Re: [sage-devel] issue when starting, setting SAGE_ROOT

[Emmanuel Charpentier]

Wups ! I forgot that I *did* create Trac#21816 
 for that... 

Le mercredi 29 novembre 2017 21:00:17 UTC+1, Emmanuel Charpentier a écrit :
>
> ISTR to have reported (no ticket, just n sage-devel or sage-release) that, 
> after installing the Sage kernel in the system's jupyter notebook, the Sage 
> kernel failed to start due to lack of definitopn for SAGE_ROOT. Trace of 
> execution :
>
>
> ===
> charpent@asus16-ec:~$ jupyter notebook
> [I 20:43:16.366 NotebookApp] Serving notebooks from local directory: 
> /home/charpent
> [I 20:43:16.366 NotebookApp] 0 active kernels
> [I 20:43:16.366 NotebookApp] The Jupyter Notebook is running at:
> [I 20:43:16.366 NotebookApp] 
> http://localhost:/?token=0eed5f7eb89f576804250b9a5351fdb923874706db8e325a
> [I 20:43:16.366 NotebookApp] Use Control-C to stop this server and shut 
> down all kernels (twice to skip confirmation).
> [C 20:43:16.368 NotebookApp] 
> 
> Copy/paste this URL into your browser when you connect for the first 
> time,
> to login with a token:
> 
> http://localhost:/?token=0eed5f7eb89f576804250b9a5351fdb923874706db8e325a
> [10704:10744:1129/204316.598038:ERROR:nss_util.cc(725)] After loading Root 
> Certs, loaded==false: NSS error code: -8018
> ATTENTION: default value of option force_s3tc_enable overridden by 
> environment.
> [I 20:43:17.210 NotebookApp] Accepting one-time-token-authenticated 
> connection from ::1
>
> 
> Here I attempt to open a pre-existing Sage notebook (generated with Sage's 
> jupyter
>
> 
> [W 20:43:18.336 NotebookApp] 404 GET 
> /static/components/moment/locale/fr.js?v=20171129204313 (::1) 6.58ms 
> referer=http://localhost:/tree
> [W 20:43:37.427 NotebookApp] 404 GET 
> /static/components/moment/locale/fr.js?v=20171129204313 (::1) 1.67ms 
> referer=http://localhost:/notebooks/Untitled.ipynb
> Error: You must set the SAGE_ROOT environment variable or run this
> script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory.
> Error setting environment variables by sourcing 
> '/usr/local/sage-8/local/bin/sage-env';
> possibly contact sage-devel (see http://groups.google.com/group/sage-devel
> ).
> [I 20:43:37.512 NotebookApp] Kernel started: 
> 0328ab43-a940-40a7-9371-c53f72f0b853
> [I 20:43:40.510 NotebookApp] KernelRestarter: restarting kernel (1/5)
> Error: You must set the SAGE_ROOT environment variable or run this
> script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory.
> Error setting environment variables by sourcing 
> '/usr/local/sage-8/local/bin/sage-env';
> possibly contact sage-devel (see http://groups.google.com/group/sage-devel
> ).
> [I 20:43:43.517 NotebookApp] KernelRestarter: restarting kernel (2/5)
> Error: You must set the SAGE_ROOT environment variable or run this
> script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory.
> Error setting environment variables by sourcing 
> '/usr/local/sage-8/local/bin/sage-env';
> possibly contact sage-devel (see http://groups.google.com/group/sage-devel
> ).
> [I 20:43:46.523 NotebookApp] KernelRestarter: restarting kernel (3/5)
> Error: You must set the SAGE_ROOT environment variable or run this
> script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory.
> Error setting environment variables by sourcing 
> '/usr/local/sage-8/local/bin/sage-env';
> possibly contact sage-devel (see http://groups.google.com/group/sage-devel
> ).
> [W 20:43:47.639 NotebookApp] Timeout waiting for kernel_info reply from 
> 0328ab43-a940-40a7-9371-c53f72f0b853
> [I 20:43:49.529 NotebookApp] KernelRestarter: restarting kernel (4/5)
> WARNING:root:kernel 0328ab43-a940-40a7-9371-c53f72f0b853 restarted
> Error: You must set the SAGE_ROOT environment variable or run this
> script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory.
> Error setting environment variables by sourcing 
> '/usr/local/sage-8/local/bin/sage-env';
> possibly contact sage-devel (see http://groups.google.com/group/sage-devel
> ).
> [W 20:43:52.535 NotebookApp] KernelRestarter: restart failed
> [W 20:43:52.535 NotebookApp] Kernel 0328ab43-a940-40a7-9371-c53f72f0b853 
> died, removing from map.
> ERROR:root:kernel 0328ab43-a940-40a7-9371-c53f72f0b853 restarted failed!
> [W 20:43:52.550 NotebookApp] 410 DELETE 
> /api/sessions/478a47ac-4621-4f7d-975e-0aad30ec3dbc (::1): Kernel deleted 
> before session
> [W 20:43:52.550 NotebookApp] Kernel deleted before session
> [W 20:43:52.550 NotebookApp] 410 DELETE 
> /api/sessions/478a47ac-4621-4f7d-975e-0aad30ec3dbc (::1) 1.49ms referer=
> http://localhost:/notebooks/Untitled.ipynb
> 
> Here, I throw the towel...
> 

Re: [sage-devel] issue when starting, setting SAGE_ROOT

[Dima Pasechnik]

On Thursday, November 30, 2017 at 8:01:59 AM UTC, tuxedomask2002 wrote:
>
> I tried "./sage" directly in the INSTALLDIR/bin directory and "sage" after 
> adding INSTALLDIR/bin to PATH. Both times resulting in the same error.
>

./sage is meant to be started in the same directory in which ./configure 
and make were run.
While this is not a standard behaviour, you might have noticed that Sage 
does not (yet) support "make install".
 

>
> Am Mittwoch, 29. November 2017 17:33:02 UTC+1 schrieb Jeroen Demeyer:
>>
>> On 2017-11-29 15:55, tuxedomask2002 wrote: 
>> > The executable, following the documentation. 
>>
>> Sorry, I cannot help you further given the explanation that you gave. 
>> There is obviously something wrong with your setup, but I cannot guess 
>> what. 
>>
>> In any case, you should not manually set SAGE_ROOT if you just want to 
>> run Sage. 
>>
>> Also note that your report is a bit inconsistent. In your first post, 
>> you talked about running "sage" and later you talked about running 
>> "./sage" The difference is important! 
>>
>

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Re: [sage-devel] issue when starting, setting SAGE_ROOT

[tuxedomask2002]

I tried "./sage" directly in the INSTALLDIR/bin directory and "sage" after 
adding INSTALLDIR/bin to PATH. Both times resulting in the same error.

Am Mittwoch, 29. November 2017 17:33:02 UTC+1 schrieb Jeroen Demeyer:
>
> On 2017-11-29 15:55, tuxedomask2002 wrote: 
> > The executable, following the documentation. 
>
> Sorry, I cannot help you further given the explanation that you gave. 
> There is obviously something wrong with your setup, but I cannot guess 
> what. 
>
> In any case, you should not manually set SAGE_ROOT if you just want to 
> run Sage. 
>
> Also note that your report is a bit inconsistent. In your first post, 
> you talked about running "sage" and later you talked about running 
> "./sage" The difference is important! 
>

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Re: [sage-devel] issue when starting, setting SAGE_ROOT

[François Bissey]

The message comes from sage-env, so something is trying to run it. Most likely 
because the kernel spec
for sage goes like this:
SAGE_LOCAL/bin/sage —python -m sage.repl.ipython_kernel -f …
While it looks like things only need to know about SAGE_LOCAL, the sage command 
will try
to source sage-env and sage-env will fail if SAGE_ROOT is not in the 
environment.

I am not sure if what you are trying to do is possible from vanilla sage 
without starting a sage shell
(sage -sh) or basically sourcing sage-env before you start.
Provided you put SAGE_LOCAL/bin in your path and defined SAGE_LOCAL  you could 
get away 
with editing the kernel spec file to call “python” directly instead of 
"SAGE_LOCAL/bin/sage —python".
And it should mostly work. The only thing really that could break is stuff 
related to package management
which need to know about SAGE_ROOT. For the rest SAGE_ROOT is dispensable once 
you have
started sage itself.

François


> On 30/11/2017, at 09:00, Emmanuel Charpentier  
> wrote:
> 
> ISTR to have reported (no ticket, just n sage-devel or sage-release) that, 
> after installing the Sage kernel in the system's jupyter notebook, the Sage 
> kernel failed to start due to lack of definitopn for SAGE_ROOT. Trace of 
> execution :
> 
> ===
> charpent@asus16-ec:~$ jupyter notebook
> [I 20:43:16.366 NotebookApp] Serving notebooks from local directory: 
> /home/charpent
> [I 20:43:16.366 NotebookApp] 0 active kernels
> [I 20:43:16.366 NotebookApp] The Jupyter Notebook is running at:
> [I 20:43:16.366 NotebookApp] 
> http://localhost:/?token=0eed5f7eb89f576804250b9a5351fdb923874706db8e325a
> [I 20:43:16.366 NotebookApp] Use Control-C to stop this server and shut down 
> all kernels (twice to skip confirmation).
> [C 20:43:16.368 NotebookApp] 
> 
> Copy/paste this URL into your browser when you connect for the first time,
> to login with a token:
> 
> http://localhost:/?token=0eed5f7eb89f576804250b9a5351fdb923874706db8e325a
> [10704:10744:1129/204316.598038:ERROR:nss_util.cc(725)] After loading Root 
> Certs, loaded==false: NSS error code: -8018
> ATTENTION: default value of option force_s3tc_enable overridden by 
> environment.
> [I 20:43:17.210 NotebookApp] Accepting one-time-token-authenticated 
> connection from ::1
> 
> Here I attempt to open a pre-existing Sage notebook (generated with Sage's 
> jupyter
> 
> [W 20:43:18.336 NotebookApp] 404 GET 
> /static/components/moment/locale/fr.js?v=20171129204313 (::1) 6.58ms 
> referer=http://localhost:/tree
> [W 20:43:37.427 NotebookApp] 404 GET 
> /static/components/moment/locale/fr.js?v=20171129204313 (::1) 1.67ms 
> referer=http://localhost:/notebooks/Untitled.ipynb
> Error: You must set the SAGE_ROOT environment variable or run this
> script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory.
> Error setting environment variables by sourcing 
> '/usr/local/sage-8/local/bin/sage-env';
> possibly contact sage-devel (see http://groups.google.com/group/sage-devel).
> [I 20:43:37.512 NotebookApp] Kernel started: 
> 0328ab43-a940-40a7-9371-c53f72f0b853
> [I 20:43:40.510 NotebookApp] KernelRestarter: restarting kernel (1/5)
> Error: You must set the SAGE_ROOT environment variable or run this
> script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory.
> Error setting environment variables by sourcing 
> '/usr/local/sage-8/local/bin/sage-env';
> possibly contact sage-devel (see http://groups.google.com/group/sage-devel).
> [I 20:43:43.517 NotebookApp] KernelRestarter: restarting kernel (2/5)
> Error: You must set the SAGE_ROOT environment variable or run this
> script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory.
> Error setting environment variables by sourcing 
> '/usr/local/sage-8/local/bin/sage-env';
> possibly contact sage-devel (see http://groups.google.com/group/sage-devel).
> [I 20:43:46.523 NotebookApp] KernelRestarter: restarting kernel (3/5)
> Error: You must set the SAGE_ROOT environment variable or run this
> script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory.
> Error setting environment variables by sourcing 
> '/usr/local/sage-8/local/bin/sage-env';
> possibly contact sage-devel (see http://groups.google.com/group/sage-devel).
> [W 20:43:47.639 NotebookApp] Timeout waiting for kernel_info reply from 
> 0328ab43-a940-40a7-9371-c53f72f0b853
> [I 20:43:49.529 NotebookApp] KernelRestarter: restarting kernel (4/5)
> WARNING:root:kernel 0328ab43-a940-40a7-9371-c53f72f0b853 restarted
> Error: You must set the SAGE_ROOT environment variable or run this
> script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory.
> Error setting environment variables 

Re: [sage-devel] issue when starting, setting SAGE_ROOT

[Emmanuel Charpentier]

ISTR to have reported (no ticket, just n sage-devel or sage-release) that, 
after installing the Sage kernel in the system's jupyter notebook, the Sage 
kernel failed to start due to lack of definitopn for SAGE_ROOT. Trace of 
execution :

===
charpent@asus16-ec:~$ jupyter notebook
[I 20:43:16.366 NotebookApp] Serving notebooks from local directory: 
/home/charpent
[I 20:43:16.366 NotebookApp] 0 active kernels
[I 20:43:16.366 NotebookApp] The Jupyter Notebook is running at:
[I 20:43:16.366 NotebookApp] 
http://localhost:/?token=0eed5f7eb89f576804250b9a5351fdb923874706db8e325a
[I 20:43:16.366 NotebookApp] Use Control-C to stop this server and shut 
down all kernels (twice to skip confirmation).
[C 20:43:16.368 NotebookApp] 

Copy/paste this URL into your browser when you connect for the first 
time,
to login with a token:

http://localhost:/?token=0eed5f7eb89f576804250b9a5351fdb923874706db8e325a
[10704:10744:1129/204316.598038:ERROR:nss_util.cc(725)] After loading Root 
Certs, loaded==false: NSS error code: -8018
ATTENTION: default value of option force_s3tc_enable overridden by 
environment.
[I 20:43:17.210 NotebookApp] Accepting one-time-token-authenticated 
connection from ::1

Here I attempt to open a pre-existing Sage notebook (generated with Sage's 
jupyter

[W 20:43:18.336 NotebookApp] 404 GET 
/static/components/moment/locale/fr.js?v=20171129204313 (::1) 6.58ms 
referer=http://localhost:/tree
[W 20:43:37.427 NotebookApp] 404 GET 
/static/components/moment/locale/fr.js?v=20171129204313 (::1) 1.67ms 
referer=http://localhost:/notebooks/Untitled.ipynb
Error: You must set the SAGE_ROOT environment variable or run this
script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory.
Error setting environment variables by sourcing 
'/usr/local/sage-8/local/bin/sage-env';
possibly contact sage-devel (see http://groups.google.com/group/sage-devel).
[I 20:43:37.512 NotebookApp] Kernel started: 
0328ab43-a940-40a7-9371-c53f72f0b853
[I 20:43:40.510 NotebookApp] KernelRestarter: restarting kernel (1/5)
Error: You must set the SAGE_ROOT environment variable or run this
script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory.
Error setting environment variables by sourcing 
'/usr/local/sage-8/local/bin/sage-env';
possibly contact sage-devel (see http://groups.google.com/group/sage-devel).
[I 20:43:43.517 NotebookApp] KernelRestarter: restarting kernel (2/5)
Error: You must set the SAGE_ROOT environment variable or run this
script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory.
Error setting environment variables by sourcing 
'/usr/local/sage-8/local/bin/sage-env';
possibly contact sage-devel (see http://groups.google.com/group/sage-devel).
[I 20:43:46.523 NotebookApp] KernelRestarter: restarting kernel (3/5)
Error: You must set the SAGE_ROOT environment variable or run this
script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory.
Error setting environment variables by sourcing 
'/usr/local/sage-8/local/bin/sage-env';
possibly contact sage-devel (see http://groups.google.com/group/sage-devel).
[W 20:43:47.639 NotebookApp] Timeout waiting for kernel_info reply from 
0328ab43-a940-40a7-9371-c53f72f0b853
[I 20:43:49.529 NotebookApp] KernelRestarter: restarting kernel (4/5)
WARNING:root:kernel 0328ab43-a940-40a7-9371-c53f72f0b853 restarted
Error: You must set the SAGE_ROOT environment variable or run this
script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory.
Error setting environment variables by sourcing 
'/usr/local/sage-8/local/bin/sage-env';
possibly contact sage-devel (see http://groups.google.com/group/sage-devel).
[W 20:43:52.535 NotebookApp] KernelRestarter: restart failed
[W 20:43:52.535 NotebookApp] Kernel 0328ab43-a940-40a7-9371-c53f72f0b853 
died, removing from map.
ERROR:root:kernel 0328ab43-a940-40a7-9371-c53f72f0b853 restarted failed!
[W 20:43:52.550 NotebookApp] 410 DELETE 
/api/sessions/478a47ac-4621-4f7d-975e-0aad30ec3dbc (::1): Kernel deleted 
before session
[W 20:43:52.550 NotebookApp] Kernel deleted before session
[W 20:43:52.550 NotebookApp] 410 DELETE 
/api/sessions/478a47ac-4621-4f7d-975e-0aad30ec3dbc (::1) 1.49ms 
referer=http://localhost:/notebooks/Untitled.ipynb

Here, I throw the towel...

[W 20:43:59.019 NotebookApp] 404 DELETE 
/api/sessions/478a47ac-4621-4f7d-975e-0aad30ec3dbc (::1): Session not 
found: session_id='478a47ac-4621-4f7d-975e-0aad30ec3dbc'
[W 20:43:59.020 NotebookApp] Session not found: 
session_id='478a47ac-4621-4f7d-975e-0aad30ec3dbc'
[W 20:43:59.020 NotebookApp] 404 DELETE 
/api/sessions/478a47ac-4621-4f7d-975e-0aad30ec3dbc (::1) 

Re: [sage-devel] issue when starting, setting SAGE_ROOT

[Jeroen Demeyer]

On 2017-11-29 15:55, tuxedomask2002 wrote:

The executable, following the documentation.


Sorry, I cannot help you further given the explanation that you gave. 
There is obviously something wrong with your setup, but I cannot guess what.


In any case, you should not manually set SAGE_ROOT if you just want to 
run Sage.


Also note that your report is a bit inconsistent. In your first post, 
you talked about running "sage" and later you talked about running 
"./sage" The difference is important!


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Re: [sage-devel] issue when starting, setting SAGE_ROOT

[tuxedomask2002]

The executable, following the documentation.

Am Mittwoch, 29. November 2017 15:13:04 UTC+1 schrieb Jeroen Demeyer:
>
> On 2017-11-29 14:15, tuxedomask2002 wrote: 
> > ./sage 
> > Error: You must set the SAGE_ROOT environment variable or run this 
> > script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory. 
>
> What is this "./sage" script that you are trying to run? 
>

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Re: [sage-devel] issue when starting, setting SAGE_ROOT

[Jeroen Demeyer]

On 2017-11-29 14:15, tuxedomask2002 wrote:

./sage
Error: You must set the SAGE_ROOT environment variable or run this
script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory.


What is this "./sage" script that you are trying to run?

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Re: [sage-devel] issue when starting, setting SAGE_ROOT

[tuxedomask2002]

./sage
Error: You must set the SAGE_ROOT environment variable or run this
script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory.
Error setting environment variables by sourcing './sage-env';
possibly contact sage-devel (see http://groups.google.com/group/sage-devel).


Am Mittwoch, 29. November 2017 14:05:30 UTC+1 schrieb tuxedomask2002:
>
> Because if I don't set it I receive the error that I have to set it.
>
>
> Am Mittwoch, 29. November 2017 13:41:32 UTC+1 schrieb Jeroen Demeyer:
>>
>> On 2017-11-29 13:30, tuxedomask2002 wrote: 
>> > prepend-path SAGE_ROOT /home/groups/sc/modules/packages/sage/8.0/ 
>> > 
>> > However, when I try to start sage via "sage", I receive: 
>> > 
>> > Error: SAGE_ROOT is set to a bad value: 
>>
>> Why are you manually setting SAGE_ROOT in the first place? Unless you 
>> have multiple Sage installations, there should be no need for that. 
>>
>

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Re: [sage-devel] issue when starting, setting SAGE_ROOT

[tuxedomask2002]

Because if I don't set it I receive the error that I have to set it.


Am Mittwoch, 29. November 2017 13:41:32 UTC+1 schrieb Jeroen Demeyer:
>
> On 2017-11-29 13:30, tuxedomask2002 wrote: 
> > prepend-path SAGE_ROOT /home/groups/sc/modules/packages/sage/8.0/ 
> > 
> > However, when I try to start sage via "sage", I receive: 
> > 
> > Error: SAGE_ROOT is set to a bad value: 
>
> Why are you manually setting SAGE_ROOT in the first place? Unless you 
> have multiple Sage installations, there should be no need for that. 
>

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Re: [sage-devel] issue when starting, setting SAGE_ROOT

[Jeroen Demeyer]

On 2017-11-29 13:30, tuxedomask2002 wrote:

prepend-path SAGE_ROOT /home/groups/sc/modules/packages/sage/8.0/

However, when I try to start sage via "sage", I receive:

Error: SAGE_ROOT is set to a bad value:


Why are you manually setting SAGE_ROOT in the first place? Unless you 
have multiple Sage installations, there should be no need for that.


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[sage-devel] issue when starting, setting SAGE_ROOT

[tuxedomask2002]

Hi,

I installed sage 8.0 to: /home/groups/sc/modules/packages/sage/8.0/ (there 
are the subfolders bin/lib) on CentOS 7 Per module file, I used the 
standard ./configure, except --prefix to change the installation direction.

I set:

set root /home/groups/sc/modules/packages/sage/8.0

prepend-path PYTHONPATH root/binprepend−pathLDLIBRARYPATH
root/binprepend−pathLDLIBRARYPATHroot/lib prepend-path LIBRARY_PATH root/lib
prepend−pathPATHroot/libprepend−pathPATHroot/bin prepend-path CPATH 
$root/include

prepend-path SAGE_ROOT /home/groups/sc/modules/packages/sage/8.0/

However, when I try to start sage via "sage", I receive:

Error: SAGE_ROOT is set to a bad value: 
SAGE_ROOT=/home/groups/sc/modules/packages/sage/8.0/ You must correct it or 
erase it and run this script from the SAGE_ROOT or SAGE_ROOT/local/bin/ 
directory. Error setting environment variables by sourcing 
'/home/groups/sc/modules/packages/sage/8.0/bin/sage-env'; possibly contact 
sage-devel (see google/group/sage-devel).

I also tried to go to "cd /home/groups/sc/modules/packages/sage/8.0/bin" 
and "./sage", but this returns the same error message. If I do not set 
"SAGE_ROOT", I get the error, that SAGE_ROOT must be set.

What am I doing wrong? Thanks in advance.

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