xplor + very large structure
Kay.Diederichs at uni-konstanz.de
Fri Oct 17 02:05:29 EST 1997
Christoph Weber wrote:
> Dear netters,
> can xplor be reconfigured to use less memory in any way? I have tried
> playing with parameters in the prexplor.dim file and also with
> parameters MAXNGR and MNCSYM in ncs.fcm, but all executables that will
> allow the job to run eventually grow to the same size.
> Also, is there a parallel version of xplor that scales relatively well?
> I hear that the regular version parallelized through pfa (on SGI) does not
> scale well and in my hands with the newer MIPSpro 7.1 compilers and pfa,
> parallelization failed altogether.
> We are trying to refine the structure of a very large virus
> (2,000,000 reflections, one size bigger than regular viruses) with xplor.
> The job has a total memory footprint of 480 MB and about
> half of the data needs to stay in memory for efficient CPU utilization.
> This creates problems on our shared SGI servers which happen to be the
> only machines on campus with sufficient memory.
> We are looking at ~6 CPU weeks on an R8000 per SA run.
> Any hints about how we can tame this job would be greatly appreciated!
> Thanks in advance,
> | Dr. Christoph Weber Sen. Research Associate
> | Research Computing, MB9 619-784-9869 (phone)
> | The Scripps Research Institute 619-784-9985 (FAX)
> | La Jolla CA 92037-1027 weber at scripps.edu
> | http://www.scripps.edu/~weber.html
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I think you can cut memory by almost a factor of two by compiling X-PLOR
in single precision: basically, remove the first C character in
I did this to make X-PLOR 3.1 work on a 8MB 486DX40, and it had the
desired effect without affecting precision too much - give it a try.
At that time, I had to use the 'generic' FFT routines (e.g. the ones in
hp735/hptime.s) as the SGI-specific C routines, as distributed, were not
affected by conversion of the Fortran routines to single precision.
Don't know what the situation currently is in that respect.
Hope this helps - and best wishes!
email: Kay.Diederichs at uni-konstanz.de Tel: +49 7531 88 4049 Fax:
Fakultaet fuer Biologie, Universitaet Konstanz
Postfach 5560 (M656), D-78434 Konstanz, Germany
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