On 01/22/2012 12:46 AM, Jonathan Gutow wrote: > Dear Jmol Users: > > I'm looking for somebody who has experience using Jmol on a server to > generate .png images. I am investigating whether this would be better for > making static images in the SageMath package than Tachyon, which they > presently use. > > I've already tried passing some .jmol files of the kind the math software can > generate to JmolData.jar, unfortunately they appear to contain some graphics > entities that JmolData cannot handle. Thus I believe I will have to run the > full Jmol on the server to make this work. My first question about this is, > do we have a script command that will cause Jmol to quit? It is important > that the application exit when it is done with its job. I can certainly add > such a command, but have learned that we have so many things in Jmol that it > is easy to overlook functionality that we already have. > There is something else that you might have to consider if you want to generate PNG images on a server with Jmol:
On Linux/Unix Jmol needs access to an 'X-Server' process which provides one or more displays (graphical screens). Usually there is no X-Server installed/available on compute servers or cluster nodes. But there exists the virtual X-Server "Xvfb" which allows to provide a virtual display on such a server. I added below a message I wrote a few years ago on the Jmol-developers list that describes this in more detail. Regards, Rolf --------------------------------------------------------------------------- Juergen Haas wrote: > Dear Jmol community, > > I am using Jmol to generate a png which is placed as a background picture > behind the jmol applet, such that when printing this picture would be printed > instead. > > on my workstation this command works beautifully: > > java -jar ~/programs/jmol-11.6.13/Jmol.jar -on -s myJMOL.script > > on the node of the cluster where the images will be generated (as a dynamic > content of web pages beta.proteinmodelportal.org, after submitting two or > more structures to be analysed), however, I get: > > Could not initialize class sun.awt.X11GraphicsEnvironment > > why does Jmol need an X11 environment when started with -n ? > I found this thread (last message id shown here): > http://www.mail-archive.com/jmol-developers@li.../msg06975.html > > since this was from 2006 I was wondering, if there now is a way to circumvent > this problem. > I couldn't access the 'www.mail-archive.com' server but I guess Juergen is refering to the thread "NO DISPLAY JMOL" from September 2006. I finally managed to use Jmol to automatically create images for all PDB entries. I ended up in using the virtual X server 'Xvfb' to circumvent the problem. Although my case is a bit different, because the server I use actually has an X server installed, 'Xvfb' might also be the solution in this case. (I never tried to run 'Xvfb' in such a case.) Since I am running 30 Jmol processes in parallel I start a virtual X server for each Jmol. My procedure is the following: 1) Distribute all PDB entries onto 30 ID lists 2) Start 30 perl scripts (1 for each list) 3) Each perl script starts a virtual X server 4) Each perl script starts Jmol for each ID (one at a time) 5) Each perl script stops the virtual X server at the end I use 30 different virtual X servers for performance reasons. I don't use permanently running virtual X servers for these reasons: 1) Image generation only once a week and usually only for new/updated PDB entries 2) Make sure that an accessible X server is available 3) Sometimes I observed a memory leak problem with a long running Xvfb server Since every X server needs a unique display number you have to make sure that you start the virtual X server with an unused display number. To avoid collisions with possibly running real X servers I start with display number 100. For starting the virtual X server I wrote a little perl script, available (temporarily) at: http://www.fli-leibniz.de/~rhuehne/jmol/start_xvfb.pl The script starts the server and returns the process ID (to be able to stop it afterwards) and the display number on standart output. It also retries to start the server up to 60 times with increasing display number if the server couldn't be started. In my perl script that starts Jmol it is invoked this way: # start virtual X server 'Xvfb' $xvfb_start_message = `$xvfb_command $display_number`; if ($xvfb_start_message =~ /ERROR:(.*)$/i) { die "ERROR: could NOT START virtual X server - $1 - ABORTED $0\n"; } if ($xvfb_start_message =~ /PID='(.*?)'/i) { $xvfb_pid = $1; } else { die "ERROR: could NOT DETERMINE PID of virtual X server 'Xvfb' - ABORTED $0\n"; } if ($xvfb_start_message =~ /DISPLAY='(.*?)'/i) { $ENV{'DISPLAY'} = $1; } else { die "ERROR: could NOT DETERMINE display_number of virtual X server 'Xvfb' - ABORTED $0\n"; } ($xvfb_command = "start_xvfb.pl"; $display_number = 100;) The command "ENV{'DISPLAY'} = $1;" in the code shown above sets the environment variable "DISPLAY" for any subsequently started programs like Jmol. Regards, Rolf ------------------------------------------------------------------------------ Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
