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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proactively, and fine-tune applications for parallel performance.
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