installation fails on SMC #12

videlec · 2016-09-15T18:29:31Z

Problems on SageMath cloud sagemathinc/cocalc#905

saliola · 2017-03-06T13:37:24Z

Has there been any progress on this? It would be good to have this installed on SMC.

I just tried "sage -pip insall pypolymake --user" in a terminal on SMC. The installation process works, but there is still the same ImportError: ... polymake/perl_object.so: undefined symbol...

videlec · 2017-03-06T14:02:24Z

Could you try with

$ sage -f polymake
$ sage -pip install git+https://github.com/videlec/pypolymake

And also give access to the full log.

saliola · 2017-03-07T13:29:52Z

I can't do this on SMC since I don't have permissions to modify the version of sage installed on SMC. Perhaps we can ask one of the SMC maintainers/developers to try this? (But, on my local machine, I have no problems installing and using pypolymake.) EDIT: I added your request over at sagemathinc/cocalc#905.

haraldschilly · 2017-06-20T13:09:19Z

Hello, I'm working on a new compute environment for CoCalc (new name for SMC), and now I have such a logfile for Sage 7.6.

Collecting git+https://github.com/videlec/pypolymake
  Cloning https://github.com/videlec/pypolymake to /tmp/pip-gWR7u0-build
    Complete output from command python setup.py egg_info:
    running egg_info
    creating pip-egg-info/pypolymake.egg-info
    writing pip-egg-info/pypolymake.egg-info/PKG-INFO
    writing top-level names to pip-egg-info/pypolymake.egg-info/top_level.txt
    writing dependency_links to pip-egg-info/pypolymake.egg-info/dependency_links.txt
    writing manifest file 'pip-egg-info/pypolymake.egg-info/SOURCES.txt'
    warning: polymake/handlers.pyx:80:19: local variable 'ans' referenced before assignment
    warning: polymake/handlers.pyx:81:14: local variable 'ans' referenced before assignment
    warning: polymake/handlers.pyx:84:26: local variable 'ans' referenced before assignment
    warning: polymake/handlers.pyx:85:14: local variable 'ans' referenced before assignment
    warning: polymake/handlers.pyx:89:21: local variable 'ans' referenced before assignment
    warning: polymake/handlers.pyx:90:14: local variable 'ans' referenced before assignment
    warning: polymake/handlers.pyx:93:28: local variable 'ans' referenced before assignment
    warning: polymake/handlers.pyx:94:14: local variable 'ans' referenced before assignment
    
    Error compiling Cython file:
    ------------------------------------------------------------
    ...
    #                  http://www.gnu.org/licenses/
    ###############################################################################
    
    from __future__ import absolute_import
    
    from .number cimport Integer, Rational
    ^
    ------------------------------------------------------------
    
    polymake/sage_conversion.pyx:15:0: 'polymake/number.pxd' not found
    
    Error compiling Cython file:
    ------------------------------------------------------------
    ...
    #                  http://www.gnu.org/licenses/
    ###############################################################################
    
    from __future__ import absolute_import
    
    from .number cimport Integer, Rational
    ^
    ------------------------------------------------------------
    
    polymake/sage_conversion.pyx:15:0: 'polymake/number/Integer.pxd' not found
    
    Error compiling Cython file:
    ------------------------------------------------------------
    ...
    #                  http://www.gnu.org/licenses/
    ###############################################################################
    
    from __future__ import absolute_import
    
    from .number cimport Integer, Rational
    ^
    ------------------------------------------------------------
    
    polymake/sage_conversion.pyx:15:0: 'polymake/number/Rational.pxd' not found
    
    Error compiling Cython file:
    ------------------------------------------------------------
    ...
    
    from __future__ import absolute_import
    
    from .number cimport Integer, Rational
    from .vector cimport VectorInteger, VectorRational
    from .matrix cimport (MatrixInt, MatrixInteger, MatrixRational,
    ^
    ------------------------------------------------------------
    
    polymake/sage_conversion.pyx:17:0: 'polymake/matrix/pm_MatrixInt_get.pxd' not found
    
    Error compiling Cython file:
    ------------------------------------------------------------
    ...
    
    from __future__ import absolute_import
    
    from .number cimport Integer, Rational
    from .vector cimport VectorInteger, VectorRational
    from .matrix cimport (MatrixInt, MatrixInteger, MatrixRational,
    ^
    ------------------------------------------------------------
    
    polymake/sage_conversion.pyx:17:0: 'polymake/matrix/pm_MatrixInteger_get.pxd' not found
    
    Error compiling Cython file:
    ------------------------------------------------------------
    ...
    
    from __future__ import absolute_import
    
    from .number cimport Integer, Rational
    from .vector cimport VectorInteger, VectorRational
    from .matrix cimport (MatrixInt, MatrixInteger, MatrixRational,
    ^
    ------------------------------------------------------------
    
    polymake/sage_conversion.pyx:17:0: 'polymake/matrix/pm_MatrixRational_get.pxd' not found
    
    Error compiling Cython file:
    ------------------------------------------------------------
    ...
    from sage.modules.vector_integer_dense cimport Vector_integer_dense as sage_Vector_integer_dense
    from sage.modules.vector_rational_dense cimport Vector_rational_dense as sage_Vector_rational_dense
    from sage.matrix.matrix_rational_dense cimport Matrix_rational_dense as sage_Matrix_rational_dense
    from sage.matrix.matrix_integer_dense cimport Matrix_integer_dense as sage_Matrix_integer_dense
    
    def Integer_to_sage(Integer n):
                       ^
    ------------------------------------------------------------
    
    polymake/sage_conversion.pyx:40:20: 'Integer' is not a type identifier
    
    Error compiling Cython file:
    ------------------------------------------------------------
    ...
    def Integer_to_sage(Integer n):
        cdef sage_Integer ans = PY_NEW(sage_Integer)
        ans.set_from_mpz(<mpz_t>n.pm_obj.get_rep())
        return ans
    
    def Rational_to_sage(Rational q):
                        ^
    ------------------------------------------------------------
    
    polymake/sage_conversion.pyx:45:21: 'Rational' is not a type identifier
    
    Error compiling Cython file:
    ------------------------------------------------------------
    ...
    from sage.matrix.matrix_rational_dense cimport Matrix_rational_dense as sage_Matrix_rational_dense
    from sage.matrix.matrix_integer_dense cimport Matrix_integer_dense as sage_Matrix_integer_dense
    
    def Integer_to_sage(Integer n):
        cdef sage_Integer ans = PY_NEW(sage_Integer)
        ans.set_from_mpz(<mpz_t>n.pm_obj.get_rep())
                        ^
    ------------------------------------------------------------
    
    polymake/sage_conversion.pyx:42:21: Casting temporary Python object to non-numeric non-Python type
    
    Error compiling Cython file:
    ------------------------------------------------------------
    ...
        ans.set_from_mpz(<mpz_t>n.pm_obj.get_rep())
        return ans
    
    def Rational_to_sage(Rational q):
        cdef sage_Rational ans = sage_Rational.__new__(sage_Rational)
        ans.set_from_mpq(<mpq_t>q.pm_obj.get_rep())
                        ^
    ------------------------------------------------------------
    
    polymake/sage_conversion.pyx:47:21: Casting temporary Python object to non-numeric non-Python type
    
    Error compiling Cython file:
    ------------------------------------------------------------
    ...
        cdef Py_ssize_t ncols = m.pm_obj.cols()
        M = MatrixSpace(ZZ, nrows, ncols)
        cdef sage_Matrix_integer_dense ans = M.zero().__copy__()
        for i in range(nrows):
            for j in range(ncols):
                ans.set_unsafe_si(i, j, pm_MatrixInt_get(m.pm_obj, i, j))
                                                         ^
    ------------------------------------------------------------
    
    polymake/sage_conversion.pyx:77:54: Cannot convert 'pm_MatrixInt' to Python object
    
    Error compiling Cython file:
    ------------------------------------------------------------
    ...
        cdef Py_ssize_t ncols = m.pm_obj.cols()
        M = MatrixSpace(ZZ, nrows, ncols)
        cdef sage_Matrix_integer_dense ans = M.zero().__copy__()
        for i in range(nrows):
            for j in range(ncols):
                ans.set_unsafe_mpz(i, j, <mpz_t> pm_MatrixInteger_get(m.pm_obj, i, j).get_rep())
                                                                      ^
    ------------------------------------------------------------
    
    polymake/sage_conversion.pyx:88:67: Cannot convert 'pm_MatrixInteger' to Python object
    
    Error compiling Cython file:
    ------------------------------------------------------------
    ...
        cdef Py_ssize_t ncols = m.pm_obj.cols()
        M = MatrixSpace(ZZ, nrows, ncols)
        cdef sage_Matrix_integer_dense ans = M.zero().__copy__()
        for i in range(nrows):
            for j in range(ncols):
                ans.set_unsafe_mpz(i, j, <mpz_t> pm_MatrixInteger_get(m.pm_obj, i, j).get_rep())
                                        ^
    ------------------------------------------------------------
    
    polymake/sage_conversion.pyx:88:37: Casting temporary Python object to non-numeric non-Python type
    
    Error compiling Cython file:
    ------------------------------------------------------------
    ...
        cdef Py_ssize_t ncols = m.pm_obj.cols()
        M = MatrixSpace(QQ, nrows, ncols)
        cdef sage_Matrix_rational_dense ans = M.zero().__copy__()
        for i in range(nrows):
            for j in range(ncols):
                mpq_set(ans._matrix[i][j], <mpq_t> pm_MatrixRational_get(m.pm_obj, i, j).get_rep())
                                                                         ^
    ------------------------------------------------------------
    
    polymake/sage_conversion.pyx:99:70: Cannot convert 'pm_MatrixRational' to Python object
    
    Error compiling Cython file:
    ------------------------------------------------------------
    ...
        cdef Py_ssize_t ncols = m.pm_obj.cols()
        M = MatrixSpace(QQ, nrows, ncols)
        cdef sage_Matrix_rational_dense ans = M.zero().__copy__()
        for i in range(nrows):
            for j in range(ncols):
                mpq_set(ans._matrix[i][j], <mpq_t> pm_MatrixRational_get(m.pm_obj, i, j).get_rep())
                                          ^
    ------------------------------------------------------------
    
    polymake/sage_conversion.pyx:99:39: Casting temporary Python object to non-numeric non-Python type
    *** Rebuilding handlers and mappings ***
    Map.h                     -->  map.pxd
    Set.h                     -->  set.pxd
    Matrix.h                  -->  matrix.pxd
    QuadraticExtension.h      -->  quadratic_extension.pxd
    PowerSet.h                -->  power_set.pxd
    Vector.h                  -->  vector.pxd
    Rational.h                -->  rational.pxd
    Polynomial.h              -->  polynomial.pxd
    Integer.h                 -->  integer.pxd
    Array.h                   -->  array.pxd
    RationalFunction.h        -->  rational_function.pxd
    IncidenceMatrix.h         -->  incidence_matrix.pxd
    SparseMatrix.h            -->  sparse_matrix.pxd
    polymake/sage_conversion.pyx: cannot find cimported module '.number'
    Compiling polymake/cygmp/utils.pyx because it changed.
    Compiling polymake/perl_object.pyx because it changed.
    Compiling polymake/main.pyx because it changed.
    Compiling polymake/handlers.pyx because it changed.
    Compiling polymake/big_object.pyx because it changed.
    Compiling polymake/array.pyx because it changed.
    Compiling polymake/incidence_matrix.pyx because it changed.
    Compiling polymake/integer.pyx because it changed.
    Compiling polymake/map.pyx because it changed.
    Compiling polymake/matrix.pyx because it changed.
    Compiling polymake/polynomial.pyx because it changed.
    Compiling polymake/power_set.pyx because it changed.
    Compiling polymake/quadratic_extension.pyx because it changed.
    Compiling polymake/rational.pyx because it changed.
    Compiling polymake/rational_function.pyx because it changed.
    Compiling polymake/set.pyx because it changed.
    Compiling polymake/sparse_matrix.pyx because it changed.
    Compiling polymake/vector.pyx because it changed.
    Compiling polymake/sage_conversion.pyx because it changed.
    [ 1/19] Cythonizing polymake/array.pyx
    [ 2/19] Cythonizing polymake/big_object.pyx
    [ 3/19] Cythonizing polymake/cygmp/utils.pyx
    [ 4/19] Cythonizing polymake/handlers.pyx
    [ 5/19] Cythonizing polymake/incidence_matrix.pyx
    [ 6/19] Cythonizing polymake/integer.pyx
    [ 7/19] Cythonizing polymake/main.pyx
    [ 8/19] Cythonizing polymake/map.pyx
    [ 9/19] Cythonizing polymake/matrix.pyx
    [10/19] Cythonizing polymake/perl_object.pyx
    [11/19] Cythonizing polymake/polynomial.pyx
    [12/19] Cythonizing polymake/power_set.pyx
    [13/19] Cythonizing polymake/quadratic_extension.pyx
    [14/19] Cythonizing polymake/rational.pyx
    [15/19] Cythonizing polymake/rational_function.pyx
    [16/19] Cythonizing polymake/sage_conversion.pyx
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-gWR7u0-build/setup.py", line 141, in <module>
        cmdclass = {'build_ext': build_ext, 'test': TestCommand}
      File "/ext/sage/sage-7.6/local/lib/python/distutils/core.py", line 151, in setup
        dist.run_commands()
      File "/ext/sage/sage-7.6/local/lib/python/distutils/dist.py", line 953, in run_commands
        self.run_command(cmd)
      File "/ext/sage/sage-7.6/local/lib/python/distutils/dist.py", line 972, in run_command
        cmd_obj.run()
      File "/ext/sage/sage-7.6/local/lib/python2.7/site-packages/setuptools/command/egg_info.py", line 279, in run
        self.find_sources()
      File "/ext/sage/sage-7.6/local/lib/python2.7/site-packages/setuptools/command/egg_info.py", line 294, in find_sources
        mm.run()
      File "/ext/sage/sage-7.6/local/lib/python2.7/site-packages/setuptools/command/egg_info.py", line 521, in run
        self.add_defaults()
      File "/ext/sage/sage-7.6/local/lib/python2.7/site-packages/setuptools/command/egg_info.py", line 557, in add_defaults
        sdist.add_defaults(self)
      File "/ext/sage/sage-7.6/local/lib/python2.7/site-packages/setuptools/command/py36compat.py", line 36, in add_defaults
        self._add_defaults_ext()
      File "/ext/sage/sage-7.6/local/lib/python2.7/site-packages/setuptools/command/py36compat.py", line 119, in _add_defaults_ext
        build_ext = self.get_finalized_command('build_ext')
      File "/ext/sage/sage-7.6/local/lib/python/distutils/cmd.py", line 312, in get_finalized_command
        cmd_obj.ensure_finalized()
      File "/ext/sage/sage-7.6/local/lib/python/distutils/cmd.py", line 109, in ensure_finalized
        self.finalize_options()
      File "/tmp/pip-gWR7u0-build/setup.py", line 123, in finalize_options
        self.distribution.ext_modules, include_path=sys.path)
      File "/ext/sage/sage-7.6/local/lib/python2.7/site-packages/Cython/Build/Dependencies.py", line 934, in cythonize
        cythonize_one(*args)
      File "/ext/sage/sage-7.6/local/lib/python2.7/site-packages/Cython/Build/Dependencies.py", line 1056, in cythonize_one
        raise CompileError(None, pyx_file)
    Cython.Compiler.Errors.CompileError: polymake/sage_conversion.pyx
    
    ----------------------------------------

videlec · 2017-06-21T13:58:22Z

Thanks for the report. There was indeed some import issues could you try again

$ sage -pip install git+https://github.com/videlec/pypolymake

I tried on 8.0.beta9 (which needed an extra hack to take care of a change of datastructure of rational matrices).

haraldschilly · 2017-06-22T15:49:43Z

Now it fails right here, and indeed, I don't this this fmpq_mat in sage 7.6. Does it only work in 8.0?

    Error compiling Cython file:
    ------------------------------------------------------------
    ...
    from .cygmp.mpz cimport mpz_set
    from .cygmp.mpq cimport mpq_set
    
    from sage.ext.stdsage cimport PY_NEW
    from sage.libs.flint.fmpq cimport fmpq_set_mpq
    from sage.libs.flint.fmpq_mat cimport fmpq_mat_entry
    ^
    ------------------------------------------------------------
    
    polymake/sage_conversion.pyx:27:0: 'sage/libs/flint/fmpq_mat.pxd' not found
    
    Error compiling Cython file:
    ------------------------------------------------------------
    ...
    from .cygmp.mpz cimport mpz_set
    from .cygmp.mpq cimport mpq_set
    
    from sage.ext.stdsage cimport PY_NEW
    from sage.libs.flint.fmpq cimport fmpq_set_mpq
    from sage.libs.flint.fmpq_mat cimport fmpq_mat_entry
    ^
    ------------------------------------------------------------
    
    polymake/sage_conversion.pyx:27:0: 'sage/libs/flint/fmpq_mat/fmpq_mat_entry.pxd' not found

and

/ext/sage/sage/src/sage/libs/flint$ ls fmpq*
fmpq.pxd  fmpq_poly.pxd

videlec · 2017-06-22T16:26:40Z

Thanks for testing again. It was my bad, commit 18e87ea makes the import conditional.

haraldschilly · 2017-06-22T16:43:01Z

Better, but I have to bother you again. Now it fails with some gcc compilation error:

    polymake/perl_object.cpp: In function ‘PyObject* __pyx_f_8polymake_11perl_object_get_properties(__pyx_obj_8polymake_11perl_object_PerlObject*, int)’:
    polymake/perl_object.cpp:1600:79: error: ‘call_function’ was not declared in this scope
         __pyx_t_4 = call_function(((std::string)__pyx_t_3), (__pyx_v_p->pm_obj[0]));
                                                                                   ^
    polymake/perl_object.cpp: In function ‘PyObject* __pyx_f_8polymake_11perl_object_get_methods(__pyx_obj_8polymake_11perl_object_PerlObject*, int)’:
    polymake/perl_object.cpp:1888:79: error: ‘call_function’ was not declared in this scope
         __pyx_t_4 = call_function(((std::string)__pyx_t_3), (__pyx_v_p->pm_obj[0]));
                                                                                   ^

Logfile: https://cocalc.com/projects/14eed217-2d3c-4975-a381-b69edcb40e0e/files/scratch/pypolymake-2.log

GCC is gcc (Ubuntu 5.4.0-6ubuntu1~16.04.4) 5.4.0 20160609

videlec · 2017-06-22T18:30:59Z

Random try... I added explicitely the namespace polymake::call_function in 39b3af3.

haraldschilly · 2017-06-23T08:33:10Z

Sorry, but this leads to almost exactly the same issue:

    /ext/sage/sage-7.6/local/include/polymake/Bitset.h: In member function ‘bool pm::Bitset_iterator::at_end() const’:
    /ext/sage/sage-7.6/local/include/polymake/Bitset.h:78:22: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
                  diff==0 && !(mpz_getlimbn(bits, n) & (mp_limb_t)(-1) << (cur%bits_per_limb));
                          ^
    polymake/perl_object.cpp: In function ‘PyObject* __pyx_f_8polymake_11perl_object_get_properties(__pyx_obj_8polymake_11perl_object_PerlObject*, int)’:
    polymake/perl_object.cpp:1600:17: error: ‘call_function’ is not a member of ‘polymake’
         __pyx_t_4 = polymake::call_function(((std::string)__pyx_t_3), (__pyx_v_p->pm_obj[0]));
                     ^
    polymake/perl_object.cpp: In function ‘PyObject* __pyx_f_8polymake_11perl_object_get_methods(__pyx_obj_8polymake_11perl_object_PerlObject*, int)’:
    polymake/perl_object.cpp:1888:17: error: ‘call_function’ is not a member of ‘polymake’
         __pyx_t_4 = polymake::call_function(((std::string)__pyx_t_3), (__pyx_v_p->pm_obj[0]));
                     ^

videlec · 2017-06-23T12:12:51Z

BTW, which polymake do you have?

haraldschilly · 2017-06-23T12:29:15Z

Well, I suppose the one in Sage? Let me check, ok, I hope this helps:

salvus@4ea60463b738:/$ sage -sh
[ ... ]
Note: SAGE_ROOT=/ext/sage/sage-7.6

(sage-sh) salvus@4ea60463b738:/$ polymake --version
polymake version 3.0
Copyright (c) 1997-2015
Ewgenij Gawrilow, Michael Joswig (TU Berlin)
http://www.polymake.org

This is free software licensed under GPL; see the source for copying conditions.
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

(sage-sh) salvus@4ea60463b738:/$ which polymake
/ext/sage/sage-7.6/local/bin/polymake

videlec · 2017-06-23T12:34:18Z

That might be the source of the troubles, I have

$ ./sage -polymake --version
polymake version 3.1

It has been upgraded for 8.0.beta0. I am recompiling sage 7.6 to see whether it can be fixed.

saliola mentioned this issue Mar 7, 2017

Upgrade Polymake; install pypolymake; install Polymake kernel for Jupyter sagemathinc/cocalc#905

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videlec mentioned this issue Jun 25, 2017

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installation fails on SMC #12

installation fails on SMC #12

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installation fails on SMC #12

installation fails on SMC #12

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