Opened 12 years ago
Closed 12 years ago
#9232 closed defect (fixed)
jmol on commandline broken
Reported by: | Volker Braun | Owned by: | Jonathan Gutow |
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Priority: | major | Milestone: | sage-4.7 |
Component: | graphics | Keywords: | |
Cc: | Karl-Dieter Crisman, Jason Grout, Jeroen Demeyer | Merged in: | sage-4.7.alpha4 |
Authors: | Jonathan Gutow, Volker Braun | Reviewers: | Jason Grout, Karl-Dieter Crisman, Volker Braun |
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | Stopgaps: |
Description (last modified by )
I can't see Graphics3d objects on the command line. For example,
sage: sphere() sage:
The command returns without starting jmol or producing any other graphical output.
Strangely enough, I can start jmol from the sage command line:
---------------------------------------------------------------------- | Sage Version 4.4.3, Release Date: 2010-06-04 | | Type notebook() for the GUI, and license() for information. | ---------------------------------------------------------------------- sage: !jmol splash_image=jar:file:/home/vbraun/opt/sage-hg/local/lib/python2.6/site-packages/sagenb-0.8-py2.6.egg/sagenb/data/jmol/Jmol.jar!/org/openscience/jmol/images/Jmol_splash.jpg history file is /home/vbraun/.jmol/history using Smarter Model Adapter (C) 2008 Jmol Development Jmol Version 11.6.16 2008-11-24 13:39 java.vendor:Sun Microsystems Inc. java.version:1.6.0_18 os.name:Linux memory:9.8/21.1 useCommandThread: false User macros dir: /home/vbraun/.jmol/macros exists: false isDirectory: false
The following also works and shows a tachyon-generated plot:
sphere(viewer='tachyon')
More verbosity:
sage: sphere(verbosity=99) Traceback (most recent call last): File "/home/vbraun/Sage/sage/local/bin/sage-pypkg-location", line 3, in <module> from pkg_resources import Requirement, working_set zipimport.ZipImportError: can't decompress data; zlib not available Jmol.jar not found
For the record, I'm running Fedora 13 x86_64
Apply trac_9232_call_jmol_correctly.patch and trac_9232-lighting.patch.
Attachments (4)
Change History (40)
comment:1 Changed 12 years ago by
comment:2 follow-up: 3 Changed 12 years ago by
I installed http://www.uwosh.edu/faculty_staff/gutow/Jmol_for_SageNoteBook-1.1.spkg (#9238) but it did not change anything. The verbose output above indicates that Jmol.jar is never opened, so it is not particularly surprising that an updated Jmol spkg has no effect.
comment:3 Changed 12 years ago by
It was worth a try as that still could have been a hidden Jmol.jar file not found error. This is different than the problem I addressed. Sorry. I would guess it is a problem with the "sphere" command. Does it work with a simple plot3d command? I've tested the 1.1 version on MacOS and Ubuntu and it seems to work for me. Replying to vbraun:
I installed http://www.uwosh.edu/faculty_staff/gutow/Jmol_for_SageNoteBook-1.1.spkg (#9238) but it did not change anything. The verbose output above indicates that Jmol.jar is never opened, so it is not particularly surprising that an updated Jmol spkg has no effect.
comment:4 follow-up: 5 Changed 12 years ago by
I only used the sphere()
command because it is the fastest way to generate 3d graphics. Other 3d plotting commands fail in the same way:
sage: plot3d(lambda x, y: x^2 + y^2, (-2,2), (-2,2)) # note: no output sage: plot3d(lambda x, y: x^2 + y^2, (-2,2), (-2,2), verbosity=99) Traceback (most recent call last): File "/home/vbraun/Sage/sage/local/bin/sage-pypkg-location", line 3, in <module> from pkg_resources import Requirement, working_set zipimport.ZipImportError: can't decompress data; zlib not available Jmol.jar not found
comment:5 Changed 12 years ago by
Try installing the Jmol for notebook again. It looks like the file on my server got corrupted and was missing the Jmol.jar application file as well as some others..Not sure what happened but we've had some power outages and the server may have been rebuilt from backups. I've uploaded a new copy.
Because the name hasn't changed you will probably have to do some surgery to get it to download and do an install. You will need to delete any copies of the .spkg (or its uncompressed directory) that you find in any of these subdirectories of your sage install before trying an install. If you don't get a message about downloading the file you missed something: spkg/build spkg/installed spkg/optional
Let us know if this fixes it. Sorry for the inconvenience. Jonathan Replying to vbraun:
I only used the
sphere()
command because it is the fastest way to generate 3d graphics. Other 3d plotting commands fail in the same way:sage: plot3d(lambda x, y: x^2 + y^2, (-2,2), (-2,2)) # note: no output sage: plot3d(lambda x, y: x^2 + y^2, (-2,2), (-2,2), verbosity=99) Traceback (most recent call last): File "/home/vbraun/Sage/sage/local/bin/sage-pypkg-location", line 3, in <module> from pkg_resources import Requirement, working_set zipimport.ZipImportError: can't decompress data; zlib not available Jmol.jar not found
comment:6 follow-up: 7 Changed 12 years ago by
I did a
[vbraun@localhost sage]$ rm ./spkg/optional/Jmol_for_SageNoteBook-1.1.spkg [vbraun@localhost sage]$ ./sage -f http://www.uwosh.edu/faculty_staff/gutow/Jmol_for_SageNoteBook-1.1.spkg
and it re-downloaded the Jmol spkg. Still fails with the same error message.
comment:7 Changed 12 years ago by
There is something special about your system...I've just retested that things work for Sage 4.4.3 on MacOS and Ubuntu Linux. Let's see if everything actually got installed: Can you please post the directory listing (ls -l please) for the following two directories: <sage directory>/local/lib/python2.6/site-packages/sagenb-0.8-py2.6.egg/sagenb/data/jmol and <sage directory>/local/lib/python2.6/site-packages/sagenb-0.8-py2.6.egg/sagenb/data/jmol/appletweb
If everything is there, I'm mystified. If everything is not, then something is wrong with the install for your system and the .spkg needs to be fixed.
Jonathan Replying to vbraun:
I did a
[vbraun@localhost sage]$ rm ./spkg/optional/Jmol_for_SageNoteBook-1.1.spkg [vbraun@localhost sage]$ ./sage -f http://www.uwosh.edu/faculty_staff/gutow/Jmol_for_SageNoteBook-1.1.spkgand it re-downloaded the Jmol spkg. Still fails with the same error message.
comment:8 Changed 12 years ago by
I saved the sys.path
within sage-pypkg-location
, and it reads:
/home/vbraun/opt/sage-4.5.alpha1/local/bin /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/setuptools-0.6c9-py2.6.egg /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/Twisted-9.0.0-py2.6-linux-x86_64.egg /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/ZODB3-3.7.0-py2.6-linux-x86_64.egg /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/zdaemon-2.0.0-py2.6.egg /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/ZConfig-2.5-py2.6.egg /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/zope.testing-3.5.0-py2.6.egg /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/zope.proxy-3.4.0-py2.6-linux-x86_64.egg /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/Pygments-0.11.1-py2.6.egg /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/Jinja-1.2-py2.6-linux-x86_64.egg /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/Jinja2-2.1.1-py2.6-linux-x86_64.egg /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/Sphinx-0.6.3-py2.6.egg /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/SQLAlchemy-0.5.8-py2.6.egg /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/pytz-2010h-py2.6.egg /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/zope.i18nmessageid-3.5.2-py2.6-linux-x86_64.egg /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/zope.event-3.5.0_1-py2.6.egg /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/ClientForm-0.2.10-py2.6.egg /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/mechanize-0.1.11-py2.6.egg /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/zope.interface-3.6.1-py2.6-linux-x86_64.egg /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/zope.schema-3.6.3-py2.6.egg /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/zope.testbrowser-3.8.1-py2.6.egg /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/sagenb-0.8-py2.6.egg /home/vbraun/opt/sage-4.5.alpha1 /home/vbraun/Sage/sage/local/lib/python /home/vbraun/Sage/sage/local/lib64/python26.zip /home/vbraun/Sage/sage/local/lib64/python2.6 /home/vbraun/Sage/sage/local/lib64/python2.6/plat-linux2 /home/vbraun/Sage/sage/local/lib64/python2.6/lib-tk /home/vbraun/Sage/sage/local/lib64/python2.6/lib-old /home/vbraun/Sage/sage/local/lib64/python2.6/lib-dynload /home/vbraun/Sage/sage/local/lib/python2.6/site-packages /home/vbraun/Sage/sage/local/lib/python2.6/site-packages/PIL
But sage install zlib in
[vbraun@volker-two sage-4.5.alpha1]$ find | grep zlib.so ./local/lib/python2.6/lib-dynload/zlib.so
Note: /lib/
, not /lib64/
. This explains why zlib cannot be imported. For the record, all libraries are 64-bit on my system.
From within Sage, on the other hand, sys.path
is set appropriately:
sage: '/home/vbraun/Sage/sage/local/lib/python2.6/lib-dynload' in sys.path True
comment:9 Changed 12 years ago by
For the record, creating a symlink $SAGE_ROOT/local/lib64 pointing to $SAGE_ROOT/local/lib works. Another workaround is adding LIBRARY_PATH to DYLD_LIBRARY_PATH in sage-native-execute (from logix/#sage-devel).
I still don't understand the underlying cause, where does python get the incorrect path from?
comment:10 Changed 12 years ago by
comment:11 Changed 12 years ago by
Owner: | changed from jason, was to Jonathan Gutow |
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comment:12 Changed 12 years ago by
Status: | new → needs_work |
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Changed 12 years ago by
Attachment: | trac_9232_plot3d_base_pyx.patch added |
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plot3d/base.pyx fixes to launch Jmol from cmd line
Changed 12 years ago by
Attachment: | trac_9232_notebook_fixes.patch added |
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Notebook fixes for launch Jmol from cmd line
comment:13 Changed 12 years ago by
Authors: | → Jonathan Gutwo |
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Cc: | Karl-Dieter Crisman Jason Grout added |
Milestone: | → sage-4.7 |
Reviewers: | → Jason Grout, Karl-Dieter Crisman |
Status: | needs_work → needs_review |
The above patches combined with installation of a newer version of Jmol fix this problem for Sage 4.6.2. To install the new Jmol
./sage -f "http://www.uwosh.edu/faculty_staff/gutow/Jmol_for_SageNoteBook-1.1.5.spkg"
Note that my linux and MacOS versions of sage seemed to have slightly different mercurial tracking. On MacOS you get a warning about the SageMenu?.mnu file, when you apply the notebook_fixes patch. That is OK, the other untracked files are properly added.
comment:14 follow-up: 15 Changed 12 years ago by
Authors: | Jonathan Gutwo → Jonathan Gutow |
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This will have to be part of a new SageNB package before it can be merged. See also #9238.
comment:15 follow-up: 16 Changed 12 years ago by
comment:16 Changed 12 years ago by
Replying to gutow:
Replying to kcrisman:
This will have to be part of a new SageNB package before it can be merged. See also #9238.
OK, so what does that involve? Does this mean make a complete .spkg of the sageNB? Then where do things have to go? Also don't we need positive reviews first?
Yes, eventually! This is just for informational purposes to someone coming to the ticket.
comment:17 Changed 12 years ago by
Getting bad news:
tar: This does not look like a tar archive tar: Skipping to next header tar: Archive contains obsolescent base-64 headers
comment:18 Changed 12 years ago by
Did you use ./sage -pkg
to create this? When I did, I got
Creating Sage package Jmol_for_SageNoteBook-1.1.5 Created package Jmol_for_SageNoteBook-1.1.5.spkg. NAME: Jmol_for_SageNoteBook VERSION: 1.1.5 SIZE: 11.1M HG REPO: Error reading repository SPKG.txt: Good Please test this package using
which is actually ok since I don't think you have an HG repo and this is a temporary package for testing. Then success:
Temporary package directory: /Users/student/Desktop/sage-4.6.2/spkg/build/Jmol_for_SageNoteBook-1.1.5 replacing Jmol.js... Jmol.js replaced. removing Jmol*.jar and license files. rm: /Users/student/Desktop/sage-4.6.2/devel/sagenb/sagenb/data/jmol/LICENSE.txt: No such file or directory installing Jmol.jar and license files… New Jmol*.jar and license files installed. real 0m1.051s user 0m0.034s sys 0m0.320s Successfully installed Jmol_for_SageNoteBook-1.1.5 Now cleaning up tmp files. Making Sage/Python scripts relocatable... Making script relocatable Finished installing Jmol_for_SageNoteBook-1.1.5.spkg
Then applying the files is ok until
applying /Users/student/.sage/temp/Dasher_03.local/468/tmp_4.patch file sagenb/data/jmol/appletweb/SageMenu.mnu already exists 1 out of 1 hunks FAILED -- saving rejects to file sagenb/data/jmol/appletweb/SageMenu.mnu.rej
Problematic is that then it's rejected? I guess I'll see what happens... but this error will probably need to be fixed.
comment:19 Changed 12 years ago by
Still zapped, probably because of the problem with the menu?
But then I tried it again, and it worked! I don't get that.
I'll try the notebook next. Okay, works, but I do not see the new stuff for the applet. I guess that's okay, since that's the other ticket, right?
Is there any way I can tell if the correct menu item is in there? (Such as something to look for in the menu for the applet?)
comment:20 follow-up: 21 Changed 12 years ago by
- The correct menu is much shorter in the notebook than in the application launched from the command line. The application launched from the command line uses the default menu. I'll look into making them match.
- Apply the patches in #9238 to see the updated notebook Jmol interface.
- The .spkg problem is odd. I've got no errors ever. I just use ./sage -f "<web address of patch>".
- The patch with the problem with the .mnu file means redoing it against a 4.6.2 that had the .mnu file in the repo. For some reason the version I got for ubuntu 10.04 lts did not.
comment:21 Changed 12 years ago by
Description: | modified (diff) |
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- The correct menu is much shorter in the notebook than in the application launched from the command line. The application launched from the command line uses the default menu. I'll look into making them match.
Well, no need on this ticket!
As for this, the first patch only suffices to fix the command line problem, and the notebook still works right.
So I would say that the second patch is not relevant to this ticket, esp. given its problems with import (which I am looking into - I think has to do with HG not applying some things correctly because of perceived line endings. Look at the view of the attachment on this ticket, and look at the lines with bond100
and bond150
and note the weirdness there. It looks like
bond100 | 0.10 √Ö = wireframe .1
instead of angstroms like I think it's supposed to
bond100 | 0.10 Å = wireframe .1
No wonder it's not applying, since it's not being interpreted right. Anyway, not relevant for the ticket.
- Apply the patches in #9238 to see the updated notebook Jmol interface.
As I thought - thanks, not relevant for reviewing this.
- The .spkg problem is odd. I've got no errors ever. I just use ./sage -f "<web address of patch>".
Yes, that is what should work. Since this isn't an spkg that would actually ever exist, it's not a problem, I hope.
- The patch with the problem with the .mnu file means redoing it against a 4.6.2 that had the .mnu file in the repo. For some reason the version I got for ubuntu 10.04 lts did not.
See above.
I get the following issue as well.
rm: /Users/.../sage-4.7.alpha2-jmol/devel/sagenb/sagenb/data/jmol/LICENSE.txt: No such file or directory
So was there not a license before? Apparently not - I can confirm that in an install that does not have the new Jmol. So it's not a big deal, but at any rate you didn't have to put that in the script.
Otherwise I think this is ready to go. It would be nice to have someone on a system where command line plotting did not work before to try this. Volker, du bist ja bei Sage Days 29, oder? Probierst du es mal aus?
comment:22 Changed 12 years ago by
Oh, and of course this can't actually be merged until a new SageNB package is produced. I think I might be willing to do that once this and #9238 and one or two other things are ready; it would sure be worth it!
comment:23 follow-up: 24 Changed 12 years ago by
I applied the jmol spkg and trac_9232_plot3d_base_pyx.patch
and jmol is still broken on the command line, Fedora 14 x86_64. I need to add trac_10286_call_jmol_correctly.patch
from #10286 on top of it. The issue is that sage-native-execute
must not be used for sage components like jmol.
comment:24 Changed 12 years ago by
Status: | needs_review → needs_work |
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Replying to vbraun:
I applied the jmol spkg and
trac_9232_plot3d_base_pyx.patch
and jmol is still broken on the command line, Fedora 14 x86_64. I need to addtrac_10286_call_jmol_correctly.patch
from #10286 on top of it. The issue is thatsage-native-execute
must not be used for sage components like jmol.
Thanks for that feedback very much. Ok, then I propose that that patch gets moved here, and then #10286 can be just about sage-native-execute. Am I correct in assuming that only that patch from #10286 is needed to fix the behavior?
comment:25 Changed 12 years ago by
Yes, it would be fine to move trac_10286_call_jmol_correctly.patch
here. Only that one-liner is needed.
comment:26 Changed 12 years ago by
Authors: | Jonathan Gutow → Jonathan Gutow, Volker Braun |
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Description: | modified (diff) |
Reviewers: | Jason Grout, Karl-Dieter Crisman → Jason Grout, Karl-Dieter Crisman, Volker Braun |
Status: | needs_work → needs_review |
Okay, this should be all okay then.
comment:27 Changed 12 years ago by
Things are a little bit of a mess because of the potential for flask changeover in SageNB. What do people think of this?
- This ticket is used just for adding Volker's patch. No sagenb change needed.
- Jonathan's patches for the menu, help, and surface lighting/spt files are moved to #9238.
- #9238 and all its attendant pieces become part of the flask notebook changeover, and henceforth the property of those doing that :)
Otherwise this has the potential to just bitrot forever.
comment:28 follow-up: 29 Changed 12 years ago by
The flask notebook has already split off of the current notebook. So any patches that are applied to the current sage notebook will also need to be applied to the new notebook, probably in parallel.
I'm already working on moving #9238 over to the new notebook. It's just a matter of applying the patch to the new notebook, as far as I can tell. (We'll find out better once we actually get jmol working with the new notebook!)
comment:29 Changed 12 years ago by
Should I continue to put my patches into #9238? I've still got some fixes that should reduce memory problems making Safari somewhat more reliable and I may be able to get the advanced controls working in IE.
comment:30 Changed 12 years ago by
Description: | modified (diff) |
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Status: | needs_review → positive_review |
Jonathan, definitely keep working on #9238. Jason can just put those things in the new notebook. Having something working completely is a very good idea, and we can continue to test it on the old notebook, which is still the current notebook, after all.
I do think we need to also add the piece of #9238 that changes the lighting. Currently I have good lighting in the command line and bad lighting in the notebook, even without the new jmol - someone the new jmol is called from the notebook, even though I didn't install it in this version!!! I even checked this in the advanced menu. Mystifying.
I'm just testing quick, and then I'll post patches. Since they aren't mine, I feel free to give positive review.
Changed 12 years ago by
Attachment: | trac_9232-lighting.patch added |
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comment:31 Changed 12 years ago by
Description: | modified (diff) |
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comment:32 Changed 12 years ago by
Cc: | Jeroen Demeyer added |
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Just a ping to let the release manager know this is ready for alpha4.
:-)
comment:34 Changed 12 years ago by
I meant to say more precisely: please confirm that the patch trac_9232_notebook_fixes.patch may be ignored.
comment:35 Changed 12 years ago by
That is correct. Only the two patches listed at the end of the description are necessary. The other two have been incorporated into ticket #9238 because they are enhancements to how Jmol works.
comment:36 Changed 12 years ago by
Merged in: | → sage-4.7.alpha4 |
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Resolution: | → fixed |
Status: | positive_review → closed |
Does it work if you install the new version of Jmol? See trac # 9238. I think this broke when the notebook was put inside an egg. I took that into account with the new version of Jmol.