Hi Warren
I set hash_max to 250 and this appears to be helping significantly.
Thanks. What exactly to these numbers mean? What is the default? If
hash_max 250 is speeding things up will hash_max 500 be even better?
Thanks,
Scott
On Jul 5, 2004, at 10:56 AM, Warren DeLano wrote:
Scott,
The optimal hash_max is somewhat scenery-dependent, but values in
the 180-250 range tend to be best for multiprocessor situations with
lots of
RAM.
Cheers,
Warren
--
mailto:war...@delsci.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
Subject: [PyMOL] having problems with batch rendering
Hello Fellow PyMOLers,
I have submitted a huge movie (i.e. 520 frames rendered at
1280x854) job to pymol on one of our linux grunts. PyMOL,
much to my surprise actually recognized that the grunt has
two multithreaded processors and subsequently split the
rendering job amongst the available processors. However, the
rendering is proceeding extremely slowly, and from the
process table (see below) it appears that PyMOL is only using
5.4% of the system memory. Is there some max_hash command I
can put in my pymol script to make things go faster? Right
now each frame is taking 25-30 minutes to render. YIKES!!!!
That means my movie won't be done until next week sometime.
Thanks,
Scott
here is the out put from top:
70 processes: 68 sleeping, 2 running, 0 zombie, 0 stopped
CPU0 states: 100.0% user 0.0% system 0.0% nice 0.0% iowait 0.0% idle
CPU1 states: 100.0% user 0.0% system 0.0% nice 0.0% iowait 0.0% idle
CPU2 states: 100.0% user 0.0% system 0.0% nice 0.0% iowait 0.0% idle
CPU3 states: 99.4% user 0.1% system 0.0% nice 0.0% iowait 0.0% idle
Mem: 2064408k av, 1980616k used, 83792k free, 0k shrd,
514360k buff 1464856k actv, 2516k in_d, 13536k in_c
Swap: 2048276k av, 7064k used, 2041212k free 932396k cached
PID USER PRI NI SIZE RSS SHARE STAT %CPU %MEM TIME CPU COMMAND
4115 classen 25 0 109M 109M 2996 R 99.9 5.4 5390m 1 pymol.exe
15131 classen 15 0 1136 1136 864 R 0.1 0.0 0:00 3 top
1 root 15 0 104 76 52 S 0.0 0.0 0:51 0 init
2 root RT 0 0 0 0 SW 0.0 0.0 0:00 0 migration/0
3 root RT 0 0 0 0 SW 0.0 0.0 0:00 1 migration/1
4 root RT 0 0 0 0 SW 0.0 0.0 0:00 2 migration/2
5 root RT 0 0 0 0 SW 0.0 0.0 0:00 3 migration/3
6 root 15 0 0 0 0 SW 0.0 0.0 0:48 2 keventd
7 root 34 19 0 0 0 SWN 0.0 0.0 0:00 0 ksoftirqd_CPU0
8 root 34 19 0 0 0 SWN 0.0 0.0 0:00 1 ksoftirqd_CPU1
9 root 34 19 0 0 0 SWN 0.0 0.0 0:00 2 ksoftirqd_CPU2
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Scott Classen, Ph.D.
ACS Postdoctoral Fellow
Department of Molecular & Cell Biology
University of California, Berkeley
237 Hildebrand Hall #3206
Berkeley, CA 94720-3206
LAB 510.643.9491
FAX 510.643.9290
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
