molecular Biology
Colorado State University
Fort Collins, CO 80523
Phone (970) 491-0469
-----Original Message-----
From: [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Sent: Fri, 19 Jan 2007 3:20 PM
Subject: announcement: OpenMP parallelization of CNS 1.2
OpenMP parallelization of CNS 1.2
=================================
I have worked out how to efficiently parallelize CNS. To use this,
you'll have to patch the source code. The patch leaves the source code
practically unchanged, because it only inserts lines that start with
"!$"
and are therefore understood as comments by the compiler, unless a specific
compiler option (-openmp in the case of ifort) is used.
The patch is for CNS 1.2 (and also works with 1.1). It was tested quite a bit
by me and others, but I cannot take any responsibility if it does
not work for you.
The speedup by parallelization occurs only for crystallographic calculations
which involve electron density calculations and FFTs. The result is a reduction
of wall-clock time for a CNS job by a factor of 1/2 - 1/3 on a Quad-processor
machine. A factor of 2/3 can be expected on a Dual-core machine.
Distribution
============
Axel Bruenger approved that I send out the patch to interested people.
Please send requests for the patch to me ([EMAIL PROTECTED]),
and please also report bugs in the patch to me.
-- Kay Diederichs http://strucbio.biologie.uni-konstanz.de
email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
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