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

[Isuru Fernando]

lRestarter:
> 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
>
> ls/2d1683ba-e9f5-4158-b989-8ff8bfbc8f51/channels?session_id=e7e7ebeb-a613-4c4c-9e1a-eb0e366
> db3d4', version='HTTP/1.1', remote_ip='::1')
>Traceback (most recent call last):
>  File "/usr/lib/python3/dist-packages/tornado/web.py", line 1713, in
> _execute
>result = await result
> 
>  File
> "/home/finotti/.local/lib/python3.11/site-packages/jupyter_server/services/kerne
> ls/websocket.py", line 67, in get
>await super().get(kernel_id=kernel_id)
>  File "/usr/lib/python3/dist-packages/tornado/websocket.py", line 277,
> in get
>await self.ws_connection.accept_connection(self)
>  File "/usr/lib/python3/dist-packages/tornado/websocket.py", line 867,
> in accept_conne
> ction
>await self._accept_connection(handler)
>  File "/usr/lib/python3/dist-packages/tornado/websocket.py", line 907,
> in _accept_conn
> ection
>self.selected_subprotocol =
> handler.select_subprotocol(subprotocols)
>
>
>  File
> "/home/finotti/.local/lib/python3.11/site-packages/jupyter_server/services/kerne
> ls/websocket.py", line 86, in select_subprotocol
>preferred_protocol = self.connection.kernel_ws_protocol
> ^^
>AttributeError: 'NoneType' object has no attribute 'kernel_ws_protocol'
> [E 2023-05-31 20:02:50.889 ServerApp] {
>  "Host": "localhost:",
>  "User-Agent": "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36
> (KHTML, like Gecko)
> Chrome/113.0.0.0 Safari/537.36"
>}
> [E 2023-05-31 20:02:50.890 ServerApp] 500 GET
> /api/kernels/2d1683ba-e9f5-4158-b989-8ff8bfbc
> 8f51/channels?session_id=e7e7ebeb-a613-4c4c-9e1a-eb0e366db3d4
> (1d8eff8bf21445009a41400a789f
> dd1f@::1) 60013.83ms referer=None
> [W 2023-05-31 20:02:51.190 ServerApp] Timeout waiting for kernel_info
> reply from 2d1683ba-e
> 9f5-4158-b989-8ff8bfbc8f51
> [E 2023-05-31 20:02:51.190 ServerApp] Uncaught exception GET
> /api/kernels/2d1683ba-e9f5-415
> 8-b989-8ff8bfbc8f51/channels?session_id=ef28bbb4-915d-49a2-9007-f81e28396ccb
> (127.0.0.1)
>HTTPServerRequest(protocol='http', host='localhost:', method='GET',
> uri='/api/kerne
>
> ls/2d1683ba-e9f5-4158-b989-8ff8bfbc8f51/channels?session_id=ef28bbb4-915d-49a2-9007-f81e283
> 96ccb', version='HTTP/1.1', remote_ip='127.0.0.1')
>Traceback (most recent call last):
>  File "/usr/lib/python3/dist-packages/tornado/web.py", line 1713, in
> _execute
>result = await result
> 
>  File
> "/home/finotti/.local/lib/python3.11/site-packages/jupyter_server/services/kerne
> ls/websocket.py", line 67, in get
>await super().get(kernel_id=kernel_id)
>  File "/usr/lib/python3/dist-packages/tornado/websocket.py", line 277,
> in get
>await self.ws_connection.accept_connection(self)
>  File "/usr/lib/python3/dist-packages/tornado/websocket.py", line 867,
> in accept_conne
> ction
>await self._accept_connection(handler)
>  File "/usr/lib/python3/dist-packages/tornado/websocket.py", line 907,
> in _accept_conn
> ection
>self.selected_su

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

[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

[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

[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.
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>>> an email to sage-support...@googlegroups.com.
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>>>  
>>> <https://groups.google.com/d/msgid/sage-support/24724ea0-edcc-4470-8b30-56cde325caf2n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>> .
>>>
>> -- 
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>>  
>> <https://groups.google.com/d/msgid/sage-support/CAAg%3Dp_0OtZQBbEV4oN8pFJshScF8L_xJ-bphtQ6EH5nixwshvg%40mail.gmail.com?utm_medium=email&utm_source=footer>
>> .
>>
>

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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.
>>
>> --
>> 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+unsubscr...@googlegroups.com.
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>> https://groups.google.com/d/msgid/sage-support/24724ea0-edcc-4470-8b30-56cde325caf2n%40googlegroups.com
>> 
>> .
>>
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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
> 

Re: [sage-support] Current advice for generic SageMath install advice

[Isuru Fernando]

> I'm not sure that's quite enough. In my experience, sagelib needs
rebuilding to interface with normaliz (I think it's "make normaliz
pynormaliz" nowadays, or perhaps one needs a pip install). I would expect
that the binary distribution of sage for conda is built without
normaliz/pynormaliz support, because those are optional packages.
Installing these as prerequisites in conda wouldn't automatically activate
the interfaces in sagemath. Does conda do something to get that to work?
Has sagemath grown better at dynamically detecting libraries to interface
with?

pynormaliz interface is indeed dynamically detected by sage. You just have
to install pynormaliz.

There are a few optional libraries that are not dynamically detected and
need to be present at build time.
See https://github.com/sagemath/sage/blob/master/src/setup.py#L82-L83
Out of those, conda builds sage with bliss and sirocco, but they are not
installed by default when you
install sage. You need to install bliss and sirocco to get that
functionality.

Isuru

On Mon, Mar 27, 2023 at 8:35 PM Nils Bruin  wrote:

> On Monday, 27 March 2023 at 17:47:54 UTC-7 Isuru Fernando wrote:
>
>
> We used to have separate architecture specific builds, but `sage` is now a
> meta-package that is architecture neutral (i.e. noarch).
> So, you get sage-9.8 for all architectures. We support sage-9.8 for the
> following OS and architecture combinations
> - linux-x86_64  (glibc>=2.12, most distros after 2010)
> - linux-aarch64  (glibc>=2.17, most distros after 2014)
> - macos-x86_64  (macos>=10.9)
> - macos-arm64  (macos>=11.0)
> You can have a look at https://anaconda.org/conda-forge/sagelib to see
> the architecture-specific builds.
>
>
> Thanks! I was hoping for an answer like that.Then it sounds like conda is
> presently the best option to get up to date binary sage.
>
>
> > Also: if students want to use packages like normaliz, can they install
> those on binary installs? When I do it on source-built versions, it
> triggers extensive recompilation.
>
> With conda, you can install binary packages for normaliz and thousands of
> other packages into the same environment as sage.
>
>
> I'm not sure that's quite enough. In my experience, sagelib needs
> rebuilding to interface with normaliz (I think it's "make normaliz
> pynormaliz" nowadays, or perhaps one needs a pip install). I would expect
> that the binary distribution of sage for conda is built without
> normaliz/pynormaliz support, because those are optional packages.
> Installing these as prerequisites in conda wouldn't automatically activate
> the interfaces in sagemath. Does conda do something to get that to work?
> Has sagemath grown better at dynamically detecting libraries to interface
> with?
>
> --
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> .
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Re: [sage-support] Current advice for generic SageMath install advice

[Isuru Fernando]

Hi,

> However: https://anaconda.org/conda-forge/sage seems to indicate that
various architecture-specific builds are woefully outdated: "noarch" seems
to be on point, but the architecture-specific ones seem stuck on 9.2. Am I
reading the info wrong? Obviously I don't want to point people to 9.2
installs.

We used to have separate architecture specific builds, but `sage` is now a
meta-package that is architecture neutral (i.e. noarch).
So, you get sage-9.8 for all architectures. We support sage-9.8 for the
following OS and architecture combinations
- linux-x86_64  (glibc>=2.12, most distros after 2010)
- linux-aarch64  (glibc>=2.17, most distros after 2014)
- macos-x86_64  (macos>=10.9)
- macos-arm64  (macos>=11.0)
You can have a look at https://anaconda.org/conda-forge/sagelib to see the
architecture-specific builds.

> Also: if students want to use packages like normaliz, can they install
those on binary installs? When I do it on source-built versions, it
triggers extensive recompilation.

With conda, you can install binary packages for normaliz and thousands of
other packages into the same environment as sage.

Isuru

On Mon, Mar 27, 2023 at 7:34 PM Nils Bruin  wrote:

> What would the current (Spring 2023) easiest instructions be for people to
> install sage? I'm asking in support of an install-fest for students, so the
> objective is to have easy solutions for giving students access on whatever
> platform they have available.
> I know about cloud-based solutions, so I'll definitely point them to
> those. I'm asking for "the next step up".
>
> In the install advice I see:
> for OSX:
>  - binary build of SageMath
>  (looks like an
> excellent solution)
> - https://anaconda.org/conda-forge/sage (would be a great place to point
> students to, because it's a rich environment for computational software).
> However: https://anaconda.org/conda-forge/sage seems to indicate that
> various architecture-specific builds are woefully outdated: "noarch" seems
> to be on point, but the architecture-specific ones seem stuck on 9.2. Am I
> reading the info wrong? Obviously I don't want to point people to 9.2
> installs.
>
> for windows:
>  - OK WSL; that's great. However, it looks like Ubuntu would be the
> easiest linux distribution to get and as far as I can see, Ubuntu has 9.5
> packaged at most? That's not great either.
>  - conda: see above
>
> for linux:
>  - same thing.
>  - conda: see above.
>
> So is building from source the only way nowadays? That's sad. I'm fine
> doing that for myself, but for an installfest, that's really not feasible.
> Probably some machines will go in thermal meltdown as a result! Or should I
> just send them to 9.2 and 9.5 etc.
>
> Also: if students want to use packages like normaliz, can they install
> those on binary installs? When I do it on source-built versions, it
> triggers extensive recompilation.
>
> --
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> 
> .
>

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Re: [sage-support] Sage Crash Report

[Isuru Fernando]

Can you try the following?

conda install mamba -n base
conda config --add channels conda-forge
conda config --set channel_priority strict
mamba create -n sagetest sage
conda activate sagetest
sage

On Sun, Aug 21, 2022 at 6:24 PM Robert Parini 
wrote:

> Using conda on macOS 12.4 (with Apple silicon) I get the attached error
> after installing sage with:
>
> conda create -n sagetest sage
> conda activate sagetest
> sage
>
> --
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> .
>

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Re: [sage-support] Sage Crash Report

[Isuru Fernando]

Can you share the output of the following command?

conda list -n sagetest

On Sun, Aug 21, 2022 at 6:24 PM Robert Parini 
wrote:

> Using conda on macOS 12.4 (with Apple silicon) I get the attached error
> after installing sage with:
>
> conda create -n sagetest sage
> conda activate sagetest
> sage
>
> --
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Re: [sage-support] tachyon not found (SageMath 9.5, running on an Intel-based Mac)

[Isuru Fernando]

conda activate sage-build  should do the trick.

Isuru

On Mon, May 9, 2022 at 6:03 AM Dima Pasechnik  wrote:

>
>
> On Mon, 9 May 2022, 11:49 harald@gmail.com, 
> wrote:
>
>> ... or add it to the PATH, I suppose. But how do I find it now?
>
>
> searching config.log for tachyon gives
>
> /Users/harald/miniconda3/envs/sage-build/bin/tachyon
>
> Indeed, searching for PATH there will tell you that
>
> Users/harald/miniconda3/envs/sage-build/bin
>
> was in your PATH while you built Sage.
>
>
>>
>> Le lundi 9 mai 2022 à 11:38:48 UTC+2, dim...@gmail.com a écrit :
>>
>>> You have built Sage with a lot of Conda packages, as can be seen from
>>> your config.log.
>>> Not sure you had Conda activated, but you had its binary directories in
>>> PATH,
>>> in particular tachyon was found there.
>>>
>>> Now tachyon is no longer in PATH. One way to remedy this would be to
>>> activate Conda and then start Sage.
>>>
>>>
>>>
>>> On Mon, 9 May 2022, 10:10 harald@gmail.com, 
>>> wrote:
>>>
 No, it is not seen. I do have conda. I don't *think* I built this
 version of Sage under it, but I am not positive.

 Le lundi 9 mai 2022 à 11:06:59 UTC+2, dim...@gmail.com a écrit :

> and if you run
>
> which tachyon
>
> outside of "sage -sh" subshell, is it seen?
>
>
> If not, it might be about activated vs non-activated Conda.
> If you built Sage under Conda, you'd need to run it under Conda, too.
>
>
>
> On Mon, 9 May 2022, 10:02 harald@gmail.com, 
> wrote:
>
>> Right, "which tachyon" gives an empty output. What to do?
>> Le lundi 9 mai 2022 à 09:11:41 UTC+2, dim...@gmail.com a écrit :
>>
>>> OK, so tachyon comes from Conda... Can you check that tachyon is in
>>> Sage's PATH, i.e.
>>> run the following two commands:
>>>
>>> ./sage -sh
>>> which tachyon
>>>
>>>
>>> On Sun, May 8, 2022 at 11:56 PM harald@gmail.com
>>>  wrote:
>>> >
>>> > Here it is.
>>> >
>>> > Le samedi 7 mai 2022 à 19:21:24 UTC+2, dim...@gmail.com a écrit :
>>> >>
>>> >> Please post the top level config.log.
>>> >>
>>> >> On Sat, 7 May 2022, 16:52 harald@gmail.com, <
>>> harald@gmail.com> wrote:
>>> >>>
>>> >>> Hi,
>>> >>>
>>> >>> I am running SageMath 9.5 (compiled from source on an
>>> Intel-based Mac). I haven't been having trouble, but today I was toying
>>> with 3D plotting, and, when I tried to do an animation, I got an error
>>> message telling me that tachyon could not be found. (I have not used
>>> tachyon before. Non-animated 3D plots work fine).
>>> >>>
>>> >>> The following example from the documentation
>>> >>> -
>>> >>> S = sphere(opacity=0.8, aspect_ratio=[1,1,1])
>>> >>> L = line3d([(0,0,0),(2,0,0)], thickness=10, color='red')
>>> >>> M = S + S.translate((2,0,0)) + L
>>> >>> M.show(viewer='tachyon')
>>> >>> -
>>> >>> gives an error message:
>>> >>> 
>>> >>> FileNotFoundError: [Errno 2] No such file or directory:
>>> 'tachyon'
>>> >>>
>>> >>>
>>> >>> What to do?
>>> >>>
>>> >>> Best
>>> >>> Harald
>>> >>>
>>> >>> --
>>> >>> You received this message because you are subscribed to the
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>>>
>>> >
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Re: [sage-support] linbox compilation failed (9.4.beta3, conda)

[Isuru Fernando]

It's fine to add that option to build/pkgs/linbox/spkg-install.in

Isuru

On Mon, Jun 28, 2021 at 10:17 AM Vincent Delecroix <
20100.delecr...@gmail.com> wrote:

> Did that. And got
>
> Successfully installed linbox-1.6.3.p1
>
> However, what is the proper long term fix for sagemath?
>
> Vincent
>
> Le 28/06/2021 à 16:58, Isuru Fernando a écrit :
> > Can you try passing `--with-ocl=no` to linbox's configure?
> >
> > Isuru
> >
> > On Mon, Jun 28, 2021 at 9:44 AM Vincent Delecroix <
> 20100.delecr...@gmail.com>
> > wrote:
> >
> >> Dear all,
> >>
> >> I am not able to compile the sage source code in a conda environment
> >> (build failure with linbox). You will find all log files in attachment
> >> (including my conda environment).
> >>
> >> Any help is appreciated!
> >>
> >> Best
> >> Vincent
> >>
> >> --
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> Groups
> >> "sage-support" group.
> >> To unsubscribe from this group and stop receiving emails from it, send
> an
> >> email to sage-support+unsubscr...@googlegroups.com.
> >> To view this discussion on the web visit
> >>
> https://groups.google.com/d/msgid/sage-support/1a9f1bb4-5e22-7329-de1b-741cd877b461%40gmail.com
> >> .
> >>
> >
>
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Re: [sage-support] linbox compilation failed (9.4.beta3, conda)

[Isuru Fernando]

Can you try passing `--with-ocl=no` to linbox's configure?

Isuru

On Mon, Jun 28, 2021 at 9:44 AM Vincent Delecroix <20100.delecr...@gmail.com>
wrote:

> Dear all,
>
> I am not able to compile the sage source code in a conda environment
> (build failure with linbox). You will find all log files in attachment
> (including my conda environment).
>
> Any help is appreciated!
>
> Best
> Vincent
>
> --
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> .
>

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Re: [sage-support] Unable to import Normaliz

[Isuru Fernando]

You need to install `pynormaliz` by doing `conda install pynormaliz`.

Isuru

On Sun, Jun 6, 2021 at 8:56 AM Dima Pasechnik  wrote:

> you should do these installations at conda prompt,
> not at Sage's prompt.
>
> On Sun, 6 Jun 2021, 13:10 Hriday Bharat Thakkar, 
> wrote:
>
>> This is an update. I followed the steps for installation of normaliz via
>> conda. I did the following and was able to install normaliz but when I
>> import normaliz there's an error "Normaliz not found."  It asks me restart
>> my kernel in order to use the updated packages. Can you please advice how I
>> can restart my kernel or what I need to do differently? It seems like conda
>> install normaliz worked.
>>
>> Attached is the steps I did:
>>
>>
>>
>> On Sunday, June 6, 2021 at 5:24:38 PM UTC+5:30 Hriday Bharat Thakkar
>> wrote:
>>
>>> I followed the instructions in
>>> https://doc.sagemath.org/html/en/installation/conda.html#sec-installation-conda
>>>
>>> but I'm still unable to install normaliz using 'sage -i normaliz'. Here
>>> is the screenshot. Can you please let me know if I've done something
>>> incorrectly or if there is some other way to install normaliz/pynormaliz.
>>> Thanks!
>>> On Sunday, June 6, 2021 at 2:44:46 PM UTC+5:30 dim...@gmail.com wrote:
>>>


 On Sun, 6 Jun 2021, 09:49 Hriday Bharat Thakkar, 
 wrote:

> I would like to use the Normaliz library to compute Ehrhart
> polynomials, etc. I have successfully installed Normaliz from their github
> and Python's IDLE environment detects it but SageMath doesn't seem to be
> able to detect this installation.
>
> Can you please advice how I can get SageMath to use Normaliz? So far,
> I've tried installing Normaliz using two ways:
> 1. sage -i normaliz (error: make: *** No rule to make target
> `all-toolchain'.  Stop.)
>

 this might need Sage built from source.

 2. conda install normaliz libnormaliz from
> https://doc.sagemath.org/html/en/reference/spkg/normaliz.html
> (error for 2. is attached as a screenshot)
>

 this needs conda channel with Sage (conda-forge). See


 https://doc.sagemath.org/html/en/installation/conda.html#sec-installation-conda




> Thanks much!
>
>
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Re: [sage-support] Sage Crash Report

[Isuru Fernando]

Mike,

Can you try creating a new conda environment? This is an issue with the
latest givaro build we had and we marked it as broken.
Details at https://github.com/conda-forge/givaro-feedstock/issues/13

(You could also try doing `conda install "givaro=4.1.1=h192cbe9_1"` to get
the older link.)

Isuru

On Wed, Mar 24, 2021 at 9:07 AM Mike Lee  wrote:

> Not sure if this is relevant, but I get the following messages when I try
> running 'conda update givaro' in my sage conda environment (attached). I
> apologize for multiple messages!
>
> On Wed, Mar 24, 2021 at 8:42 AM Mike Lee  wrote:
>
>> I believe the following line in the output of the nm command you
>> suggested is the corresponding symbol?
>>
>> 00017da0 T Givaro::Integer::operator
>> std::__cxx11::basic_string,
>> std::allocator >() const
>>
>> I've also attached the full output of the nm command as a txt file below
>> in case it's helpful!
>>
>> On Wed, Mar 24, 2021 at 5:41 AM Dima Pasechnik  wrote:
>>
>>> On Tue, Mar 23, 2021 at 10:27 PM Mike Lee  wrote:
>>> >
>>> > Hi,
>>> >
>>> > I'm facing a similar issue when I tried to install Sage through conda
>>> (I followed the 'Setting Up' directions in
>>> https://wiki.sagemath.org/Conda). I get the following error in my
>>> Sage_crash_report.txt (attached)
>>> >
>>> > 'ImportError:
>>> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/
>>> matrix_modn_sparse.cpython-39-x86_64-linux-gnu.so: undefined symbol:
>>> _ZNK6Givaro7IntegercvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEB5cxx11Ev'
>>>
>>> this is, demangled:
>>>
>>> $ c++filt
>>> _ZNK6Givaro7IntegercvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEB5cxx11Ev
>>> Givaro::Integer::operator std::__cxx11::basic_string>> std::char_traits, std::allocator >[abi:cxx11]() const
>>>
>>> Can you find this in the output of
>>>
>>> $ nm -D --demangle
>>> /home/msl/software/miniconda3/envs/sage/lib/libgivaro.so.9
>>>
>>> Perhaps, wrong C++ standard version chosen somewhere?
>>>
>>> Maybe Isuru knows what's wrong there.
>>>
>>> >
>>> > What could I do to fix this issue? Thank you in advance for the help!
>>> >
>>> > By the way, when I run 'ldd
>>> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/
>>> matrix_modn_sparse.cpython-39-x86_64-linux-gnu.so ' I get the following
>>> output:
>>> >
>>> > linux-vdso.so.1 (0x7ffde17a7000)
>>> > liblinbox.so.0 =>
>>> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../liblinbox.so.0
>>> (0x7fa325ba)
>>> > libfflas.so.1 =>
>>> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libfflas.so.1
>>> (0x7fa325ad4000)
>>> > libblas.so.3 =>
>>> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libblas.so.3
>>> (0x7fa323ae3000)
>>> > libgivaro.so.9 =>
>>> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libgivaro.so.9
>>> (0x7fa323a88000)
>>> > libflint.so.14 =>
>>> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libflint.so.14
>>> (0x7fa32320d000)
>>> > libntl.so.43 =>
>>> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libntl.so.43
>>> (0x7fa322fca000)
>>> > libgmp.so.10 =>
>>> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libgmp.so.10
>>> (0x7fa322f24000)
>>> > libstdc++.so.6 =>
>>> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libstdc++.so.6
>>> (0x7fa322daf000)
>>> > libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x7fa3229fb000)
>>> > libgcc_s.so.1 =>
>>> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libgcc_s.so.1
>>> (0x7fa3229e7000)
>>> > libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x7fa3225f6000)
>>> > libffpack.so.1 =>
>>> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libffpack.so.1
>>> (0x7fa3224e3000)
>>> > libgmpxx.so.4 =>
>>> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libgmpxx.so.4
>>> (0x7fa3224da000)
>>> > libmpfr.so.6 =>
>>> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libmpfr.so.6
>>> (0x7fa32245b000)
>>> > libiml.so.0 =>
>>> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libiml.so.0
>>> (0x7fa322436000)
>>> > libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
>>> (0x7fa322217000)
>>> > libgfortran.so.5 =>
>>> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libgfortran.so.5
>>> (0x7fa322075000)
>>> > /lib64/ld-linux-x86-64.so.2 (0x7fa325aa8000)
>>> > libgf2x.so.3 =>
>>> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packa

Re: [sage-support] problems again installing Sage9.1 (and 9.2)

[Isuru Fernando]

>  (Not sure whether with Conda one would get it, or it's not in Conda)

It's not in conda. We have almost all the gap packages except for a few
problematic ones. (compile failures)
`kbmag` is one of them.
https://github.com/conda-forge/gap-feedstock/blob/19ff5a3e3365bd1ef9ed9bd9315f0596d9e7de21/recipe/build.sh#L44-L48

Isuru

On Thu, Mar 18, 2021 at 2:35 PM Dima Pasechnik  wrote:

> On Thu, Mar 18, 2021 at 7:14 PM Nathan Dunfield 
> wrote:
> >
> > Anita,
> >
> > 1. The version at:
> >
> > https://github.com/3-manifolds/Sage_macOS/releases/tag/v1.0-beta
> >
> > was just updated last night.  Now double-clicking the icon should
> produce a window which offers a choice of terminal or Jupyter.
> >
> > 2. I don't think kbmag comes with Sage, or at least your command failed
> on three different versions of Sage I tried (one Mac, two Linux).  So I
> assume this is a file in one of your own directories that you are trying to
> load.  If so, probably the file is not in the directory where Sage starts
> (which is /Users/anita or similar).
>
> kbmag is a part of Sage's optional package gap-packages
>
> One can certainly get it, but it might entail building Sage from source.
> (Not sure whether with Conda one would get it, or it's not in Conda)
>
> Dima
>
> >
> > Best,
> >
> > Nathan
> >
> > On Thursday, March 18, 2021 at 9:45:12 AM UTC-5 roja...@gmail.com wrote:
> >>
> >> Dear Samuel,
> >> thank you very much for your help. I installed the version you told me.
> It worked in the basics, so thanks!
> >> But I still have some problems. I write them here, hoping you can help
> me. Thanks in advance!
> >> 1. I double click on SageMath icon, and it opens in a Terminal. I do
> not know how to open it as a Sage notebook in
> >> jupyter. In my macbook I run sage -n jupyter.
> >> 2. I have some routines using the underlying GAP. They do not work
> here. I tried (and fail) the following:
> >> sage:  libgap.eval('LoadPackage("kbmag")')
> >> fail
> >>
> >> Thank you very much for all your help and support.
> >> With best regards,
> >> Anita
> >>
> >>
> >> On Thu, Mar 18, 2021 at 8:50 AM Samuel Lelièvre 
> wrote:
> >>>
> >>> ¡Hola Anita!
> >>>
> >>> You could try the new macOS app, currently in beta testing at:
> >>>
> >>> https://github.com/3-manifolds/Sage_macOS/releases/
> >>> Let us know if it solves your problems.  --Samuel
> >>>
> >>> --
> >>> You received this message because you are subscribed to a topic in the
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> .
> >>
> >>
> >>
> >> --
> >> Anita M. Rojas
> >> Departamento de Matemáticas
> >> Facultad de Ciencias
> >> Universidad de Chile
> >>
> >> https://sites.google.com/a/u.uchile.cl/mat-ciencias-prof-anita-rojas/
> >
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Re: [sage-support] Apple M1 Chip

[Isuru Fernando]

Yes, I managed to cross compile quite a few. What remains is at
https://raw.githubusercontent.com/regro/cf-graph-countyfair/master/status/armosxaddition.svg?sanitize=true

Isuru

On Sat, Dec 19, 2020 at 7:27 AM Dima Pasechnik  wrote:

>
>
> On Fri, 18 Dec 2020, 18:27 Isuru Fernando,  wrote:
>
>> miniforge, a conda installer by conda-forge works fine on Apple silicon
>> chips with native binaries. You can install python 3.8 and 3.9.
>> packages like python, numpy, scipy, notebook, scikit-image are known to
>> work.
>>
>> See https://github.com/conda-forge/miniforge
>>
>
> have you managed to build more sage dependencies natively on M1?
>
>>
>>
>> Isuru
>>
>> On Thu, Dec 17, 2020 at 12:36 PM Tom Judson  wrote:
>>
>>> Homebrew is a quick and easy install under Rosetta (the Intel
>>> emulator).  Python 3.8 is there, and I finally got Jupyter Notebook
>>> installed.  However, when JN opens I have a problem.  I gave up last night
>>> but may try to work on it later today. - Tom
>>>
>>> On Wednesday, December 16, 2020 at 12:34:10 PM UTC-7 kcrisman wrote:
>>>
>>>> On Wednesday, December 16, 2020 at 10:46:47 AM UTC-5 dim...@gmail.com
>>>> wrote:
>>>>
>>>>> On Wed, Dec 16, 2020 at 3:19 PM Thomas Judson 
>>>>> wrote:
>>>>> >
>>>>> > I have a new MacBook Air with an Apple M1 chip. Does the Intel
>>>>> version of Sage 9.2 work on this machine?
>>>>>
>>>>> 9.2 is not known to work on macOS 11 (the one you have on M1), as far
>>>>> as I know.
>>>>> You might try building the latest beta in Homebrew installed into the
>>>>> Intel emulator.
>>>>> We are very curious to know how far one can go this way.
>>>>>
>>>>>
>>>> Tom, anything you can do along these lines will be fantastic - I am
>>>> slated to get one of those soon too, and we'll need lots of guinea pigs to
>>>> help.
>>>>
>>> --
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>>>
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Re: [sage-support] Apple M1 Chip

[Isuru Fernando]

miniforge, a conda installer by conda-forge works fine on Apple silicon
chips with native binaries. You can install python 3.8 and 3.9.
packages like python, numpy, scipy, notebook, scikit-image are known to
work.

See https://github.com/conda-forge/miniforge

Isuru

On Thu, Dec 17, 2020 at 12:36 PM Tom Judson  wrote:

> Homebrew is a quick and easy install under Rosetta (the Intel emulator).
> Python 3.8 is there, and I finally got Jupyter Notebook installed.
> However, when JN opens I have a problem.  I gave up last night but may try
> to work on it later today. - Tom
>
> On Wednesday, December 16, 2020 at 12:34:10 PM UTC-7 kcrisman wrote:
>
>> On Wednesday, December 16, 2020 at 10:46:47 AM UTC-5 dim...@gmail.com
>> wrote:
>>
>>> On Wed, Dec 16, 2020 at 3:19 PM Thomas Judson 
>>> wrote:
>>> >
>>> > I have a new MacBook Air with an Apple M1 chip. Does the Intel version
>>> of Sage 9.2 work on this machine?
>>>
>>> 9.2 is not known to work on macOS 11 (the one you have on M1), as far as
>>> I know.
>>> You might try building the latest beta in Homebrew installed into the
>>> Intel emulator.
>>> We are very curious to know how far one can go this way.
>>>
>>>
>> Tom, anything you can do along these lines will be fantastic - I am
>> slated to get one of those soon too, and we'll need lots of guinea pigs to
>> help.
>>
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Re: [sage-support] SageMath-9.2 does not start with Jupyter on macOS 10.15.7

[Isuru Fernando]

Looks to me like you are using gcc,g++ from the system and ar, ranlib from
homebrew. Can you try switching all to system or all to homebrew?

Isuru

On Wed, Nov 4, 2020 at 3:09 PM phiparis19  wrote:

> /usr/bin/gcc
>
> /usr/bin/g++
>
> /usr/local/bin/ar
>
> /usr/local/bin/ranlib
>
>
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld
>
> /Applications/sage-9.2/local/var/tmp/sage/build/gf2x-1.3.0/.libs/libtuneup-s1.a:
> cannot open
> `/Applications/sage-9.2/local/var/tmp/sage/build/gf2x-1.3.0/.libs/libtuneup-s1.a'
> (No such file or directory)
>
> Philippe
>
> Le mercredi 4 novembre 2020 à 21:45:52 UTC+1, isu...@gmail.com a écrit :
>
>> What do you get for each of the commands?
>>
>> which gcc
>> which g++
>> which ar
>> which ranlib
>> gcc -print-prog-name=ld
>> file
>> /Applications/sage-9.2/local/var/tmp/sage/build/gf2x-1.3.0/.libs/libtuneup-s1.a
>>
>> Isuru
>>
>> On Wed, Nov 4, 2020 at 2:30 PM phiparis19  wrote:
>>
>>> Here is the file
>>> Thank you
>>>
>>> Le mercredi 4 novembre 2020 à 21:04:09 UTC+1, isu...@gmail.com a écrit :
>>>
 > I get ld: warning: ignoring file ./.libs/libtuneup-s1.a, building for
 macOS-x86_64 but attempting to link with file built for unknown-unsupported
 file format ( 0x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A 0x2F 0x20 0x20 0x20
 0x20 0x20 0x20 0x20 )

 Can you send `gf2x`'s `config.log`?

 This happens when you are using a linker without LTO support.

 Isuru

 On Wed, Nov 4, 2020 at 1:53 PM phiparis19  wrote:

>
> Thank you for helping me.
>
> I followed the instructions at the end of ./configure output  (brew
> install ...)
>
> I get ld: warning: ignoring file ./.libs/libtuneup-s1.a, building for
> macOS-x86_64 but attempting to link with file built for 
> unknown-unsupported
> file format ( 0x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A 0x2F 0x20 0x20 0x20
> 0x20 0x20 0x20 0x20 )
>
> Error installing package gf2x-1.3.0
>
> I have also tried to compile sage-9.2 on another partition of my mac :
> il fails after 4h of compilation for the same reason for one of the last
> packages.
> Le mercredi 4 novembre 2020 à 18:18:41 UTC+1, John H Palmieri a écrit :
>
>>
>>
>> On Tuesday, November 3, 2020 at 11:30:54 PM UTC-8, Dima Pasechnik
>> wrote:
>>>
>>> As far as building from source is concerned, I'd recommend using
>>> Homebrew, instead of trying
>>> to build most packages from scratch (as it is the case if you don't
>>> use it).
>>> Please pay attention that you need to run
>>>
>>> source .homebrew-build-env
>>>
>>>
>>> and to the list of packages you'd install printed out by ./configure
>>> (at the end of its run)
>>>
>>
>> And after installing new system packages, it's a good idea to run
>> 'make distclean' and then rerun './configure' (with whatever options you
>> want to pass to it).
>>
>>
>>>
>>> On Wed, Nov 4, 2020 at 6:18 AM phiparis19 
>>> wrote:
>>> >
>>> > Hello,
>>> >
>>> > After upgrading from SageMath-9.1 to SageMath-9.2,
>>> >
>>> > ./sage -n jupyter fails
>>> >
>>> > ModuleNotFoundError: No module named '_ssl'
>>> >
>>> > The Jupyter notebook requires ssl, even if you do not use https.
>>> Install the openssl development packages in your system and then rebuild
>>> Python (sage -f python3).
>>> >
>>> > Unfortunately,  openssl installation has failed :
>>> >
>>> > [openssl-1.1.1g] Undefined symbols for architecture x86_64:
>>> >
>>> > 
>>> >
>>> > [openssl-1.1.1g] ld: symbol(s) not found for architecture x86_64
>>> >
>>> > [openssl-1.1.1g] clang: error: linker command failed with exit
>>> code 1 (use -v to see invocation)
>>> >
>>> > Same issue when recompiling sage from sage-9.2.tar.gz
>>> >
>>> > ./configure --enable-openssl=yes
>>> >
>>> > make
>>> >
>>> > [patch-2.7.5] ld: symbol(s) not found for architecture x86_64
>>> >
>>> >
>>> > I have macports and hombres installed
>>> >
>>> > So I dit
>>> >
>>> >  sudo mv /opt/local /opt/local_old
>>> >
>>> > sudo mv /usr/local/Homebrew /usr/local/Homebrew_old
>>>
>>> Unless you use a non-standard installaI don't think you achieve much
>>> by the latter, as Homebrew installs several packages directly into
>>> /usr/local (i.e. /usr/local/bin, etc), so this is more or less just
>>> breaks Homebrew, but is very far from uninstalling it.
>>>
>>>
>>> >
>>> > before typing make for sage
>>> >
>>> > See file enclose for configure output
>>> >
>>> > Thank you for helping
>>> >
>>> > --
>>> > You received this message because you are subscribed to the Google
>>> Groups "sage-support" group.
>>>
>> > To unsubscribe from this group and stop

Re: [sage-support] SageMath-9.2 does not start with Jupyter on macOS 10.15.7

[Isuru Fernando]

What do you get for each of the commands?

which gcc
which g++
which ar
which ranlib
gcc -print-prog-name=ld
file
/Applications/sage-9.2/local/var/tmp/sage/build/gf2x-1.3.0/.libs/libtuneup-s1.a

Isuru

On Wed, Nov 4, 2020 at 2:30 PM phiparis19  wrote:

> Here is the file
> Thank you
>
> Le mercredi 4 novembre 2020 à 21:04:09 UTC+1, isu...@gmail.com a écrit :
>
>> > I get ld: warning: ignoring file ./.libs/libtuneup-s1.a, building for
>> macOS-x86_64 but attempting to link with file built for unknown-unsupported
>> file format ( 0x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A 0x2F 0x20 0x20 0x20
>> 0x20 0x20 0x20 0x20 )
>>
>> Can you send `gf2x`'s `config.log`?
>>
>> This happens when you are using a linker without LTO support.
>>
>> Isuru
>>
>> On Wed, Nov 4, 2020 at 1:53 PM phiparis19  wrote:
>>
>>>
>>> Thank you for helping me.
>>>
>>> I followed the instructions at the end of ./configure output  (brew
>>> install ...)
>>>
>>> I get ld: warning: ignoring file ./.libs/libtuneup-s1.a, building for
>>> macOS-x86_64 but attempting to link with file built for unknown-unsupported
>>> file format ( 0x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A 0x2F 0x20 0x20 0x20
>>> 0x20 0x20 0x20 0x20 )
>>>
>>> Error installing package gf2x-1.3.0
>>>
>>> I have also tried to compile sage-9.2 on another partition of my mac :
>>> il fails after 4h of compilation for the same reason for one of the last
>>> packages.
>>> Le mercredi 4 novembre 2020 à 18:18:41 UTC+1, John H Palmieri a écrit :
>>>


 On Tuesday, November 3, 2020 at 11:30:54 PM UTC-8, Dima Pasechnik wrote:
>
> As far as building from source is concerned, I'd recommend using
> Homebrew, instead of trying
> to build most packages from scratch (as it is the case if you don't
> use it).
> Please pay attention that you need to run
>
> source .homebrew-build-env
>
>
> and to the list of packages you'd install printed out by ./configure
> (at the end of its run)
>

 And after installing new system packages, it's a good idea to run 'make
 distclean' and then rerun './configure' (with whatever options you want to
 pass to it).


>
> On Wed, Nov 4, 2020 at 6:18 AM phiparis19  wrote:
> >
> > Hello,
> >
> > After upgrading from SageMath-9.1 to SageMath-9.2,
> >
> > ./sage -n jupyter fails
> >
> > ModuleNotFoundError: No module named '_ssl'
> >
> > The Jupyter notebook requires ssl, even if you do not use https.
> Install the openssl development packages in your system and then rebuild
> Python (sage -f python3).
> >
> > Unfortunately,  openssl installation has failed :
> >
> > [openssl-1.1.1g] Undefined symbols for architecture x86_64:
> >
> > 
> >
> > [openssl-1.1.1g] ld: symbol(s) not found for architecture x86_64
> >
> > [openssl-1.1.1g] clang: error: linker command failed with exit code
> 1 (use -v to see invocation)
> >
> > Same issue when recompiling sage from sage-9.2.tar.gz
> >
> > ./configure --enable-openssl=yes
> >
> > make
> >
> > [patch-2.7.5] ld: symbol(s) not found for architecture x86_64
> >
> >
> > I have macports and hombres installed
> >
> > So I dit
> >
> >  sudo mv /opt/local /opt/local_old
> >
> > sudo mv /usr/local/Homebrew /usr/local/Homebrew_old
>
> Unless you use a non-standard installaI don't think you achieve much
> by the latter, as Homebrew installs several packages directly into
> /usr/local (i.e. /usr/local/bin, etc), so this is more or less just
> breaks Homebrew, but is very far from uninstalling it.
>
>
> >
> > before typing make for sage
> >
> > See file enclose for configure output
> >
> > Thank you for helping
> >
> > --
> > 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-s...@googlegroups.com.
>
 > To view this discussion on the web visit
> https://groups.google.com/d/msgid/sage-support/d13b96e9-92ec-4128-b219-92384d3e3110n%40googlegroups.com.
>
>
 --
>>> 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/6c90038f-0d0c-4935-bb3e-20170e82dcdbn%40googlegroups.com
>>> 
>>> .
>>>
>> --
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> "sage-support" group.
> To unsubscribe from this group and stop receiving emails from it, se

Re: [sage-support] SageMath-9.2 does not start with Jupyter on macOS 10.15.7

[Isuru Fernando]

> I get ld: warning: ignoring file ./.libs/libtuneup-s1.a, building for
macOS-x86_64 but attempting to link with file built for unknown-unsupported
file format ( 0x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A 0x2F 0x20 0x20 0x20
0x20 0x20 0x20 0x20 )

Can you send `gf2x`'s `config.log`?

This happens when you are using a linker without LTO support.

Isuru

On Wed, Nov 4, 2020 at 1:53 PM phiparis19  wrote:

>
> Thank you for helping me.
>
> I followed the instructions at the end of ./configure output  (brew
> install ...)
>
> I get ld: warning: ignoring file ./.libs/libtuneup-s1.a, building for
> macOS-x86_64 but attempting to link with file built for unknown-unsupported
> file format ( 0x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A 0x2F 0x20 0x20 0x20
> 0x20 0x20 0x20 0x20 )
>
> Error installing package gf2x-1.3.0
>
> I have also tried to compile sage-9.2 on another partition of my mac : il
> fails after 4h of compilation for the same reason for one of the last
> packages.
> Le mercredi 4 novembre 2020 à 18:18:41 UTC+1, John H Palmieri a écrit :
>
>>
>>
>> On Tuesday, November 3, 2020 at 11:30:54 PM UTC-8, Dima Pasechnik wrote:
>>>
>>> As far as building from source is concerned, I'd recommend using
>>> Homebrew, instead of trying
>>> to build most packages from scratch (as it is the case if you don't use
>>> it).
>>> Please pay attention that you need to run
>>>
>>> source .homebrew-build-env
>>>
>>>
>>> and to the list of packages you'd install printed out by ./configure
>>> (at the end of its run)
>>>
>>
>> And after installing new system packages, it's a good idea to run 'make
>> distclean' and then rerun './configure' (with whatever options you want to
>> pass to it).
>>
>>
>>>
>>> On Wed, Nov 4, 2020 at 6:18 AM phiparis19  wrote:
>>> >
>>> > Hello,
>>> >
>>> > After upgrading from SageMath-9.1 to SageMath-9.2,
>>> >
>>> > ./sage -n jupyter fails
>>> >
>>> > ModuleNotFoundError: No module named '_ssl'
>>> >
>>> > The Jupyter notebook requires ssl, even if you do not use https.
>>> Install the openssl development packages in your system and then rebuild
>>> Python (sage -f python3).
>>> >
>>> > Unfortunately,  openssl installation has failed :
>>> >
>>> > [openssl-1.1.1g] Undefined symbols for architecture x86_64:
>>> >
>>> > 
>>> >
>>> > [openssl-1.1.1g] ld: symbol(s) not found for architecture x86_64
>>> >
>>> > [openssl-1.1.1g] clang: error: linker command failed with exit code 1
>>> (use -v to see invocation)
>>> >
>>> > Same issue when recompiling sage from sage-9.2.tar.gz
>>> >
>>> > ./configure --enable-openssl=yes
>>> >
>>> > make
>>> >
>>> > [patch-2.7.5] ld: symbol(s) not found for architecture x86_64
>>> >
>>> >
>>> > I have macports and hombres installed
>>> >
>>> > So I dit
>>> >
>>> >  sudo mv /opt/local /opt/local_old
>>> >
>>> > sudo mv /usr/local/Homebrew /usr/local/Homebrew_old
>>>
>>> Unless you use a non-standard installaI don't think you achieve much
>>> by the latter, as Homebrew installs several packages directly into
>>> /usr/local (i.e. /usr/local/bin, etc), so this is more or less just
>>> breaks Homebrew, but is very far from uninstalling it.
>>>
>>>
>>> >
>>> > before typing make for sage
>>> >
>>> > See file enclose for configure output
>>> >
>>> > Thank you for helping
>>> >
>>> > --
>>> > 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-s...@googlegroups.com.
>>>
>> > To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/sage-support/d13b96e9-92ec-4128-b219-92384d3e3110n%40googlegroups.com.
>>>
>>>
>> --
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> "sage-support" group.
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> 
> .
>

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Re: [sage-support] Re: Jupyter kernels for R, gp, gap, etc

[Isuru Fernando]

I suggest installing sage through conda.
https://doc.sagemath.org/html/en/installation/conda.html

Conda is a package manager that runs on linux and osx and sagemath is
available as a binary package. There are lots of jupyter kernels
pre-packaged, so it's only a matter of typing,

  conda install sage=9.1 r-irkernel pari_jupyter gap

to get sage, R, gp, gap kernels.

Isuru

On Tue, Aug 4, 2020 at 1:21 AM Nils Bruin  wrote:

> On Monday, August 3, 2020 at 9:26:38 PM UTC-7, Tim McLarnan wrote:
>>
>> I tried copying the kernel folders from CoCalc and editing them in what I
>> thought was the right way and putting them with the kernel folders on my
>> machine.  This produced kernels that show up in Jupyter, but that don't
>> work.  No doubt someone who knows the right things to put in the .json
>> files could make this work, but I can't.  This has to be an absurdly
>> complicated approach, though.  Surely there's just some trivial thing I
>> don't know about.
>>
>
> That got you the configuration of the kernels, but likely not the actual
> code that implements them. Jupyter kernels are basically stand-alone
> programs. Often, they are written in python (but they don't have to be!)
> and installing them consists of two steps: installing the software and
> informing the jupyter notebook installation of their presence.
>
> For kernels written in python, you end up needing to install python
> software, for which there are excellent tools.
>
> A very simple example, that I happen to have written myself, so that's why
> I'm familiar with it, but needs "magma" present on your machine to work.
>
> https://github.com/nbruin/magma_kernel
>
> The instructions indeed show two installation steps: one for installing
> the python package and the other for setting up the jupyter notebook
> registration.
>
> To make extra kernels known to the *sage* jupyter notebook server, you
> have to make sure that you run the configurations in the sage copy of
> python. You'd want to do something like "sage -sh" (on linux or OSX) to get
> a shell that is set up with the sage environment, and run the
> configurations in there.
>
> An alternative is to register the sage kernel with the system-wide jupyter
> notebook. This has the advantage that other kernels that come prepackaged
> with your OS distribution are easier to install (just use your OS tools).
> It has the big disadvantage that currently, rhis is still not a
> straightforward process; it requires some hackery, so I would not recomment
> it as your first experiment.
>
> A big disadvantage of the python ecosystem is that one often end up with
> multiple copies of python living side-by-side on your OS and it's often
> hard to tell which version gets run for what.
>
> --
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> 
> .
>

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Re: [sage-support] Sage Crash Report

[Isuru Fernando]

Looks like you are using ccache, but CCACHE_DIR is not pointing to the
scratch folder.
Delete $HOME/.ccache and set CCACHE_DIR env variable to some place like
/scratch/user/hhuang235/.ccache

Isuru

On Mon, Apr 13, 2020 at 8:45 PM HANG HUANG  wrote:

> Thanks very much for your reply. In fact, my scratch folder has almost 1T
> of free space. So I am really confused of why I got that error message.
>
>
> Best,
> Amy
>
>
> 'Justin C. Walker' via sage-support 
> 于2020年4月13日周一 下午6:16写道：
>
>>
>>
>> > On Apr 13, 2020, at 14:59 , HANG HUANG  wrote:
>> >
>> > I am trying to install Sage version 9.0 on the High performance cluster
>> at my university, which runs Linux (CentOS 7). I am installing to my local
>> "scratch" folder since I do not have administrative permissions. I am
>> trying to install from source code as the installing from pre-built
>> binaries also gives me some other error. I was able  to run ./configure
>> without any issues and then when i did make, I received the following log
>> file (attached) and error:
>> >
>> > Error building Sage.
>> >
>> > The following package(s) may have failed to build (not necessarily
>> > during this run of 'make all-start'):
>> >
>> > * package: flint-2.5.2.p5
>> >   log file:
>> /scratch/user/hhuang235/sage-9.0/logs/pkgs/flint-2.5.2.p5.log
>> >   build directory:
>> /scratch/user/hhuang235/sage-9.0/local/var/tmp/sage/build/flint-2.5.2.p5
>> >
>> > The build directory may contain configuration files and other
>> potentially
>> > helpful information. WARNING: if you now run 'make' again, the build
>> > directory will, by default, be deleted. Set the environment variable
>> > SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.
>> >
>> > make[1]: *** [all-start] Error 1
>> > make[1]: Leaving directory `/scratch/user/hhuang235/sage-9.0'
>> > make: *** [all] Error 2
>>
>> Checking the log file for flint that you attached, there is this:
>>
>> ccache: error: Failed to create temporary file for
>> /home/hhuang235/.ccache/2/9/8e02d78d68b9638edd65c3e5744171-2001.manifest.tmp:
>> Disk quota exceeded
>>
>> I think that should explain the problem you are having.  Is the “scratch
>> folder” on a disk of small size, or does it have a small amount of free
>> space?  The source build of Sage does take a lot of space.  On my system,
>> Sage 9.0 uses about 7.5 GB (when complete).
>>
>> HTH
>>
>> Justin
>>
>> --
>> Justin C. Walker
>> Curmudgeon-at-large
>> Director
>> Institute for the Absorption of Federal Funds
>> 
>> 186,000 Miles per Second
>> Not just a good idea:
>>   it's the law!
>> 
>>
>> --
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>> "sage-support" group.
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>> email to sage-support+unsubscr...@googlegroups.com.
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>> https://groups.google.com/d/msgid/sage-support/8F194F5B-3706-4290-AB20-9E16425014D4%40mac.com
>> .
>>
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> .
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Re: [sage-support] Sage Crash Report

[Isuru Fernando]

No, it doesn't require sudo privileges. It can be installed in your home
directory.

Isuru

On Wed, Mar 18, 2020 at 8:05 PM  wrote:

> Hi!
>  Thanks for responding! Will this require any administrative permissions?
> I do not have any sudo privileges.
>
> On Mar 18, 2020, at 6:48 PM, Isuru Fernando  wrote:
>
> 
> One alternative to installing sage is by using the conda package manager.
> https://github.com/conda-forge/miniforge#download
> It's know to work on CentOS 6 and above.
> See https://github.com/conda-forge/sage-feedstock#installing-sage
>
> Isuru
>
> On Wed, Mar 18, 2020 at 6:00 PM Kashif Bari  wrote:
>
>> I am trying to install Sage version 8.9 on the High performance cluster
>> at my university, which runs Linux (CentOS 7). I am installing to my
>> local "scratch" folder since I do not have administrative permissions. I am
>> trying to install from source code as the pre-built binaries are for Ubuntu
>> and Debian and did not work for me and I was unsure if they would work on
>> CentOS 7. I was able to run ./configure without any issues and then when i
>> did make, I received the following log file (attached) and error:
>>
>> Error building Sage.
>>
>> The following package(s) may have failed to build (not necessarily
>> during this run of 'make all-start'):
>>
>> * package: mpfr-4.0.1.p0
>>   log file: /scratch/user/kbari/sage-8.9/logs/pkgs/mpfr-4.0.1.p0.log
>>   build directory:
>> /scratch/user/kbari/sage-8.9/local/var/tmp/sage/build/mpfr-4.0.1.p0
>>
>> The build directory may contain configuration files and other potentially
>> helpful information. WARNING: if you now run 'make' again, the build
>> directory will, by default, be deleted. Set the environment variable
>> SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.
>>
>> make[1]: *** [all-start] Error 1
>> make[1]: Leaving directory `/scratch/user/kbari/sage-8.9'
>> make: *** [all] Error 2
>>
>>
>>  I have tried to contact the help and support for the cluster, but they
>> do not know much about Sage. Any help would be greatly appreciated! Thank
>> you for your time!
>>
>> --
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>> "sage-support" group.
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>> .
>>
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Re: [sage-support] Sage Crash Report

[Isuru Fernando]

One alternative to installing sage is by using the conda package manager.
https://github.com/conda-forge/miniforge#download
It's know to work on CentOS 6 and above.
See https://github.com/conda-forge/sage-feedstock#installing-sage

Isuru

On Wed, Mar 18, 2020 at 6:00 PM Kashif Bari  wrote:

> I am trying to install Sage version 8.9 on the High performance cluster at
> my university, which runs Linux (CentOS 7). I am installing to my local
> "scratch" folder since I do not have administrative permissions. I am
> trying to install from source code as the pre-built binaries are for Ubuntu
> and Debian and did not work for me and I was unsure if they would work on
> CentOS 7. I was able to run ./configure without any issues and then when i
> did make, I received the following log file (attached) and error:
>
> Error building Sage.
>
> The following package(s) may have failed to build (not necessarily
> during this run of 'make all-start'):
>
> * package: mpfr-4.0.1.p0
>   log file: /scratch/user/kbari/sage-8.9/logs/pkgs/mpfr-4.0.1.p0.log
>   build directory:
> /scratch/user/kbari/sage-8.9/local/var/tmp/sage/build/mpfr-4.0.1.p0
>
> The build directory may contain configuration files and other potentially
> helpful information. WARNING: if you now run 'make' again, the build
> directory will, by default, be deleted. Set the environment variable
> SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.
>
> make[1]: *** [all-start] Error 1
> make[1]: Leaving directory `/scratch/user/kbari/sage-8.9'
> make: *** [all] Error 2
>
>
>  I have tried to contact the help and support for the cluster, but they do
> not know much about Sage. Any help would be greatly appreciated! Thank you
> for your time!
>
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Re: [sage-support] Sage not loading after conda install (Catalina)

[Isuru Fernando]

I'm not a Mac user, so not sure about what's needed.

Can you try the solution in
https://support.apple.com/en-gb/guide/mac-help/mh40616/mac or
https://community.wappler.io/t/solving-python-error-in-macos-catalina-when-using-docker/13497
?

Isuru



On Mon, Jan 6, 2020 at 3:51 PM Christian Bean 
wrote:

> After following the instructions from
> http://doc.sagemath.org/html/en/installation/conda.html, with python=3,
> opening sage then failed. My computer is macOS Catalina 10.15.2. I have
> attached the crash report.
>
> https://hastebin.com/oleluxotoq.pl
>
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Re: [sage-support] Re: Sage Crash Report: Missing symbols in conda build for macOS?

[Isuru Fernando]

Hi,

Can you try doing the following?

conda install -n sage27 "pynac=0.7.26=py27ha01bd41_0"

Isuru

On Tue, Nov 19, 2019 at 11:23 AM Michael Boyle <
michael.oliver.bo...@gmail.com> wrote:

> Sure.  Here it is:
>
> > conda list
> # packages in environment at
> /Users/myusername/.continuum/miniconda3.7/envs/sage27:
> #
> # NameVersion   Build  Channel
> _r-mutex  1.0.1   anacondar_1conda-forge
> alabaster 0.7.12 py_0conda-forge
> appdirs   1.4.3  py_1conda-forge
> appnope   0.1.0 py27_1000conda-forge
> arb   2.16.0h3aece09_1000conda-forge
> attrs 19.3.0 py_0conda-forge
> automat   0.8.0  py_0conda-forge
> babel 2.7.0  py_0conda-forge
> backports 1.0py_2conda-forge
> backports.functools_lru_cache 1.6.1  py_0
> conda-forge
> backports.os  0.1.1 py27_1001conda-forge
> backports.shutil_get_terminal_size 1.0.0  py_3
> conda-forge
> backports_abc 0.5py_1conda-forge
> bdw-gc8.0.4ha1b3eb9_0conda-forge
> bleach3.1.0  py_0conda-forge
> brial 1.2.5  py_1conda-forge
> bwidget   1.9.130conda-forge
> bzip2 1.0.8h01d97ff_1conda-forge
> ca-certificates   2019.9.11hecc5488_0conda-forge
> cairo 1.16.0he1c11cd_1002conda-forge
> cctools   921  h5ba7a2e_4conda-forge
> cddlib1!0.94j   h65ac59c_1001conda-forge
> certifi   2019.9.11py27_0conda-forge
> cffi  1.13.2   py27h33e799b_0conda-forge
> chardet   3.0.4 py27_1003conda-forge
> clang 9.0.0   default_hf57f61e_4conda-forge
> clang_osx-64  9.0.0h22b1bf0_3conda-forge
> clangxx   9.0.0   default_hf57f61e_4conda-forge
> clangxx_osx-649.0.0h22b1bf0_3conda-forge
> click 7.0py_0conda-forge
> cliquer   1.21  h1de35cc_1000conda-forge
> compiler-rt   9.0.0h2b4a0d1_1conda-forge
> configparser  3.7.3py27_1conda-forge
> constantly15.1.0 py_0conda-forge
> contextlib2   0.6.0.post1py_0conda-forge
> cryptography  2.8  py27hafa8578_0conda-forge
> curl  7.65.3   h22ea746_0conda-forge
> cvxopt1.2.3   py27h43946de_203conda-forge
> cycler0.10.0 py_2conda-forge
> cypari2   2.1.1py27h7c56200_0conda-forge
> cysignals 1.10.2   py27hba7914e_1conda-forge
> cython0.29.14  py27h4a8c4bd_0conda-forge
> decorator 4.4.1  py_0conda-forge
> defusedxml0.6.0  py_0conda-forge
> docutils  0.15.2   py27_0conda-forge
> dsdp  5.8   h7674d01_1203conda-forge
> ecl   16.1.2h0672242_1004conda-forge
> eclib 20190226 he5f4af6_2conda-forge
> ecm   7.0.4 h65ac59c_1002conda-forge
> entrypoints   0.3   py27_1000conda-forge
> enum341.1.6 py27_1002conda-forge
> expat 2.2.5 h4a8c4bd_1004conda-forge
> fastcache 1.1.0py27h0b31af3_0conda-forge
> fflas-ffpack  2.4.3h75e9206_1conda-forge
> fftw  3.3.8   nompi_h44ae4c8_1110
> conda-forge
> flask 0.11.1 py_1conda-forge
> flask-autoindex   0.6.2  py_0conda-forge
> flask-babel   0.12.2 py_0conda-forge
> flask-oldsessions 0.10   py_0conda-forge
> flask-openid  1.2.5 py27_1003conda-forge
> flask-silk0.2py_0conda-forge
> flintqs 

Re: [sage-support] Ubuntu 18.04 binaries for Sage 8.9?

[Isuru Fernando]

On Thu, Oct 17, 2019 at 12:31 PM henri.gir...@gmail.com <
henri.gir...@gmail.com> wrote:

> I tried sage conda is not really recent too and didn't work for me on
> ubuntu
>

What was the issue with the conda package? If you report the problems, then
we can fix them.

Isuru

>
> The best is to compile it when possible
>
> Le 17/10/2019 à 18:37, Dima Pasechnik a écrit :
> > On Thu, Oct 17, 2019 at 5:27 PM Tom Flyer  wrote:
> >> I can't find any Ubuntu 18.04 binary for Sage 8.9 on the mirrors listed
> at http://www.sagemath.org/download-linux.html.
> >> Are there any issues in creating these binary?
> > the only issue is the absence of a building host running Ubuntu 18.04
> > in our automatic binaries building system, run by a very small (about
> > 1 person, I gather)
> > team of volunteers...
> > Just build it from source, it should be very easy, or use
> > an alternative package manager (e.g. conda, nix, etc...)
> >
> >> --
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Re: [sage-support] Re: A case of immaculate conception...

[Isuru Fernando]

Hi Simon,

Yes, that's what I meant. I see it as a problem because if you had a python
variable x, it will be overwritten by the symbolic value.

Isuru

On Wed, Mar 20, 2019, 4:25 AM Simon King  wrote:

> Hi Isuru,
>
> On 2019-03-19, Isuru Fernando  wrote:
> > If the sage preparser did something like,
> >
> > __tmp__ = SR.var("x, y"); __tmp_g__ = lambda x, y:
> > symbolic_expression(x+y**Integer(2)).function(x,y); f =
> __tmp_g__(*__tmp__)
> >
> > for
> >
> > f(x, y)  = x + y ** 2
> >
> > you wouldn't have this problem and it should be easy enough to change in
> > the preparsesr.
>
> By "problem" you mean that f(x,y)=x+y^2 creates symbolic variables
> called x and y? I don't think that's a problem, but a useful feature.
>
> Best regards,
> Simon
>
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Re: [sage-support] Re: A case of immaculate conception...

[Isuru Fernando]

If the sage preparser did something like,

__tmp__ = SR.var("x, y"); __tmp_g__ = lambda x, y:
symbolic_expression(x+y**Integer(2)).function(x,y); f = __tmp_g__(*__tmp__)

for

f(x, y)  = x + y ** 2

you wouldn't have this problem and it should be easy enough to change in
the preparsesr.

Isuru

On Tue, Mar 19, 2019 at 12:38 PM john_perry_usm  wrote:

> Apologies for the pedantry, but unless the indeterminates so generated are
> free of all bugs, then strictly speaking this is not immaculate conception;
> it is spontaneous generation, or perhaps virginal conception. ;-)
>
> john perry
>
> On Tuesday, March 19, 2019 at 6:52:19 AM UTC-5, Emmanuel Charpentier wrote:
>>
>> Defining a symbolic function seems to declare its arguments. Case
>> illustrated in this sagecell example
>> 
>>  :
>>
>> reset()
>> Id1=set(show_identifiers())
>> foo(p,a,b)=p^(a-1)*(1-p)^(b-1)
>> Id2=set(show_identifiers())
>> Id2 - Id1
>>
>> which happily prints :
>>
>> {'Id1', 'a', 'b', 'foo', 'p'}
>>
>>
>> Is this expected ?
>>
>>
>>
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Re: [sage-support] Fwd: Sage Crash Report

[Isuru Fernando]

This is a known issue with the conda package as the sage package hasn't
been updated yet for the new compiler runtimes on conda-forge.

Try,

conda create -n sage sage -c conda-forge/label/cf201901

Isuru

On Tue, Feb 19, 2019 at 1:11 PM Douglas Webster <
douglas.webster2...@gmail.com> wrote:

>
>
>
> Operating system: See Attached file.
>
> I installed Sage using conda giving the following commands during the
> session as per the instructions on the sage website:
>
> conda update --all
> anaconda-navigator
> conda create -n sage sage
> conda activate sage
> sage
>
>
> I then removed the conda environment and reinstalled it following the
> above method.  The complete re-instillation session record is detailed in
> the file CrashReproduction.txt.
> Also included is the SystemInfo as reported by the Linux Mint app.
> There are two crash reports, Sage_crash_report_1st.txt being generated
> from the original installation and Sage_crash_report.txt from the
> reinstallation
>
> I have previously installed sage successfully as a binary package.  This I
> removed before trying it as a conda package.
>
> Hopefully this will be of some help.
>
> Best regards
> Douglas
>
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Re: [sage-support] Scipy 1.1.0 instead of 1.2.0 built for Sage 8.6 ??? ALso cannot find libgfortran???

[Isuru Fernando]

What's your binutils version? (You can find that out by doing "ld
--version")

Isuru

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Re: [sage-support] Sage Crash Report

[Isuru Fernando]

Ah, that package was marked broken. conda-forge and defaults channels are
not ABI compatible, (it'll be in a month or so once the conda-forge rebuild
is done)
You should prioritize conda-forge over defaults and see what happens. Let
me know if it doesn't work and I'll send you the env file for a new
environment.

Isuru

On Sun, Nov 18, 2018 at 4:20 PM Kolen Cheung 
wrote:

> Interesting, it failed.
>
> sage ❯❯❯ conda env create -f env.yml
> Solving environment: failed
>
> ResolvePackageNotFound:
>   - sagenb==1.0.3=py_0
>
> Searching it on https://anaconda.org/conda-forge/sagenb/files shows it
> doesn’t exist. Has it been removed?
>
> Another question, I noticed that you prioritize conda-forge over defaults,
> why?
>
> Thanks.
> ​
>
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Re: [sage-support] Sage Crash Report

[Isuru Fernando]

Can you try doing `conda update libgd`? Python 3 builds are experimental 
and don't work correctly. (But they should be able to start sage.)

I've attached an env file that works for me on linux.

Isuru

On Sunday, November 18, 2018 at 5:26:46 AM UTC-6, Dima Pasechnik wrote:
>
> I guess the place to report such issues is here: 
> https://github.com/conda-forge/sage-feedstock 
> On Sun, Nov 18, 2018 at 10:58 AM Kolen Cheung  > wrote: 
> > 
> > I actually tried a whole bunch of combinations. Build with and without 
> the intel channel, with python 2 or 3, on 3 different systems (macOS, 
> ArchLinux, and SUSE), all through conda. They all have some problems (that 
> upon `sage` there's an error, but this is the only one I reported so they 
> can in principle be all not working for a different reason. 
> > 
> > But may be a more general question, is the conda-forge formula really 
> works? If so are there a reproducible build that is tested to be working? 
> If so, can the environment be shared (like the environment.yml I generated 
> above.) 
> > 
> > Among the supported installation methods, conda is preferred, because it 
> is reproducible and extensible and isolated. And conda is designed to 
> handle exactly the situation like Sage, that has a lot of non-python 
> dependencies, and conda has a lot of compiler stacks as well. 
> > 
> > Who's maintaining the conda-forge formula? May be they can take a look 
> at this? 
> > 
> > Regards, 
> > Kolen 
> > On Nov 18, 2018, 1:56 AM -0800, Dima Pasechnik  >, wrote: 
> > 
> > Oh, wait, these are all Python3 libraries, correct? This looks fishy 
> > to me. As well, 
> > Sage's libgd does not link ICU libraries (all these libicu*), 
> > fontconfig and webp, all these must be conda-forge 
> > modifications. 
> > So that's not something we could realistically fix without conda people. 
> > 
> > The usual suggestion - build Sage from source... 
> > 
> > On Sun, Nov 18, 2018 at 1:41 AM Kolen Cheung  > wrote: 
> > 
> > 
> > sage ~ ❯❯❯ ls -alh 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../../libgd.so.3
>  
>
> > lrwxrwxrwx 1 sage sage 14 Nov 17 17:34 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../../libgd.so.3
>  
> -> libgd.so.3.0.5 
> > sage ~ ❯❯❯ ldd 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../../libgd.so.3
>  
>
> > linux-vdso.so.1 (0x7ffd5f589000) 
> > libm.so.6 => /usr/lib/libm.so.6 (0x7f0a078fe000) 
> > libpng16.so.16 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././libpng16.so.16
>  
> (0x7f0a076c3000) 
> > libz.so.1 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././libz.so.1
>  
> (0x7f0a074a8000) 
> > libfontconfig.so.1 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././libfontconfig.so.1
>  
> (0x7f0a07263000) 
> > libfreetype.so.6 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././libfreetype.so.6
>  
> (0x7f0a06f87000) 
> > libjpeg.so.9 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././libjpeg.so.9
>  
> (0x7f0a06d49000) 
> > libtiff.so.5 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././libtiff.so.5
>  
> (0x7f0a06acf000) 
> > libwebp.so.6 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././libwebp.so.6
>  
> (0x7f0a06831000) 
> > libpthread.so.0 => /usr/lib/libpthread.so.0 (0x7f0a0681) 
> > libc.so.6 => /usr/lib/libc.so.6 (0x7f0a0664c000) 
> > /usr/lib64/ld-linux-x86-64.so.2 (0x7f0a07d04000) 
> > libxml2.so.2 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../../././libxml2.so.2
>  
> (0x7f0a062e5000) 
> > libdl.so.2 => /usr/lib/libdl.so.2 (0x7f0a062de000) 
> > libicui18n.so.58 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../../././libicui18n.so.58
>  
> (0x7f0a05e69000) 
> > libicuuc.so.58 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../../././libicuuc.so.58
>  
> (0x7f0a05abb000) 
> > libicudata.so.58 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../../././libicudata.so.58
>  
> (0x7f0a03fbb000) 
> > liblzma.so.5 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../../././liblzma.so.5
>  
> (0x7f0a03d8d000) 
> > librt.so.1 => /usr/lib/librt.so.1 (0x7f0a03d83000) 
> > libstdc++.so.6 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././././libstdc++.so.6
>  
> (0x7f0a03c4) 
> > libgcc_s.so.1 => 
> /home/sage/.conda/envs/sage/lib/python3.6/site-packages/sage/matrix/../../../.././././libgcc_s.so.1
>  
> (0x7f0a03c2b000) 
> > 
> > -- 
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> Groups