To add to that, users interested in compiling sage on nix may be interested to help with https://trac.sagemath.org/ticket/29130 ("Add nix package information, extend dockerfile generator to nix").
It looks like that this particular compile error will be addressed by https://trac.sagemath.org/ticket/27705 ("Check for more strictly required extension modules in Python build: zlib sqlite3"). On Monday, February 17, 2020 at 12:38:49 PM UTC-8, vdelecroix wrote: > > By default, the Sage sources does not allow that. Though, you > might want to have a look at the ongoing effort in that direction in > > https://trac.sagemath.org/ticket/27824 > https://trac.sagemath.org/ticket/29032 > > As Francois mentioned, many distros package SageMath (without requiring > an extra Python). But this involves each time some level of patching. > > Vincent > > Le 17/02/2020 à 21:26, Maxime Boissonneault a écrit : > > We're not quite using Nix either for that either. Nix is just a > > compatibility layer on top of which we build the scientific software > > stack (through EasyBuild). > > > > Maxime > > > > > > Le 20-02-17 à 15:22, François Bissey a écrit : > >> Timo Kaufmann (eisf...@gmail.com <javascript:>) is packaging for nix. > You should > >> ask him for tips. > >> > >> François > >> > >>> On 18/02/2020, at 9:17 AM, Maxime Boissonneault > >>> <maxime.bo...@calculquebec.ca <javascript:>> wrote: > >>> > >>> Hi Vincent, > >>> > >>> It is a rather complex setup, as this is for a national network of > >>> HPC clusters. We have thousands of software packages installed, with > >>> basically what amounts to an operating system (NixOS) in user space. > >>> You can see a description of our system in this paper : > >>> > >>> > https://ssl.linklings.net/conferences/pearc/pearc19_program/views/includes/files/pap139s3-file1.pdf > > >>> > >>> > >>> This setup is rather complex, but it also means that you can actually > >>> mount all of our software environment on any Linux computer and have > >>> thousands of software available to you in a matter of seconds. > >>> > >>> https://docs.computecanada.ca/wiki/Accessing_CVMFS > >>> > >>> > >>> > >>> My main question is : how do I make sage use the python that we > >>> already have and which works perfectly well ? > >>> > >>> It should *not* install python and pip. > >>> > >>> > >>> Attached is a tarball with the log file. > >>> > >>> Maxime Boissonneault > >>> > >>> > >>> Le 20-02-17 à 16:12, Vincent Delecroix a écrit : > >>>> Dear Maxime, > >>>> > >>>> Could you describe precisely your computer and the steps you follow > >>>> to install SageMath 9.0? There are dozen of different OS and dozens > >>>> of ways to install SageMath on each of them. > >>>> > >>>> Also, if you compile from source, you should provide the files > >>>> - config.log > >>>> - logs/install.log > >>>> > >>>> Vincent > >>>> > >>>> Le 17/02/2020 à 20:50, Maxime Boissonneault a écrit : > >>>>> Hi, > >>>>> I get the following error when installing SageMath 9.0. I am not > >>>>> sure why > >>>>> SageMath is trying at all to install python and pip, as those are > >>>>> already > >>>>> working just fine on our system. > >>>>> > >>>>> > >>>>> > >>>>> [pip-18.1] > >>>>> > ************************************************************************ > >>>>> > >>>>> [pip-18.1] Error installing package pip-18.1 > >>>>> [pip-18.1] > >>>>> > ************************************************************************ > >>>>> > >>>>> [pip-18.1] Please email sage-devel > >>>>> (http://groups.google.com/group/sage-devel) > >>>>> [pip-18.1] explaining the problem and including the log file > >>>>> [pip-18.1] > >>>>> > /home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/logs/pkgs/pip-18.1.log > > > >>>>> > >>>>> [pip-18.1] Describe your computer, operating system, etc. > >>>>> [pip-18.1] If you want to try to fix the problem yourself, *don't* > >>>>> just cd > >>>>> to > >>>>> [pip-18.1] > >>>>> > /home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/local/var/tmp/sage/build/pip-18.1 > > > >>>>> > >>>>> and type 'make' or whatever is appropriate. > >>>>> [pip-18.1] Instead, the following commands setup all environment > >>>>> variables > >>>>> [pip-18.1] correctly and load a subshell for you to debug the error: > >>>>> [pip-18.1] (cd > >>>>> > '/home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/local/var/tmp/sage/build/pip-18.1' > > > >>>>> > >>>>> && > >>>>> > '/home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/sage' > > > >>>>> > >>>>> --sh) > >>>>> [pip-18.1] When you are done debugging, you can type "exit" to > >>>>> leave the > >>>>> subshell. > >>>>> [pip-18.1] > >>>>> > ************************************************************************ > >>>>> > >>>>> make[3]: *** [Makefile:2152: > >>>>> > /home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/local/var/lib/sage/installed/pip-18.1] > > > >>>>> > >>>>> Error 1 > >>>>> make[3]: Leaving directory > >>>>> > '/home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/build/make' > > > >>>>> > >>>>> make[2]: *** [Makefile:1830: all-start] Error 2 > >>>>> make[2]: Leaving directory > >>>>> > '/home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/build/make' > > > >>>>> > >>>>> > >>>>> real 0m1.189s > >>>>> user 0m0.818s > >>>>> sys 0m0.269s > >>>>> > >>>>> > >>>>> > >>>>> Below is the content of the log file : > >>>>> > >>>>> Found local metadata for pip-18.1 > >>>>> Using cached file > >>>>> > /home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/upstream/pip-18.1.tar.gz > > > >>>>> > >>>>> pip-18.1 > >>>>> ==================================================== > >>>>> Setting up build directory for pip-18.1 > >>>>> Finished extraction > >>>>> No patch files found in ../patches > >>>>> **************************************************** > >>>>> Host system: > >>>>> Linux build-node.computecanada.ca 3.10.0-1062.12.1.el7.x86_64 #1 > >>>>> SMP Tue > >>>>> Feb 4 23:02:59 UTC 2020 x86_64 GNU/Linux > >>>>> **************************************************** > >>>>> C compiler: gcc > >>>>> C compiler version: > >>>>> Using built-in specs. > >>>>> COLLECT_GCC=/cvmfs/ > soft.computecanada.ca/nix/var/nix/profiles/gcc-7.3.0/bin/gcc > >>>>> > >>>>> COLLECT_LTO_WRAPPER=/cvmfs/ > soft.computecanada.ca/nix/store/c9qaklf3dvjvlbky3fiakmafb1p8l106-gfortran-7.3.0/libexec/gcc/x86_64-pc-linux-gnu/7.3.0/lto-wrapper > > >>>>> > >>>>> OFFLOAD_TARGET_NAMES=nvptx-none > >>>>> Target: x86_64-pc-linux-gnu > >>>>> Configured with: > >>>>> Thread model: posix > >>>>> gcc version 7.3.0 (GCC) > >>>>> **************************************************** > >>>>> Package 'pip' is currently not installed > >>>>> No legacy uninstaller found for 'pip'; nothing to do > >>>>> Traceback (most recent call last): > >>>>> File > >>>>> > "/home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/local/lib/python3.7/runpy.py", > > > >>>>> > >>>>> line 193, in _run_module_as_main > >>>>> "__main__", mod_spec) > >>>>> File > >>>>> > "/home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/local/lib/python3.7/runpy.py", > > > >>>>> > >>>>> line 85, in _run_code > >>>>> exec(code, run_globals) > >>>>> File > >>>>> > "/home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/local/var/tmp/sage/build/pip-18.1/src/src/pip/__main__.py", > > > >>>>> > >>>>> line 16, in <module> > >>>>> from pip._internal import main as _main # isort:skip # noqa > >>>>> File > >>>>> > "/home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/local/var/tmp/sage/build/pip-18.1/src/src/pip/_internal/__init__.py", > > > >>>>> > >>>>> line 19, in <module> > >>>>> from pip._vendor.urllib3.exceptions import DependencyWarning > >>>>> File > >>>>> > "/home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/local/var/tmp/sage/build/pip-18.1/src/src/pip/_vendor/urllib3/__init__.py", > > > >>>>> > >>>>> line 8, in <module> > >>>>> from .connectionpool import ( > >>>>> File > >>>>> > "/home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/local/var/tmp/sage/build/pip-18.1/src/src/pip/_vendor/urllib3/connectionpool.py", > > > >>>>> > >>>>> line 36, in <module> > >>>>> from .response import HTTPResponse > >>>>> File > >>>>> > "/home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/local/var/tmp/sage/build/pip-18.1/src/src/pip/_vendor/urllib3/response.py", > > > >>>>> > >>>>> line 3, in <module> > >>>>> import zlib > >>>>> ModuleNotFoundError: No module named 'zlib' > >>>>> > ********************************************************************************************************************************************************************************************************************************************** > > > >>>>> > >>>>> Error building / installing pip3 > >>>>> > ********************************************************************************************************************************************************************************************************************************************** > > > >>>>> > >>>>> > >>>>> real 0m0.147s > >>>>> user 0m0.120s > >>>>> sys 0m0.031s > >>>>> > ************************************************************************ > >>>>> > >>>>> Error installing package pip-18.1 > >>>>> > ************************************************************************ > >>>>> > >>>>> Please email sage-devel (http://groups.google.com/group/sage-devel) > >>>>> explaining the problem and including the log file > >>>>> > /home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/logs/pkgs/pip-18.1.log > > > >>>>> > >>>>> Describe your computer, operating system, etc. > >>>>> If you want to try to fix the problem yourself, *don't* just cd to > >>>>> > /home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/local/var/tmp/sage/build/pip-18.1 > > > >>>>> > >>>>> 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 > >>>>> > '/home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/local/var/tmp/sage/build/pip-18.1' > > > >>>>> > >>>>> && > >>>>> > '/home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/sage' > > > >>>>> > >>>>> --sh) > >>>>> When you are done debugging, you can type "exit" to leave the > >>>>> subshell. > >>>>> > ************************************************************************ > >>>>> > >>>>> Found local metadata for pip-18.1 > >>>>> Using cached file > >>>>> > /home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/upstream/pip-18.1.tar.gz > > > >>>>> > >>>>> pip-18.1 > >>>>> ==================================================== > >>>>> Setting up build directory for pip-18.1 > >>>>> Finished extraction > >>>>> No patch files found in ../patches > >>>>> **************************************************** > >>>>> Host system: > >>>>> Linux build-node.computecanada.ca 3.10.0-1062.12.1.el7.x86_64 #1 > >>>>> SMP Tue > >>>>> Feb 4 23:02:59 UTC 2020 x86_64 GNU/Linux > >>>>> **************************************************** > >>>>> C compiler: gcc > >>>>> C compiler version: > >>>>> Using built-in specs. > >>>>> COLLECT_GCC=/cvmfs/ > soft.computecanada.ca/nix/var/nix/profiles/gcc-7.3.0/bin/gcc > >>>>> > >>>>> COLLECT_LTO_WRAPPER=/cvmfs/ > soft.computecanada.ca/nix/store/c9qaklf3dvjvlbky3fiakmafb1p8l106-gfortran-7.3.0/libexec/gcc/x86_64-pc-linux-gnu/7.3.0/lto-wrapper > > >>>>> > >>>>> OFFLOAD_TARGET_NAMES=nvptx-none > >>>>> Target: x86_64-pc-linux-gnu > >>>>> Configured with: > >>>>> Thread model: posix > >>>>> gcc version 7.3.0 (GCC) > >>>>> **************************************************** > >>>>> Package 'pip' is currently not installed > >>>>> No legacy uninstaller found for 'pip'; nothing to do > >>>>> Traceback (most recent call last): > >>>>> File > >>>>> > "/home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/local/lib/python3.7/runpy.py", > > > >>>>> > >>>>> line 193, in _run_module_as_main > >>>>> "__main__", mod_spec) > >>>>> File > >>>>> > "/home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/local/lib/python3.7/runpy.py", > > > >>>>> > >>>>> line 85, in _run_code > >>>>> exec(code, run_globals) > >>>>> File > >>>>> > "/home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/local/var/tmp/sage/build/pip-18.1/src/src/pip/__main__.py", > > > >>>>> > >>>>> line 16, in <module> > >>>>> from pip._internal import main as _main # isort:skip # noqa > >>>>> File > >>>>> > "/home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/local/var/tmp/sage/build/pip-18.1/src/src/pip/_internal/__init__.py", > > > >>>>> > >>>>> line 19, in <module> > >>>>> from pip._vendor.urllib3.exceptions import DependencyWarning > >>>>> File > >>>>> > "/home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/local/var/tmp/sage/build/pip-18.1/src/src/pip/_vendor/urllib3/__init__.py", > > > >>>>> > >>>>> line 8, in <module> > >>>>> from .connectionpool import ( > >>>>> File > >>>>> > "/home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/local/var/tmp/sage/build/pip-18.1/src/src/pip/_vendor/urllib3/connectionpool.py", > > > >>>>> > >>>>> line 36, in <module> > >>>>> from .response import HTTPResponse > >>>>> File > >>>>> > "/home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/local/var/tmp/sage/build/pip-18.1/src/src/pip/_vendor/urllib3/response.py", > > > >>>>> > >>>>> line 3, in <module> > >>>>> import zlib > >>>>> ModuleNotFoundError: No module named 'zlib' > >>>>> > ********************************************************************************************************************************************************************************************************************************************** > > > >>>>> > >>>>> Error building / installing pip3 > >>>>> > ********************************************************************************************************************************************************************************************************************************************** > > > >>>>> > >>>>> > >>>>> real 0m0.150s > >>>>> user 0m0.124s > >>>>> sys 0m0.031s > >>>>> > ************************************************************************ > >>>>> > >>>>> Error installing package pip-18.1 > >>>>> > ************************************************************************ > >>>>> > >>>>> Please email sage-devel (http://groups.google.com/group/sage-devel) > >>>>> explaining the problem and including the log file > >>>>> > /home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/logs/pkgs/pip-18.1.log > > > >>>>> > >>>>> Describe your computer, operating system, etc. > >>>>> If you want to try to fix the problem yourself, *don't* just cd to > >>>>> > /home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/local/var/tmp/sage/build/pip-18.1 > > > >>>>> > >>>>> 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 > >>>>> > '/home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/local/var/tmp/sage/build/pip-18.1' > > > >>>>> > >>>>> && > >>>>> > '/home/mboisson/.local/easybuild/software/2017/avx2/Compiler/gcc7.3/sagemath/9.0/sage' > > > >>>>> > >>>>> --sh) > >>>>> When you are done debugging, you can type "exit" to leave the > >>>>> subshell. > >>>>> > ************************************************************************ > >>>>> > >>>>> > >>> -- > >>> You received this message because you are subscribed to the Google > >>> Groups "sage-devel" group. > >>> To unsubscribe from this group and stop receiving emails from it, > >>> send an email to sage-...@googlegroups.com <javascript:>. > >>> To view this discussion on the web visit > >>> > https://groups.google.com/d/msgid/sage-devel/2f2c357f-1b25-0f02-a411-9b20ad0f4316%40calculquebec.ca. > > > >>> > >>> <logs.tar.gz> > > > -- You received this message because you are subscribed to the Google Groups "sage-devel" group. 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