[SciPy-Dev] Building SciPy from source for development
Matt Haberland
haberland at ucla.edu
Tue Sep 10 23:51:38 EDT 2019
Hi Isabel, Mark -
There has been a lot of work on the developer documentation since 1.3 was
released, so in general I would suggest using the development version of
the documentation:
http://scipy.github.io/devdocs/
Rather than those links.
However, there are important updates to the new Linux development
environment quickstart guide in progress:
https://github.com/scipy/scipy/pull/10461
Isabel, would you try following the very latest Linux instructions:
https://15105-1460385-gh.circle-artifacts.com/0/html-scipyorg/dev/contributor/quickstart_ubuntu.html#quickstart-ubuntu
And let me know if you run into any issues? They are written for full
Anaconda, but you can do it with Miniconda with minor adaptations (e.g. you
might be prompted to install `conda-build` if you try to use the `conda
develop` command) if you prefer.
Matt
On Tue, Sep 10, 2019, 8:03 PM Dr. Mark Alexander Mikofski PhD <
mikofski at berkeley.edu> wrote:
> Probably a more experienced contributor will also answer better, but what
> worked for me was to use the runtest.py script in a virtualenv:
> https://github.com/scipy/scipy/blob/master/runtests.py
>
> there's good info here in the docs, look for "runtest" under "recommended
> dev setup"
> https://docs.scipy.org/doc/scipy/reference/hacking.html
>
> there's some more info in the numpy docs on runtest.py and recommended dev
> setup:
> https://docs.scipy.org/doc/numpy/dev/development_environment.html
>
> If you are trying to build scipy to install or package, then you may need
> to change the settings in site.cfg (or setup.cfg), see the example
> https://github.com/scipy/scipy/blob/master/site.cfg.example
>
> I guess for Linux the INSTALL instructions are similar to the docs, but I
> don't think they will work with Anaconda/miniconda
> https://github.com/scipy/scipy/blob/master/INSTALL.rst.txt
>
> Here's more info in the documentation:
> * building from source:
> https://docs.scipy.org/doc/scipy/reference/building/index.html
> * dev guide: https://docs.scipy.org/doc/scipy/reference/dev/index.html
> * hacking: https://docs.scipy.org/doc/scipy/reference/hacking.html
>
> From your diagnostic messages, SciPy seems to think you are on a Windows
> machine instead of a Linux machine, not sure why:
> >Warning: Can't read registry to find the necessary compiler setting
> >Make sure that Python modules winreg, win32api or win32con are installed.
>
> Linux doesn't have a "registry" does it? And winreg, win32api, and
> win32con are python bindings for Windows machines right?
>
> As I said, I first created a virtualenv, activated the venv, installed the
> requirements (Numpy, pytest, cython, etc., see build docs), and then used
> runtest.py - I did not use anaconda/miniconda
>
> Are you on a mac, linux, or windows machine? On mac I used homebrew, and
> on windows I used WSL.
> https://brew.sh/
> https://docs.microsoft.com/en-us/windows/wsl/install-win10
>
> Good luck!
>
> PS: If I have given any incorrect information, I do apologize.
>
>
> On Tue, Sep 10, 2019 at 5:50 PM Isabel Kaspriskie <ikaspriskie at gmail.com>
> wrote:
>
>> Hello,
>>
>> I am setting up my development environment in order to start contributing
>> to the scipy repo. I have run into an error that I have not been able to
>> diagnose myself. When running `python setup.py install --user`, I find the
>> following error. The output is large, so I have only copied the end of it,
>> but please let me know if it is acceptable to attach a text file of the
>> output if that helps.
>>
>> ...
>> building 'rectangular_lsap' library
>> compiling C++ sources
>> C compiler: g++ -pthread -B
>> /home/isabelgk/miniconda3/envs/scipy-dev/compiler_compat -Wl,--sysroot=/
>> -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC
>>
>> creating build/temp.linux-x86_64-3.7/scipy/optimize/rectangular_lsap
>> compile options:
>> '-I/home/isabelgk/miniconda3/envs/scipy-dev/lib/python3.7/site-packages/numpy/core/include
>> -I/home/isabelgk/miniconda3/envs/scipy-dev/include/python3.7m -c'
>> g++: scipy/optimize/rectangular_lsap/rectangular_lsap.cpp
>> error: Command "g++ -pthread -B
>> /home/isabelgk/miniconda3/envs/scipy-dev/compiler_compat -Wl,--sysroot=/
>> -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC
>> -I/home/isabelgk/miniconda3/envs/scipy-dev/lib/python3.7/site-packages/numpy/core/include
>> -I/home/isabelgk/miniconda3/envs/scipy-dev/include/python3.7m -c
>> scipy/optimize/rectangular_lsap/rectangular_lsap.cpp -o
>> build/temp.linux-x86_64-3.7/scipy/optimize/rectangular_lsap/rectangular_lsap.o
>> -MMD -MF
>> build/temp.linux-x86_64-3.7/scipy/optimize/rectangular_lsap/rectangular_lsap.o.d"
>> failed with exit status 127
>>
>>
>>
>> I have run the numpy diagnose utility, and it seems that there is a
>> warning about being unable to read the registry to find my Fortran compiler
>> setting.
>>
>> >>> python -c 'from numpy.f2py.diagnose import run; run()'
>>
>> ------
>> os.name='posix'
>> ------
>> sys.platform='linux'
>> ------
>> sys.version:
>> 3.7.4 (default, Aug 13 2019, 20:35:49)
>> [GCC 7.3.0]
>> ------
>> sys.prefix:
>> /home/isabelgk/miniconda3/envs/scipy-dev
>> ------
>> sys.path=':/home/isabelgk/miniconda3/envs/scipy-dev/lib/python37.zip:/home/isabelgk/miniconda3/envs/scipy-dev/lib/python3.7:/home/isabelgk/miniconda3/envs/scipy-dev/lib/python3.7/lib-dynload:/home/isabelgk/.local/lib/python3.7/site-packages:/home/isabelgk/miniconda3/envs/scipy-dev/lib/python3.7/site-packages'
>> ------
>> Found new numpy version '1.16.4' in /home/isabelgk/miniconda3/envs/scipy-dev/lib/python3.7/site-packages/numpy/__init__.py
>> Found f2py2e version '2' in /home/isabelgk/miniconda3/envs/scipy-dev/lib/python3.7/site-packages/numpy/f2py/f2py2e.py
>> Found numpy.distutils version '0.4.0' in '/home/isabelgk/miniconda3/envs/scipy-dev/lib/python3.7/site-packages/numpy/distutils/__init__.py'
>> ------
>> Importing numpy.distutils.fcompiler ... ok
>> ------
>> Checking availability of supported Fortran compilers:
>> Warning: Can't read registry to find the necessary compiler setting
>> Make sure that Python modules winreg, win32api or win32con are installed.
>> Gnu95FCompiler instance properties:
>> archiver = ['/usr/bin/gfortran', '-cr']
>> compile_switch = '-c'
>> compiler_f77 = ['/usr/bin/gfortran', '-Wall', '-g', '-ffixed-form', '-
>> fno-second-underscore', '-fPIC', '-O3', '-funroll-loops']
>> compiler_f90 = ['/usr/bin/gfortran', '-Wall', '-g', '-fno-second-
>> underscore', '-fPIC', '-O3', '-funroll-loops']
>> compiler_fix = ['/usr/bin/gfortran', '-Wall', '-g', '-ffixed-form', '-
>> fno-second-underscore', '-Wall', '-g', '-fno-second-
>> underscore', '-fPIC', '-O3', '-funroll-loops']
>> libraries = ['gfortran']
>> library_dirs = ['/usr/lib/gcc/x86_64-linux-gnu/7', '/usr/lib/gcc/x86_64
>> -linux-gnu/7']
>> linker_exe = ['/usr/bin/gfortran', '-Wall', '-Wall']
>> linker_so = ['/usr/bin/gfortran', '-Wall', '-g', '-Wall', '-g', '-
>> shared']
>> object_switch = '-o '
>> ranlib = ['/usr/bin/gfortran']
>> version = LooseVersion ('7')
>> version_cmd = ['/usr/bin/gfortran', '-dumpversion']
>> Fortran compilers found:
>> --fcompiler=gnu95 GNU Fortran 95 compiler (7)
>> Compilers available for this platform, but not found:
>> --fcompiler=absoft Absoft Corp Fortran Compiler
>> --fcompiler=compaq Compaq Fortran Compiler
>> --fcompiler=g95 G95 Fortran Compiler
>> --fcompiler=gnu GNU Fortran 77 compiler
>> --fcompiler=intel Intel Fortran Compiler for 32-bit apps
>> --fcompiler=intele Intel Fortran Compiler for Itanium apps
>> --fcompiler=intelem Intel Fortran Compiler for 64-bit apps
>> --fcompiler=lahey Lahey/Fujitsu Fortran 95 Compiler
>> --fcompiler=nag NAGWare Fortran 95 Compiler
>> --fcompiler=nagfor NAG Fortran Compiler
>> --fcompiler=pathf95 PathScale Fortran Compiler
>> --fcompiler=pg Portland Group Fortran Compiler
>> --fcompiler=vast Pacific-Sierra Research Fortran 90 Compiler
>> Compilers not available on this platform:
>> --fcompiler=flang Portland Group Fortran LLVM Compiler
>> --fcompiler=hpux HP Fortran 90 Compiler
>> --fcompiler=ibm IBM XL Fortran Compiler
>> --fcompiler=intelev Intel Visual Fortran Compiler for Itanium apps
>> --fcompiler=intelv Intel Visual Fortran Compiler for 32-bit apps
>> --fcompiler=intelvem Intel Visual Fortran Compiler for 64-bit apps
>> --fcompiler=mips MIPSpro Fortran Compiler
>> --fcompiler=none Fake Fortran compiler
>> --fcompiler=sun Sun or Forte Fortran 95 Compiler
>> For compiler details, run 'config_fc --verbose' setup command.
>> ------
>> Importing numpy.distutils.cpuinfo ... ok
>> ------
>> CPU information: CPUInfoBase__get_nbits getNCPUs has_mmx has_sse has_sse2 has_sse3 has_ssse3 is_64bit is_Intel is_i686 ------
>>
>>
>> Thank you in advance,
>>
>> Isabel
>>
>> _______________________________________________
>> SciPy-Dev mailing list
>> SciPy-Dev at python.org
>> https://mail.python.org/mailman/listinfo/scipy-dev
>>
>
>
> --
> Mark Mikofski, PhD (2005)
> *Fiat Lux*
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev at python.org
> https://mail.python.org/mailman/listinfo/scipy-dev
>
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