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no module named crcm #408

Closed lbertolotti closed 7 years ago

lbertolotti commented 7 years ago 
lucas@lucas-K55VD:~/sfepy$ sfepy-run -v
sfepy-run 2017.2
lucas@lucas-K55VD:~/sfepy$ ./simple.py
Traceback (most recent call last):
  File "./simple.py", line 21, in <module>
    from sfepy.applications import PDESolverApp
  File "/home/lucas/sfepy/sfepy/applications/__init__.py", line 3, in <module>
    from .pde_solver_app import PDESolverApp, solve_pde, assign_standard_hooks
  File "/home/lucas/sfepy/sfepy/applications/pde_solver_app.py", line 7, in <module>
    from sfepy.discrete import Problem
  File "/home/lucas/sfepy/sfepy/discrete/__init__.py", line 9, in <module>
    from .variables import Variables, Variable, FieldVariable, create_adof_conns
  File "/home/lucas/sfepy/sfepy/discrete/variables.py", line 14, in <module>
    import sfepy.linalg as la
  File "/home/lucas/sfepy/sfepy/linalg/__init__.py", line 2, in <module>
    from .extmods.crcm import rcm, permute_in_place
ImportError: No module named crcm
rc commented 7 years ago

This happens when the extension modules in C/cython are not compiled. Did you run the following in your terminal?

$ python setup.py build_ext --inplace

or

$ make
lbertolotti commented 7 years ago

I had run "python setup.py install".

lucas@lucas-K55VD:~/sfepy$ sudo python setup.py build_ext --inplace
sympy (optional) is missing; some tests are going to fail!
igakit (optional) is missing; you may get run-time errors
petsc4py (optional) is missing; you may get run-time errors
pymetis (optional) is missing; you may get run-time errors
scikits.umfpack (optional) is missing; you may get run-time errors
/usr/local/lib/python2.7/dist-packages/setuptools/dist.py:343: UserWarning: The version specified ('2017.2-git-ff8b2712f5cbd2ce78cd2df1853884af8d543df1') is an invalid version, this may not work as expected with newer versions of setuptools, pip, and PyPI. Please see PEP 440 for more details.
  "details." % self.metadata.version
running build_ext
running build_src
build_src
building library "sfepy_common" sources
building library "sfepy_terms" sources
building extension "sfepy.discrete.common.extmods._fmfield" sources
building extension "sfepy.discrete.common.extmods.mappings" sources
building extension "sfepy.discrete.common.extmods.assemble" sources
building extension "sfepy.discrete.common.extmods.cmesh" sources
building extension "sfepy.discrete.common.extmods.crefcoors" sources
building extension "sfepy.discrete.common.extmods._geommech" sources
building extension "sfepy.discrete.fem.extmods.bases" sources
building extension "sfepy.discrete.fem.extmods.lobatto_bases" sources
building extension "sfepy.discrete.iga.extmods.igac" sources
building extension "sfepy.linalg.extmods.crcm" sources
building extension "sfepy.terms.extmods.terms" sources
building data_files sources
build_src: building npy-pkg config files
customize UnixCCompiler
customize UnixCCompiler using build_clib
customize UnixCCompiler
customize UnixCCompiler using build_ext
extending extension 'sfepy.discrete.common.extmods._fmfield' defined_macros with [('__SDIR__', '\\"sfepy/discrete/common/extmods\\"'), ('SFEPY_PLATFORM', 0), ('inline', 'inline')]
extending extension 'sfepy.discrete.common.extmods.mappings' defined_macros with [('__SDIR__', '\\"sfepy/discrete/common/extmods\\"'), ('SFEPY_PLATFORM', 0), ('inline', 'inline')]
extending extension 'sfepy.discrete.common.extmods.crefcoors' defined_macros with [('__SDIR__', '\\"sfepy/discrete/common/extmods\\"'), ('SFEPY_PLATFORM', 0), ('inline', 'inline')]
extending extension 'sfepy.discrete.common.extmods._geommech' defined_macros with [('__SDIR__', '\\"sfepy/discrete/common/extmods\\"'), ('SFEPY_PLATFORM', 0), ('inline', 'inline')]
extending extension 'sfepy.discrete.fem.extmods.bases' defined_macros with [('__SDIR__', '\\"sfepy/discrete/common/extmods\\"'), ('SFEPY_PLATFORM', 0), ('inline', 'inline')]
extending extension 'sfepy.discrete.fem.extmods.lobatto_bases' defined_macros with [('__SDIR__', '\\"sfepy/discrete/common/extmods\\"'), ('SFEPY_PLATFORM', 0), ('inline', 'inline')]
extending extension 'sfepy.terms.extmods.terms' defined_macros with [('__SDIR__', '\\"sfepy/terms/extmods\\"'), ('SFEPY_PLATFORM', 0), ('inline', 'inline'), ('__SDIR__', '\\"sfepy/discrete/common/extmods\\"')]
building 'sfepy.discrete.common.extmods._fmfield' extension
compiling C sources
C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC

compile options: '-D__SDIR__=\"sfepy/discrete/common/extmods\" -DSFEPY_PLATFORM=0 -Dinline=inline -D__SDIR__=\"sfepy/discrete/common/extmods\" -DSFEPY_PLATFORM=0 -Dinline=inline -Isfepy/discrete/common/extmods -I/usr/local/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'
extra options: '-g -O2'
x86_64-linux-gnu-gcc: sfepy/discrete/common/extmods/_fmfield.c
In file included from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from sfepy/discrete/common/extmods/_fmfield.c:435:
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/sfepy/discrete/common/extmods/_fmfield.o -Lbuild/temp.linux-x86_64-2.7 -lsfepy_common -o sfepy/discrete/common/extmods/_fmfield.so
building 'sfepy.discrete.common.extmods.mappings' extension
compiling C sources
C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC

compile options: '-D__SDIR__=\"sfepy/discrete/common/extmods\" -DSFEPY_PLATFORM=0 -Dinline=inline -D__SDIR__=\"sfepy/discrete/common/extmods\" -DSFEPY_PLATFORM=0 -Dinline=inline -Isfepy/discrete/common/extmods -I/usr/local/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'
extra options: '-g -O2'
x86_64-linux-gnu-gcc: sfepy/discrete/common/extmods/mappings.c
In file included from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from sfepy/discrete/common/extmods/mappings.c:435:
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/sfepy/discrete/common/extmods/mappings.o -Lbuild/temp.linux-x86_64-2.7 -lsfepy_common -o sfepy/discrete/common/extmods/mappings.so
building 'sfepy.discrete.common.extmods.assemble' extension
compiling C sources
C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC

compile options: '-D__SDIR__=\"sfepy/discrete/common/extmods\" -DSFEPY_PLATFORM=0 -Dinline=inline -Isfepy/discrete/common/extmods -I/usr/local/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'
extra options: '-g -O2'
x86_64-linux-gnu-gcc: sfepy/discrete/common/extmods/assemble.c
In file included from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from sfepy/discrete/common/extmods/assemble.c:435:
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/sfepy/discrete/common/extmods/assemble.o -Lbuild/temp.linux-x86_64-2.7 -o sfepy/discrete/common/extmods/assemble.so
building 'sfepy.discrete.common.extmods.cmesh' extension
compiling C sources
C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC

compile options: '-D__SDIR__=\"sfepy/discrete/common/extmods\" -DSFEPY_PLATFORM=0 -Dinline=inline -Isfepy/discrete/common/extmods -I/usr/local/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'
extra options: '-g -O2'
x86_64-linux-gnu-gcc: sfepy/discrete/common/extmods/common_python.c
x86_64-linux-gnu-gcc: sfepy/discrete/common/extmods/meshutils.c
x86_64-linux-gnu-gcc: sfepy/discrete/common/extmods/mesh.c
x86_64-linux-gnu-gcc: sfepy/discrete/common/extmods/geomtrans.c
x86_64-linux-gnu-gcc: sfepy/discrete/common/extmods/sort.c
sfepy/discrete/common/extmods/sort.c: In function ‘int32_sort_rows’:
sfepy/discrete/common/extmods/sort.c:80:70: warning: pointer targets in passing argument 6 of ‘int32_mtx_aquicksort’ differ in signedness [-Wpointer-sign]
   int32_mtx_aquicksort( array, n_row, n_col, i_sort_col, n_sort_col, perm );
                                                                      ^
In file included from sfepy/discrete/common/extmods/sort.c:18:0:
sfepy/discrete/common/extmods/sort.h:13:7: note: expected ‘intp * {aka unsigned int *}’ but argument is of type ‘int32 * {aka int *}’
 int32 int32_mtx_aquicksort( int32 *v, int32 n_row, int32 n_col,
       ^
x86_64-linux-gnu-gcc: sfepy/discrete/common/extmods/cmesh.c
In file included from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from sfepy/discrete/common/extmods/cmesh.c:435:
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/sfepy/discrete/common/extmods/cmesh.o build/temp.linux-x86_64-2.7/sfepy/discrete/common/extmods/geomtrans.o build/temp.linux-x86_64-2.7/sfepy/discrete/common/extmods/mesh.o build/temp.linux-x86_64-2.7/sfepy/discrete/common/extmods/meshutils.o build/temp.linux-x86_64-2.7/sfepy/discrete/common/extmods/sort.o build/temp.linux-x86_64-2.7/sfepy/discrete/common/extmods/common_python.o -Lbuild/temp.linux-x86_64-2.7 -o sfepy/discrete/common/extmods/cmesh.so
building 'sfepy.discrete.common.extmods.crefcoors' extension
compiling C sources
C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC

compile options: '-D__SDIR__=\"sfepy/discrete/common/extmods\" -DSFEPY_PLATFORM=0 -Dinline=inline -D__SDIR__=\"sfepy/discrete/common/extmods\" -DSFEPY_PLATFORM=0 -Dinline=inline -Isfepy/discrete/common/extmods -I/usr/local/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'
extra options: '-g -O2'
x86_64-linux-gnu-gcc: sfepy/discrete/common/extmods/refcoors.c
x86_64-linux-gnu-gcc: sfepy/discrete/common/extmods/mesh.c
x86_64-linux-gnu-gcc: sfepy/discrete/common/extmods/geomtrans.c
x86_64-linux-gnu-gcc: sfepy/discrete/common/extmods/crefcoors.c
In file included from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from sfepy/discrete/common/extmods/crefcoors.c:435:
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/sfepy/discrete/common/extmods/crefcoors.o build/temp.linux-x86_64-2.7/sfepy/discrete/common/extmods/refcoors.o build/temp.linux-x86_64-2.7/sfepy/discrete/common/extmods/geomtrans.o build/temp.linux-x86_64-2.7/sfepy/discrete/common/extmods/mesh.o -Lbuild/temp.linux-x86_64-2.7 -lsfepy_common -o sfepy/discrete/common/extmods/crefcoors.so
building 'sfepy.discrete.common.extmods._geommech' extension
compiling C sources
C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC

compile options: '-D__SDIR__=\"sfepy/discrete/common/extmods\" -DSFEPY_PLATFORM=0 -Dinline=inline -D__SDIR__=\"sfepy/discrete/common/extmods\" -DSFEPY_PLATFORM=0 -Dinline=inline -Isfepy/discrete/common/extmods -I/usr/local/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'
extra options: '-g -O2'
x86_64-linux-gnu-gcc: sfepy/discrete/common/extmods/_geommech.c
In file included from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from sfepy/discrete/common/extmods/_geommech.c:435:
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/sfepy/discrete/common/extmods/_geommech.o -Lbuild/temp.linux-x86_64-2.7 -lsfepy_common -o sfepy/discrete/common/extmods/_geommech.so
building 'sfepy.discrete.fem.extmods.bases' extension
compiling C sources
C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC

compile options: '-D__SDIR__=\"sfepy/discrete/fem/extmods\" -DSFEPY_PLATFORM=0 -Dinline=inline -D__SDIR__=\"sfepy/discrete/common/extmods\" -DSFEPY_PLATFORM=0 -Dinline=inline -Isfepy/discrete/fem/extmods -Isfepy/discrete/common/extmods -I/usr/local/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'
extra options: '-g -O2'
x86_64-linux-gnu-gcc: sfepy/discrete/fem/extmods/lagrange.c
<command-line>:0:0: warning: "__SDIR__" redefined
<command-line>:0:0: note: this is the location of the previous definition
x86_64-linux-gnu-gcc: sfepy/discrete/fem/extmods/bases.c
<command-line>:0:0: warning: "__SDIR__" redefined
<command-line>:0:0: note: this is the location of the previous definition
In file included from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from sfepy/discrete/fem/extmods/bases.c:435:
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/sfepy/discrete/fem/extmods/bases.o build/temp.linux-x86_64-2.7/sfepy/discrete/fem/extmods/lagrange.o -Lbuild/temp.linux-x86_64-2.7 -lsfepy_common -o sfepy/discrete/fem/extmods/bases.so
building 'sfepy.discrete.fem.extmods.lobatto_bases' extension
compiling C sources
C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC

compile options: '-D__SDIR__=\"sfepy/discrete/fem/extmods\" -DSFEPY_PLATFORM=0 -Dinline=inline -D__SDIR__=\"sfepy/discrete/common/extmods\" -DSFEPY_PLATFORM=0 -Dinline=inline -Isfepy/discrete/fem/extmods -Isfepy/discrete/common/extmods -I/usr/local/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'
extra options: '-g -O2'
x86_64-linux-gnu-gcc: sfepy/discrete/fem/extmods/lobatto1d.c
<command-line>:0:0: warning: "__SDIR__" redefined
<command-line>:0:0: note: this is the location of the previous definition
x86_64-linux-gnu-gcc: sfepy/discrete/fem/extmods/lobatto.c
<command-line>:0:0: warning: "__SDIR__" redefined
<command-line>:0:0: note: this is the location of the previous definition
x86_64-linux-gnu-gcc: sfepy/discrete/fem/extmods/lobatto_bases.c
<command-line>:0:0: warning: "__SDIR__" redefined
<command-line>:0:0: note: this is the location of the previous definition
In file included from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from sfepy/discrete/fem/extmods/lobatto_bases.c:435:
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/sfepy/discrete/fem/extmods/lobatto_bases.o build/temp.linux-x86_64-2.7/sfepy/discrete/fem/extmods/lobatto.o build/temp.linux-x86_64-2.7/sfepy/discrete/fem/extmods/lobatto1d.o -Lbuild/temp.linux-x86_64-2.7 -lsfepy_common -o sfepy/discrete/fem/extmods/lobatto_bases.so
building 'sfepy.discrete.iga.extmods.igac' extension
compiling C sources
C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC

compile options: '-D__SDIR__=\"sfepy/discrete/iga/extmods\" -DSFEPY_PLATFORM=0 -Dinline=inline -Isfepy/discrete/iga/extmods -Isfepy/discrete/common/extmods -I/usr/local/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'
extra options: '-g -O2'
x86_64-linux-gnu-gcc: sfepy/discrete/iga/extmods/igac.c
In file included from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from sfepy/discrete/iga/extmods/igac.c:435:
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
x86_64-linux-gnu-gcc: sfepy/discrete/common/extmods/fmfield.c
x86_64-linux-gnu-gcc: sfepy/discrete/common/extmods/common_python.c
x86_64-linux-gnu-gcc: sfepy/discrete/iga/extmods/nurbs.c
x86_64-linux-gnu-gcc: sfepy/discrete/common/extmods/geommech.c
sfepy/discrete/common/extmods/geommech.c: In function ‘geme_mulAVSB3’:
sfepy/discrete/common/extmods/geommech.c:400:31: warning: variable ‘sym’ set but not used [-Wunused-but-set-variable]
   int32 iqp, ir, ic, ii, dim, sym, nQP, nc;
                               ^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/sfepy/discrete/iga/extmods/igac.o build/temp.linux-x86_64-2.7/sfepy/discrete/iga/extmods/nurbs.o build/temp.linux-x86_64-2.7/sfepy/discrete/common/extmods/fmfield.o build/temp.linux-x86_64-2.7/sfepy/discrete/common/extmods/geommech.o build/temp.linux-x86_64-2.7/sfepy/discrete/common/extmods/common_python.o -Lbuild/temp.linux-x86_64-2.7 -o sfepy/discrete/iga/extmods/igac.so
building 'sfepy.linalg.extmods.crcm' extension
compiling C sources
C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC

compile options: '-D__SDIR__=\"sfepy/linalg/extmods\" -DSFEPY_PLATFORM=0 -Dinline=inline -Isfepy/linalg/extmods -Isfepy/discrete/common/extmods -I/usr/local/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'
extra options: '-g -O2'
x86_64-linux-gnu-gcc: sfepy/linalg/extmods/crcm.c
In file included from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from sfepy/linalg/extmods/crcm.c:435:
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
x86_64-linux-gnu-gcc: sfepy/linalg/extmods/rcm.c
x86_64-linux-gnu-gcc: sfepy/discrete/common/extmods/common_python.c
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/sfepy/linalg/extmods/crcm.o build/temp.linux-x86_64-2.7/sfepy/linalg/extmods/rcm.o build/temp.linux-x86_64-2.7/sfepy/discrete/common/extmods/common_python.o -Lbuild/temp.linux-x86_64-2.7 -o sfepy/linalg/extmods/crcm.so
building 'sfepy.terms.extmods.terms' extension
compiling C sources
C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC

compile options: '-D__SDIR__=\"sfepy/terms/extmods\" -DSFEPY_PLATFORM=0 -Dinline=inline -D__SDIR__=\"sfepy/terms/extmods\" -DSFEPY_PLATFORM=0 -Dinline=inline -D__SDIR__=\"sfepy/discrete/common/extmods\" -Isfepy/terms/extmods -Isfepy/discrete/common/extmods -I/usr/local/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'
extra options: '-g -O2'
x86_64-linux-gnu-gcc: sfepy/terms/extmods/terms.c
<command-line>:0:0: warning: "__SDIR__" redefined
<command-line>:0:0: note: this is the location of the previous definition
In file included from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from sfepy/terms/extmods/terms.c:435:
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/sfepy/terms/extmods/terms.o -Lbuild/temp.linux-x86_64-2.7 -lsfepy_terms -lsfepy_common -o sfepy/terms/extmods/terms.so

Required and optional packages found:

cython is available in version 0.25.2
numpy is available in version 1.13.0
scipy is available in version 0.19.0
matplotlib is available in version 2.0.2
pyparsing is available in version 2.2.0
tables is available in version 3.4.2
mayavi (optional) is available in version 4.5.0
sympy (optional) is missing; some tests are going to fail!
igakit (optional) is missing; you may get run-time errors
petsc4py (optional) is missing; you may get run-time errors
mpi4py (optional) is available in version 1.3.1
pymetis (optional) is missing; you may get run-time errors
scikits.umfpack (optional) is missing; you may get run-time errors
pysparse (optional) is available in version 1.1
lucas@lucas-K55VD:~/sfepy$ ./simple.py
usage: simple.py [-h] [--version] [--debug] [-c "key : value, ..."]
                 [-O "key : value, ..."] [-d "key : value, ..."] [-o filename]
                 [--format format] [--save-restart mode]
                 [--load-restart filename] [--log file] [-q] [--save-ebc]
                 [--save-ebc-nodes] [--save-regions]
                 [--save-regions-as-groups] [--save-field-meshes]
                 [--solve-not] [--list what]
                 [filename_in]
simple.py: error: one of the arguments --list filename_in is required
lucas@lucas-K55VD:~/sfepy$ ./simple.py examples/diffusion/poisson_short_syntax.py
sfepy: left over: ['verbose', '__builtins__', 'absolute_import', '__file__', '__doc__', '__name__', 'data_dir', '__package__', '_filename']
sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] (/home/lucas/sfepy/meshes/3d/cylinder.mesh)...
sfepy: ...done in 0.01 s
sfepy: creating regions...
sfepy:     Gamma_Right
sfepy:     Omega
sfepy:     Gamma_Left
sfepy: ...done in 0.07 s
sfepy: equation "Temperature":
sfepy: dw_laplace.i.Omega( coef.val, s, t ) = 0
sfepy: using solvers:
                ts: no ts
               nls: newton
                ls: ls
sfepy: updating variables...
sfepy: ...done
sfepy: setting up dof connectivities...
sfepy: ...done in 0.00 s
sfepy: matrix shape: (300, 300)
sfepy: assembling matrix graph...
sfepy: ...done in 0.00 s
sfepy: matrix structural nonzeros: 3538 (3.93e-02% fill)
sfepy: updating materials...
sfepy:     coef
sfepy: ...done in 0.04 s
sfepy: nls: iter: 0, residual: 1.176265e-01 (rel: 1.000000e+00)
sfepy:   rezidual:    0.01 [s]
sfepy:      solve:    0.11 [s]
sfepy:     matrix:    0.00 [s]
sfepy: nls: iter: 1, residual: 1.905741e-16 (rel: 1.620162e-15)

I this expected?


lucas@lucas-K55VD:~/sfepy$ ./postproc.py cylinder.vtk
********************************************************************************
WARNING: Imported VTK version (6.2) does not match the one used
         to build the TVTK classes (5.1). This may cause problems.
         Please rebuild TVTK.
********************************************************************************

sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] (cylinder.vtk)...
sfepy: ...done in 0.02 s
Segmentation fault (core dumped)
rc commented 7 years ago

On 06/21/2017 08:10 PM, lbertolotti wrote:

I had run "python setup.py install".

This installs sfepy system-wide, but in order to use the sfepy from its source directory, you need to use the in-place build.

lucas@lucas-K55VD:~/sfepy$ ./simple.py usage: simple.py [-h] [--version] [--debug] [-c "key : value, ..."] [-O "key : value, ..."] [-d "key : value, ..."] [-o filename] [--format format] [--save-restart mode] [--load-restart filename] [--log file] [-q] [--save-ebc] [--save-ebc-nodes] [--save-regions] [--save-regions-as-groups] [--save-field-meshes] [--solve-not] [--list what] [filename_in] simple.py: error: one of the arguments --list filename_in is required lucas@lucas-K55VD:~/sfepy$ ./simple.py examples/diffusion/poisson_short_syntax.py sfepy: left over: ['verbose', 'builtins', 'absolute_import', 'file', 'doc', 'name', 'data_dir', 'package', '_filename'] sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] (/home/lucas/sfepy/meshes/3d/cylinder.mesh)... sfepy: ...done in 0.01 s sfepy: creating regions... sfepy: Gamma_Right sfepy: Omega sfepy: Gamma_Left sfepy: ...done in 0.07 s sfepy: equation "Temperature": sfepy: dw_laplace.i.Omega( coef.val, s, t ) = 0 sfepy: using solvers: ts: no ts nls: newton ls: ls sfepy: updating variables... sfepy: ...done sfepy: setting up dof connectivities... sfepy: ...done in 0.00 s sfepy: matrix shape: (300, 300) sfepy: assembling matrix graph... sfepy: ...done in 0.00 s sfepy: matrix structural nonzeros: 3538 (3.93e-02% fill) sfepy: updating materials... sfepy: coef sfepy: ...done in 0.04 s sfepy: nls: iter: 0, residual: 1.176265e-01 (rel: 1.000000e+00) sfepy: rezidual: 0.01 [s] sfepy: solve: 0.11 [s] sfepy: matrix: 0.00 [s] sfepy: nls: iter: 1, residual: 1.905741e-16 (rel: 1.620162e-15)


I this expected?

Yes, this is what you should see - the solution was saved correctly into cylinder.vtk


lucas@lucas-K55VD:~/sfepy$ ./postproc.py cylinder.vtk
********************************************************************************
WARNING: Imported VTK version (6.2) does not match the one used
          to build the TVTK classes (5.1). This may cause problems.
          Please rebuild TVTK.
********************************************************************************

sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] (cylinder.vtk)...
sfepy: ...done in 0.02 s
Segmentation fault (core dumped)

This looks like a problem with your mayavi/VTK installation. If you are unable to resolve that, try another VTK visualization software, for example paraview.

lbertolotti commented 7 years ago

This looks like a problem with your mayavi/VTK installation. If you are unable to resolve that, try another VTK visualization software, for example paraview.

This fault is due to VTK.

lucas@lucas-K55VD:~/sfepy$ ./postproc.py cylinder.vtk
sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] (cylinder.vtk)...
sfepy: ...done in 0.02 s
sfepy: point scalars t at [-0.05 -0.02  0.  ]
sfepy: range: -2.00e+00 2.00e+00 l2 norm range: 1.06e-02 2.00e+00

cylinder