I'm confused by the 2400% CPU usage claimed below. Does this imply that 24
cores of a multicore machine are running at 100%?
I have not been able to get Jmol to run on more than one core of my Mac 8 core
machine. In looking at the source code for Jmol 11.8.not_too_long_ago there
seems to be a spot in the script interpreter to launch multiple threads which
could exploit a multicore machine, but seems to launch only one thread to run
the script itself. The code for this version's interpreter doesn't seem thread
safe at first blush, so it doesn't seem like it is possible to get more than
100% CPU usage there.
So, my questions are:
- Does Jmol 12 exploit Java multi-threading?
- If so, is this multi-threading for "file loading only" or a side-effect of
something in Java or the operating system?
- Is there a way to exploit multi-threading in Jmol?
My Jmol app uses isosurface rendering for quaternary structure of proteins.
Right now, seven of the cores on my machine are idle and one is very busy. It
would be nice to be able to put the calculation of every chain's isosurface on
a thread to take advantage of whatever multicore capacity a user's machine has.
--Chuck
--- Original Message -----
From: Robert Hanson
To: jmol-users@lists.sourceforge.net
Sent: Wednesday, April 07, 2010 8:10 AM
Subject: Re: [Jmol-users] Jmol -- two major advances
Wow, thanks, Rolf. I thought perhaps you could do that! Oh, so close!
First,
write PNG
just sends the image to your clipboard as an actual system-dependent image
since you didn't specify a file name. So it was trying to create that when the
error occurred. I'm guessing that happened not because the file was so large
but instead because the ribbon was so tiny. I'll see if I can reproduce that.
JPG64
should not be there at all.
Bob
On Wed, Apr 7, 2010 at 4:32 AM, Rolf Huehne <rhue...@fli-leibniz.de> wrote:
On 04/05/2010 06:50 PM, Robert Hanson wrote:
> Thanks, Peter. Yes, that's a killer. Definitely not ready to read
16,000,000
> atoms! But I have added a new option that lets you load some smaller
number
> of biomolecule transformations. Looks like we'll have to let Rolf open
that
> one for us.... ;)
>
Using Jmol 12.0.RC4_dev rev 12773 I opened the full 1m4x biological unit
file with all atoms successfully. It took about 520 minutes CPU time and
21 GB of memory. (Until the memory was filled the CPU usage raised up to
2400%, then it stayed at 100% for several hours.)
(When I tried this before the same amount of memory was used but Jmol
somehow got stuck and I never got anything rendered.)
You can't really work interactively (unless you have a CPU that is at
least 600 times faster than a 1.6 GHz Itanium processor) because it
takes about one minute for a command to work on all atoms.
But at least you can work with script commands.
When I tried to export an image with "write png" I got the following
error message:
JPG64
java.lang.ArrayIndexOutOfBoundsException: -1
at org.jmol.g3d.Hermite3D.renderHermiteRibbon(Unknown Source)
at org.jmol.g3d.Graphics3D.drawHermite(Unknown Source)
at org.jmol.shapebio.BioShapeRenderer.renderHermiteRibbon(Unknown
Source)
at org.jmol.shapebio.CartoonRenderer.render1(Unknown Source)
at org.jmol.shapebio.CartoonRenderer.renderBioShape(Unknown Source)
at org.jmol.shapebio.BioShapeRenderer.render(Unknown Source)
at org.jmol.shape.ShapeRenderer.render(Unknown Source)
at org.jmol.viewer.RepaintManager.render1(Unknown Source)
at org.jmol.viewer.RepaintManager.render(Unknown Source)
at org.jmol.viewer.Viewer.render(Unknown Source)
at org.jmol.viewer.Viewer.getImage(Unknown Source)
at org.jmol.viewer.Viewer.getScreenImage(Unknown Source)
at org.jmol.viewer.Viewer.renderScreenImage(Unknown Source)
at org.jmol.viewer.Viewer.renderScreenImage(Unknown Source)
at org.openscience.jmol.app.jmolpanel.DisplayPanel.paint(Unknown
Source)
at javax.swing.JComponent.paintToOffscreen(JComponent.java:5124)
at
javax.swing.BufferStrategyPaintManager.paint(BufferStrategyPaintManager.java:278)
at javax.swing.RepaintManager.paint(RepaintManager.java:1224)
at javax.swing.JComponent._paintImmediately(JComponent.java:5072)
at javax.swing.JComponent.paintImmediately(JComponent.java:4882)
at
javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:785)
at
javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:713)
at
javax.swing.RepaintManager.seqPaintDirtyRegions(RepaintManager.java:693)
at
javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(SystemEventQueueUtilities.java:125)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:597)
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
rendering error?
Regards,
Rolf
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
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