Errors in Python Installation #28

wielandbrendel · 2019-03-04T16:06:03Z

I am running into a few issues when trying to install the Python version. After calling sudo python3 setup.py install I get (sorry for the long traceback):

Namespace(blas64=False, extraverbose=False, float32=False, gpu=False, int32=False, root_dir='../', scs=False)
/usr/local/lib/python3.6/dist-packages/numpy/distutils/system_info.py:636: UserWarning: 
    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [atlas]) or by setting
    the ATLAS environment variable.
  self.calc_info()
/usr/bin/ld: cannot find -lcblas
collect2: error: ld returned 1 exit status
{'define_macros': [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)], 'libraries': ['blas', 'blas'], 'library_dirs': ['/usr/lib'], 'include_dirs': ['/usr/local/include', '/usr/include'], 'language': 'c'}
/usr/local/lib/python3.6/dist-packages/numpy/distutils/system_info.py:636: UserWarning: 
    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [atlas]) or by setting
    the ATLAS environment variable.
  self.calc_info()
{'define_macros': [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)], 'libraries': ['lapack', 'lapack', 'blas', 'blas'], 'library_dirs': ['/usr/lib'], 'language': 'c', 'include_dirs': ['/usr/local/include', '/usr/include']}
running install
running bdist_egg
running egg_info
writing superscs.egg-info/PKG-INFO
writing dependency_links to superscs.egg-info/dependency_links.txt
writing requirements to superscs.egg-info/requires.txt
writing top-level names to superscs.egg-info/top_level.txt
reading manifest file 'superscs.egg-info/SOURCES.txt'
writing manifest file 'superscs.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
running build_ext
##################################################
# failed to compile with OpenMP;                 #
# some sections of SCS will not be parallelized. #
##################################################
building '_superscs_direct' extension
C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

compile options: '-DPYTHON -DCTRLC=1 -DCOPYAMATRIX -DUSE_LAPACK=1 -DLAPACK_LIB_FOUND=1 -DSVD_ACTIVATED=1 -DLAPACK_LIB_FOUND -DNO_ATLAS_INFO=1 -DHAVE_CBLAS -DNO_ATLAS_INFO=1 -DHAVE_CBLAS -DDLONG=0 -I../ -I../include -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I../linsys -I/usr/local/include -I/usr/include -I/usr/local/include -I/usr/include -I../linsys/direct/ -I../linsys/direct/external/ -I/usr/include/python3.6m -c'
extra options: '-O3 -std=c99'
x86_64-linux-gnu-gcc: ../src/ctrlc.c
x86_64-linux-gnu-gcc: ../src/directions.c
x86_64-linux-gnu-gcc: scsmodule.c
x86_64-linux-gnu-gcc: ../src/cs.c
x86_64-linux-gnu-gcc: ../src/scs_parser.c
x86_64-linux-gnu-gcc: ../src/cones.c
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
x86_64-linux-gnu-gcc: ../src/linAlg.c
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
x86_64-linux-gnu-gcc: ../src/scs.c
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
x86_64-linux-gnu-gcc: ../src/scs_version.c
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
x86_64-linux-gnu-gcc: ../src/unit_test_util.c
x86_64-linux-gnu-gcc: ../src/util.c
x86_64-linux-gnu-gcc: ../linsys/common.c
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
x86_64-linux-gnu-gcc: ../linsys/direct/private.c
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
x86_64-linux-gnu-gcc: ../linsys/direct/external/amd_1.c
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
x86_64-linux-gnu-gcc: ../linsys/direct/external/SuiteSparse_config.c
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
x86_64-linux-gnu-gcc: ../linsys/direct/external/amd_aat.c
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
x86_64-linux-gnu-gcc: ../linsys/direct/external/amd_control.c
x86_64-linux-gnu-gcc: ../linsys/direct/external/amd_2.c
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
x86_64-linux-gnu-gcc: ../linsys/direct/external/amd_defaults.c
x86_64-linux-gnu-gcc: ../linsys/direct/external/amd_dump.c
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
x86_64-linux-gnu-gcc: ../linsys/direct/external/amd_global.c
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
x86_64-linux-gnu-gcc: ../linsys/direct/external/amd_info.c
x86_64-linux-gnu-gcc: ../linsys/direct/external/amd_order.c
x86_64-linux-gnu-gcc: ../linsys/direct/external/amd_postorder.c
x86_64-linux-gnu-gcc: ../linsys/direct/external/amd_preprocess.c
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
x86_64-linux-gnu-gcc: ../linsys/direct/external/amd_post_tree.c
x86_64-linux-gnu-gcc: ../linsys/direct/external/amd_valid.c
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
x86_64-linux-gnu-gcc: ../linsys/direct/external/ldl.c
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'

Do you have any idea what's going wrong?

The text was updated successfully, but these errors were encountered:

wielandbrendel · 2019-03-04T18:04:47Z

To make this easier to reproduce, I extended your Dockerfile with the following lines:

COPY python/ /superscs/python
RUN apt-get install -y python3-pip
RUN pip3 install --upgrade pip
RUN pip3 install numpy scipy
RUN cd /superscs/python && python3 setup.py install

This basically gives the same errors as reported above.

alphaville · 2019-03-04T18:11:03Z

@wielandbrendel The Python interface of SuperSCS needs python2 (it has been tested with Python v2.7).

wielandbrendel · 2019-03-04T18:24:57Z

@alphaville Great, thanks for the quick response! Python2 solves some but not all problems: changing the lines above to

RUN apt-get install -y python-pip
RUN pip install --upgrade pip
RUN pip install numpy scipy
RUN cd /superscs/python && python setup.py install

still leaves some of the errors:

gcc: ../src/util.c
gcc: scsmodule.c
gcc: ../src/unit_test_util.c
gcc: ../linsys/direct/external/amd_postorder.c
gcc: ../linsys/direct/external/amd_dump.c
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
gcc: ../linsys/direct/external/amd_2.c
gcc: ../linsys/direct/external/amd_control.c
gcc: ../linsys/direct/external/SuiteSparse_config.c
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
gcc: ../linsys/direct/external/amd_valid.c
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'
cc1: error: argument to '-O' should be a non-negative integer, 'g', 's' or 'fast'

I'd love to help with a Python3 version but fear that my non-existent knowledge of C is not much of a help here :(.

wmtonkin · 2019-04-10T19:05:43Z

I think the problem here is that in python/setup.py
extra_compile_args = ["-O3 -std=c99"]

Changing this to
extra_compile_args = ['-O3', '-std=c99']

gets ride of the "cc1: error: argument to '-O' should be " ... errors

alphaville · 2019-04-11T11:38:12Z

@wmtonkin In python/setup.py, line 185, the extra compilation arguments are

extra_compile_args = [""]

which version of SuperSCS are you using? You could download the latest version.

wmtonkin · 2019-04-11T14:33:34Z

Hello Pantelis, Thank you for getting back to me, I very much appreciate it. I was building from master, commit ff0ee5b If one runs the following from the top level "scs" dir: git diff v1.3.2..ff0ee5b -- python/setup.py It will show (snipped for brevity): @@ -157,14 +182,14 @@ def install_scs(**kwargs): blas_info = kwargs['blas_info'] lapack_info = kwargs['lapack_info'] - extra_compile_args = ["-O3"] + extra_compile_args = ["-O3 -std=c99"] library_dirs = [] extra_link_args = [] libraries = [] extra_define_macros = [] sources = ['scsmodule.c', ] + glob(os.path.join(root_dir, 'src/*.c')) + glob(os.path.join(root_dir, 'linsys/*.c')) include_dirs = [root_dir, os.path.join(root_dir, 'include'), get_include(), os.path.join(root_dir, 'linsys')] I believe this change was introduced in commit `ef306c18094eb46fd846db72232ab4cdd54971b9` Running git diff ef306c1^..ef306c1 -- python/setup.py diff --git a/python/setup.py b/python/setup.py index fc98245b..f7d1aa5b 100644 --- a/python/setup.py +++ b/python/setup.py @@ -157,7 +157,7 @@ def install_scs(**kwargs): blas_info = kwargs['blas_info'] lapack_info = kwargs['lapack_info'] - extra_compile_args = ["-O3"] + extra_compile_args = ["-O3 -std=c99"] library_dirs = [] extra_link_args = [] libraries = [] @@ -182,7 +182,7 @@ def install_scs(**kwargs): extra_link_args += blas_info.pop('extra_link_args', []) + lapack_info.pop('extra_link_args', []) extra_compile_args += blas_info.pop('extra_compile_args', []) + lapack_info.pop('extra_compile_args', []) if not args.int32: - extra_define_macros += [('DLONG', 1)] # longs for integer type + extra_define_macros += [('DLONG', 0)] # longs for integer type _superscs_direct = Extension( name='_superscs_direct', Best Regards, Bill Tonkin

web2webs · 2020-05-16T00:58:18Z

I think the problem here is that in python/setup.py
extra_compile_args = ["-O3 -std=c99"]

Changing this to
extra_compile_args = ['-O3', '-std=c99']

gets ride of the "cc1: error: argument to '-O' should be " ... errors

Thanks, it works!

alphaville self-assigned this Mar 4, 2019

alphaville added the python issue related to python label Mar 4, 2019

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Errors in Python Installation #28

Errors in Python Installation #28

wielandbrendel commented Mar 4, 2019

wielandbrendel commented Mar 4, 2019

alphaville commented Mar 4, 2019

wielandbrendel commented Mar 4, 2019

wmtonkin commented Apr 10, 2019

alphaville commented Apr 11, 2019

wmtonkin commented Apr 11, 2019 via email •

edited by alphaville

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web2webs commented May 16, 2020

Errors in Python Installation #28

Errors in Python Installation #28

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wielandbrendel commented Mar 4, 2019

wielandbrendel commented Mar 4, 2019

alphaville commented Mar 4, 2019

wielandbrendel commented Mar 4, 2019

wmtonkin commented Apr 10, 2019

alphaville commented Apr 11, 2019

wmtonkin commented Apr 11, 2019 via email • edited by alphaville Loading

web2webs commented May 16, 2020

wmtonkin commented Apr 11, 2019 via email •

edited by alphaville

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