Scott,
The hash_max setting changes the maximum linear dimension of the
three-dimensional hash table used by PyMOL's internal ray-tracer.
Worst-case memory usage increases as the third power of this number (i.e.
doubling hash_max can increase RAM usage by up to 800%), but that's a rare
scenario. Optimum rendering performance value usually lies around 170, but
can be much lower (90) for sphere-only scenes and much higher (250-300) for
complex scenes with a mixture of geometries. The default value of 100 is
supposed to avoid blowing out the RAM on 256 MB systems. If you have 512MB
or above, it's usually worth setting hash-max to at least 150 or so.
Cheers,
Warren
PS. Hopefully, we'll eventually replace the render's hash table with
something more efficient that doesn't require any configuration to deliver
maximum performance.
--
mailto:war...@delsci.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -----Original Message-----
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Scott Classen
> Sent: Monday, July 05, 2004 12:02 PM
> To: Warren DeLano
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] having problems with batch rendering
>
> 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
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
