Re: [Jmol-developers] Do we need to initialize the graphics environment when Jmol is running headless?
I was able to successfully embed it in the SAGE web server. Now for lots of code cleanup... Jonathan On Mar 20, 2012, at 7:43 PM, Robert Hanson wrote: OK, so I definitely learned something! On Tue, Mar 20, 2012 at 5:48 PM, Jonathan Gutow gu...@uwosh.edu wrote: Bob, You did it! My preliminary tests show it works. I have to do some modifications to get it embedded in Sage, but I think it will work fine. Thanks, Jonathan On Mar 19, 2012, at 9:53 PM, Robert Hanson wrote: OK, Jonathan. I think I found the problem. Please try what I just checked in -- do a build, and then use jmolData.jar instead of jmol.jar. Formerly: JmolData.jar -s foo.spt execute the script foo.spt with absolutely no graphics and no rendering, including no image creation now: JmolData.jar -s foo.spt execute the script foo.spt still with rending for image creation, just not for screen display Jmoldata.jar -n -s foo.spt as before, now for performance enhancement, no graphics of any kind. Let's see how that works. Bob On Mon, Mar 19, 2012 at 8:30 PM, Robert Hanson hans...@stolaf.edu wrote: If awt is not there, you are out of luck. But with the -n flag there is no creation of Display. But there might be a reference to it. Let me see. Based on this discussion: http://java.sun.com/developer/technicalArticles/J2SE/Desktop/headless/ we should be able to do it. Bob On Mon, Mar 19, 2012 at 6:06 PM, Jonathan Gutow gu...@uwosh.edu wrote: Bob, Thanks for trying...Your changes definitely reduce the error messages, but the application is still looking for screen dimensions somewhere in the tree after entering JmolPanel. It is making a call to the awt package. I'm suspicious this is all associated with the allocation of a Display near line 242 in JmolPanel. I've got a solution for Sage, but we should keep picking at this as more people would be able to use Jmol as a server side image generator. Some people really don't like running a GUI on their servers. Jonathan On Mar 19, 2012, at 3:51 PM, Robert Hanson wrote: Could be I'm wrong.Try what I just checked in. Be sure to use the -ions t.spt option (silent/no console/no graphics) You won't get THAT error. but will it create an image? I used this script: load $tylenol write image 300 300 t.png Bob On Mon, Mar 19, 2012 at 7:55 AM, Gutow, Jonathan H gu...@uwosh.edu wrote: I dug a little and agree it would be a significant undertaking to make the image generation work without the GUI. That said, we might want to put that on a long term to-do list. -- 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- 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 -- 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-developers
Re: [Jmol-developers] Do we need to initialize the graphics environment when Jmol is running headless?
superb! On Wed, Mar 21, 2012 at 11:26 AM, Jonathan Gutow gu...@uwosh.edu wrote: I was able to successfully embed it in the SAGE web server. Now for lots of code cleanup... Jonathan On Mar 20, 2012, at 7:43 PM, Robert Hanson wrote: OK, so I definitely learned something! On Tue, Mar 20, 2012 at 5:48 PM, Jonathan Gutow gu...@uwosh.edu wrote: Bob, You did it! My preliminary tests show it works. I have to do some modifications to get it embedded in Sage, but I think it will work fine. Thanks, Jonathan On Mar 19, 2012, at 9:53 PM, Robert Hanson wrote: OK, Jonathan. I think I found the problem. Please try what I just checked in -- do a build, and then use jmolData.jar instead of jmol.jar. Formerly: JmolData.jar -s foo.spt execute the script foo.spt with absolutely no graphics and no rendering, including no image creation now: JmolData.jar -s foo.spt execute the script foo.spt still with rending for image creation, just not for screen display Jmoldata.jar -n -s foo.spt as before, now for performance enhancement, no graphics of any kind. Let's see how that works. Bob On Mon, Mar 19, 2012 at 8:30 PM, Robert Hanson hans...@stolaf.eduwrote: If awt is not there, you are out of luck. But with the -n flag there is no creation of Display. But there might be a reference to it. Let me see. Based on this discussion: http://java.sun.com/developer/technicalArticles/J2SE/Desktop/headless/ we should be able to do it. Bob On Mon, Mar 19, 2012 at 6:06 PM, Jonathan Gutow gu...@uwosh.edu wrote: Bob, Thanks for trying...Your changes definitely reduce the error messages, but the application is still looking for screen dimensions somewhere in the tree after entering JmolPanel. It is making a call to the awt package. I'm suspicious this is all associated with the allocation of a Display near line 242 in JmolPanel. I've got a solution for Sage, but we should keep picking at this as more people would be able to use Jmol as a server side image generator. Some people really don't like running a GUI on their servers. Jonathan On Mar 19, 2012, at 3:51 PM, Robert Hanson wrote: Could be I'm wrong.Try what I just checked in. Be sure to use the -ions t.spt option (silent/no console/no graphics) You won't get THAT error. but will it create an image? I used this script: load $tylenol write image 300 300 t.png Bob On Mon, Mar 19, 2012 at 7:55 AM, Gutow, Jonathan H gu...@uwosh.eduwrote: I dug a little and agree it would be a significant undertaking to make the image generation work without the GUI. That said, we might want to put that on a long term to-do list. -- 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- 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 -- 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___
Re: [Jmol-developers] Do we need to initialize the graphics environment when Jmol is running headless?
Bob, You did it! My preliminary tests show it works. I have to do some modifications to get it embedded in Sage, but I think it will work fine. Thanks, Jonathan On Mar 19, 2012, at 9:53 PM, Robert Hanson wrote: OK, Jonathan. I think I found the problem. Please try what I just checked in -- do a build, and then use jmolData.jar instead of jmol.jar. Formerly: JmolData.jar -s foo.spt execute the script foo.spt with absolutely no graphics and no rendering, including no image creation now: JmolData.jar -s foo.spt execute the script foo.spt still with rending for image creation, just not for screen display Jmoldata.jar -n -s foo.spt as before, now for performance enhancement, no graphics of any kind. Let's see how that works. Bob On Mon, Mar 19, 2012 at 8:30 PM, Robert Hanson hans...@stolaf.edu wrote: If awt is not there, you are out of luck. But with the -n flag there is no creation of Display. But there might be a reference to it. Let me see. Based on this discussion: http://java.sun.com/developer/technicalArticles/J2SE/Desktop/headless/ we should be able to do it. Bob On Mon, Mar 19, 2012 at 6:06 PM, Jonathan Gutow gu...@uwosh.edu wrote: Bob, Thanks for trying...Your changes definitely reduce the error messages, but the application is still looking for screen dimensions somewhere in the tree after entering JmolPanel. It is making a call to the awt package. I'm suspicious this is all associated with the allocation of a Display near line 242 in JmolPanel. I've got a solution for Sage, but we should keep picking at this as more people would be able to use Jmol as a server side image generator. Some people really don't like running a GUI on their servers. Jonathan On Mar 19, 2012, at 3:51 PM, Robert Hanson wrote: Could be I'm wrong.Try what I just checked in. Be sure to use the -ions t.spt option (silent/no console/no graphics) You won't get THAT error. but will it create an image? I used this script: load $tylenol write image 300 300 t.png Bob On Mon, Mar 19, 2012 at 7:55 AM, Gutow, Jonathan H gu...@uwosh.edu wrote: I dug a little and agree it would be a significant undertaking to make the image generation work without the GUI. That said, we might want to put that on a long term to-do list. -- 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- 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 -- 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh
Re: [Jmol-developers] Do we need to initialize the graphics environment when Jmol is running headless?
OK, so I definitely learned something! On Tue, Mar 20, 2012 at 5:48 PM, Jonathan Gutow gu...@uwosh.edu wrote: Bob, You did it! My preliminary tests show it works. I have to do some modifications to get it embedded in Sage, but I think it will work fine. Thanks, Jonathan On Mar 19, 2012, at 9:53 PM, Robert Hanson wrote: OK, Jonathan. I think I found the problem. Please try what I just checked in -- do a build, and then use jmolData.jar instead of jmol.jar. Formerly: JmolData.jar -s foo.spt execute the script foo.spt with absolutely no graphics and no rendering, including no image creation now: JmolData.jar -s foo.spt execute the script foo.spt still with rending for image creation, just not for screen display Jmoldata.jar -n -s foo.spt as before, now for performance enhancement, no graphics of any kind. Let's see how that works. Bob On Mon, Mar 19, 2012 at 8:30 PM, Robert Hanson hans...@stolaf.edu wrote: If awt is not there, you are out of luck. But with the -n flag there is no creation of Display. But there might be a reference to it. Let me see. Based on this discussion: http://java.sun.com/developer/technicalArticles/J2SE/Desktop/headless/ we should be able to do it. Bob On Mon, Mar 19, 2012 at 6:06 PM, Jonathan Gutow gu...@uwosh.edu wrote: Bob, Thanks for trying...Your changes definitely reduce the error messages, but the application is still looking for screen dimensions somewhere in the tree after entering JmolPanel. It is making a call to the awt package. I'm suspicious this is all associated with the allocation of a Display near line 242 in JmolPanel. I've got a solution for Sage, but we should keep picking at this as more people would be able to use Jmol as a server side image generator. Some people really don't like running a GUI on their servers. Jonathan On Mar 19, 2012, at 3:51 PM, Robert Hanson wrote: Could be I'm wrong.Try what I just checked in. Be sure to use the -ions t.spt option (silent/no console/no graphics) You won't get THAT error. but will it create an image? I used this script: load $tylenol write image 300 300 t.png Bob On Mon, Mar 19, 2012 at 7:55 AM, Gutow, Jonathan H gu...@uwosh.eduwrote: I dug a little and agree it would be a significant undertaking to make the image generation work without the GUI. That said, we might want to put that on a long term to-do list. -- 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- 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 -- 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu
Re: [Jmol-developers] Do we need to initialize the graphics environment when Jmol is running headless?
I dug a little and agree it would be a significant undertaking to make the image generation work without the GUI. That said, we might want to put that on a long term to-do list. My solution is to run an Xsession using xpra winswitch. As long as I launch the server process in the xpra Xsession, there is always a graphics environment available. Jonathan On Mar 17, 2012, at 8:38 AM, Jonathan Gutow wrote: I've been working on using 12.0.45 as a server-side static graphics engine for the SageMath group. I've run into the following problem. The server does not run in an X-session, so there is no graphics environment. This causes an error when Jmol is run as Jmol.jar -ionx. The error seems to imply that we are still initializing the look-and-feel, even when there is no GUI. Is there any reason we can't switch this off? Here's the error: Exception in thread main java.lang.NoClassDefFoundError: Could not initialize class sun.awt.X11GraphicsEnvironment at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:186) at java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnviron\ ment.java:82) at sun.awt.X11.XToolkit.clinit(XToolkit.java:112) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:186) at java.awt.Toolkit$2.run(Toolkit.java:849) at java.security.AccessController.doPrivileged(Native Method) at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:841) at sun.swing.SwingUtilities2$AATextInfo.getAATextInfo(SwingUtilities2.java:\ 121) at javax.swing.plaf.metal.MetalLookAndFeel.initComponentDefaults(MetalLookA\ ndFeel.java:1564) at javax.swing.plaf.basic.BasicLookAndFeel.getDefaults(BasicLookAndFeel.jav\ a:147) at javax.swing.plaf.metal.MetalLookAndFeel.getDefaults(MetalLookAndFeel.jav\ a:1599) at javax.swing.UIManager.setLookAndFeel(UIManager.java:530) at javax.swing.UIManager.setLookAndFeel(UIManager.java:570) at javax.swing.UIManager.initializeDefaultLAF(UIManager.java:1320) at javax.swing.UIManager.initialize(UIManager.java:1407) at javax.swing.UIManager.maybeInitialize(UIManager.java:1395) at javax.swing.UIManager.getDefaults(UIManager.java:644) at javax.swing.UIManager.put(UIManager.java:973) at org.jmol.export.dialog.Dialog.setupUIManager(Unknown Source) at org.openscience.jmol.app.jmolpanel.JmolPanel.startJmol(Unknown Source) at org.openscience.jmol.app.Jmol.main(Unknown Source) Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers Dr. Jonathan H. Gutow Chemistry Department gu...@uwosh.edu UW-Oshkosh Office:920-424-1326 800 Algoma Boulevard FAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow/ -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Do we need to initialize the graphics environment when Jmol is running headless?
Hi, You can check also tools like xvfb which can create a virtual display. Even without the GUI, image generation may require a display for some image operations (like fonts, ...), this is a Java limitation. I used xvfb in several projects where I needed to create images without having a real display. Nico On Mon, Mar 19, 2012 at 1:55 PM, Gutow, Jonathan H gu...@uwosh.edu wrote: I dug a little and agree it would be a significant undertaking to make the image generation work without the GUI. That said, we might want to put that on a long term to-do list. My solution is to run an Xsession using xpra winswitch. As long as I launch the server process in the xpra Xsession, there is always a graphics environment available. Jonathan On Mar 17, 2012, at 8:38 AM, Jonathan Gutow wrote: I've been working on using 12.0.45 as a server-side static graphics engine for the SageMath group. I've run into the following problem. The server does not run in an X-session, so there is no graphics environment. This causes an error when Jmol is run as Jmol.jar -ionx. The error seems to imply that we are still initializing the look-and-feel, even when there is no GUI. Is there any reason we can't switch this off? Here's the error: Exception in thread main java.lang.NoClassDefFoundError: Could not initialize class sun.awt.X11GraphicsEnvironment at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:186) at java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnviron\ ment.java:82) at sun.awt.X11.XToolkit.clinit(XToolkit.java:112) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:186) at java.awt.Toolkit$2.run(Toolkit.java:849) at java.security.AccessController.doPrivileged(Native Method) at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:841) at sun.swing.SwingUtilities2$AATextInfo.getAATextInfo(SwingUtilities2.java:\ 121) at javax.swing.plaf.metal.MetalLookAndFeel.initComponentDefaults(MetalLookA\ ndFeel.java:1564) at javax.swing.plaf.basic.BasicLookAndFeel.getDefaults(BasicLookAndFeel.jav\ a:147) at javax.swing.plaf.metal.MetalLookAndFeel.getDefaults(MetalLookAndFeel.jav\ a:1599) at javax.swing.UIManager.setLookAndFeel(UIManager.java:530) at javax.swing.UIManager.setLookAndFeel(UIManager.java:570) at javax.swing.UIManager.initializeDefaultLAF(UIManager.java:1320) at javax.swing.UIManager.initialize(UIManager.java:1407) at javax.swing.UIManager.maybeInitialize(UIManager.java:1395) at javax.swing.UIManager.getDefaults(UIManager.java:644) at javax.swing.UIManager.put(UIManager.java:973) at org.jmol.export.dialog.Dialog.setupUIManager(Unknown Source) at org.openscience.jmol.app.jmolpanel.JmolPanel.startJmol(Unknown Source) at org.openscience.jmol.app.Jmol.main(Unknown Source) Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers Dr. Jonathan H. Gutow Chemistry Department gu...@uwosh.edu UW-Oshkosh Office:920-424-1326 800 Algoma Boulevard FAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow/ -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Do we need to initialize the graphics environment when Jmol is running headless?
Nico, I had forgot about fonts. Since we want to be able to put text in our graphics, that may pretty much require us to have a GUI. For your information, it appears that xpra/winswitch is an extension of the facilities provided by xvfb and in some cases makes use of xvfb. Jonathan On Mar 19, 2012, at 8:04 AM, Nicolas Vervelle wrote: Hi, You can check also tools like xvfb which can create a virtual display. Even without the GUI, image generation may require a display for some image operations (like fonts, ...), this is a Java limitation. I used xvfb in several projects where I needed to create images without having a real display. Nico On Mon, Mar 19, 2012 at 1:55 PM, Gutow, Jonathan H gu...@uwosh.edu wrote: I dug a little and agree it would be a significant undertaking to make the image generation work without the GUI. That said, we might want to put that on a long term to-do list. My solution is to run an Xsession using xpra winswitch. As long as I launch the server process in the xpra Xsession, there is always a graphics environment available. Jonathan Dr. Jonathan H. Gutow Chemistry Department gu...@uwosh.edu UW-Oshkosh Office:920-424-1326 800 Algoma Boulevard FAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow/ -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Do we need to initialize the graphics environment when Jmol is running headless?
Could be I'm wrong.Try what I just checked in. Be sure to use the -ions t.spt option (silent/no console/no graphics) You won't get THAT error. but will it create an image? I used this script: load $tylenol write image 300 300 t.png Bob On Mon, Mar 19, 2012 at 7:55 AM, Gutow, Jonathan H gu...@uwosh.edu wrote: I dug a little and agree it would be a significant undertaking to make the image generation work without the GUI. That said, we might want to put that on a long term to-do list. -- 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Do we need to initialize the graphics environment when Jmol is running headless?
Bob, Thanks for trying...Your changes definitely reduce the error messages, but the application is still looking for screen dimensions somewhere in the tree after entering JmolPanel. It is making a call to the awt package. I'm suspicious this is all associated with the allocation of a Display near line 242 in JmolPanel. I've got a solution for Sage, but we should keep picking at this as more people would be able to use Jmol as a server side image generator. Some people really don't like running a GUI on their servers. Jonathan On Mar 19, 2012, at 3:51 PM, Robert Hanson wrote: Could be I'm wrong.Try what I just checked in. Be sure to use the -ions t.spt option (silent/no console/no graphics) You won't get THAT error. but will it create an image? I used this script: load $tylenol write image 300 300 t.png Bob On Mon, Mar 19, 2012 at 7:55 AM, Gutow, Jonathan H gu...@uwosh.edu wrote: I dug a little and agree it would be a significant undertaking to make the image generation work without the GUI. That said, we might want to put that on a long term to-do list. -- 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] Do we need to initialize the graphics environment when Jmol is running headless?
I've been working on using 12.0.45 as a server-side static graphics engine for the SageMath group. I've run into the following problem. The server does not run in an X-session, so there is no graphics environment. This causes an error when Jmol is run as Jmol.jar -ionx. The error seems to imply that we are still initializing the look-and-feel, even when there is no GUI. Is there any reason we can't switch this off? Here's the error: Exception in thread main java.lang.NoClassDefFoundError: Could not initialize class sun.awt.X11GraphicsEnvironment at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:186) at java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnviron\ ment.java:82) at sun.awt.X11.XToolkit.clinit(XToolkit.java:112) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:186) at java.awt.Toolkit$2.run(Toolkit.java:849) at java.security.AccessController.doPrivileged(Native Method) at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:841) at sun.swing.SwingUtilities2$AATextInfo.getAATextInfo(SwingUtilities2.java:\ 121) at javax.swing.plaf.metal.MetalLookAndFeel.initComponentDefaults(MetalLookA\ ndFeel.java:1564) at javax.swing.plaf.basic.BasicLookAndFeel.getDefaults(BasicLookAndFeel.jav\ a:147) at javax.swing.plaf.metal.MetalLookAndFeel.getDefaults(MetalLookAndFeel.jav\ a:1599) at javax.swing.UIManager.setLookAndFeel(UIManager.java:530) at javax.swing.UIManager.setLookAndFeel(UIManager.java:570) at javax.swing.UIManager.initializeDefaultLAF(UIManager.java:1320) at javax.swing.UIManager.initialize(UIManager.java:1407) at javax.swing.UIManager.maybeInitialize(UIManager.java:1395) at javax.swing.UIManager.getDefaults(UIManager.java:644) at javax.swing.UIManager.put(UIManager.java:973) at org.jmol.export.dialog.Dialog.setupUIManager(Unknown Source) at org.openscience.jmol.app.jmolpanel.JmolPanel.startJmol(Unknown Source) at org.openscience.jmol.app.Jmol.main(Unknown Source) Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Do we need to initialize the graphics environment when Jmol is running headless?
Is this because of the try{...} at line 513 of JmolPanel.java? Shouldn't this
be inside the preceding if..., which checks to see if the display and splash
are enabled?
Jonathan
On Mar 17, 2012, at 8:38 AM, Jonathan Gutow wrote:
I've been working on using 12.0.45 as a server-side static graphics engine
for the SageMath group. I've run into the following problem. The server
does not run in an X-session, so there is no graphics environment. This
causes an error when Jmol is run as Jmol.jar -ionx. The error seems to imply
that we are still initializing the look-and-feel, even when there is no GUI.
Is there any reason we can't switch this off? Here's the error:
Exception in thread main java.lang.NoClassDefFoundError: Could not
initialize class sun.awt.X11GraphicsEnvironment
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:186)
at
java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnviron\
ment.java:82)
at sun.awt.X11.XToolkit.clinit(XToolkit.java:112)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:186)
at java.awt.Toolkit$2.run(Toolkit.java:849)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:841)
at
sun.swing.SwingUtilities2$AATextInfo.getAATextInfo(SwingUtilities2.java:\
121)
at
javax.swing.plaf.metal.MetalLookAndFeel.initComponentDefaults(MetalLookA\
ndFeel.java:1564)
at
javax.swing.plaf.basic.BasicLookAndFeel.getDefaults(BasicLookAndFeel.jav\
a:147)
at
javax.swing.plaf.metal.MetalLookAndFeel.getDefaults(MetalLookAndFeel.jav\
a:1599)
at javax.swing.UIManager.setLookAndFeel(UIManager.java:530)
at javax.swing.UIManager.setLookAndFeel(UIManager.java:570)
at javax.swing.UIManager.initializeDefaultLAF(UIManager.java:1320)
at javax.swing.UIManager.initialize(UIManager.java:1407)
at javax.swing.UIManager.maybeInitialize(UIManager.java:1395)
at javax.swing.UIManager.getDefaults(UIManager.java:644)
at javax.swing.UIManager.put(UIManager.java:973)
at org.jmol.export.dialog.Dialog.setupUIManager(Unknown Source)
at org.openscience.jmol.app.jmolpanel.JmolPanel.startJmol(Unknown
Source)
at org.openscience.jmol.app.Jmol.main(Unknown Source)
Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow
--
This SF email is sponsosred by:
Try Windows Azure free for 90 days Click Here
http://p.sf.net/sfu/sfd2d-msazure
___
Jmol-developers mailing list
Jmol-developers@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-developers
Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow
--
This SF email is sponsosred by:
Try Windows Azure free for 90 days Click Here
http://p.sf.net/sfu/sfd2d-msazure
___
Jmol-developers mailing list
Jmol-developers@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Do we need to initialize the graphics environment when Jmol is running headless?
You can't run it without graphics if you are going to create JPG files. . If you are doing something else, you can use JmolData.jar, which has no graphics. On Sat, Mar 17, 2012 at 8:38 AM, Jonathan Gutow gu...@uwosh.edu wrote: I've been working on using 12.0.45 as a server-side static graphics engine for the SageMath group. I've run into the following problem. The server does not run in an X-session, so there is no graphics environment. This causes an error when Jmol is run as Jmol.jar -ionx. The error seems to imply that we are still initializing the look-and-feel, even when there is no GUI. Is there any reason we can't switch this off? Here's the error: Exception in thread main java.lang.NoClassDefFoundError: Could not initialize class sun.awt.X11GraphicsEnvironment at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:186) at java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnviron\ ment.java:82) at sun.awt.X11.XToolkit.clinit(XToolkit.java:112) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:186) at java.awt.Toolkit$2.run(Toolkit.java:849) at java.security.AccessController.doPrivileged(Native Method) at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:841) at sun.swing.SwingUtilities2$AATextInfo.getAATextInfo(SwingUtilities2.java:\ 121) at javax.swing.plaf.metal.MetalLookAndFeel.initComponentDefaults(MetalLookA\ ndFeel.java:1564) at javax.swing.plaf.basic.BasicLookAndFeel.getDefaults(BasicLookAndFeel.jav\ a:147) at javax.swing.plaf.metal.MetalLookAndFeel.getDefaults(MetalLookAndFeel.jav\ a:1599) at javax.swing.UIManager.setLookAndFeel(UIManager.java:530) at javax.swing.UIManager.setLookAndFeel(UIManager.java:570) at javax.swing.UIManager.initializeDefaultLAF(UIManager.java:1320) at javax.swing.UIManager.initialize(UIManager.java:1407) at javax.swing.UIManager.maybeInitialize(UIManager.java:1395) at javax.swing.UIManager.getDefaults(UIManager.java:644) at javax.swing.UIManager.put(UIManager.java:973) at org.jmol.export.dialog.Dialog.setupUIManager(Unknown Source) at org.openscience.jmol.app.jmolpanel.JmolPanel.startJmol(Unknown Source) at org.openscience.jmol.app.Jmol.main(Unknown Source) Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
