#14358: Notebook server should run Java for JMol inside temporary directory
----------------------------------+----------------------------------
Reporter: ppurka | Owner: jason, mpatel, was
Type: defect | Status: needs_review
Priority: major | Milestone: sage-5.13
Component: graphics | Resolution:
Keywords: | Merged in:
Authors: Jeroen Demeyer | Reviewers:
Report Upstream: N/A | Work issues:
Branch: | Commit:
Dependencies: | Stopgaps:
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Description changed by jdemeyer:
Old description:
> When a Sage notebook server needs to create a static 3D image, it runs
> JMol server-side to create this image (if Java is available). However, it
> does this inside a directory to which the worker process might not have
> access to.
>
> ----
>
> '''Old report''' (before we diagnosed the problem):
>
> We have been running the sage worksheets as an unprivileged user. The
> setup is as follows.
>
> 1. A user, say user1, starts the sage server using
> {{{
> sage -n port=8888 accounts=True interface=''
> server_pool=['sagenb@localhost'] openid=True automatic_login=False
> port_tries=0 directory=/home/user1/a.sagenb
> }}}
> 2. Because of the server_pool command, any worksheet is opened as an
> unprivileged user called ''sagenb''. Here is some more info on how to set
> up the environment.
> 1. Create user sagenb by doing (as root)
> {{{
> $ groupadd sagenb
> $ useradd -g sagenb -m sagenb
> }}}
> 2. Create a ssh key for user1
> {{{
> $ ssh-keygen -t rsa # run as user1 and make it passwordless
> }}}
> 3. Copy the id_rsa.pub to `~sagenb/.ssh/authorized_keys`.
> {{{
> $ cp -a ~user1/.ssh/id_rsa.pub /tmp/authorized_keys # Run as user1
> $ mkdir ~sagenb/.ssh # Run as sagenb
> $ cp /tmp/authorized_keys .ssh # Run as sagenb
> }}}
> 3. With default sage-5.2 there is no problem with this and everything
> works.
> 4. With sage-5.2 + "#13121 without new jmol", jmol works but one needs to
> close the worksheet and then reopen the worksheet and then the jmol pops
> up.
> 5. With sage-5.2 + #13121, jmol works partially:
> 1. First, the static image can not be created and there is a permission
> denied error. See [attachment:permission_error.jpg].
> 2. However, once the 3D output is toggled, jmol loads fine. The
> permission denied error is still there.
> 3. The error obtained is of the form
> {{{
> script ERROR: script ERROR: io error reading
> /home/user1/a.sagenb/home/__store__/0/09/098/098f/te\
> st/0/cells/7/sage0-size500-499889951.jmol.zip|SCRIPT:
> java.io.FileNotFoundException:
> /home/user1/a.sagenb/home/__store__/0/09/098/098f/te\
> st/0/cells/7/sage0-size500-499889951.jmol.zip (Permission denied)
> Sleeping...Make Interactive
> }}}
> 6. When run locally, i.e., without server_pool, the jmol loads and runs
> fine. For instance, this is fine:
> {{{
> sage -n directory=a.sagenb
> }}}
>
> This problem has made it difficult for me to upgrade a server from 5.2
> and I think the error is introduced by some change in jmol. The error
> itself stems from some java component. A diff of the changes between the
> directory `$SAGE_ROOT/devel/sagenb/sagenb/data/sage3d` for sage-5.2 and
> sage-5.7.rc0 has not yielded any difference. So, I believe the difference
> is really in the jmol spkg introduced in #12299.
>
> I have traced it back and reproduced it in sage-5.2 + new notebook + new
> jmol. Although I wrote sage-5.2 above, the error is present in all the
> sage versions I have tried - sage-5.4 till sage-5.9.beta0.
New description:
When a Sage notebook server needs to create a static 3D image, it runs
JMol server-side to create this image (if Java is available). However, it
does this inside a directory to which the worker process might not have
access to.
'''Apply''' [attachment:14358_java.patch]
----
'''Old report''' (before we diagnosed the problem):
We have been running the sage worksheets as an unprivileged user. The
setup is as follows.
1. A user, say user1, starts the sage server using
{{{
sage -n port=8888 accounts=True interface=''
server_pool=['sagenb@localhost'] openid=True automatic_login=False
port_tries=0 directory=/home/user1/a.sagenb
}}}
2. Because of the server_pool command, any worksheet is opened as an
unprivileged user called ''sagenb''. Here is some more info on how to set
up the environment.
1. Create user sagenb by doing (as root)
{{{
$ groupadd sagenb
$ useradd -g sagenb -m sagenb
}}}
2. Create a ssh key for user1
{{{
$ ssh-keygen -t rsa # run as user1 and make it passwordless
}}}
3. Copy the id_rsa.pub to `~sagenb/.ssh/authorized_keys`.
{{{
$ cp -a ~user1/.ssh/id_rsa.pub /tmp/authorized_keys # Run as user1
$ mkdir ~sagenb/.ssh # Run as sagenb
$ cp /tmp/authorized_keys .ssh # Run as sagenb
}}}
3. With default sage-5.2 there is no problem with this and everything
works.
4. With sage-5.2 + "#13121 without new jmol", jmol works but one needs to
close the worksheet and then reopen the worksheet and then the jmol pops
up.
5. With sage-5.2 + #13121, jmol works partially:
1. First, the static image can not be created and there is a permission
denied error. See [attachment:permission_error.jpg].
2. However, once the 3D output is toggled, jmol loads fine. The
permission denied error is still there.
3. The error obtained is of the form
{{{
script ERROR: script ERROR: io error reading
/home/user1/a.sagenb/home/__store__/0/09/098/098f/te\
st/0/cells/7/sage0-size500-499889951.jmol.zip|SCRIPT:
java.io.FileNotFoundException:
/home/user1/a.sagenb/home/__store__/0/09/098/098f/te\
st/0/cells/7/sage0-size500-499889951.jmol.zip (Permission denied)
Sleeping...Make Interactive
}}}
6. When run locally, i.e., without server_pool, the jmol loads and runs
fine. For instance, this is fine:
{{{
sage -n directory=a.sagenb
}}}
This problem has made it difficult for me to upgrade a server from 5.2 and
I think the error is introduced by some change in jmol. The error itself
stems from some java component. A diff of the changes between the
directory `$SAGE_ROOT/devel/sagenb/sagenb/data/sage3d` for sage-5.2 and
sage-5.7.rc0 has not yielded any difference. So, I believe the difference
is really in the jmol spkg introduced in #12299.
I have traced it back and reproduced it in sage-5.2 + new notebook + new
jmol. Although I wrote sage-5.2 above, the error is present in all the
sage versions I have tried - sage-5.4 till sage-5.9.beta0.
--
--
Ticket URL: <http://trac.sagemath.org/ticket/14358#comment:32>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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