Re: [sage-support] Re: sage-10.0 not working in Jupyter Lab

[Jan Groenewald]

Check this:

File
"/home/finotti/src/sage-10.0/src/sage/repl/ipython_kernel/__main__.py",
line 1
   import sage.all
IndentationError: unexpected indent

On Thu, 1 Jun 2023 at 03:15, Luis Finotti  wrote:

> Here is one with your suggested change:
> https://web.math.utk.edu/~finotti/misc/jl1.out
>
> Here is one with the original version:
> https://web.math.utk.edu/~finotti/misc/jl2.out
>
> Again, thanks for your help!
>
> On Wednesday, May 31, 2023 at 9:03:15 PM UTC-4 Isuru Fernando wrote:
>
>> Can you upload the full log with `LD_DEBUG=libs` and jupyterlab somewhere
>> and post a link?
>>
>> Isuru
>>
>> On Wed, May 31, 2023 at 3:46 PM Luis Finotti  wrote:
>>
>>> Hello,
>>>
>>> Thanks for the help!
>>>
>>> On Wednesday, May 31, 2023 at 4:24:11 PM UTC-4 Isuru Fernando wrote:
>>>
>>> Try running JupyterLab in a shell with `export LD_DEBUG=libs` and import
>>> sage with that jupyterlab instance.
>>> That should tell you where givaro is loaded from.
>>>
>>> Isuru
>>>
>>>
>>> The output is very long, but maybe this is what you mean:
>>>
>>> 916747: find library=libgivaro.so.9 [0]; searching
>>> 916747:  search path=/usr/lib/R/lib (LD_LIBRARY_PATH)
>>> 916747:   trying file=/usr/lib/R/lib/libgivaro.so.9
>>> 916747:  search path=/usr/lib/x86_64-linux-gnu (system search path)
>>> 916747:   trying file=/usr/lib/x86_64-linux-gnu/libgivaro.so.9
>>> 916747:
>>> 916747: find library=libgmpxx.so.4 [0]; searching
>>> 916747:  search path=/usr/lib/R/lib (LD_LIBRARY_PATH)
>>> 916747:   trying file=/usr/lib/R/lib/libgmpxx.so.4
>>> 916747:  search path=/usr/lib/x86_64-linux-gnu (system search path)
>>> 916747:   trying file=/usr/lib/x86_64-linux-gnu/libgmpxx.so.4
>>> 916747:
>>> 916747:
>>> 916747: calling init: /usr/lib/x86_64-linux-gnu/libgmpxx.so.4
>>> 916747:
>>> 916747:
>>> 916747: calling init: /usr/lib/x86_64-linux-gnu/libgivaro.so.9
>>> 916747:
>>> 916747:
>>> 916747: calling init:
>>> /home/finotti/src/sage-test/sage-10.0/src/sage/rings/finite_rings/
>>> element_givaro.cpython-311-x86_64-linux-gnu.so
>>>
>>> Later we see the error
>>>
>>> 916747: /home/finotti/src/sage-test/sage-10.0/src/sage/matrix/
>>> matrix_modn_dense_float.cpython-311-x86_64-linux-gnu.so: error: symbol
>>> lookup error: undefined symbol:
>>> _ZNK6Givaro7IntegercvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEB5cxx11Ev
>>> (fatal)
>>>
>>> Any ideas?
>>>
>>> --
>>> You received this message because you are subscribed to a topic in the
>>> Google Groups "sage-support" group.
>>> To unsubscribe from this topic, visit
>>> https://groups.google.com/d/topic/sage-support/we-BvSt6WRk/unsubscribe.
>>> To unsubscribe from this group and all its topics, send an email to
>>> sage-support...@googlegroups.com.
>>> To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/sage-support/d6430e5a-929e-4662-8852-0bb9ff6f948an%40googlegroups.com
>>> 
>>> .
>>>
>> --
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> 
> .
>

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Re: [sage-support] Re: sage-10.0 not working in Jupyter Lab

[Luis Finotti]

Here is one with your suggested change: 
https://web.math.utk.edu/~finotti/misc/jl1.out

Here is one with the original version: 
https://web.math.utk.edu/~finotti/misc/jl2.out

Again, thanks for your help!

On Wednesday, May 31, 2023 at 9:03:15 PM UTC-4 Isuru Fernando wrote:

> Can you upload the full log with `LD_DEBUG=libs` and jupyterlab somewhere 
> and post a link?
>
> Isuru
>
> On Wed, May 31, 2023 at 3:46 PM Luis Finotti  wrote:
>
>> Hello,
>>
>> Thanks for the help!
>>
>> On Wednesday, May 31, 2023 at 4:24:11 PM UTC-4 Isuru Fernando wrote:
>>
>> Try running JupyterLab in a shell with `export LD_DEBUG=libs` and import 
>> sage with that jupyterlab instance.
>> That should tell you where givaro is loaded from.
>>
>> Isuru
>>
>>
>> The output is very long, but maybe this is what you mean:
>>
>> 916747: find library=libgivaro.so.9 [0]; searching
>> 916747:  search path=/usr/lib/R/lib (LD_LIBRARY_PATH)
>> 916747:   trying file=/usr/lib/R/lib/libgivaro.so.9
>> 916747:  search path=/usr/lib/x86_64-linux-gnu (system search path)
>> 916747:   trying file=/usr/lib/x86_64-linux-gnu/libgivaro.so.9
>> 916747: 
>> 916747: find library=libgmpxx.so.4 [0]; searching
>> 916747:  search path=/usr/lib/R/lib (LD_LIBRARY_PATH)
>> 916747:   trying file=/usr/lib/R/lib/libgmpxx.so.4
>> 916747:  search path=/usr/lib/x86_64-linux-gnu (system search path)
>> 916747:   trying file=/usr/lib/x86_64-linux-gnu/libgmpxx.so.4
>> 916747: 
>> 916747: 
>> 916747: calling init: /usr/lib/x86_64-linux-gnu/libgmpxx.so.4
>> 916747: 
>> 916747: 
>> 916747: calling init: /usr/lib/x86_64-linux-gnu/libgivaro.so.9
>> 916747: 
>> 916747: 
>> 916747: calling init: 
>> /home/finotti/src/sage-test/sage-10.0/src/sage/rings/finite_rings/
>> element_givaro.cpython-311-x86_64-linux-gnu.so
>>
>> Later we see the error
>>
>> 916747: /home/finotti/src/sage-test/sage-10.0/src/sage/matrix/
>> matrix_modn_dense_float.cpython-311-x86_64-linux-gnu.so: error: symbol 
>> lookup error: undefined symbol: 
>> _ZNK6Givaro7IntegercvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEB5cxx11Ev
>>  
>> (fatal)
>>
>> Any ideas?
>>
>> -- 
>> You received this message because you are subscribed to a topic in the 
>> Google Groups "sage-support" group.
>> To unsubscribe from this topic, visit 
>> https://groups.google.com/d/topic/sage-support/we-BvSt6WRk/unsubscribe.
>> To unsubscribe from this group and all its topics, send an email to 
>> sage-support...@googlegroups.com.
>> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/sage-support/d6430e5a-929e-4662-8852-0bb9ff6f948an%40googlegroups.com
>>  
>> 
>> .
>>
>

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Re: [sage-support] Re: sage-10.0 not working in Jupyter Lab

[Isuru Fernando]

Can you upload the full log with `LD_DEBUG=libs` and jupyterlab somewhere
and post a link?

Isuru

On Wed, May 31, 2023 at 3:46 PM Luis Finotti  wrote:

> Hello,
>
> Thanks for the help!
>
> On Wednesday, May 31, 2023 at 4:24:11 PM UTC-4 Isuru Fernando wrote:
>
> Try running JupyterLab in a shell with `export LD_DEBUG=libs` and import
> sage with that jupyterlab instance.
> That should tell you where givaro is loaded from.
>
> Isuru
>
>
> The output is very long, but maybe this is what you mean:
>
> 916747: find library=libgivaro.so.9 [0]; searching
> 916747:  search path=/usr/lib/R/lib (LD_LIBRARY_PATH)
> 916747:   trying file=/usr/lib/R/lib/libgivaro.so.9
> 916747:  search path=/usr/lib/x86_64-linux-gnu (system search path)
> 916747:   trying file=/usr/lib/x86_64-linux-gnu/libgivaro.so.9
> 916747:
> 916747: find library=libgmpxx.so.4 [0]; searching
> 916747:  search path=/usr/lib/R/lib (LD_LIBRARY_PATH)
> 916747:   trying file=/usr/lib/R/lib/libgmpxx.so.4
> 916747:  search path=/usr/lib/x86_64-linux-gnu (system search path)
> 916747:   trying file=/usr/lib/x86_64-linux-gnu/libgmpxx.so.4
> 916747:
> 916747:
> 916747: calling init: /usr/lib/x86_64-linux-gnu/libgmpxx.so.4
> 916747:
> 916747:
> 916747: calling init: /usr/lib/x86_64-linux-gnu/libgivaro.so.9
> 916747:
> 916747:
> 916747: calling init:
> /home/finotti/src/sage-test/sage-10.0/src/sage/rings/finite_rings/
> element_givaro.cpython-311-x86_64-linux-gnu.so
>
> Later we see the error
>
> 916747: /home/finotti/src/sage-test/sage-10.0/src/sage/matrix/
> matrix_modn_dense_float.cpython-311-x86_64-linux-gnu.so: error: symbol
> lookup error: undefined symbol:
> _ZNK6Givaro7IntegercvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEB5cxx11Ev
> (fatal)
>
> Any ideas?
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "sage-support" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/sage-support/we-BvSt6WRk/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
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> https://groups.google.com/d/msgid/sage-support/d6430e5a-929e-4662-8852-0bb9ff6f948an%40googlegroups.com
> 
> .
>

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Re: [sage-support] Re: sage-10.0 not working in Jupyter Lab

[Luis Finotti]

Ah, sorry!  I've fixed,  but it is still not working:

[I 2023-05-31 20:13:22.480 ServerApp] Connecting to kernel 
28308c3f-6fa3-4b63-91b6-cc5e1278
2d4d. 
[I 2023-05-31 20:13:22.500 ServerApp] Connecting to kernel 
28308c3f-6fa3-4b63-91b6-cc5e1278
2d4d. 
[IPKernelApp] WARNING | Unknown message type: 'comm_open' 
[I 2023-05-31 20:13:22.526 ServerApp] Connecting to kernel 
28308c3f-6fa3-4b63-91b6-cc5e1278
2d4d. 
[IPKernelApp] WARNING | Unknown message type: 'comm_msg' 
[W 2023-05-31 20:13:22.551 ServerApp] Got events for closed stream 
 
Traceback (most recent call last): 
 File "", line 198, in _run_module_as_main 
 File "", line 88, in _run_code 
 File 
"/home/finotti/src/sage-10.0/src/sage/repl/ipython_kernel/__main__.py", 
line 1, in <
module> 
   import sage.all 
 File "/home/finotti/src/sage-10.0/src/sage/all.py", line 91, in  
   from sage.algebras.all   import * 
 File "/home/finotti/src/sage-10.0/src/sage/algebras/all.py", line 21, in 
 
   import sage.algebras.catalog as algebras 
 File "/home/finotti/src/sage-10.0/src/sage/algebras/catalog.py", line 86, 
in  
   from sage.algebras.quatalg.quaternion_algebra import QuaternionAlgebra 
as Quaternion 
 File 
"/home/finotti/src/sage-10.0/src/sage/algebras/quatalg/quaternion_algebra.py", 
line 
73, in  
   from . import quaternion_algebra_cython 
 File "sage/algebras/quatalg/quaternion_algebra_cython.pyx", line 1, in 
init sage.algebras
.quatalg.quaternion_algebra_cython 
 File "sage/matrix/matrix_integer_dense.pyx", line 1, in init 
sage.matrix.matrix_integer_d
ense 
ImportError: 
/home/finotti/src/sage-10.0/src/sage/matrix/matrix_modn_dense_float.cpython-31
1-x86_64-linux-gnu.so: undefined symbol: 
_ZNK6Givaro7IntegercvNSt7__cxx1112basic_stringIcSt
11char_traitsIcESaIcEEEB5cxx11Ev

On Wednesday, May 31, 2023 at 8:07:23 PM UTC-4 Isuru Fernando wrote:

> Following seems to indicate that there were some space before `import 
> sage.all`
>
> Isuru
>
>  File 
> "/home/finotti/src/sage-10.0/src/sage/repl/ipython_kernel/__main__.py", 
> line 1 
>import sage.all 
> IndentationError: unexpected indent 
> On Wed, May 31, 2023 at 7:05 PM Luis Finotti  wrote:
>
>> Thanks again for the help!  It is really appreciated!
>>
>> Unfortunately, it did not work:
>>
>> [I 2023-05-31 20:01:40.186 ServerApp] Kernel started: 
>> b7d122c3-383b-463b-b196-193ba26373aa 
>> \0.00s - Debugger warning: It seems that frozen modules are being used, 
>> which may 
>> 0.00s - make the debugger miss breakpoints. Please pass 
>> -Xfrozen_modules=off 
>> 0.00s - to python to disable frozen modules. 
>> 0.00s - Note: Debugging will proceed. Set 
>> PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this 
>> validation. 
>> -[I 2023-05-31 20:01:41.577 ServerApp] Connecting to kernel 
>> b7d122c3-383b-463b-b196-193ba26
>> 373aa. 
>> [I 2023-05-31 20:01:41.580 ServerApp] Connecting to kernel 
>> b7d122c3-383b-463b-b196-193ba263
>> 73aa. 
>> [I 2023-05-31 20:01:41.595 ServerApp] Connecting to kernel 
>> b7d122c3-383b-463b-b196-193ba263
>> 73aa. 
>> \[IPKernelApp] WARNING | Unknown message type: 'comm_open' 
>> [IPKernelApp] WARNING | Unknown message type: 'comm_msg' 
>> [W 2023-05-31 20:01:41.657 ServerApp] Got events for closed stream 
>> > .ZMQStream object at 0x7f8f0c2cf990> 
>> [I 2023-05-31 20:01:50.449 ServerApp] Creating new notebook in 
>> [I 2023-05-31 20:01:50.844 ServerApp] Kernel started: 
>> 2d1683ba-e9f5-4158-b989-8ff8bfbc8f51 
>> Traceback (most recent call last): 
>>  File "", line 189, in _run_module_as_main 
>>  File "", line 148, in _get_module_details 
>>  File "", line 159, in _get_module_details 
>>  File "", line 1074, in get_code 
>>  File "", line 1004, in 
>> source_to_code 
>>  File "", line 241, in 
>> _call_with_frames_removed 
>>  File 
>> "/home/finotti/src/sage-10.0/src/sage/repl/ipython_kernel/__main__.py", 
>> line 1 
>>import sage.all 
>> IndentationError: unexpected indent 
>> [I 2023-05-31 20:01:53.834 ServerApp] AsyncIOLoopKernelRestarter: 
>> restarting kernel (1/5), 
>> new random ports 
>> Traceback (most recent call last): 
>>  File "", line 189, in _run_module_as_main 
>>  File "", line 148, in _get_module_details 
>>  File "", line 159, in _get_module_details 
>>  File "", line 1074, in get_code 
>>  File "", line 1004, in 
>> source_to_code 
>>  File "", line 241, in 
>> _call_with_frames_removed 
>>  File 
>> "/home/finotti/src/sage-10.0/src/sage/repl/ipython_kernel/__main__.py", 
>> line 1 
>>import sage.all 
>> IndentationError: unexpected indent 
>> [I 2023-05-31 20:01:56.846 ServerApp] AsyncIOLoopKernelRestarter: 
>> restarting kernel (2/5), 
>> new random ports 
>> Traceback (most recent call last): 
>>  File "", line 189, in _run_module_as_main 
>>  File "", line 148, in _get_module_details 
>>  File "", line 159, in _get_module_details 
>>  File "", line 1074, in get_code 
>>  File "", line 1004, in 
>> source_to_code 
>>  File "", line 241, in 
>> _call_with_frames_removed 
>>  File 
>> 

Re: [sage-support] Re: sage-10.0 not working in Jupyter Lab

[Isuru Fernando]

Following seems to indicate that there were some space before `import
sage.all`

Isuru

 File
"/home/finotti/src/sage-10.0/src/sage/repl/ipython_kernel/__main__.py",
line 1
   import sage.all
IndentationError: unexpected indent

On Wed, May 31, 2023 at 7:05 PM Luis Finotti  wrote:

> Thanks again for the help!  It is really appreciated!
>
> Unfortunately, it did not work:
>
> [I 2023-05-31 20:01:40.186 ServerApp] Kernel started:
> b7d122c3-383b-463b-b196-193ba26373aa
> \0.00s - Debugger warning: It seems that frozen modules are being used,
> which may
> 0.00s - make the debugger miss breakpoints. Please pass
> -Xfrozen_modules=off
> 0.00s - to python to disable frozen modules.
> 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1
> to disable this
> validation.
> -[I 2023-05-31 20:01:41.577 ServerApp] Connecting to kernel
> b7d122c3-383b-463b-b196-193ba26
> 373aa.
> [I 2023-05-31 20:01:41.580 ServerApp] Connecting to kernel
> b7d122c3-383b-463b-b196-193ba263
> 73aa.
> [I 2023-05-31 20:01:41.595 ServerApp] Connecting to kernel
> b7d122c3-383b-463b-b196-193ba263
> 73aa.
> \[IPKernelApp] WARNING | Unknown message type: 'comm_open'
> [IPKernelApp] WARNING | Unknown message type: 'comm_msg'
> [W 2023-05-31 20:01:41.657 ServerApp] Got events for closed stream
>  .ZMQStream object at 0x7f8f0c2cf990>
> [I 2023-05-31 20:01:50.449 ServerApp] Creating new notebook in
> [I 2023-05-31 20:01:50.844 ServerApp] Kernel started:
> 2d1683ba-e9f5-4158-b989-8ff8bfbc8f51
> Traceback (most recent call last):
>  File "", line 189, in _run_module_as_main
>  File "", line 148, in _get_module_details
>  File "", line 159, in _get_module_details
>  File "", line 1074, in get_code
>  File "", line 1004, in
> source_to_code
>  File "", line 241, in
> _call_with_frames_removed
>  File
> "/home/finotti/src/sage-10.0/src/sage/repl/ipython_kernel/__main__.py",
> line 1
>import sage.all
> IndentationError: unexpected indent
> [I 2023-05-31 20:01:53.834 ServerApp] AsyncIOLoopKernelRestarter:
> restarting kernel (1/5),
> new random ports
> Traceback (most recent call last):
>  File "", line 189, in _run_module_as_main
>  File "", line 148, in _get_module_details
>  File "", line 159, in _get_module_details
>  File "", line 1074, in get_code
>  File "", line 1004, in
> source_to_code
>  File "", line 241, in
> _call_with_frames_removed
>  File
> "/home/finotti/src/sage-10.0/src/sage/repl/ipython_kernel/__main__.py",
> line 1
>import sage.all
> IndentationError: unexpected indent
> [I 2023-05-31 20:01:56.846 ServerApp] AsyncIOLoopKernelRestarter:
> restarting kernel (2/5),
> new random ports
> Traceback (most recent call last):
>  File "", line 189, in _run_module_as_main
>  File "", line 148, in _get_module_details
>  File "", line 159, in _get_module_details
>  File "", line 1074, in get_code
>  File "", line 1004, in
> source_to_code
>  File "", line 241, in
> _call_with_frames_removed
>  File
> "/home/finotti/src/sage-10.0/src/sage/repl/ipython_kernel/__main__.py",
> line 1
>import sage.all
> IndentationError: unexpected indent
> [I 2023-05-31 20:01:59.861 ServerApp] AsyncIOLoopKernelRestarter:
> restarting kernel (3/5),
> new random ports
> Traceback (most recent call last):
>  File "", line 189, in _run_module_as_main
>  File "", line 148, in _get_module_details
>  File "", line 159, in _get_module_details
>  File "", line 1074, in get_code
>  File "", line 1004, in
> source_to_code
>  File "", line 241, in
> _call_with_frames_removed
>  File
> "/home/finotti/src/sage-10.0/src/sage/repl/ipython_kernel/__main__.py",
> line 1
>import sage.all
> IndentationError: unexpected indent
> [I 2023-05-31 20:02:02.875 ServerApp] AsyncIOLoopKernelRestarter:
> restarting kernel (4/5),
> new random ports
> Traceback (most recent call last):
>  File "", line 189, in _run_module_as_main
>  File "", line 148, in _get_module_details
>  File "", line 159, in _get_module_details
>  File "", line 1074, in get_code
>  File "", line 1004, in
> source_to_code
>  File "", line 241, in
> _call_with_frames_removed
>  File
> "/home/finotti/src/sage-10.0/src/sage/repl/ipython_kernel/__main__.py",
> line 1
>import sage.all
> IndentationError: unexpected indent
> [I 2023-05-31 20:02:05.888 ServerApp] AsyncIOLoopKernelRestarter:
> restarting kernel (5/5),
> new random ports
> Traceback (most recent call last):
>  File "", line 189, in _run_module_as_main
>  File "", line 148, in _get_module_details
>  File "", line 159, in _get_module_details
>  File "", line 1074, in get_code
>  File "", line 1004, in
> source_to_code
>  File "", line 241, in
> _call_with_frames_removed
>  File
> "/home/finotti/src/sage-10.0/src/sage/repl/ipython_kernel/__main__.py",
> line 1
>import sage.all
> IndentationError: unexpected indent
> [W 2023-05-31 20:02:08.901 ServerApp] AsyncIOLoopKernelRestarter: restart
> failed
> [W 2023-05-31 20:02:08.901 ServerApp] Kernel
> 2d1683ba-e9f5-4158-b989-8ff8bfbc8f51 died, rem
> oving from map.
> [W 

Re: [sage-support] Re: sage-10.0 not working in Jupyter Lab

[Luis Finotti]

Thanks again for the help!  It is really appreciated!

Unfortunately, it did not work:

[I 2023-05-31 20:01:40.186 ServerApp] Kernel started: 
b7d122c3-383b-463b-b196-193ba26373aa 
\0.00s - Debugger warning: It seems that frozen modules are being used, 
which may 
0.00s - make the debugger miss breakpoints. Please pass 
-Xfrozen_modules=off 
0.00s - to python to disable frozen modules. 
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 
to disable this 
validation. 
-[I 2023-05-31 20:01:41.577 ServerApp] Connecting to kernel 
b7d122c3-383b-463b-b196-193ba26
373aa. 
[I 2023-05-31 20:01:41.580 ServerApp] Connecting to kernel 
b7d122c3-383b-463b-b196-193ba263
73aa. 
[I 2023-05-31 20:01:41.595 ServerApp] Connecting to kernel 
b7d122c3-383b-463b-b196-193ba263
73aa. 
\[IPKernelApp] WARNING | Unknown message type: 'comm_open' 
[IPKernelApp] WARNING | Unknown message type: 'comm_msg' 
[W 2023-05-31 20:01:41.657 ServerApp] Got events for closed stream 
 
[I 2023-05-31 20:01:50.449 ServerApp] Creating new notebook in 
[I 2023-05-31 20:01:50.844 ServerApp] Kernel started: 
2d1683ba-e9f5-4158-b989-8ff8bfbc8f51 
Traceback (most recent call last): 
 File "", line 189, in _run_module_as_main 
 File "", line 148, in _get_module_details 
 File "", line 159, in _get_module_details 
 File "", line 1074, in get_code 
 File "", line 1004, in 
source_to_code 
 File "", line 241, in 
_call_with_frames_removed 
 File 
"/home/finotti/src/sage-10.0/src/sage/repl/ipython_kernel/__main__.py", 
line 1 
   import sage.all 
IndentationError: unexpected indent 
[I 2023-05-31 20:01:53.834 ServerApp] AsyncIOLoopKernelRestarter: 
restarting kernel (1/5), 
new random ports 
Traceback (most recent call last): 
 File "", line 189, in _run_module_as_main 
 File "", line 148, in _get_module_details 
 File "", line 159, in _get_module_details 
 File "", line 1074, in get_code 
 File "", line 1004, in 
source_to_code 
 File "", line 241, in 
_call_with_frames_removed 
 File 
"/home/finotti/src/sage-10.0/src/sage/repl/ipython_kernel/__main__.py", 
line 1 
   import sage.all 
IndentationError: unexpected indent 
[I 2023-05-31 20:01:56.846 ServerApp] AsyncIOLoopKernelRestarter: 
restarting kernel (2/5), 
new random ports 
Traceback (most recent call last): 
 File "", line 189, in _run_module_as_main 
 File "", line 148, in _get_module_details 
 File "", line 159, in _get_module_details 
 File "", line 1074, in get_code 
 File "", line 1004, in 
source_to_code 
 File "", line 241, in 
_call_with_frames_removed 
 File 
"/home/finotti/src/sage-10.0/src/sage/repl/ipython_kernel/__main__.py", 
line 1 
   import sage.all 
IndentationError: unexpected indent 
[I 2023-05-31 20:01:59.861 ServerApp] AsyncIOLoopKernelRestarter: 
restarting kernel (3/5), 
new random ports 
Traceback (most recent call last): 
 File "", line 189, in _run_module_as_main 
 File "", line 148, in _get_module_details 
 File "", line 159, in _get_module_details 
 File "", line 1074, in get_code 
 File "", line 1004, in 
source_to_code 
 File "", line 241, in 
_call_with_frames_removed 
 File 
"/home/finotti/src/sage-10.0/src/sage/repl/ipython_kernel/__main__.py", 
line 1 
   import sage.all 
IndentationError: unexpected indent 
[I 2023-05-31 20:02:02.875 ServerApp] AsyncIOLoopKernelRestarter: 
restarting kernel (4/5), 
new random ports 
Traceback (most recent call last): 
 File "", line 189, in _run_module_as_main 
 File "", line 148, in _get_module_details 
 File "", line 159, in _get_module_details 
 File "", line 1074, in get_code 
 File "", line 1004, in 
source_to_code 
 File "", line 241, in 
_call_with_frames_removed 
 File 
"/home/finotti/src/sage-10.0/src/sage/repl/ipython_kernel/__main__.py", 
line 1 
   import sage.all 
IndentationError: unexpected indent 
[I 2023-05-31 20:02:05.888 ServerApp] AsyncIOLoopKernelRestarter: 
restarting kernel (5/5), 
new random ports 
Traceback (most recent call last): 
 File "", line 189, in _run_module_as_main 
 File "", line 148, in _get_module_details 
 File "", line 159, in _get_module_details 
 File "", line 1074, in get_code 
 File "", line 1004, in 
source_to_code 
 File "", line 241, in 
_call_with_frames_removed 
 File 
"/home/finotti/src/sage-10.0/src/sage/repl/ipython_kernel/__main__.py", 
line 1 
   import sage.all 
IndentationError: unexpected indent 
[W 2023-05-31 20:02:08.901 ServerApp] AsyncIOLoopKernelRestarter: restart 
failed 
[W 2023-05-31 20:02:08.901 ServerApp] Kernel 
2d1683ba-e9f5-4158-b989-8ff8bfbc8f51 died, rem
oving from map. 
[W 2023-05-31 20:02:50.881 ServerApp] Timeout waiting for kernel_info reply 
from 2d1683ba-e
9f5-4158-b989-8ff8bfbc8f51 
[E 2023-05-31 20:02:50.881 ServerApp] Uncaught exception GET 
/api/kernels/2d1683ba-e9f5-415
8-b989-8ff8bfbc8f51/channels?session_id=e7e7ebeb-a613-4c4c-9e1a-eb0e366db3d4 
(::1) 
   HTTPServerRequest(protocol='http', host='localhost:', method='GET', 
uri='/api/kerne

Re: [sage-support] Re: sage-10.0 not working in Jupyter Lab

[Isuru Fernando]

Try adding

   import sage.all

to the top of
/home/finotti/src/sage-10.0/src/sage/repl/ipython_kernel/__main__.py

Isuru

On Wed, May 31, 2023 at 5:23 PM Luis Finotti  wrote:

>
> On Wednesday, May 31, 2023 at 6:10:42 PM UTC-4 Isuru Fernando wrote:
>
> Which givaro library is loaded when you do `export LD_DEBUG=libs` and run
> sage from the command line?
>
>
> I get:
>
>1028008: find library=libgivaro.so.9 [0]; searching
>1028008:  search path=/home/finotti/src/sage-10.0/local/lib
>  (RUNPATH from file
> /home/finotti/src/sage-10.0/local/var/lib/sage/venv-python3.11/lib/python3.11/site-packages/cysignals/
> signals.cpython-311-x86_64-linux-gnu.so)
>1028008:   trying
> file=/home/finotti/src/sage-10.0/local/lib/libgivaro.so.9
>1028008:
>1028008: find library=libgmpxx.so.4 [0]; searching
>1028008:  search path=/home/finotti/src/sage-10.0/local/lib
>  (RUNPATH from file
> /home/finotti/src/sage-10.0/local/var/lib/sage/venv-python3.11/lib/python3.11/site-packages/cysignals/
> signals.cpython-311-x86_64-linux-gnu.so)
>1028008:   trying
> file=/home/finotti/src/sage-10.0/local/lib/libgmpxx.so.4
>1028008:  search cache=/etc/ld.so.cache
>1028008:   trying file=/lib/x86_64-linux-gnu/libgmpxx.so.4
>1028008:
>1028008:
>1028008: calling init: /lib/x86_64-linux-gnu/libgmpxx.so.4
>1028008:
>1028008:
>1028008: calling init:
> /home/finotti/src/sage-10.0/local/lib/libgivaro.so.9
>1028008:
>1028008:
>1028008: calling init:
> /home/finotti/src/sage-10.0/src/sage/rings/finite_rings/
> element_givaro.cpython-311-x86_64-linux-gnu.so
> [snip]
>1028008: calling fini:
> /home/finotti/src/sage-10.0/src/sage/rings/finite_rings/
> element_givaro.cpython-311-x86_64-linux-gnu.so [0
>1028008:
>1028008:
>1028008: calling fini:
> /home/finotti/src/sage-10.0/local/lib/libgivaro.so.9 [0]
>
> --
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> 
> .
>

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Re: [sage-support] Re: sage-10.0 not working in Jupyter Lab

[Luis Finotti]

On Wednesday, May 31, 2023 at 6:10:42 PM UTC-4 Isuru Fernando wrote:

Which givaro library is loaded when you do `export LD_DEBUG=libs` and run 
sage from the command line?


I get:

   1028008: find library=libgivaro.so.9 [0]; searching
   1028008:  search path=/home/finotti/src/sage-10.0/local/lib 
 (RUNPATH from file 
/home/finotti/src/sage-10.0/local/var/lib/sage/venv-python3.11/lib/python3.11/site-packages/cysignals/signals.cpython-311-x86_64-linux-gnu.so)
   1028008:   trying 
file=/home/finotti/src/sage-10.0/local/lib/libgivaro.so.9
   1028008:
   1028008: find library=libgmpxx.so.4 [0]; searching
   1028008:  search path=/home/finotti/src/sage-10.0/local/lib 
 (RUNPATH from file 
/home/finotti/src/sage-10.0/local/var/lib/sage/venv-python3.11/lib/python3.11/site-packages/cysignals/signals.cpython-311-x86_64-linux-gnu.so)
   1028008:   trying 
file=/home/finotti/src/sage-10.0/local/lib/libgmpxx.so.4
   1028008:  search cache=/etc/ld.so.cache
   1028008:   trying file=/lib/x86_64-linux-gnu/libgmpxx.so.4
   1028008:
   1028008:
   1028008: calling init: /lib/x86_64-linux-gnu/libgmpxx.so.4
   1028008:
   1028008:
   1028008: calling init: 
/home/finotti/src/sage-10.0/local/lib/libgivaro.so.9
   1028008:
   1028008:
   1028008: calling init: 
/home/finotti/src/sage-10.0/src/sage/rings/finite_rings/element_givaro.cpython-311-x86_64-linux-gnu.so
[snip]
   1028008: calling fini: 
/home/finotti/src/sage-10.0/src/sage/rings/finite_rings/element_givaro.cpython-311-x86_64-linux-gnu.so
 
[0
   1028008:
   1028008:
   1028008: calling fini: 
/home/finotti/src/sage-10.0/local/lib/libgivaro.so.9 [0]

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Re: [sage-support] Re: sage-10.0 not working in Jupyter Lab

[Isuru Fernando]

Which givaro library is loaded when you do `export LD_DEBUG=libs` and run
sage from the command line?

Isuru

On Wed, May 31, 2023 at 5:02 PM Luis Finotti  wrote:

>
>
> On Wednesday, May 31, 2023 at 5:29:25 PM UTC-4 Isuru Fernando wrote:
>
> Does `import sage.all` in a sage shell work?
>
>
> In a regular sage shell (from the command line, not in Jupyter Lab)?  Yes,
> no errors (or output).
>
> --
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> 
> .
>

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Re: [sage-support] Re: sage-10.0 not working in Jupyter Lab

[Luis Finotti]

On Wednesday, May 31, 2023 at 5:29:25 PM UTC-4 Isuru Fernando wrote:

Does `import sage.all` in a sage shell work?


In a regular sage shell (from the command line, not in Jupyter Lab)?  Yes, 
no errors (or output). 

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Re: [sage-support] Re: sage-10.0 not working in Jupyter Lab

[Isuru Fernando]

Does `import sage.all` in a sage shell work?

Isuru

On Wed, May 31, 2023 at 3:46 PM Luis Finotti  wrote:

> Hello,
>
> Thanks for the help!
>
> On Wednesday, May 31, 2023 at 4:24:11 PM UTC-4 Isuru Fernando wrote:
>
> Try running JupyterLab in a shell with `export LD_DEBUG=libs` and import
> sage with that jupyterlab instance.
> That should tell you where givaro is loaded from.
>
> Isuru
>
>
> The output is very long, but maybe this is what you mean:
>
> 916747: find library=libgivaro.so.9 [0]; searching
> 916747:  search path=/usr/lib/R/lib (LD_LIBRARY_PATH)
> 916747:   trying file=/usr/lib/R/lib/libgivaro.so.9
> 916747:  search path=/usr/lib/x86_64-linux-gnu (system search path)
> 916747:   trying file=/usr/lib/x86_64-linux-gnu/libgivaro.so.9
> 916747:
> 916747: find library=libgmpxx.so.4 [0]; searching
> 916747:  search path=/usr/lib/R/lib (LD_LIBRARY_PATH)
> 916747:   trying file=/usr/lib/R/lib/libgmpxx.so.4
> 916747:  search path=/usr/lib/x86_64-linux-gnu (system search path)
> 916747:   trying file=/usr/lib/x86_64-linux-gnu/libgmpxx.so.4
> 916747:
> 916747:
> 916747: calling init: /usr/lib/x86_64-linux-gnu/libgmpxx.so.4
> 916747:
> 916747:
> 916747: calling init: /usr/lib/x86_64-linux-gnu/libgivaro.so.9
> 916747:
> 916747:
> 916747: calling init:
> /home/finotti/src/sage-test/sage-10.0/src/sage/rings/finite_rings/
> element_givaro.cpython-311-x86_64-linux-gnu.so
>
> Later we see the error
>
> 916747: /home/finotti/src/sage-test/sage-10.0/src/sage/matrix/
> matrix_modn_dense_float.cpython-311-x86_64-linux-gnu.so: error: symbol
> lookup error: undefined symbol:
> _ZNK6Givaro7IntegercvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEB5cxx11Ev
> (fatal)
>
> Any ideas?
>
> --
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> 
> .
>

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Re: [sage-support] Re: sage-10.0 not working in Jupyter Lab

[Luis Finotti]

Hello,

Thanks for the help!

On Wednesday, May 31, 2023 at 4:24:11 PM UTC-4 Isuru Fernando wrote:

Try running JupyterLab in a shell with `export LD_DEBUG=libs` and import 
sage with that jupyterlab instance.
That should tell you where givaro is loaded from.

Isuru


The output is very long, but maybe this is what you mean:

916747: find library=libgivaro.so.9 [0]; searching
916747:  search path=/usr/lib/R/lib (LD_LIBRARY_PATH)
916747:   trying file=/usr/lib/R/lib/libgivaro.so.9
916747:  search path=/usr/lib/x86_64-linux-gnu (system search path)
916747:   trying file=/usr/lib/x86_64-linux-gnu/libgivaro.so.9
916747: 
916747: find library=libgmpxx.so.4 [0]; searching
916747:  search path=/usr/lib/R/lib (LD_LIBRARY_PATH)
916747:   trying file=/usr/lib/R/lib/libgmpxx.so.4
916747:  search path=/usr/lib/x86_64-linux-gnu (system search path)
916747:   trying file=/usr/lib/x86_64-linux-gnu/libgmpxx.so.4
916747: 
916747: 
916747: calling init: /usr/lib/x86_64-linux-gnu/libgmpxx.so.4
916747: 
916747: 
916747: calling init: /usr/lib/x86_64-linux-gnu/libgivaro.so.9
916747: 
916747: 
916747: calling init: 
/home/finotti/src/sage-test/sage-10.0/src/sage/rings/finite_rings/element_givaro.cpython-311-x86_64-linux-gnu.so

Later we see the error

916747: 
/home/finotti/src/sage-test/sage-10.0/src/sage/matrix/matrix_modn_dense_float.cpython-311-x86_64-linux-gnu.so:
 
error: symbol lookup error: undefined symbol: 
_ZNK6Givaro7IntegercvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEB5cxx11Ev
 
(fatal)

Any ideas?

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Re: [sage-support] Re: sage-10.0 not working in Jupyter Lab

[Isuru Fernando]

Try running JupyterLab in a shell with `export LD_DEBUG=libs` and import 
sage with that jupyterlab instance.
That should tell you where givaro is loaded from.

Isuru

On Wednesday, May 31, 2023 at 2:46:14 PM UTC-5 Isuru Fernando wrote:

> That's a different issue than this.
>
> Isuru
>
> On Wed, May 31, 2023 at 2:37 PM Jan Groenewald  
> wrote:
>
>> Hi
>>
>> This 
>> https://groups.google.com/g/sage-support/c/egP7I9eGLuI/m/MsUUNLEUAQAJ
>> suggests trying clang 14 for compiling sage or waiting for givaro 
>> compiled with clang 15.
>>
>> (or just try rebuild the deb for givaro with clang15 
>> https://raphaelhertzog.com/2010/12/15/howto-to-rebuild-debian-packages/)
>>
>> Regards,
>> Jan
>>
>> On Tue, 30 May 2023 at 18:48, Nils Bruin  wrote:
>>
>>> On Tuesday, 30 May 2023 at 06:09:23 UTC-7 Luis Finotti wrote:
>>>
>>>
>>> I looked at it, but I cannot tell if it is really the same issue, or how 
>>> I could check.
>>>
>>> well ... it looks like the symbol that is found undefined is indeed of 
>>> the type mentioned there. So that would suggest that indeed a system givaro 
>>> is picked up while sage is apparently compiled with a "too advanced" c++ 
>>> ABI for that library. However, you're not getting errors when you just run 
>>> sage-10.0, so it would seem there is a givaro library that can satisfy the 
>>> needs (it probably built its own givaro)
>>>
>>> So in your case there seems to be something about the environment in 
>>> which jupyter starts sage that confuses the library resolution process. I 
>>> imagine it could be something where juoyter runs using a python that has 
>>> its own venv and that the initialization of sage (which should set up its 
>>> venv) somehow misses overriding something or erroneously inherits something 
>>> from the jupyter venv. 
>>>
>>> In that case I would expect this issue was basically always present, but 
>>> has only recently become relevant because now the system givaro doesn't cut 
>>> it any more.
>>>
>>> -- 
>>> You received this message because you are subscribed to the Google 
>>> Groups "sage-support" group.
>>> To unsubscribe from this group and stop receiving emails from it, send 
>>> an email to sage-support...@googlegroups.com.
>>> To view this discussion on the web visit 
>>> https://groups.google.com/d/msgid/sage-support/24724ea0-edcc-4470-8b30-56cde325caf2n%40googlegroups.com
>>>  
>>> 
>>> .
>>>
>> -- 
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>> email to sage-support...@googlegroups.com.
>>
> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/sage-support/CAAg%3Dp_0OtZQBbEV4oN8pFJshScF8L_xJ-bphtQ6EH5nixwshvg%40mail.gmail.com
>>  
>> 
>> .
>>
>

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Re: [sage-support] Re: sage-10.0 not working in Jupyter Lab

[Isuru Fernando]

That's a different issue than this.

Isuru

On Wed, May 31, 2023 at 2:37 PM Jan Groenewald 
wrote:

> Hi
>
> This https://groups.google.com/g/sage-support/c/egP7I9eGLuI/m/MsUUNLEUAQAJ
> suggests trying clang 14 for compiling sage or waiting for givaro compiled
> with clang 15.
>
> (or just try rebuild the deb for givaro with clang15
> https://raphaelhertzog.com/2010/12/15/howto-to-rebuild-debian-packages/)
>
> Regards,
> Jan
>
> On Tue, 30 May 2023 at 18:48, Nils Bruin  wrote:
>
>> On Tuesday, 30 May 2023 at 06:09:23 UTC-7 Luis Finotti wrote:
>>
>>
>> I looked at it, but I cannot tell if it is really the same issue, or how
>> I could check.
>>
>> well ... it looks like the symbol that is found undefined is indeed of
>> the type mentioned there. So that would suggest that indeed a system givaro
>> is picked up while sage is apparently compiled with a "too advanced" c++
>> ABI for that library. However, you're not getting errors when you just run
>> sage-10.0, so it would seem there is a givaro library that can satisfy the
>> needs (it probably built its own givaro)
>>
>> So in your case there seems to be something about the environment in
>> which jupyter starts sage that confuses the library resolution process. I
>> imagine it could be something where juoyter runs using a python that has
>> its own venv and that the initialization of sage (which should set up its
>> venv) somehow misses overriding something or erroneously inherits something
>> from the jupyter venv.
>>
>> In that case I would expect this issue was basically always present, but
>> has only recently become relevant because now the system givaro doesn't cut
>> it any more.
>>
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Re: [sage-support] Re: sage-10.0 not working in Jupyter Lab

[Jan Groenewald]

Hi

This https://groups.google.com/g/sage-support/c/egP7I9eGLuI/m/MsUUNLEUAQAJ
suggests trying clang 14 for compiling sage or waiting for givaro compiled
with clang 15.

(or just try rebuild the deb for givaro with clang15
https://raphaelhertzog.com/2010/12/15/howto-to-rebuild-debian-packages/)

Regards,
Jan

On Tue, 30 May 2023 at 18:48, Nils Bruin  wrote:

> On Tuesday, 30 May 2023 at 06:09:23 UTC-7 Luis Finotti wrote:
>
>
> I looked at it, but I cannot tell if it is really the same issue, or how I
> could check.
>
> well ... it looks like the symbol that is found undefined is indeed of the
> type mentioned there. So that would suggest that indeed a system givaro is
> picked up while sage is apparently compiled with a "too advanced" c++ ABI
> for that library. However, you're not getting errors when you just run
> sage-10.0, so it would seem there is a givaro library that can satisfy the
> needs (it probably built its own givaro)
>
> So in your case there seems to be something about the environment in which
> jupyter starts sage that confuses the library resolution process. I imagine
> it could be something where juoyter runs using a python that has its own
> venv and that the initialization of sage (which should set up its venv)
> somehow misses overriding something or erroneously inherits something from
> the jupyter venv.
>
> In that case I would expect this issue was basically always present, but
> has only recently become relevant because now the system givaro doesn't cut
> it any more.
>
> --
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> "sage-support" group.
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> 
> .
>

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Re: [sage-support] Re: Sage Crash Report

[Isuru Fernando]

This is an ABI incompatibility with clang 14 and 15 where givaro was
compiled with 14 and sage was compiled with 15.
I suggest downgrading to clang 14 or set flags like
https://github.com/conda-forge/sagelib-feedstock/blob/5542b278f642b772ae243b323c7cbc7a170a5f9a/recipe/build.sh#L21-L25
until we rebuild givaro with clang 15.

Isuru

On Wed, May 31, 2023 at 2:01 PM Matthias Goerner  wrote:

> I am focusing on the Sage 9.8 issue of the missing symbol
> __ZN6FFPACK8CharPolyIN6Givaro8Poly1DomINS1_7ModularIddvEENS1_5DenseERNT_7ElementERKS7_S9_mNS7_8Domain_t11Element_ptrEmRNSC_8RandIterENS_19FFPACK_CHARPOLY_TAGEm
>
> Demangled with c++filt, the missing symbol is:
> Givaro::Poly1Dom,
> Givaro::Dense>::Element&
> FFPACK::CharPoly,
> Givaro::Dense> >(Givaro::Poly1Dom,
> Givaro::Dense> const&, Givaro::Poly1Dom void>, Givaro::Dense>::Element&, unsigned long,
> Givaro::Poly1Dom,
> Givaro::Dense>::Domain_t::Element_ptr, unsigned long,
> Givaro::Poly1Dom,
> Givaro::Dense>::Domain_t::RandIter&, FFPACK::FFPACK_CHARPOLY_TAG, unsigned
> long)
>
> I expect this to be in ffpack, so I made sure that ffpack is indeed picked
> up from the dedicated conda environment:
>
> lsof -p 70202 | grep -i ffpack
> python3.1 70202 matthias  txt  REG   1,15  1132624 5917685
> /Users/matthias/anaconda3/envs/sage98-py311/lib/libffpack.1.dylib
>
> I then looked whether similar symbols are available in ffpack with the
> following command:
> nm /Users/matthias/anaconda3/envs/sage98-py311/lib/libffpack.1.dylib |
> grep
> __ZN6FFPACK8CharPolyIN6Givaro8Poly1DomINS1_7ModularIddvEENS1_5DenseERNT_7ElementERKS7_S9_mNS7_8Domain_t11Element_ptrEm
>
> Which gave:
> 0004f17c T
> __ZN6FFPACK8CharPolyIN6Givaro8Poly1DomINS1_7ModularIddvEENS1_5DenseERNT_7ElementERKS7_S9_mNS7_8Domain_t11Element_ptrEmNS_19FFPACK_CHARPOLY_TAGEm
> 0004ec10 T
> __ZN6FFPACK8CharPolyIN6Givaro8Poly1DomINS1_7ModularIddvEENS1_5DenseERNT_7ElementERKS7_S9_mNS7_8Domain_t11Element_ptrEmRNS7_8Domain_t8RandIterENS_19FFPACK_CHARPOLY_TAGEm
>
> which demangled gives:
> Givaro::Poly1Dom,
> Givaro::Dense>::Element&
> FFPACK::CharPoly,
> Givaro::Dense> >(Givaro::Poly1Dom,
> Givaro::Dense> const&, Givaro::Poly1Dom void>, Givaro::Dense>::Element&, unsigned long,
> Givaro::Poly1Dom,
> Givaro::Dense>::Domain_t::Element_ptr, unsigned long,
> FFPACK::FFPACK_CHARPOLY_TAG, unsigned long)
> Givaro::Poly1Dom,
> Givaro::Dense>::Element&
> FFPACK::CharPoly,
> Givaro::Dense> >(Givaro::Poly1Dom,
> Givaro::Dense> const&, Givaro::Poly1Dom void>, Givaro::Dense>::Element&, unsigned long,
> Givaro::Poly1Dom,
> Givaro::Dense>::Domain_t::Element_ptr, unsigned long,
> Givaro::Poly1Dom,
> Givaro::Dense>::Domain_t::RandIter&, FFPACK::FFPACK_CHARPOLY_TAG, unsigned
> long)
>
> And then I got confused: the latter demangled method has the same
> signature as the missing one.
>
> In other words: from a C++ perspective, the missing method is there, it is
> just that the way the name and signature get mangled is different between
> linbox_flint_interface.cpython-311-darwin.so and libffpack.1.dylib
>
> So it seems it is an ABI problem where we get two different managled names
> for the same function signature.
>
> I am not sure what to make out of this and have only two explanations:
> 1. It is a bug in the C++ compiler.
> 2. The two libraries were compiled with different C++ compilers or with
> different compiler options.
>
> On Wednesday, May 31, 2023 at 11:01:20 AM UTC-7 Matthias Goerner wrote:
>
> Sorry for the late reply. Here are the details about my conda environment.
> I am not exactly sure what other information is useful to debug this. I am
> familiar with the linux tools, but am struggling with otool and vmmap to
> figure out what is going on here and see whether I am picking up any
> library from something that is not in the dedicated conda environment.
>
> On Friday, May 26, 2023 at 8:05:04 AM UTC-7 Matthias Koeppe wrote:
>
> config.log please
>
> On Wednesday, May 24, 2023 at 3:16:25 PM UTC-7 Matthias Goerner wrote:
>
> Hi!
>
> I can't get sage to work when installing it with conda on a new MacBook
> Pro with M2 chip and Ventura 13.3.
>
> I tried
> conda -n sage create sage=9.X python=3.Y
> for (X,Y) = (5,10), (8,10), (8,11).
> With Sage 9.5, I get the attached crash report.
> With Sage 9.8, I get the following linking error below.
>
> Cheers,
> Matthias
>
> (sage-py310) matthias@matthiass-air-2 ~ % sage
> ┌┐
> │ SageMath version 9.8, Release Date: 2023-02-11 │
> │ Using Python 3.10.11. Type "help()" for help.  │
> └┘
> ┏┓
> ┃ Warning: sage.all is not available; this is a limited REPL.┃
> ┗┛
> sage: import sage.all
> 

[sage-support] Re: Sage Crash Report

[Matthias Goerner]

I am focusing on the Sage 9.8 issue of the missing symbol 
__ZN6FFPACK8CharPolyIN6Givaro8Poly1DomINS1_7ModularIddvEENS1_5DenseERNT_7ElementERKS7_S9_mNS7_8Domain_t11Element_ptrEmRNSC_8RandIterENS_19FFPACK_CHARPOLY_TAGEm

Demangled with c++filt, the missing symbol is:
Givaro::Poly1Dom, 
Givaro::Dense>::Element& 
FFPACK::CharPoly, 
Givaro::Dense> >(Givaro::Poly1Dom, 
Givaro::Dense> const&, Givaro::Poly1Dom, Givaro::Dense>::Element&, unsigned long, 
Givaro::Poly1Dom, 
Givaro::Dense>::Domain_t::Element_ptr, unsigned long, 
Givaro::Poly1Dom, 
Givaro::Dense>::Domain_t::RandIter&, FFPACK::FFPACK_CHARPOLY_TAG, unsigned 
long)

I expect this to be in ffpack, so I made sure that ffpack is indeed picked 
up from the dedicated conda environment:

lsof -p 70202 | grep -i ffpack
python3.1 70202 matthias  txt  REG   1,15  1132624 5917685 
/Users/matthias/anaconda3/envs/sage98-py311/lib/libffpack.1.dylib

I then looked whether similar symbols are available in ffpack with the 
following command:
nm /Users/matthias/anaconda3/envs/sage98-py311/lib/libffpack.1.dylib | grep 
__ZN6FFPACK8CharPolyIN6Givaro8Poly1DomINS1_7ModularIddvEENS1_5DenseERNT_7ElementERKS7_S9_mNS7_8Domain_t11Element_ptrEm

Which gave:
0004f17c T 
__ZN6FFPACK8CharPolyIN6Givaro8Poly1DomINS1_7ModularIddvEENS1_5DenseERNT_7ElementERKS7_S9_mNS7_8Domain_t11Element_ptrEmNS_19FFPACK_CHARPOLY_TAGEm
0004ec10 T 
__ZN6FFPACK8CharPolyIN6Givaro8Poly1DomINS1_7ModularIddvEENS1_5DenseERNT_7ElementERKS7_S9_mNS7_8Domain_t11Element_ptrEmRNS7_8Domain_t8RandIterENS_19FFPACK_CHARPOLY_TAGEm

which demangled gives:
Givaro::Poly1Dom, 
Givaro::Dense>::Element& 
FFPACK::CharPoly, 
Givaro::Dense> >(Givaro::Poly1Dom, 
Givaro::Dense> const&, Givaro::Poly1Dom, Givaro::Dense>::Element&, unsigned long, 
Givaro::Poly1Dom, 
Givaro::Dense>::Domain_t::Element_ptr, unsigned long, 
FFPACK::FFPACK_CHARPOLY_TAG, unsigned long)
Givaro::Poly1Dom, 
Givaro::Dense>::Element& 
FFPACK::CharPoly, 
Givaro::Dense> >(Givaro::Poly1Dom, 
Givaro::Dense> const&, Givaro::Poly1Dom, Givaro::Dense>::Element&, unsigned long, 
Givaro::Poly1Dom, 
Givaro::Dense>::Domain_t::Element_ptr, unsigned long, 
Givaro::Poly1Dom, 
Givaro::Dense>::Domain_t::RandIter&, FFPACK::FFPACK_CHARPOLY_TAG, unsigned 
long)

And then I got confused: the latter demangled method has the same signature 
as the missing one.

In other words: from a C++ perspective, the missing method is there, it is 
just that the way the name and signature get mangled is different 
between linbox_flint_interface.cpython-311-darwin.so and libffpack.1.dylib

So it seems it is an ABI problem where we get two different managled names 
for the same function signature.

I am not sure what to make out of this and have only two explanations:
1. It is a bug in the C++ compiler.
2. The two libraries were compiled with different C++ compilers or with 
different compiler options.

On Wednesday, May 31, 2023 at 11:01:20 AM UTC-7 Matthias Goerner wrote:

Sorry for the late reply. Here are the details about my conda environment. 
I am not exactly sure what other information is useful to debug this. I am 
familiar with the linux tools, but am struggling with otool and vmmap to 
figure out what is going on here and see whether I am picking up any 
library from something that is not in the dedicated conda environment.

On Friday, May 26, 2023 at 8:05:04 AM UTC-7 Matthias Koeppe wrote:

config.log please

On Wednesday, May 24, 2023 at 3:16:25 PM UTC-7 Matthias Goerner wrote:

Hi!

I can't get sage to work when installing it with conda on a new MacBook Pro 
with M2 chip and Ventura 13.3.

I tried
conda -n sage create sage=9.X python=3.Y
for (X,Y) = (5,10), (8,10), (8,11).
With Sage 9.5, I get the attached crash report.
With Sage 9.8, I get the following linking error below.

Cheers,
Matthias

(sage-py310) matthias@matthiass-air-2 ~ % sage
┌┐
│ SageMath version 9.8, Release Date: 2023-02-11 │
│ Using Python 3.10.11. Type "help()" for help.  │
└┘
┏┓
┃ Warning: sage.all is not available; this is a limited REPL.┃
┗┛
sage: import sage.all
---
ImportError   Traceback (most recent call last)
Cell In[1], line 1
> 1 import sage.all

File 
~/anaconda3/envs/sage-py310/lib/python3.10/site-packages/sage/all.py:168
166 from sage.modules.allimport *
167 from sage.monoids.allimport *
--> 168 from sage.algebras.all   import *
169 from sage.modular.allimport *
170 from sage.sat.allimport *

File 
~/anaconda3/envs/sage-py310/lib/python3.10/site-packages/sage/algebras/all.py:21
  5 

[sage-support] Re: Sage Crash Report

[Matthias Goerner]

Sorry for the late reply. Here are the details about my conda environment. 
I am not exactly sure what other information is useful to debug this. I am 
familiar with the linux tools, but am struggling with otool and vmmap to 
figure out what is going on here and see whether I am picking up any 
library from something that is not in the dedicated conda environment.

On Friday, May 26, 2023 at 8:05:04 AM UTC-7 Matthias Koeppe wrote:

> config.log please
>
> On Wednesday, May 24, 2023 at 3:16:25 PM UTC-7 Matthias Goerner wrote:
>
>> Hi!
>>
>> I can't get sage to work when installing it with conda on a new MacBook 
>> Pro with M2 chip and Ventura 13.3.
>>
>> I tried
>> conda -n sage create sage=9.X python=3.Y
>> for (X,Y) = (5,10), (8,10), (8,11).
>> With Sage 9.5, I get the attached crash report.
>> With Sage 9.8, I get the following linking error below.
>>
>> Cheers,
>> Matthias
>>
>> (sage-py310) matthias@matthiass-air-2 ~ % sage
>> ┌┐
>> │ SageMath version 9.8, Release Date: 2023-02-11 │
>> │ Using Python 3.10.11. Type "help()" for help.  │
>> └┘
>> ┏┓
>> ┃ Warning: sage.all is not available; this is a limited REPL.┃
>> ┗┛
>> sage: import sage.all
>>
>> ---
>> ImportError   Traceback (most recent call 
>> last)
>> Cell In[1], line 1
>> > 1 import sage.all
>>
>> File 
>> ~/anaconda3/envs/sage-py310/lib/python3.10/site-packages/sage/all.py:168
>> 166 from sage.modules.allimport *
>> 167 from sage.monoids.allimport *
>> --> 168 from sage.algebras.all   import *
>> 169 from sage.modular.allimport *
>> 170 from sage.sat.allimport *
>>
>> File 
>> ~/anaconda3/envs/sage-py310/lib/python3.10/site-packages/sage/algebras/all.py:21
>>   5 
>> #*
>>   6 #   Copyright (C) 2005 William Stein 
>>   7 #
>>(...)
>>  17 #  http://www.gnu.org/licenses/
>>  18 
>> #*
>>  19 from sage.misc.lazy_import import lazy_import
>> ---> 21 import sage.algebras.catalog as algebras
>>  23 from .quatalg.all import *
>>  24 from .steenrod.all import *
>>
>> File 
>> ~/anaconda3/envs/sage-py310/lib/python3.10/site-packages/sage/algebras/catalog.py:84
>>   1 r"""
>>   2 Catalog of Algebras
>>   3
>>(...)
>>  80   `
>>  81 """
>>  83 from sage.algebras.free_algebra import FreeAlgebra as Free
>> ---> 84 from sage.algebras.quatalg.quaternion_algebra import 
>> QuaternionAlgebra as Quaternion
>>  85 from sage.algebras.steenrod.steenrod_algebra import 
>> SteenrodAlgebra as Steenrod
>>  86 from 
>> sage.algebras.finite_dimensional_algebras.finite_dimensional_algebra import 
>> FiniteDimensionalAlgebra as FiniteDimensional
>>
>> File 
>> ~/anaconda3/envs/sage-py310/lib/python3.10/site-packages/sage/algebras/quatalg/quaternion_algebra.py:68
>>  61 from operator import itemgetter
>>  63 from .quaternion_algebra_element import (
>>  64 QuaternionAlgebraElement_abstract,
>>  65 QuaternionAlgebraElement_generic,
>>  66 QuaternionAlgebraElement_rational_field,
>>  67 QuaternionAlgebraElement_number_field)
>> ---> 68 from . import quaternion_algebra_cython
>>  70 from sage.modular.modsym.p1list import P1List
>>  72 from sage.misc.cachefunc import cached_method
>>
>> File 
>> ~/anaconda3/envs/sage-py310/lib/python3.10/site-packages/sage/algebras/quatalg/quaternion_algebra_cython.pyx:1,
>>  
>> in init sage.algebras.quatalg.quaternion_algebra_cython 
>> (build/cythonized/sage/algebras/quatalg/quaternion_algebra_cython.cpp:6484)()
>> > 1 # distutils: language = c++
>>   2 # distutils: libraries = gmp m NTL_LIBRARIES
>>   3 # distutils: extra_compile_args = NTL_CFLAGS
>>
>> File 
>> ~/anaconda3/envs/sage-py310/lib/python3.10/site-packages/sage/matrix/matrix_integer_dense.pyx:1,
>>  
>> in init sage.matrix.matrix_integer_dense 
>> (build/cythonized/sage/matrix/matrix_integer_dense.cpp:59322)()
>> > 1 # -*- coding: utf-8 -*-
>>   2 # distutils: extra_compile_args = NTL_CFLAGS M4RI_CFLAGS
>>   3 # distutils: libraries = iml NTL_LIBRARIES gmp m CBLAS_LIBRARIES
>>
>> ImportError: 
>> dlopen(/Users/matthias/anaconda3/envs/sage-py310/lib/python3.10/site-packages/sage/libs/linbox/
>> linbox_flint_interface.cpython-310-darwin.so, 0x0002): symbol not found 
>> in flat namespace 
>>