Open videlec opened 7 years ago
saliola
commented
7 years ago 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
commented
7 years ago Could you try with
$ sage -f polymake
$ sage -pip install git+https://github.com/videlec/pypolymakeAnd also give access to the full log.
saliola
commented
7 years ago 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/smc#905.
haraldschilly
commented
7 years ago 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
----------------------------------------Thanks for the report. There was indeed some import issues could you try again
$ sage -pip install git+https://github.com/videlec/pypolymakeI tried on 8.0.beta9 (which needed an extra hack to take care of a change of datastructure of rational matrices).
haraldschilly
commented
7 years ago 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 foundand
/ext/sage/sage/src/sage/libs/flint$ ls fmpq*
fmpq.pxd fmpq_poly.pxdThanks for testing again. It was my bad, commit 18e87ea makes the import conditional.
haraldschilly
commented
7 years ago 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
commented
7 years ago Random try... I added explicitely the namespace polymake::call_function in 39b3af3.
haraldschilly
commented
7 years ago 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]));
^
BTW, which polymake do you have?
haraldschilly
commented
7 years ago 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
That might be the source of the troubles, I have
$ ./sage -polymake --version
polymake version 3.1It has been upgraded for 8.0.beta0. I am recompiling sage 7.6 to see whether it can be fixed.
Problems on SageMath cloud sagemathinc/smc#905