Build error in sfepy/linalg/extmods and possible fix to sfepy/linalg/extmods/setup.py
Hi,
I just did a git pull from [1]. I was getting the following build error (see (1) below) using the "distutils" method. It seems to be due to missing paths to sfepy/fem/extmods/* in sfepy/linalg/extmods, so I followed the example of sfepy/terms/extmods to put in the missing paths. This is available from [2] (it's on the master branch, should I have made a new branch for this?). It's a pretty quick fix to get the build to work, so I wouldn't be surprised if I'm overlooking something. :)
After putting in the fix, I'm getting a test failure in tests/test_permutations.py (see (2)). I figure I missed something else in the distutils configuration. The "make" build method works before and after the fix.
I know sfepy/linalg is new, so probably everything isn't in place for distutils building yet, but I thought I could at least help get the build working again. :)
Thanks! Logan
[1] git://git.sympy.org/sfepy.git [2] git://github.com/logansorenson/electrostatic_structural_test.git
(1) logan@quantumdot:~/phoenix/projects/sfepy$ python setup.py build_ext --inplace
['sfepy', '/home/logan/phoenix/projects/sfepy/sfepy', '/home/logan/phoenix/projects/sfepy', '/home/logan/phoenix/projects/sfepy', '/usr/lib/python2.5/site-packages/numpydoc-0.2-py2.5.egg', '/usr/lib/python2.5/site-packages/scikits.umfpack-5.1.0-py2.5-linux-i686.egg', '/usr/lib/python2.5', '/usr/lib/python2.5/plat-linux2', '/usr/lib/python2.5/lib-tk', '/usr/lib/python2.5/lib-dynload', '/usr/local/lib/python2.5/site-packages', '/usr/lib/python2.5/site-packages', '/usr/lib/python2.5/site-packages/Numeric', '/usr/lib/python2.5/site-packages/PIL', '/usr/lib/python2.5/site-packages/gst-0.10', '/usr/lib/pymodules/python2.5', '/usr/lib/pymodules/python2.5/gtk-2.0', '/usr/lib/python2.5/site-packages/wx-2.8-gtk2-unicode']
non-existing path in 'sfepy/linalg/extmods': 'common_python.c'
non-existing path in 'sfepy/linalg/extmods': 'array.i'
non-existing path in 'sfepy/linalg/extmods': 'common.i'
<snip>
building extension "sfepy.linalg.extmods._rcm" sources swig: sfepy/linalg/extmods/rcm.i swig -python -Isfepy/linalg/extmods -o sfepy/linalg/extmods/rcm_wrap.c -outdir sfepy/linalg/extmods sfepy/linalg/extmods/rcm.i sfepy/linalg/extmods/rcm.i:9: Error: Unable to find 'types.h' sfepy/linalg/extmods/rcm.i:11: Error: Unable to find 'common.i' sfepy/linalg/extmods/rcm.i:12: Error: Unable to find 'array.i' error: command 'swig' failed with exit status 1
(2) tests/test_permutations.py
--- test_rcm: failed!
test instance prepared (1 test(s)) <type 'exceptions.ImportError'> Traceback (most recent call last): File "./runTests.py", line 226, in <module> main() File "./runTests.py", line 217, in main run_tests(stats, dirname, [filename]) File "./runTests.py", line 148, in run_tests n_fail, n_total, test_time = run_test( conf_name, options ) File "./runTests.py", line 111, in run_test ok, n_fail, n_total = test.run( options.debug ) File "/home/logan/phoenix/projects/sfepy/sfepy/base/testing.py", line 38, in run ret = test_method() File "tests/test_permutations.py", line 11, in test_rcm from sfepy.linalg import rcm, permute_in_place, save_sparse_txt File "/home/logan/phoenix/projects/sfepy/sfepy/linalg/__init__.py", line 1, in <module> from extmods.rcm import rcm, permute_in_place File "/home/logan/phoenix/projects/sfepy/sfepy/linalg/extmods/rcm.py",
logan@quantumdot:~/phoenix/projects/sfepy$ ./runTests.py --debug tests/test_permutations.py <<< directory: tests, test files: 1 <<< tests/test_permutations.py sfepy: left over: ['__builtins__', '_filename', '__file__', 'TestCommon', '__name__', 'assert_', '__doc__', 'op'] line 28, in <module> import _rcm ImportError: /home/logan/phoenix/projects/sfepy/sfepy/linalg/extmods/_rcm.so: undefined symbol: g_error
Hi!
Logan Sorenson wrote:
Hi,
I just did a git pull from [1]. I was getting the following build error (see (1) below) using the "distutils" method. It seems to be due to missing paths to sfepy/fem/extmods/* in sfepy/linalg/extmods, so I followed the example of sfepy/terms/extmods to put in the missing paths. This is available from [2] (it's on the master branch, should I have made a new branch for this?). It's a pretty quick fix to get the build to work, so I wouldn't be surprised if I'm overlooking something. :)
Whoops, sorry about that - I had this already working, but pushed only to my github site, not the master site...
After putting in the fix, I'm getting a test failure in tests/test_permutations.py (see (2)). I figure I missed something else in the distutils configuration. The "make" build method works before and after the fix.
I know sfepy/linalg is new, so probably everything isn't in place for distutils building yet, but I thought I could at least help get the build working again. :)
Yes, that was the case. The master branch now passes all the tests no matter how you build it (make, or python setup.py build_ext --inplace). I have also fixed some ViewerGUI issues pointed out by Vladimir.
Sorry for the trouble :) r.
[1] git://git.sympy.org/sfepy.git [2] git://github.com/logansorenson/electrostatic_structural_test.git
(1) logan@quantumdot:~/phoenix/projects/sfepy$ python setup.py build_ext --inplace
['sfepy', '/home/logan/phoenix/projects/sfepy/sfepy', '/home/logan/phoenix/projects/sfepy', '/home/logan/phoenix/projects/sfepy', '/usr/lib/python2.5/site-packages/numpydoc-0.2-py2.5.egg', '/usr/lib/python2.5/site-packages/scikits.umfpack-5.1.0-py2.5-linux-i686.egg', '/usr/lib/python2.5', '/usr/lib/python2.5/plat-linux2', '/usr/lib/python2.5/lib-tk', '/usr/lib/python2.5/lib-dynload', '/usr/local/lib/python2.5/site-packages', '/usr/lib/python2.5/site-packages', '/usr/lib/python2.5/site-packages/Numeric', '/usr/lib/python2.5/site-packages/PIL', '/usr/lib/python2.5/site-packages/gst-0.10', '/usr/lib/pymodules/python2.5', '/usr/lib/pymodules/python2.5/gtk-2.0', '/usr/lib/python2.5/site-packages/wx-2.8-gtk2-unicode']
non-existing path in 'sfepy/linalg/extmods': 'common_python.c'
non-existing path in 'sfepy/linalg/extmods': 'array.i'
non-existing path in 'sfepy/linalg/extmods': 'common.i'
<snip>
building extension "sfepy.linalg.extmods._rcm" sources swig: sfepy/linalg/extmods/rcm.i swig -python -Isfepy/linalg/extmods -o sfepy/linalg/extmods/rcm_wrap.c -outdir sfepy/linalg/extmods sfepy/linalg/extmods/rcm.i sfepy/linalg/extmods/rcm.i:9: Error: Unable to find 'types.h' sfepy/linalg/extmods/rcm.i:11: Error: Unable to find 'common.i' sfepy/linalg/extmods/rcm.i:12: Error: Unable to find 'array.i' error: command 'swig' failed with exit status 1
(2) tests/test_permutations.py
--- test_rcm: failed!
test instance prepared (1 test(s)) <type 'exceptions.ImportError'> Traceback (most recent call last): File "./runTests.py", line 226, in <module> main() File "./runTests.py", line 217, in main run_tests(stats, dirname, [filename]) File "./runTests.py", line 148, in run_tests n_fail, n_total, test_time = run_test( conf_name, options ) File "./runTests.py", line 111, in run_test ok, n_fail, n_total = test.run( options.debug ) File "/home/logan/phoenix/projects/sfepy/sfepy/base/testing.py", line 38, in run ret = test_method() File "tests/test_permutations.py", line 11, in test_rcm from sfepy.linalg import rcm, permute_in_place, save_sparse_txt File "/home/logan/phoenix/projects/sfepy/sfepy/linalg/__init__.py", line 1, in <module> from extmods.rcm import rcm, permute_in_place File "/home/logan/phoenix/projects/sfepy/sfepy/linalg/extmods/rcm.py",
logan@quantumdot:~/phoenix/projects/sfepy$ ./runTests.py --debug tests/test_permutations.py <<< directory: tests, test files: 1 <<< tests/test_permutations.py sfepy: left over: ['__builtins__', '_filename', '__file__', 'TestCommon', '__name__', 'assert_', '__doc__', 'op'] line 28, in <module> import _rcm ImportError: /home/logan/phoenix/projects/sfepy/sfepy/linalg/extmods/_rcm.so: undefined symbol: g_error
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Hi Robert,
On Fri, Nov 20, 2009 at 4:13 AM, Robert Cimrman <cimr...@ntc.zcu.cz> wrote:
Hi!
Logan Sorenson wrote:
Hi,
I just did a git pull from [1]. I was getting the following build error (see (1) below) using the "distutils" method. It seems to be due to missing paths to sfepy/fem/extmods/* in sfepy/linalg/extmods, so I followed the example of sfepy/terms/extmods to put in the missing paths. This is available from [2] (it's on the master branch, should I have made a new branch for this?). It's a pretty quick fix to get the build to work, so I wouldn't be surprised if I'm overlooking something. :)
Whoops, sorry about that - I had this already working, but pushed only to my github site, not the master site...
Oh, ok, no worries then! :)
After putting in the fix, I'm getting a test failure in tests/test_permutations.py (see (2)). I figure I missed something else in the distutils configuration. The "make" build method works before and after the fix.
I know sfepy/linalg is new, so probably everything isn't in place for distutils building yet, but I thought I could at least help get the build working again. :)
Yes, that was the case. The master branch now passes all the tests no matter how you build it (make, or python setup.py build_ext --inplace). I have also fixed some ViewerGUI issues pointed out by Vladimir.
Sorry for the trouble :) r.
No trouble, I was treating it as a debugging exercise. :)
Thanks! Logan
[1] git://git.sympy.org/sfepy.git [2] git://github.com/logansorenson/electrostatic_structural_test.git
(1) logan@quantumdot:~/phoenix/projects/sfepy$ python setup.py build_ext --inplace
['sfepy', '/home/logan/phoenix/projects/sfepy/sfepy', '/home/logan/phoenix/projects/sfepy', '/home/logan/phoenix/projects/sfepy', '/usr/lib/python2.5/site-packages/numpydoc-0.2-py2.5.egg', '/usr/lib/python2.5/site-packages/scikits.umfpack-5.1.0-py2.5-linux-i686.egg', '/usr/lib/python2.5', '/usr/lib/python2.5/plat-linux2', '/usr/lib/python2.5/lib-tk', '/usr/lib/python2.5/lib-dynload', '/usr/local/lib/python2.5/site-packages', '/usr/lib/python2.5/site-packages', '/usr/lib/python2.5/site-packages/Numeric', '/usr/lib/python2.5/site-packages/PIL', '/usr/lib/python2.5/site-packages/gst-0.10', '/usr/lib/pymodules/python2.5', '/usr/lib/pymodules/python2.5/gtk-2.0', '/usr/lib/python2.5/site-packages/wx-2.8-gtk2-unicode']
non-existing path in 'sfepy/linalg/extmods': 'common_python.c'
non-existing path in 'sfepy/linalg/extmods': 'array.i'
non-existing path in 'sfepy/linalg/extmods': 'common.i'
<snip>
building extension "sfepy.linalg.extmods._rcm" sources swig: sfepy/linalg/extmods/rcm.i swig -python -Isfepy/linalg/extmods -o sfepy/linalg/extmods/rcm_wrap.c -outdir sfepy/linalg/extmods sfepy/linalg/extmods/rcm.i sfepy/linalg/extmods/rcm.i:9: Error: Unable to find 'types.h' sfepy/linalg/extmods/rcm.i:11: Error: Unable to find 'common.i' sfepy/linalg/extmods/rcm.i:12: Error: Unable to find 'array.i' error: command 'swig' failed with exit status 1
(2) tests/test_permutations.py
--- test_rcm: failed!
test instance prepared (1 test(s)) <type 'exceptions.ImportError'> Traceback (most recent call last): File "./runTests.py", line 226, in <module> main() File "./runTests.py", line 217, in main run_tests(stats, dirname, [filename]) File "./runTests.py", line 148, in run_tests n_fail, n_total, test_time = run_test( conf_name, options ) File "./runTests.py", line 111, in run_test ok, n_fail, n_total = test.run( options.debug ) File "/home/logan/phoenix/projects/sfepy/sfepy/base/testing.py", line 38, in run ret = test_method() File "tests/test_permutations.py", line 11, in test_rcm from sfepy.linalg import rcm, permute_in_place, save_sparse_txt File "/home/logan/phoenix/projects/sfepy/sfepy/linalg/__init__.py", line 1, in <module> from extmods.rcm import rcm, permute_in_place File "/home/logan/phoenix/projects/sfepy/sfepy/linalg/extmods/rcm.py",
logan@quantumdot:~/phoenix/projects/sfepy$ ./runTests.py --debug tests/test_permutations.py <<< directory: tests, test files: 1 <<< tests/test_permutations.py sfepy: left over: ['__builtins__', '_filename', '__file__', 'TestCommon', '__name__', 'assert_', '__doc__', 'op'] line 28, in <module> import _rcm ImportError: /home/logan/phoenix/projects/sfepy/sfepy/linalg/extmods/_rcm.so: undefined symbol: g_error
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participants (2)
-
Logan Sorenson -
Robert Cimrman