On Thu, Apr 24, 2025 at 4:01 PM Aram Dermenjian <
aram.dermenjian.m...@gmail.com> wrote:
> I ran gap and it said it's version 4.13.1, so it theoretically should be
> ok?
>
what does this mean, exactly, you ran GAP? How? Did you run Sage's GAP, or
a system-wide GAP?
>
> I ran the `ldd` code you said, but I'm not sure how to read the output.
> Here's what I get:
>
> (sage-sh) aram@Cali-Alien:sd$ ldd /sage/sd/src/sage/libs/gap/
> libgap.cpython-312-x86_64-linux-gnu.so
> linux-vdso.so.1 (0x00007ffd603ee000)
> libgap.so.7 => /lib/x86_64-linux-gnu/libgap.so.7
> (0x00007f333560a000)
>
The above line says that /lib/x86_64-linux-gnu/libgap.so.7 (a system-wide
libgap) is linked to Sage's libgap interface.
libgap.so.7 is from GAP 4.11, so it's too old.
If you uninstall system-wide GAP, then the output of this ldd command
should change, and point to a libgap.so.9 or something like this in the
directory you built Sage in.
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f33353e1000)
> libgmp.so.10 => /lib/x86_64-linux-gnu/libgmp.so.10
> (0x00007f333535f000)
> libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f3335343000)
> libreadline.so.8 => /lib/x86_64-linux-gnu/libreadline.so.8
> (0x00007f33352ef000)
> libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f3335206000)
> /lib64/ld-linux-x86-64.so.2 (0x00007f3336169000)
> libtinfo.so.6 => /lib/x86_64-linux-gnu/libtinfo.so.6
> (0x00007f33351d4000)
>
> On Thu, 24 Apr 2025 at 22:48, Dima Pasechnik <dimp...@gmail.com> wrote:
>
>>
>>
>> On Thu, Apr 24, 2025 at 12:02 PM Aram Dermenjian <
>> aram.dermenjian.m...@gmail.com> wrote:
>>
>>> Yeah a few times I tried doing make after and there seemed to be *some*
>>> success sometimes. Anyway, my internet is a little more stable so it seemed
>>> to download everything correctly.
>>>
>>> Now I seem to be getting a sagemath_doc_html error (log attached). It
>>> looks like something to do with trying to import libgap? I checked apt to
>>> see what libgap I have and here's what it gave:
>>> libgap-dev/jammy,now 4.11.1-1 amd64 [installed]
>>> libgap7/jammy,now 4.11.1-1 amd64 [installed,automatic]
>>>
>>> But I'm not 100% sure. When I try to run sage, I get the following error
>>> (which seems very similar to the doc error)
>>>
>>> --------------------------------------------------------
>>> Error in sys.excepthook:
>>> Traceback (most recent call last):
>>> File
>>> "/sage/sd/local/var/lib/sage/venv-python3.12.5/lib/python3.12/site-packages/IPython/core/application.py",
>>> line 284, in excepthook
>>> return self.crash_handler(etype, evalue, tb)
>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>>> File
>>> "/sage/sd/local/var/lib/sage/venv-python3.12.5/lib/python3.12/site-packages/IPython/core/crashhandler.py",
>>> line 163, in __call__
>>> if rptdir is None or not Path.is_dir(rptdir):
>>> ^^^^^^^^^^^^^^^^^^^
>>> File
>>> "/sage/sd/local/var/lib/sage/venv-python3.12.5/lib/python3.12/pathlib.py",
>>> line 875, in is_dir
>>> return S_ISDIR(self.stat().st_mode)
>>> ^^^^^^^^^
>>> AttributeError: 'str' object has no attribute 'stat'
>>>
>>> Original exception was:
>>> Traceback (most recent call last):
>>> File "/sage/sd/src/bin/sage-ipython", line 15, in <module>
>>> app.initialize()
>>> File
>>> "/sage/sd/local/var/lib/sage/venv-python3.12.5/lib/python3.12/site-packages/traitlets/config/application.py",
>>> line 118, in inner
>>> return method(app, *args, **kwargs)
>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>>> File
>>> "/sage/sd/local/var/lib/sage/venv-python3.12.5/lib/python3.12/site-packages/IPython/terminal/ipapp.py",
>>> line 278, in initialize
>>> self.init_shell()
>>> File "/sage/sd/src/sage/repl/interpreter.py", line 854, in init_shell
>>> self.shell.extension_manager.load_extension(SAGE_EXTENSION)
>>> File
>>> "/sage/sd/local/var/lib/sage/venv-python3.12.5/lib/python3.12/site-packages/IPython/core/extensions.py",
>>> line 76, in load_extension
>>> return self._load_extension(module_str)
>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>>> File
>>> "/sage/sd/local/var/lib/sage/venv-python3.12.5/lib/python3.12/site-packages/IPython/core/extensions.py",
>>> line 93, in _load_extension
>>> if self._call_load_ipython_extension(mod):
>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>>> File
>>> "/sage/sd/local/var/lib/sage/venv-python3.12.5/lib/python3.12/site-packages/IPython/core/extensions.py",
>>> line 145, in _call_load_ipython_extension
>>> mod.load_ipython_extension(self.shell)
>>> File "/sage/sd/src/sage/repl/__init__.py", line 6, in
>>> load_ipython_extension
>>> sage.repl.ipython_extension.load_ipython_extension(*args)
>>> File "/sage/sd/src/sage/misc/misc.py", line 1030, in wrapper
>>> result = func(*args, **kwargs)
>>> ^^^^^^^^^^^^^^^^^^^^^
>>> File "/sage/sd/src/sage/repl/ipython_extension.py", line 747, in
>>> load_ipython_extension
>>> SageCustomizations(shell=ip)
>>> File "/sage/sd/src/sage/repl/ipython_extension.py", line 592, in
>>> __init__
>>> import sage.all # noqa: F401
>>> ^^^^^^^^^^^^^^^
>>> File "/sage/sd/src/sage/all.py", line 98, in <module>
>>> from sage.groups.all import *
>>> File "/sage/sd/src/sage/groups/all.py", line 5, in <module>
>>> from sage.groups.matrix_gps.all import *
>>> File "/sage/sd/src/sage/groups/matrix_gps/all.py", line 13, in <module>
>>> import sage.groups.matrix_gps.pickling_overrides
>>> File "/sage/sd/src/sage/groups/matrix_gps/pickling_overrides.py", line
>>> 7, in <module>
>>> from sage.groups.matrix_gps.finitely_generated_gap import
>>> FinitelyGeneratedMatrixGroup_gap
>>> File "/sage/sd/src/sage/groups/matrix_gps/finitely_generated_gap.py",
>>> line 30, in <module>
>>> from sage.groups.matrix_gps.matrix_group_gap import MatrixGroup_gap
>>> File "/sage/sd/src/sage/groups/matrix_gps/matrix_group_gap.py", line
>>> 24, in <module>
>>> from sage.groups.libgap_mixin import GroupMixinLibGAP
>>> File "/sage/sd/src/sage/groups/libgap_mixin.py", line 15, in <module>
>>> from sage.libs.gap.libgap import libgap
>>> ImportError: /sage/sd/src/sage/libs/gap/
>>> libgap.cpython-312-x86_64-linux-gnu.so: undefined symbol:
>>> GAP_CollectBags
>>>
>>
>> Sage needs GAP 4.13 or newer.
>> Assuming you actually built GAP spkg OK, the error might be due to the
>> system-wide installed old version of GAP (and libgap)
>> interfering with the normal operations of Sage interface.
>>
>> One way to debug this is to fire up Sage shell (i.e. ./sage --sh, or
>> ./sage --buildsh) and run
>>
>> ldd /sage/sd/src/sage/libs/gap/libgap.cpython-312-x86_64-linux-gnu.so
>>
>> which will print the full paths to the libraries this Python module is
>> linked to..
>>
>> I'd uninstall the old system-wide GAP, and see if it helps.
>>
>> Dima
>>
>>
>>> On Thu, 24 Apr 2025 at 18:51, Dima Pasechnik <dimp...@gmail.com> wrote:
>>>
>>>> You can try to restart make after you hit ctrl-C. Sometimes it just
>>>> works.
>>>>
>>>> > Also, I'm thinking I should create a ticket along the lines of "if
>>>> unable to download xxx, then an error should be thrown instead of just
>>>> hanging and waiting forever",
>>>>
>>>> it might help to trim the list of mirrors in upstream/mirror_list -
>>>> only leave few mirrors geographically nearby.
>>>>
>>>>
>>>> On Wed, Apr 23, 2025 at 12:17 PM Aram Dermenjian <
>>>> aram.dermenjian.m...@gmail.com> wrote:
>>>>
>>>>> This definitely solves the sci-py problem! Thanks.
>>>>>
>>>>> I'm still getting hung up on the 2nd issue though where for some
>>>>> reason matplotlib just won't install. The terminal goes to something like:
>>>>> ```
>>>>> [sagenb_export-3.3] [spkg-pipinst] Installing collected packages:
>>>>> sagenb_export
>>>>> [sagenb_export-3.3] [spkg-pipinst] changing mode of
>>>>> /sage/sagedev/local/var/lib/sage/venv-python3.12.5/bin/sagenb-export to
>>>>> 755
>>>>> [sagenb_export-3.3] [spkg-pipinst] Successfully installed
>>>>> sagenb_export-3.3
>>>>> [sagenb_export-3.3] Deleting build directory
>>>>> /sage/sagedev/local/var/lib/sage/venv-python3.12.5/var/tmp/sage/build/sagenb_export-3.3
>>>>> [sagenb_export-3.3] Finished installing sagenb_export-3.3
>>>>> ```
>>>>> (each time something slightly different) and then it just stalls
>>>>> there. (I Left it like that for 4 hours and no change. Then when I ctrl+c
>>>>> to stop the running process matplotlib throws an error.
>>>>>
>>>>> -Aram
>>>>>
>>>>> On Wed, 23 Apr 2025 at 13:25, Eric Gourgoulhon <egourgoul...@gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> This line in the scipy log:
>>>>>> [spkg-install] g++: fatal error: Killed signal terminated program
>>>>>> cc1plus
>>>>>> points towards a memory issue. Could you increase the RAM devoted to
>>>>>> WSL2 or decrease the number of processes if you are performing a parallel
>>>>>> build (e.g use make -j4 instead of make -j8) ?
>>>>>>
>>>>>> Eric.
>>>>>>
>>>>>>
>>>>>> Le mercredi 23 avril 2025 à 11:41:37 UTC+2, aram.derme...@gmail.com
>>>>>> a écrit :
>>>>>>
>>>>>>> Hey all,
>>>>>>>
>>>>>>> I'm trying to update to the latest devel version in order to code
>>>>>>> some things up, but I can't seem to get the latest devel version
>>>>>>> "making"
>>>>>>> properly. Not sure if I'm doing something wrong, so I'm attaching my
>>>>>>> logs.
>>>>>>>
>>>>>>> - First time, I ran it, I got a scipy error (logs attached) and it
>>>>>>> wouldn't build
>>>>>>> - I tried running `make` again (without doing a `make distclean`)
>>>>>>> and the 2nd time scipy installs correctly, but then the instlaler just
>>>>>>> hangs and doesn't finish.
>>>>>>> -> When I `ctrl+c` to quit, it shows `matplotlib-3.10.1` errors,
>>>>>>> so seems like it's getting stuck in `matplotlib-3.10.1`. (Which I'm
>>>>>>> attaching the log file for)
>>>>>>> -> Analyzying the log file, looks like it can't properly get
>>>>>>> `matplotlib-3.10.1`. Version 10.6 doesn't have it (only has
>>>>>>> `matplotlib-3.8` and the URL it's trying to download from for 10.7 is
>>>>>>> wrong
>>>>>>> (It should be:
>>>>>>> https://github.com/sagemath/sage/releases/download/10.7.beta1/matplotlib-3.10.1.tar.gz
>>>>>>> )
>>>>>>>
>>>>>>> I tried installing a fresh copy of sagedev (not my forked version)
>>>>>>> and a similar thing happens, but this time it failed when trying to
>>>>>>> install
>>>>>>> numpy.
>>>>>>>
>>>>>>> Wanted to see what the best way to approach fixing my development
>>>>>>> version is.
>>>>>>>
>>>>>>> Also, I'm thinking I should create a ticket along the lines of "if
>>>>>>> unable to download xxx, then an error should be thrown instead of just
>>>>>>> hanging and waiting forever", but before doing that I want to make sure
>>>>>>> that it is really a problem with the dev version and not a problem on my
>>>>>>> end (as my internet is a little weird here, so it could potentially be
>>>>>>> my
>>>>>>> internet being weird)
>>>>>>>
>>>>>>> Kindly,
>>>>>>> Aram
>>>>>>>
>>>>>> --
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