On Tue, Nov 2, 2021 at 9:00 PM Matthias Köppe <matthiaskoe...@gmail.com> wrote:
> It's really just the command "tox -e > docker-ubuntu-groovy-standard-arm64v8" - try it Thanks. Some more details I figured out in a few moments, in case anybody else is interested: 1. What is tox? Answer: it is a Python package you can install by typing "pip3 install tox". The homepage is https://tox.wiki/en/latest/, which explains that it is a test automation system. 2. How do you use it? Answer: Get the Sage source code and from the top level type "tox -e docker-ubuntu-groovy-standard-arm64v8". This uses the file tox.ini that is in the top of the Sage source tree. 3. What is tox.ini? Where does it come from? Answer: Matthias added it to Sage a year ago. I don't know how it gets generated, but it seems very comprehensive. 4. Does it install tachyon from Ubuntu packages? Answer: I don't know, though "grep -i tachyon tox.ini" doesn't output anything, so I'm guessing it doesn't. William > > On Tuesday, November 2, 2021 at 8:37:54 PM UTC-7 William Stein wrote: > >> What did you do exactly? For example did you install tachyon >> systemwide? >> >> Thanks! >> >> On Tue, Nov 2, 2021 at 8:02 PM Matthias Köppe <matthia...@gmail.com> >> wrote: >> >>> I just built for this architecture successfully using "tox -e >>> docker-ubuntu-groovy-standard-arm64v8" (on my Intel MBP). That's slightly >>> newer than ubuntu-focal (20.04) >>> >>> sage -t --random-seed=0 >>> src/sage/algebras/quatalg/quaternion_algebra_cython.pyx >>> [10 tests, 0.17 s] >>> >>> ---------------------------------------------------------------------- >>> >>> All tests passed! >>> >>> >>> >>> >>> On Tuesday, November 2, 2021 at 9:13:25 AM UTC-7 William Stein wrote: >>> >>>> This is a quick update about building the 9.5.beta5 version of Sage on >>>> an M1 Mac under Docker aarch64 Linux. >>>> >>>> After installing Tachyon system wide, the build completes. This >>>> Cython module won't import due to an issue with libgomp, which >>>> is evidently some openMP parallel computing library, failing with >>>> " /lib/aarch64-linux-gnu/libgomp.so.1: cannot allocate memory in static TLS >>>> block". >>>> See below for the failed test. >>>> >>>> A quick search reveals this discussion of exactly this sort of problem: >>>> >>>> https://github.com/opencv/opencv/issues/14884 >>>> >>>> It sounds like a bug in how SageMath is built (or the library is >>>> imported) that will need a workaround on aarch64. This comment >>>> >>>> https://github.com/opencv/opencv/issues/14884#issuecomment-815632861 >>>> >>>> seems most actionable. >>>> >>>> I was NOT able to reproduce this by just starting sage or Python and >>>> importing modules. It has something to >>>> do with how doctests are run. >>>> >>>> The suggestion in the github issue I link to above to use LD_PRELOAD >>>> *does* work, i.e., >>>> >>>> LD_PRELOAD=/lib/aarch64-linux-gnu/libgomp.so.1 ./sage -t >>>> src/sage/algebras/quatalg/quaternion_algebra_cython.pyx >>>> ... >>>> works fine. I might just set LD_PRELOAD for cocalc-docker if nobody >>>> has a better idea. I'm keeping track of all these >>>> issues with Sage + aarch64 here: >>>> https://github.com/sagemathinc/cocalc-docker/issues/138 >>>> >>>> --- >>>> >>>> root@8bff70fbbc1c:/usr/local/sage# ./sage -t >>>> src/sage/algebras/quatalg/quaternion_algebra_cython.pyx >>>> no stored timings available >>>> Running doctests with ID 2021-11-02-15-54-57-8a128eb1. >>>> Git branch: HEAD >>>> Using >>>> --optional=build,debian,dochtml,pip,sage,sage.geometry.polyhedron,sage.rings.real_double,sage_spkg >>>> Doctesting 1 file. >>>> Traceback (most recent call last): >>>> File "/usr/local/sage/src/bin/sage-runtests", line 151, in <module> >>>> err = DC.run() >>>> File >>>> "/usr/local/sage/local/var/lib/sage/venv-python3.8/lib/python3.8/site-packages/sage/doctest/control.py", >>>> line 1254, in run >>>> self.run_doctests() >>>> File >>>> "/usr/local/sage/local/var/lib/sage/venv-python3.8/lib/python3.8/site-packages/sage/doctest/control.py", >>>> line 951, in run_doctests >>>> self.dispatcher = DocTestDispatcher(self) >>>> File >>>> "/usr/local/sage/local/var/lib/sage/venv-python3.8/lib/python3.8/site-packages/sage/doctest/forker.py", >>>> line 1614, in __init__ >>>> init_sage(controller) >>>> File >>>> "/usr/local/sage/local/var/lib/sage/venv-python3.8/lib/python3.8/site-packages/sage/doctest/forker.py", >>>> line 192, in init_sage >>>> controller.load_environment() >>>> File >>>> "/usr/local/sage/local/var/lib/sage/venv-python3.8/lib/python3.8/site-packages/sage/doctest/control.py", >>>> line 572, in load_environment >>>> return import_module(self.options.environment) >>>> File "/usr/lib/python3.8/importlib/__init__.py", line 127, in >>>> import_module >>>> return _bootstrap._gcd_import(name[level:], package, level) >>>> File "<frozen importlib._bootstrap>", line 1014, in _gcd_import >>>> File "<frozen importlib._bootstrap>", line 991, in _find_and_load >>>> File "<frozen importlib._bootstrap>", line 975, in >>>> _find_and_load_unlocked >>>> File "<frozen importlib._bootstrap>", line 671, in _load_unlocked >>>> File "<frozen importlib._bootstrap_external>", line 848, in >>>> exec_module >>>> File "<frozen importlib._bootstrap>", line 219, in >>>> _call_with_frames_removed >>>> File >>>> "/usr/local/sage/local/var/lib/sage/venv-python3.8/lib/python3.8/site-packages/sage/repl/ipython_kernel/all_jupyter.py", >>>> line 5, in <module> >>>> from sage.all_cmdline import * >>>> File >>>> "/usr/local/sage/local/var/lib/sage/venv-python3.8/lib/python3.8/site-packages/sage/all_cmdline.py", >>>> line 19, in <module> >>>> from sage.all import * >>>> File >>>> "/usr/local/sage/local/var/lib/sage/venv-python3.8/lib/python3.8/site-packages/sage/all.py", >>>> line 129, in <module> >>>> from sage.algebras.all import * >>>> File >>>> "/usr/local/sage/local/var/lib/sage/venv-python3.8/lib/python3.8/site-packages/sage/algebras/all.py", >>>> line 21, in <module> >>>> import sage.algebras.catalog as algebras >>>> File >>>> "/usr/local/sage/local/var/lib/sage/venv-python3.8/lib/python3.8/site-packages/sage/algebras/catalog.py", >>>> line 80, in <module> >>>> from sage.algebras.quatalg.quaternion_algebra import >>>> QuaternionAlgebra as Quaternion >>>> File >>>> "/usr/local/sage/local/var/lib/sage/venv-python3.8/lib/python3.8/site-packages/sage/algebras/quatalg/quaternion_algebra.py", >>>> line 69, in <module> >>>> from . import quaternion_algebra_cython >>>> File "sage/algebras/quatalg/quaternion_algebra_cython.pyx", line 1, >>>> in init sage.algebras.quatalg.quaternion_algebra_cython >>>> (build/cythonized/sage/algebras/quatalg/quaternion_algebra_cython.cpp:6215) >>>> File "sage/matrix/matrix_integer_dense.pyx", line 1, in init >>>> sage.matrix.matrix_integer_dense >>>> (build/cythonized/sage/matrix/matrix_integer_dense.cpp:57704) >>>> ImportError: /lib/aarch64-linux-gnu/libgomp.so.1: cannot allocate >>>> memory in static TLS block >>>> >>>> On Mon, Nov 1, 2021 at 5:33 PM William Stein <wst...@gmail.com> wrote: >>>> >>>>> >>>>> >>>>> On Mon, Nov 1, 2021 at 4:35 PM Dima Pasechnik <dim...@gmail.com> >>>>> wrote: >>>>> >>>>>> >>>>>> >>>>>> On Mon, Nov 1, 2021 at 11:28 PM William Stein <wst...@gmail.com> >>>>>> wrote: >>>>>> >>>>>>> Great idea. Thanks Dima! >>>>>>> >>>>>>> On Mon, Nov 1, 2021 at 3:37 PM Dima Pasechnik <dim...@gmail.com> >>>>>>> wrote: >>>>>>> >>>>>> >>>>>>>> >>>>>>>> On Mon, Nov 1, 2021 at 10:18 PM William Stein <wst...@gmail.com> >>>>>>>> wrote: >>>>>>>> >>>>>>>>> I tried to build sage-9.5.beta5 on a very clean Linux Ubuntu:20.04 >>>>>>>>> image with standard dev packages (in Docker) but on an ARM aarch64 >>>>>>>>> architecture instead of Intel. It fails with Tachyon simply saying >>>>>>>>> "Error: >>>>>>>>> Sorry, your platform isn't supported by Tachyon and/or Sage. >>>>>>>>> Exiting...". >>>>>>>>> I don't know what that is about. >>>>>>>>> >>>>>>>> I found https://trac.sagemath.org/ticket/23712 which is a 2-year >>>>>>>>> old ticket about how upgrading Tachyon is needed " to make Sage >>>>>>>>> work on arm64/aarch64." >>>>>>>>> >>>>>>>>> Any suggestions? My goal is to make an aarch64 version of the >>>>>>>>> cocalc-docker image. Is there an easy workaround for this problem, >>>>>>>>> or >>>>>>>>> should I just do some hack to disable building tachyon (since it is a >>>>>>>>> runtime only dependency)? Is the right way to disable building a >>>>>>>>> standard >>>>>>>>> package these days still to touch some file somewhere, or did that >>>>>>>>> change? >>>>>>>>> >>>>>>>> >>>>>> by the way, it would be great to know if our usual "install as many >>>>>> system packages as ./configure advises >>>>>> at the end" scheme works well on aarch64, don't stop at tachyon >>>>>> please. >>>>>> >>>>> >>>>> Good idea, definitely. >>>>> >>>>> Is there an official Dockerfile for building Sage these days >>>>> somewhere? I'm using one that I found years ago from @ebray, and all >>>>> that advertisement about the fantastic support for system-wide packages >>>>> (which I forgot about) is hidden behind automation. [searches...]. Yes, >>>>> there is: >>>>> >>>>> https://github.com/sagemath/sage/blob/develop/docker/Dockerfile >>>>> >>>>> That's a pretty enormous Dockerfile, and I imagine it solves many >>>>> subtle problems. A cursory glance suggests that it installs a minimal >>>>> collection of system-wide packages. Maybe somebody should try what you >>>>> just suggested (modify it to depend on system packages) starting with that >>>>> Dockerfile too, to see how it goes (or as a different CI test)... >>>>> >>>>> William >>>>> >>>>> >>>>> >>>>> >>>> >>>>>> >>>>>> >>>>>>>> Just install the system tachyon package, and let ./configure do its >>>>>>>> job. >>>>>>>> You don't need to build it. >>>>>>>> >>>>>>>> >>>>>>> >>>>>>>>> gcc version 9.3.0 (Ubuntu 9.3.0-17ubuntu1~20.04) >>>>>>>>> **************************************************** >>>>>>>>> Package 'tachyon' is currently not installed >>>>>>>>> No legacy uninstaller found for 'tachyon'; nothing to do >>>>>>>>> >>>>>>>>> **************************************************************************************** >>>>>>>>> Error: Sorry, your platform isn't supported by Tachyon and/or >>>>>>>>> Sage. Exiting... >>>>>>>>> >>>>>>>>> **************************************************************************************** >>>>>>>>> >>>>>>>>> real 0m0.013s >>>>>>>>> user 0m0.007s >>>>>>>>> sys 0m0.009s >>>>>>>>> >>>>>>>>> ************************************************************************ >>>>>>>>> Error installing package tachyon-0.98.9.p7 >>>>>>>>> >>>>>>>>> ************************************************************************ >>>>>>>>> Please email sage-devel (http://groups.google.com/group/sage-devel >>>>>>>>> ) >>>>>>>>> explaining the problem and including the log files >>>>>>>>> /usr/local/sage/logs/pkgs/tachyon-0.98.9.p7.log >>>>>>>>> and >>>>>>>>> /usr/local/sage/config.log >>>>>>>>> Describe your computer, operating system, etc. >>>>>>>>> If you want to try to fix the problem yourself, *don't* just cd to >>>>>>>>> /usr/local/sage/local/var/tmp/sage/build/tachyon-0.98.9.p7 and >>>>>>>>> type 'make' or whatever is appropriate. >>>>>>>>> Instead, the following commands setup all environment variables >>>>>>>>> correctly and load a subshell for you to debug the error: >>>>>>>>> (cd '/usr/local/sage/local/var/tmp/sage/build/tachyon-0.98.9.p7' >>>>>>>>> && '/usr/local/sage/sage' --buildsh) >>>>>>>>> When you are done debugging, you can type "exit" to leave the >>>>>>>>> subshell. >>>>>>>>> >>>>>>>>> ************************************************************************ >>>>>>>>> >>>>>>>>> On Sat, Oct 30, 2021 at 2:54 PM Samuel Lelievre < >>>>>>>>> samuel....@gmail.com> wrote: >>>>>>>>> >>>>>>>> 2021-10-30 18:34:21 UTC, Emmanuel Charpentier: >>>>>>>>>> > >>>>>>>>>> > After rebuilding and reinstalling the same (really) >>>>>>>>>> > optional packages, `ptestlong` gets exactly one >>>>>>>>>> > (reproducible) failure, i. e. the one reported by >>>>>>>>>> > Samuel Lelièvre. >>>>>>>>>> > >>>>>>>>>> > I am at loss as to why I needed to rebuild 9.5 >>>>>>>>>> > from sratch instead of upgrading from 9.3. Ideas? >>>>>>>>>> >>>>>>>>>> I'm sure you mean: "why I needed to rebuild 9.5.beta5 >>>>>>>>>> from scratch instead of upgrading from 9.5.beta3". >>>>>>>>>> >>>>>>>>>> Not sure why a distclean was needed in that case. >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> You received this message because you are subscribed to the >>>>>>>>>> Google Groups "sage-release" group. >>>>>>>>>> >>>>>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>>>>>> send an email to sage-release...@googlegroups.com. >>>>>>>>>> To view this discussion on the web visit >>>>>>>>>> https://groups.google.com/d/msgid/sage-release/422c4441-dfb2-4b97-85d6-7f706a2be402n%40googlegroups.com >>>>>>>>>> <https://groups.google.com/d/msgid/sage-release/422c4441-dfb2-4b97-85d6-7f706a2be402n%40googlegroups.com?utm_medium=email&utm_source=footer> >>>>>>>>>> . >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> William (http://wstein.org) >>>>>>>>> >>>>>>>>> -- >>>>>>>>> You received this message because you are subscribed to the Google >>>>>>>>> Groups "sage-release" group. >>>>>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>>>>> send an email to sage-release...@googlegroups.com. >>>>>>>>> To view this discussion on the web visit >>>>>>>>> https://groups.google.com/d/msgid/sage-release/CACLE5GBVsNZbe%2BnikwGR-uxsL8WWVSk1EzEqziR--DT-ERTs_A%40mail.gmail.com >>>>>>>>> <https://groups.google.com/d/msgid/sage-release/CACLE5GBVsNZbe%2BnikwGR-uxsL8WWVSk1EzEqziR--DT-ERTs_A%40mail.gmail.com?utm_medium=email&utm_source=footer> >>>>>>>>> . >>>>>>>>> >>>>>>>> -- >>>>>>>> You received this message because you are subscribed to the Google >>>>>>>> Groups "sage-release" group. >>>>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>>>> send an email to sage-release...@googlegroups.com. >>>>>>>> To view this discussion on the web visit >>>>>>>> https://groups.google.com/d/msgid/sage-release/CAAWYfq3FDgxH_UOcEhMY1wvbLkvEPkMhjchtPMDJ1X6YzG7DmQ%40mail.gmail.com >>>>>>>> <https://groups.google.com/d/msgid/sage-release/CAAWYfq3FDgxH_UOcEhMY1wvbLkvEPkMhjchtPMDJ1X6YzG7DmQ%40mail.gmail.com?utm_medium=email&utm_source=footer> >>>>>>>> . >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> William (http://wstein.org) >>>>>>> >>>>>>> -- >>>>>>> You received this message because you are subscribed to the Google >>>>>>> Groups "sage-release" group. >>>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>>> send an email to sage-release...@googlegroups.com. >>>>>>> To view this discussion on the web visit >>>>>>> https://groups.google.com/d/msgid/sage-release/CACLE5GAHQpnqrfC74jimwXA-UXU4j%2BLSE98tvW2%3DyMQ%2BC05okw%40mail.gmail.com >>>>>>> <https://groups.google.com/d/msgid/sage-release/CACLE5GAHQpnqrfC74jimwXA-UXU4j%2BLSE98tvW2%3DyMQ%2BC05okw%40mail.gmail.com?utm_medium=email&utm_source=footer> >>>>>>> . >>>>>>> >>>>>> -- >>>>>> You received this message because you are subscribed to the Google >>>>>> Groups "sage-release" group. >>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>> send an email to sage-release...@googlegroups.com. >>>>>> To view this discussion on the web visit >>>>>> https://groups.google.com/d/msgid/sage-release/CAAWYfq3HSp6ZsRqWPQBSJPQU3%3DQa1owhk4tMGpa3j5Wsqxg3zQ%40mail.gmail.com >>>>>> <https://groups.google.com/d/msgid/sage-release/CAAWYfq3HSp6ZsRqWPQBSJPQU3%3DQa1owhk4tMGpa3j5Wsqxg3zQ%40mail.gmail.com?utm_medium=email&utm_source=footer> >>>>>> . >>>>>> >>>>> >>>>> >>>>> -- >>>>> William (http://wstein.org) >>>>> >>>> >>>> >>>> -- >>>> William (http://wstein.org) >>>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "sage-release" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to sage-release...@googlegroups.com. >>> >> To view this discussion on the web visit >>> https://groups.google.com/d/msgid/sage-release/9497b1ce-756a-4605-973a-cc577ea65355n%40googlegroups.com >>> <https://groups.google.com/d/msgid/sage-release/9497b1ce-756a-4605-973a-cc577ea65355n%40googlegroups.com?utm_medium=email&utm_source=footer> >>> . >>> >> -- >> -- William Stein >> > -- > You received this message because you are subscribed to the Google Groups > "sage-release" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-release+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-release/40ae90a8-e48a-40a7-81d5-6d9f37a5a557n%40googlegroups.com > <https://groups.google.com/d/msgid/sage-release/40ae90a8-e48a-40a7-81d5-6d9f37a5a557n%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- William (http://wstein.org) -- You received this message because you are subscribed to the Google Groups "sage-release" group. 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