Rolf, Thank you! I'm not sure this is exactly equivalent, but all of this looks useful in some way. I can definitely use the perl scripts.
Thanks, Jonathan On Jan 23, 2012, at 4:06 PM, jmol-users-requ...@lists.sourceforge.net wrote: > Message: 3 > Date: Mon, 23 Jan 2012 17:03:34 +0100 > From: Rolf Huehne <rhue...@fli-leibniz.de> > Subject: Re: [Jmol-users] Need some advice on server side static image > processing with Jmol... > To: jmol-users@lists.sourceforge.net > Message-ID: <4f1d84d6.1020...@fli-leibniz.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > 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 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/faculty_staff/gutow/ ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! 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-d2d _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
