From: Moon C. <mo...@gm...> - 2011-12-03 12:25:23
|
Hi, When i use system call in c to call Jmol under Linux(the code is "(void)system("/opt/QtSDK/Projects/jmol-12.2.7/jmol.sh -s /opt/QtSDK/Projects/testing3.pdb.spt")") And testing3.pdb.spt is a Rasmol Script in the code. There is a problem that the Jmol will stop running at Setting up drag and drop. This situation will occur 1 around 5 times. What can i do with this situation? Best Regards, Moon |
From: Robert H. <ha...@st...> - 2011-12-04 00:29:10
|
Does Jmol.sh run generally on your machine from the command line? On Sat, Dec 3, 2011 at 6:25 AM, Moon Cheung <mo...@gm...> wrote: > Hi, > > When i use system call in c to call Jmol under Linux(the code is > "(void)system("/opt/QtSDK/Projects/jmol-12.2.7/jmol.sh -s > /opt/QtSDK/Projects/testing3.pdb.spt")") > And testing3.pdb.spt is a Rasmol Script in the code. > There is a problem that the Jmol will stop running at Setting up drag and > drop. > This situation will occur 1 around 5 times. > What can i do with this situation? > > Best Regards, > Moon > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > 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 |
From: Moon C. <mo...@gm...> - 2011-12-04 06:44:37
|
It has the same problem in running Jmol.sh from the command line.This time Jmol will stop at "Creating main window". And once the problem occurs, it will occur continuously after i kill the process. Best Regards Moon 2011/12/4 Robert Hanson <ha...@st...> > Does Jmol.sh run generally on your machine from the command line? > > On Sat, Dec 3, 2011 at 6:25 AM, Moon Cheung <mo...@gm...> wrote: > >> Hi, >> >> When i use system call in c to call Jmol under Linux(the code is >> "(void)system("/opt/QtSDK/Projects/jmol-12.2.7/jmol.sh -s >> /opt/QtSDK/Projects/testing3.pdb.spt")") >> And testing3.pdb.spt is a Rasmol Script in the code. >> There is a problem that the Jmol will stop running at Setting up drag and >> drop. >> This situation will occur 1 around 5 times. >> What can i do with this situation? >> >> Best Regards, >> Moon >> >> >> ------------------------------------------------------------------------------ >> All the data continuously generated in your IT infrastructure >> contains a definitive record of customers, application performance, >> security threats, fraudulent activity, and more. Splunk takes this >> data and makes sense of it. IT sense. And common sense. >> http://p.sf.net/sfu/splunk-novd2d >> _______________________________________________ >> Jmol-developers mailing list >> Jmo...@li... >> 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 > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > |
From: Robert H. <ha...@st...> - 2011-12-04 18:02:39
|
Hellow, Linux experts? What can you suggest for Moon? On Sun, Dec 4, 2011 at 12:44 AM, Moon Cheung <mo...@gm...> wrote: > It has the same problem in running Jmol.sh from the command line.This time > Jmol will stop at "Creating main window". > And once the problem occurs, it will occur continuously after i kill the > process. > > Best Regards > Moon > > > 2011/12/4 Robert Hanson <ha...@st...> > >> Does Jmol.sh run generally on your machine from the command line? >> >> On Sat, Dec 3, 2011 at 6:25 AM, Moon Cheung <mo...@gm...> wrote: >> >>> Hi, >>> >>> When i use system call in c to call Jmol under Linux(the code is >>> "(void)system("/opt/QtSDK/Projects/jmol-12.2.7/jmol.sh -s >>> /opt/QtSDK/Projects/testing3.pdb.spt")") >>> And testing3.pdb.spt is a Rasmol Script in the code. >>> There is a problem that the Jmol will stop running at Setting up drag >>> and drop. >>> This situation will occur 1 around 5 times. >>> What can i do with this situation? >>> >>> Best Regards, >>> Moon >>> >>> >>> ------------------------------------------------------------------------------ >>> All the data continuously generated in your IT infrastructure >>> contains a definitive record of customers, application performance, >>> security threats, fraudulent activity, and more. Splunk takes this >>> data and makes sense of it. IT sense. And common sense. >>> http://p.sf.net/sfu/splunk-novd2d >>> _______________________________________________ >>> Jmol-developers mailing list >>> Jmo...@li... >>> 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 >> >> >> ------------------------------------------------------------------------------ >> All the data continuously generated in your IT infrastructure >> contains a definitive record of customers, application performance, >> security threats, fraudulent activity, and more. Splunk takes this >> data and makes sense of it. IT sense. And common sense. >> http://p.sf.net/sfu/splunk-novd2d >> _______________________________________________ >> Jmol-developers mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-developers >> >> > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > 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 |
From: Robert H. <ha...@st...> - 2011-12-05 12:41:38
|
Well, that's extremely odd, because that message is followed IMMEDIATELY by another at the very start of the process: splash.showStatus(GT._("Creating main window...")); splash.showStatus(GT._("Initializing Swing...")); There is nothing between them, the JmolPanel class has not been constructed yet, and basically there is almost no memory being used. I can think of nothing that would do this except GT, which is the internationalization package. But you are getting English messages, so that should not be the issue. Please try adding -Duser.language=en just before the -jar flag on the command line of your shell: java -Duser.language=en -jar Jmol.jar Q: Can you run other Java applications? Also, you could try running Jmol without graphics once: java -jar Jmol.jar -n -j "print 'OK' " You could also try that with JmolData.jar, which has absolutely no graphics: java -jar JmolData.jar -n -j "print 'ok' " For sure, try this: java -jar Jmol.jar -h Are you getting anything? Bob On Sun, Dec 4, 2011 at 12:44 AM, Moon Cheung <mo...@gm...> wrote: > It has the same problem in running Jmol.sh from the command line.This time > Jmol will stop at "Creating main window". > And once the problem occurs, it will occur continuously after i kill the > process. > > Best Regards > Moon > > > 2011/12/4 Robert Hanson <ha...@st...> > >> Does Jmol.sh run generally on your machine from the command line? >> >> On Sat, Dec 3, 2011 at 6:25 AM, Moon Cheung <mo...@gm...> wrote: >> >>> Hi, >>> >>> When i use system call in c to call Jmol under Linux(the code is >>> "(void)system("/opt/QtSDK/Projects/jmol-12.2.7/jmol.sh -s >>> /opt/QtSDK/Projects/testing3.pdb.spt")") >>> And testing3.pdb.spt is a Rasmol Script in the code. >>> There is a problem that the Jmol will stop running at Setting up drag >>> and drop. >>> This situation will occur 1 around 5 times. >>> What can i do with this situation? >>> >>> Best Regards, >>> Moon >>> >>> >>> ------------------------------------------------------------------------------ >>> All the data continuously generated in your IT infrastructure >>> contains a definitive record of customers, application performance, >>> security threats, fraudulent activity, and more. Splunk takes this >>> data and makes sense of it. IT sense. And common sense. >>> http://p.sf.net/sfu/splunk-novd2d >>> _______________________________________________ >>> Jmol-developers mailing list >>> Jmo...@li... >>> 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 >> >> >> ------------------------------------------------------------------------------ >> All the data continuously generated in your IT infrastructure >> contains a definitive record of customers, application performance, >> security threats, fraudulent activity, and more. Splunk takes this >> data and makes sense of it. IT sense. And common sense. >> http://p.sf.net/sfu/splunk-novd2d >> _______________________________________________ >> Jmol-developers mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-developers >> >> > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > 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 |
From: Jonathan G. <gu...@uw...> - 2011-12-04 19:20:54
|
I don't use the jmol.sh script very often, but one possibility is that the memory defaults in it are too small for the virtual machine he is using. Another guess is that he is using the IceTea JVM and not the Sun/Oracle JVM. IceTea is getting better, but I've still had occasional problems with it. Jonathan On Dec 4, 2011, at 12:02 PM, Robert Hanson wrote: > Hellow, Linux experts? What can you suggest for Moon? > > On Sun, Dec 4, 2011 at 12:44 AM, Moon Cheung <mo...@gm...> wrote: > It has the same problem in running Jmol.sh from the command line.This time Jmol will stop at "Creating main window". > And once the problem occurs, it will occur continuously after i kill the process. > > Best Regards > Moon > > > 2011/12/4 Robert Hanson <ha...@st...> > Does Jmol.sh run generally on your machine from the command line? > > On Sat, Dec 3, 2011 at 6:25 AM, Moon Cheung <mo...@gm...> wrote: > Hi, > > When i use system call in c to call Jmol under Linux(the code is "(void)system("/opt/QtSDK/Projects/jmol-12.2.7/jmol.sh -s /opt/QtSDK/Projects/testing3.pdb.spt")") > And testing3.pdb.spt is a Rasmol Script in the code. > There is a problem that the Jmol will stop running at Setting up drag and drop. > This situation will occur 1 around 5 times. > What can i do with this situation? > > Best Regards, > Moon > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > 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 > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > 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 > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers Dr. Jonathan H. Gutow Chemistry Department gu...@uw... UW-Oshkosh Office: 920-424-1326 800 Algoma Boulevard FAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow |
From: Moon C. <mo...@gm...> - 2011-12-05 08:30:50
|
I set the memory to 2GB in my virtual machine and have already change the JVM to SUN, the problem is still here! Any ideas? Best Regards, Moon 2011/12/5 Jonathan Gutow <gu...@uw...> > I don't use the jmol.sh script very often, but one possibility is that > the memory defaults in it are too small for the virtual machine he is > using. Another guess is that he is using the IceTea JVM and not the > Sun/Oracle JVM. IceTea is getting better, but I've still had occasional > problems with it. > > Jonathan > > On Dec 4, 2011, at 12:02 PM, Robert Hanson wrote: > > Hellow, Linux experts? What can you suggest for Moon? > > On Sun, Dec 4, 2011 at 12:44 AM, Moon Cheung <mo...@gm...> wrote: > >> It has the same problem in running Jmol.sh from the command line.This >> time Jmol will stop at "Creating main window". >> And once the problem occurs, it will occur continuously after i kill the >> process. >> >> Best Regards >> Moon >> >> >> 2011/12/4 Robert Hanson <ha...@st...> >> >>> Does Jmol.sh run generally on your machine from the command line? >>> >>> On Sat, Dec 3, 2011 at 6:25 AM, Moon Cheung <mo...@gm...> wrote: >>> >>>> Hi, >>>> >>>> When i use system call in c to call Jmol under Linux(the code is >>>> "(void)system("/opt/QtSDK/Projects/jmol-12.2.7/jmol.sh -s >>>> /opt/QtSDK/Projects/testing3.pdb.spt")") >>>> And testing3.pdb.spt is a Rasmol Script in the code. >>>> There is a problem that the Jmol will stop running at Setting up drag >>>> and drop. >>>> This situation will occur 1 around 5 times. >>>> What can i do with this situation? >>>> >>>> Best Regards, >>>> Moon >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> All the data continuously generated in your IT infrastructure >>>> contains a definitive record of customers, application performance, >>>> security threats, fraudulent activity, and more. Splunk takes this >>>> data and makes sense of it. IT sense. And common sense. >>>> http://p.sf.net/sfu/splunk-novd2d >>>> _______________________________________________ >>>> Jmol-developers mailing list >>>> Jmo...@li... >>>> 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 >>> >>> >>> ------------------------------------------------------------------------------ >>> All the data continuously generated in your IT infrastructure >>> contains a definitive record of customers, application performance, >>> security threats, fraudulent activity, and more. Splunk takes this >>> data and makes sense of it. IT sense. And common sense. >>> http://p.sf.net/sfu/splunk-novd2d >>> _______________________________________________ >>> Jmol-developers mailing list >>> Jmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>> >>> >> >> >> ------------------------------------------------------------------------------ >> All the data continuously generated in your IT infrastructure >> contains a definitive record of customers, application performance, >> security threats, fraudulent activity, and more. Splunk takes this >> data and makes sense of it. IT sense. And common sense. >> http://p.sf.net/sfu/splunk-novd2d >> _______________________________________________ >> Jmol-developers mailing list >> Jmo...@li... >> 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 > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > > Dr. Jonathan H. Gutow > Chemistry Department gu...@uw... > UW-Oshkosh Office: 920-424-1326 > 800 Algoma Boulevard FAX:920-424-2042 > Oshkosh, WI 54901 > http://www.uwosh.edu/facstaff/gutow > > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > |
From: A. H. <ang...@ua...> - 2011-12-05 08:51:41
|
Hello Moon I think that Jonathan's comment was noot so much about the memory in your VM, but the memory allocated to Java (and so to Jmol) You can try http://wiki.jmol.org/index.php/Jmol_Application#Giving_Jmol_more_memory_to_work_with and see if it fixes your problem. I cannot help with setting up the Jmol.sh details though |