[sage-devel] Re: sage notebook with many Jmol viewers
Dan, I'm glad you like most of what has been done. If you manage to get anything to fail please report that as well. As to the speed, there's not a lot we can do. That is limited by how fast information is passed from the server and how fast your computer is. Jmol is doing quite a bit of computation to produce the live figures. Because of JavaVM memory constraints within browsers things do not work well if more than one applet is loading at once. This means that each applet has to finish loading before the next one can start. One thought is to make it clearer what is happening. Would a pop-up progress window indicating which applet is loading help with the way it feels? Long term, I will probably make it so that old pages load with all the applets replaced by static images, but this requires changes to the plot3d functions. I was worrying about the interface first. Jonathan On Mar 31, 8:44 pm, Dan Drake dr...@kaist.edu wrote: On Thu, 31 Mar 2011 at 06:08AM -0700, Jonathan wrote: If you want to see what is coming down the pike in the next few weeks, take a look at the published samples on my test server: http:///141.233.197.45:. I could really use some comments on how it works. I'm using Firefox 4.0 on Ubuntu 10.10 with the Sun/Oracle Java andhttp://141.233.197.45:/home/pub/0/is working great. I really like the new controls -- putting it in a new window, changing the size, turning the spin on and off. The sleeping/interactive thing is also nice. The only slight problem is that it did take quite a long time for all the applets to load, but I suppose it's better to get things working first before we worry about speed. I tried the lots of applets worksheet, and tried to get every applet interactive and spinning. I see that some will automatically sleep, rather than have too many applets running. That's nice. Excellent work! Thanks so much for your efforts. Jmol is absolutely essential to me when I teach multivariable calc. Dan -- --- Dan Drake - http://mathsci.kaist.ac.kr/~drake --- signature.asc 1KViewDownload -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Re: sage notebook with many Jmol viewers
One thought is to make it clearer what is happening. Would a pop-up progress window indicating which applet is loading help with the way it feels? Long term, I will probably make it so that old pages load Yes. But that can be added after this. Let's make sure your valuable improvements actually make it in before adding more stuff. with all the applets replaced by static images, but this requires changes to the plot3d functions. I was worrying about the interface first. Can you expand on this? Do you mean that any given page would have a static image, and it would only turn into an applet if one clicked on it (or evaluated it)? Or do you mean that only pages produced before this change would do so, or ...? - kcrisman -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Re: sage notebook with many Jmol viewers
On Apr 1, 1:49 pm, kcrisman kcris...@gmail.com wrote: with all the applets replaced by static images, but this requires changes to the plot3d functions. I was worrying about the interface first. Can you expand on this? Do you mean that any given page would have a static image, and it would only turn into an applet if one clicked on it (or evaluated it)? Or do you mean that only pages produced before this change would do so, or ...? What I'm thinking about is that when re-opening a worksheet the 3-D plots would initially load as static images each with a Make Interactive button. This would increase load speed. Then only the plots the user wants to interact with would have to load applets. I think that when the output cell contents are created by an evaluate call it should default to a live Jmol. This will require some reworking of how 3-D plots are generated. Jonathan -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Re: sage notebook with many Jmol viewers
On Apr 1, 4:35 pm, Jonathan gu...@uwosh.edu wrote: On Apr 1, 1:49 pm, kcrisman kcris...@gmail.com wrote: with all the applets replaced by static images, but this requires changes to the plot3d functions. I was worrying about the interface first. Can you expand on this? Do you mean that any given page would have a static image, and it would only turn into an applet if one clicked on it (or evaluated it)? Or do you mean that only pages produced before this change would do so, or ...? What I'm thinking about is that when re-opening a worksheet the 3-D plots would initially load as static images each with a Make Interactive button. This would increase load speed. Then only the plots the user wants to interact with would have to load applets. I think that when the output cell contents are created by an evaluate call it should default to a live Jmol. This will require some reworking of how 3-D plots are generated. As you said. But not a bad idea. -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Re: sage notebook with many Jmol viewers
On 4/1/11 1:18 PM, Jonathan wrote: Dan, I'm glad you like most of what has been done. If you manage to get anything to fail please report that as well. As to the speed, there's not a lot we can do. That is limited by how fast information is passed from the server and how fast your computer is. Jmol is doing quite a bit of computation to produce the live figures. Because of JavaVM memory constraints within browsers things do not work well if more than one applet is loading at once. This means that each applet has to finish loading before the next one can start. One thought is to make it clearer what is happening. Would a pop-up progress window indicating which applet is loading help with the way it feels? If we end up doing a pop-up progress window, how about instead a little spinning icon in the place of the jmol applet, like a typical circular thing chasing its tail, or a progress bar loader. If it's in the place of the applets that haven't loaded yet, it's not intrusive on the experience, whereas a pop-up progress window I think intrudes too much on the user. I agree that we should get something in that we've been testing a long time first, and then we can worry more about adding additional things on. Thanks, Jason -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Re: sage notebook with many Jmol viewers
Jon, We are sorting this out. Ticket #9238 is the one you want. The .spkg you used is out-of-date. All the fixes are not in, but if you follow the patching instructions on #9238 you should get something that will work cleanly on MacOS + Chrome. FF has been inconsistent, so we are having trouble tracing the error and Safari appears to have a memory leak (the latest patches have a clunky work-around for this). If you want to see what is coming down the pike in the next few weeks, take a look at the published samples on my test server: http:///141.233.197.45:. I could really use some comments on how it works. Thanks, Jonathan On Mar 30, 12:02 am, jtyard jty...@gmail.com wrote: I am having issues with sage notebooks that contain more than five instances of the Jmol viewer. In short, if I create a notebook with more than 5 Jmol viewers, save, then reload it, I get an unresponsive script error in Firefox, Safari and Chrome. I've done some peeking around on the trac server and it seems that this is a well-documented problem for which a fix may exist, having to do with the tickets #9232 and #9238. So I apologize if this is not the correct place to ask about this, but I'm having trouble following what has been done on these tickets and, more importantly, what I would need to do in order to incorporate the fix to my sage distribution. I'm running sage 4.6.2 on osx 10.6.7, and I upgraded to Jmol_for_SageNoteBook-1.1.4.spkg so that I could use google Chrome. I'm sure that if I wait long enough this will all be incorporated into an upcoming release of sage, but I'd be very happy to resolve this issue asap so that I can use my notebooks without deleting all the 3d plots. I'm also more than happy to test the changes, but any pointer to how I can incorporate the new code would be helpful. Thanks, Jon -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Re: sage notebook with many Jmol viewers
Hi Jonathan, Thanks for your reply. I tried last night to figure out how to patch my notebook, and I ended up giving up after several hours. I also couldn't find any documentation for hg_sagenb.apply. After updating jmol to 1.1.5, I tried to follow the directions at http://www.sagemath.org/doc/developer/walk_through.html#reviewing-a-patch only replacing hg_sage.apply with hg_sagenb.apply, but things seem not to be as simple as described on that page. Running the command on a patch drops me into a vim editor that shows the text of the whole patch. Not knowing what to do, I press q and I am then asked to enter a commit message. No matter what I seem to do, when I try to quit vim it warns me that there was no write since last change, and if I quit with :q! then it seems I am back where I started. It doesn't help that I am next to clueless about vim, having been raised on emacs, but I really am beyond confused about why I am being dropped into the editor in the first place. Any pointers you could give me to get the new notebook up and running would be much appreciated. I'll be more than happy to test it. Thanks, Jon On Mar 31, 7:08 am, Jonathan gu...@uwosh.edu wrote: Jon, We are sorting this out. Ticket #9238 is the one you want. The .spkg you used is out-of-date. All the fixes are not in, but if you follow the patching instructions on #9238 you should get something that will work cleanly on MacOS + Chrome. FF has been inconsistent, so we are having trouble tracing the error and Safari appears to have a memory leak (the latest patches have a clunky work-around for this). If you want to see what is coming down the pike in the next few weeks, take a look at the published samples on my test server: http:///141.233.197.45:. I could really use some comments on how it works. Thanks, Jonathan On Mar 30, 12:02 am, jtyard jty...@gmail.com wrote: I am having issues with sage notebooks that contain more than five instances of the Jmol viewer. In short, if I create a notebook with more than 5 Jmol viewers, save, then reload it, I get an unresponsive script error in Firefox, Safari and Chrome. I've done some peeking around on the trac server and it seems that this is a well-documented problem for which a fix may exist, having to do with the tickets #9232 and #9238. So I apologize if this is not the correct place to ask about this, but I'm having trouble following what has been done on these tickets and, more importantly, what I would need to do in order to incorporate the fix to my sage distribution. I'm running sage 4.6.2 on osx 10.6.7, and I upgraded to Jmol_for_SageNoteBook-1.1.4.spkg so that I could use google Chrome. I'm sure that if I wait long enough this will all be incorporated into an upcoming release of sage, but I'd be very happy to resolve this issue asap so that I can use my notebooks without deleting all the 3d plots. I'm also more than happy to test the changes, but any pointer to how I can incorporate the new code would be helpful. Thanks, Jon -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Re: sage notebook with many Jmol viewers
Your description sounds like you are doing a hg_sagenb.commit(), not a hg_sagenb.apply(http://patchname.patch). If you just copy the link to the listed patches as shown above they should work. That's what I do. Jonathan P.S. Great name! On Mar 31, 11:32 am, jtyard jty...@gmail.com wrote: Hi Jonathan, Thanks for your reply. I tried last night to figure out how to patch my notebook, and I ended up giving up after several hours. I also couldn't find any documentation for hg_sagenb.apply. After updating jmol to 1.1.5, I tried to follow the directions at http://www.sagemath.org/doc/developer/walk_through.html#reviewing-a-p... only replacing hg_sage.apply with hg_sagenb.apply, but things seem not to be as simple as described on that page. Running the command on a patch drops me into a vim editor that shows the text of the whole patch. Not knowing what to do, I press q and I am then asked to enter a commit message. No matter what I seem to do, when I try to quit vim it warns me that there was no write since last change, and if I quit with :q! then it seems I am back where I started. It doesn't help that I am next to clueless about vim, having been raised on emacs, but I really am beyond confused about why I am being dropped into the editor in the first place. Any pointers you could give me to get the new notebook up and running would be much appreciated. I'll be more than happy to test it. Thanks, Jon On Mar 31, 7:08 am, Jonathan gu...@uwosh.edu wrote: Jon, We are sorting this out. Ticket #9238 is the one you want. The .spkg you used is out-of-date. All the fixes are not in, but if you follow the patching instructions on #9238 you should get something that will work cleanly on MacOS + Chrome. FF has been inconsistent, so we are having trouble tracing the error and Safari appears to have a memory leak (the latest patches have a clunky work-around for this). If you want to see what is coming down the pike in the next few weeks, take a look at the published samples on my test server: http:///141.233.197.45:. I could really use some comments on how it works. Thanks, Jonathan On Mar 30, 12:02 am, jtyard jty...@gmail.com wrote: I am having issues with sage notebooks that contain more than five instances of the Jmol viewer. In short, if I create a notebook with more than 5 Jmol viewers, save, then reload it, I get an unresponsive script error in Firefox, Safari and Chrome. I've done some peeking around on the trac server and it seems that this is a well-documented problem for which a fix may exist, having to do with the tickets #9232 and #9238. So I apologize if this is not the correct place to ask about this, but I'm having trouble following what has been done on these tickets and, more importantly, what I would need to do in order to incorporate the fix to my sage distribution. I'm running sage 4.6.2 on osx 10.6.7, and I upgraded to Jmol_for_SageNoteBook-1.1.4.spkg so that I could use google Chrome. I'm sure that if I wait long enough this will all be incorporated into an upcoming release of sage, but I'd be very happy to resolve this issue asap so that I can use my notebooks without deleting all the 3d plots. I'm also more than happy to test the changes, but any pointer to how I can incorporate the new code would be helpful. Thanks, Jon -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: sage notebook with many Jmol viewers
On 03/31/11 05:32 PM, jtyard wrote: Hi Jonathan, Thanks for your reply. I tried last night to figure out how to patch my notebook, and I ended up giving up after several hours. I also couldn't find any documentation for hg_sagenb.apply. After updating jmol to 1.1.5, I tried to follow the directions at http://www.sagemath.org/doc/developer/walk_through.html#reviewing-a-patch only replacing hg_sage.apply with hg_sagenb.apply, but things seem not to be as simple as described on that page. Running the command on a patch drops me into a vim editor that shows the text of the whole patch. Not knowing what to do, I press q and I am then asked to enter a commit message. No matter what I seem to do, when I try to quit vim it warns me that there was no write since last change, and if I quit with :q! then it seems I am back where I started. It doesn't help that I am next to clueless about vim, having been raised on emacs, but I really am beyond confused about why I am being dropped into the editor in the first place. Any pointers you could give me to get the new notebook up and running would be much appreciated. I'll be more than happy to test it. Thanks, Jon If you make changes to the code and try to commit them, then you must give a message why. I must admit I can't see why that should be so with you applying a patch though. I personally never use the hg commands in Sage, but use a version of hg on my system, so I can't really say too much about your issues. If set this: EDITOR=emacs export EDITOR then instead of firing up vim, you will get emacs. (I had the almost the opposite problem to you - my system kept firing up the GUI editor gedit, but I wanted vi!) I believe there's a variable you can use that selects the editor for Mercurial (i.e. hg) only. I'm not sure what it is, but Google would find it. But I just use EDITOR as I use vi for everything anyway. I must admit though, I'm still puzzled why you are asked to supply a commit message. Dave -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
[sage-devel] Re: sage notebook with many Jmol viewers
Thanks guys. I was definitely using hg_sagenb.apply() and not hg_sagenb.commit(), so I am not sure why it was asking me to commit. The only difference from what you say Jonathan was that I was applying the patches from a local directory and not an http:, so I doubt that makes a difference. I will play with it some more tonight and see if I can get somewhere. Jon On Mar 31, 3:13 pm, Dr. David Kirkby david.kir...@onetel.net wrote: On 03/31/11 05:32 PM, jtyard wrote: Hi Jonathan, Thanks for your reply. I tried last night to figure out how to patch my notebook, and I ended up giving up after several hours. I also couldn't find any documentation for hg_sagenb.apply. After updating jmol to 1.1.5, I tried to follow the directions at http://www.sagemath.org/doc/developer/walk_through.html#reviewing-a-p... only replacing hg_sage.apply with hg_sagenb.apply, but things seem not to be as simple as described on that page. Running the command on a patch drops me into a vim editor that shows the text of the whole patch. Not knowing what to do, I press q and I am then asked to enter a commit message. No matter what I seem to do, when I try to quit vim it warns me that there was no write since last change, and if I quit with :q! then it seems I am back where I started. It doesn't help that I am next to clueless about vim, having been raised on emacs, but I really am beyond confused about why I am being dropped into the editor in the first place. Any pointers you could give me to get the new notebook up and running would be much appreciated. I'll be more than happy to test it. Thanks, Jon If you make changes to the code and try to commit them, then you must give a message why. I must admit I can't see why that should be so with you applying a patch though. I personally never use the hg commands in Sage, but use a version of hg on my system, so I can't really say too much about your issues. If set this: EDITOR=emacs export EDITOR then instead of firing up vim, you will get emacs. (I had the almost the opposite problem to you - my system kept firing up the GUI editor gedit, but I wanted vi!) I believe there's a variable you can use that selects the editor for Mercurial (i.e. hg) only. I'm not sure what it is, but Google would find it. But I just use EDITOR as I use vi for everything anyway. I must admit though, I'm still puzzled why you are asked to supply a commit message. Dave -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
Re: [sage-devel] Re: sage notebook with many Jmol viewers
On Thu, 31 Mar 2011 at 06:08AM -0700, Jonathan wrote: If you want to see what is coming down the pike in the next few weeks, take a look at the published samples on my test server: http:///141.233.197.45:. I could really use some comments on how it works. I'm using Firefox 4.0 on Ubuntu 10.10 with the Sun/Oracle Java and http://141.233.197.45:/home/pub/0/ is working great. I really like the new controls -- putting it in a new window, changing the size, turning the spin on and off. The sleeping/interactive thing is also nice. The only slight problem is that it did take quite a long time for all the applets to load, but I suppose it's better to get things working first before we worry about speed. I tried the lots of applets worksheet, and tried to get every applet interactive and spinning. I see that some will automatically sleep, rather than have too many applets running. That's nice. Excellent work! Thanks so much for your efforts. Jmol is absolutely essential to me when I teach multivariable calc. Dan -- --- Dan Drake - http://mathsci.kaist.ac.kr/~drake --- signature.asc Description: Digital signature
[sage-devel] Re: sage notebook with many Jmol viewers
So I just made a fresh build of sage and the patching went smoothly. Not sure what was causing the problem. So far, everything works great! I also noticed that it did seem to take a long time for the applets to load, and somehow it seems that the image resolution is not as good as it was before I did the update. Presumably this is to save memory, but it would be nice if this could be a global option somehow. Thanks! Jon On Mar 31, 4:05 pm, jtyard jty...@gmail.com wrote: Thanks guys. I was definitely using hg_sagenb.apply() and not hg_sagenb.commit(), so I am not sure why it was asking me to commit. The only difference from what you say Jonathan was that I was applying the patches from a local directory and not an http:, so I doubt that makes a difference. I will play with it some more tonight and see if I can get somewhere. Jon On Mar 31, 3:13 pm, Dr. David Kirkby david.kir...@onetel.net wrote: On 03/31/11 05:32 PM, jtyard wrote: Hi Jonathan, Thanks for your reply. I tried last night to figure out how to patch my notebook, and I ended up giving up after several hours. I also couldn't find any documentation for hg_sagenb.apply. After updating jmol to 1.1.5, I tried to follow the directions at http://www.sagemath.org/doc/developer/walk_through.html#reviewing-a-p... only replacing hg_sage.apply with hg_sagenb.apply, but things seem not to be as simple as described on that page. Running the command on a patch drops me into a vim editor that shows the text of the whole patch. Not knowing what to do, I press q and I am then asked to enter a commit message. No matter what I seem to do, when I try to quit vim it warns me that there was no write since last change, and if I quit with :q! then it seems I am back where I started. It doesn't help that I am next to clueless about vim, having been raised on emacs, but I really am beyond confused about why I am being dropped into the editor in the first place. Any pointers you could give me to get the new notebook up and running would be much appreciated. I'll be more than happy to test it. Thanks, Jon If you make changes to the code and try to commit them, then you must give a message why. I must admit I can't see why that should be so with you applying a patch though. I personally never use the hg commands in Sage, but use a version of hg on my system, so I can't really say too much about your issues. If set this: EDITOR=emacs export EDITOR then instead of firing up vim, you will get emacs. (I had the almost the opposite problem to you - my system kept firing up the GUI editor gedit, but I wanted vi!) I believe there's a variable you can use that selects the editor for Mercurial (i.e. hg) only. I'm not sure what it is, but Google would find it. But I just use EDITOR as I use vi for everything anyway. I must admit though, I'm still puzzled why you are asked to supply a commit message. Dave -- To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
