sieve-dev FIAT import question

Tue Mar 25 08:47:10 CDT 2008

On Tue 2008-03-25 08:24, Matthew Knepley wrote:
> On Tue, Mar 25, 2008 at 7:22 AM, Jed Brown <jed at 59a2.org> wrote:
> > When I try to build the sieve examples, I get errors like the one below.  If I
> >  move the `import FIAT.shapes' up to the top of the file, it works just fine.  I
> >  don't know if there is something peculiar about my configuration, but this
> >  problem hasn't gone away in the last weeks so I thought I'd mention it.  My
> >  configuration included the options:
> 
> Do you have numpy in a weird place? You are the first to report this
> error, and I
> am not sure sure how moving an import would matter, but evidently on your
> system it does somehow. In order to debug it, I need to know how you installed
> numpy.

No, it is in /usr/lib/python2.5/site-packages/numpy/.  I see the same problem on
two systems, an x86 Ubuntu system with numpy installed via apt and an x86_64
Archlinux system with numpy built from source and installed with package
manager.  I have PYTHONPATH=/home/jed/usr/lib/python2.5/site-packages because
that is where I installed FIAT and other fenics packages.  What exactly is the
build system trying to do in this case?  As noted above, when I just import FIAT
at the top instead of in run(), everything works fine.  Since this modification
is easy, if it doesn't affect any one else, no problem, but these systems are
really quite standard so I'm surprised it hasn't popped up.  I have attached
verbose output from my python session.

Jed
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Script started on Tue 25 Mar 2008 02:45:17 PM CET
k\14:45[;1m[35m[;0m [33mjed[31mbrakk[36m10 [32m~[0m$ python -v
# installing zipimport hook
import zipimport # builtin
# installed zipimport hook
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Python 2.5.2 (r252:60911, Feb 23 2008, 21:07:14) 
[GCC 4.2.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
dlopen("/usr/lib/python2.5/lib-dynload/readline.so", 2);
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>>> import numpy
import numpy # directory /usr/lib/python2.5/site-packages/numpy
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import numpy # precompiled from /usr/lib/python2.5/site-packages/numpy/__init__.pyc
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dlopen("/usr/lib/python2.5/site-packages/numpy/lib/_compiled_base.so", 2);
import numpy.lib._compiled_base # dynamically loaded from /usr/lib/python2.5/site-packages/numpy/lib/_compiled_base.so
# /usr/lib/python2.5/site-packages/numpy/lib/arraysetops.pyc matches /usr/lib/python2.5/site-packages/numpy/lib/arraysetops.py
import numpy.lib.arraysetops # precompiled from /usr/lib/python2.5/site-packages/numpy/lib/arraysetops.pyc
# /usr/lib/python2.5/site-packages/numpy/lib/scimath.pyc matches /usr/lib/python2.5/site-packages/numpy/lib/scimath.py
import numpy.lib.scimath # precompiled from /usr/lib/python2.5/site-packages/numpy/lib/scimath.pyc
# /usr/lib/python2.5/site-packages/numpy/lib/polynomial.pyc matches /usr/lib/python2.5/site-packages/numpy/lib/polynomial.py
import numpy.lib.polynomial # precompiled from /usr/lib/python2.5/site-packages/numpy/lib/polynomial.pyc
# /usr/lib/python2.5/site-packages/numpy/lib/getlimits.pyc matches /usr/lib/python2.5/site-packages/numpy/lib/getlimits.py
import numpy.lib.getlimits # precompiled from /usr/lib/python2.5/site-packages/numpy/lib/getlimits.pyc
# /usr/lib/python2.5/site-packages/numpy/lib/machar.pyc matches /usr/lib/python2.5/site-packages/numpy/lib/machar.py
import numpy.lib.machar # precompiled from /usr/lib/python2.5/site-packages/numpy/lib/machar.pyc
# /usr/lib/python2.5/site-packages/numpy/lib/utils.pyc matches /usr/lib/python2.5/site-packages/numpy/lib/utils.py
import numpy.lib.utils # precompiled from /usr/lib/python2.5/site-packages/numpy/lib/utils.pyc
# /usr/lib/python2.5/inspect.pyc matches /usr/lib/python2.5/inspect.py
import inspect # precompiled from /usr/lib/python2.5/inspect.pyc
# /usr/lib/python2.5/dis.pyc matches /usr/lib/python2.5/dis.py
import dis # precompiled from /usr/lib/python2.5/dis.pyc
# /usr/lib/python2.5/opcode.pyc matches /usr/lib/python2.5/opcode.py
import opcode # precompiled from /usr/lib/python2.5/opcode.pyc
# /usr/lib/python2.5/tokenize.pyc matches /usr/lib/python2.5/tokenize.py
import tokenize # precompiled from /usr/lib/python2.5/tokenize.pyc
# /usr/lib/python2.5/token.pyc matches /usr/lib/python2.5/token.py
import token # precompiled from /usr/lib/python2.5/token.pyc
import numpy.linalg # directory /usr/lib/python2.5/site-packages/numpy/linalg
# /usr/lib/python2.5/site-packages/numpy/linalg/__init__.pyc matches /usr/lib/python2.5/site-packages/numpy/linalg/__init__.py
import numpy.linalg # precompiled from /usr/lib/python2.5/site-packages/numpy/linalg/__init__.pyc
# /usr/lib/python2.5/site-packages/numpy/linalg/info.pyc matches /usr/lib/python2.5/site-packages/numpy/linalg/info.py
import numpy.linalg.info # precompiled from /usr/lib/python2.5/site-packages/numpy/linalg/info.pyc
# /usr/lib/python2.5/site-packages/numpy/linalg/linalg.pyc matches /usr/lib/python2.5/site-packages/numpy/linalg/linalg.py
import numpy.linalg.linalg # precompiled from /usr/lib/python2.5/site-packages/numpy/linalg/linalg.pyc
dlopen("/usr/lib/python2.5/site-packages/numpy/linalg/lapack_lite.so", 2);
import numpy.linalg.lapack_lite # dynamically loaded from /usr/lib/python2.5/site-packages/numpy/linalg/lapack_lite.so
import numpy.fft # directory /usr/lib/python2.5/site-packages/numpy/fft
# /usr/lib/python2.5/site-packages/numpy/fft/__init__.pyc matches /usr/lib/python2.5/site-packages/numpy/fft/__init__.py
import numpy.fft # precompiled from /usr/lib/python2.5/site-packages/numpy/fft/__init__.pyc
# /usr/lib/python2.5/site-packages/numpy/fft/info.pyc matches /usr/lib/python2.5/site-packages/numpy/fft/info.py
import numpy.fft.info # precompiled from /usr/lib/python2.5/site-packages/numpy/fft/info.pyc
# /usr/lib/python2.5/site-packages/numpy/fft/fftpack.pyc matches /usr/lib/python2.5/site-packages/numpy/fft/fftpack.py
import numpy.fft.fftpack # precompiled from /usr/lib/python2.5/site-packages/numpy/fft/fftpack.pyc
dlopen("/usr/lib/python2.5/site-packages/numpy/fft/fftpack_lite.so", 2);
import numpy.fft.fftpack_lite # dynamically loaded from /usr/lib/python2.5/site-packages/numpy/fft/fftpack_lite.so
# /usr/lib/python2.5/site-packages/numpy/fft/helper.pyc matches /usr/lib/python2.5/site-packages/numpy/fft/helper.py
import numpy.fft.helper # precompiled from /usr/lib/python2.5/site-packages/numpy/fft/helper.pyc
import numpy.random # directory /usr/lib/python2.5/site-packages/numpy/random
# /usr/lib/python2.5/site-packages/numpy/random/__init__.pyc matches /usr/lib/python2.5/site-packages/numpy/random/__init__.py
import numpy.random # precompiled from /usr/lib/python2.5/site-packages/numpy/random/__init__.pyc
# /usr/lib/python2.5/site-packages/numpy/random/info.pyc matches /usr/lib/python2.5/site-packages/numpy/random/info.py
import numpy.random.info # precompiled from /usr/lib/python2.5/site-packages/numpy/random/info.pyc
dlopen("/usr/lib/python2.5/site-packages/numpy/random/mtrand.so", 2);
import numpy.random.mtrand # dynamically loaded from /usr/lib/python2.5/site-packages/numpy/random/mtrand.so
# /usr/lib/python2.5/site-packages/numpy/ctypeslib.pyc matches /usr/lib/python2.5/site-packages/numpy/ctypeslib.py
import numpy.ctypeslib # precompiled from /usr/lib/python2.5/site-packages/numpy/ctypeslib.pyc
import ctypes # directory /usr/lib/python2.5/ctypes
# /usr/lib/python2.5/ctypes/__init__.pyc matches /usr/lib/python2.5/ctypes/__init__.py
import ctypes # precompiled from /usr/lib/python2.5/ctypes/__init__.pyc
dlopen("/usr/lib/python2.5/lib-dynload/_ctypes.so", 2);
import _ctypes # dynamically loaded from /usr/lib/python2.5/lib-dynload/_ctypes.so
# /usr/lib/python2.5/struct.pyc matches /usr/lib/python2.5/struct.py
import struct # precompiled from /usr/lib/python2.5/struct.pyc
dlopen("/usr/lib/python2.5/lib-dynload/_struct.so", 2);
import _struct # dynamically loaded from /usr/lib/python2.5/lib-dynload/_struct.so
# /usr/lib/python2.5/ctypes/_endian.pyc matches /usr/lib/python2.5/ctypes/_endian.py
import ctypes._endian # precompiled from /usr/lib/python2.5/ctypes/_endian.pyc
# /usr/lib/python2.5/site-packages/numpy/add_newdocs.pyc matches /usr/lib/python2.5/site-packages/numpy/add_newdocs.py
import numpy.add_newdocs # precompiled from /usr/lib/python2.5/site-packages/numpy/add_newdocs.pyc
>>> from FIAT import shapes, Lagrange, quadrature
import FIAT # directory /home/jed/usr/lib/python2.5/site-packages/FIAT
# /home/jed/usr/lib/python2.5/site-packages/FIAT/__init__.pyc matches /home/jed/usr/lib/python2.5/site-packages/FIAT/__init__.py
import FIAT # precompiled from /home/jed/usr/lib/python2.5/site-packages/FIAT/__init__.pyc
# /home/jed/usr/lib/python2.5/site-packages/FIAT/shapes.pyc matches /home/jed/usr/lib/python2.5/site-packages/FIAT/shapes.py
import FIAT.shapes # precompiled from /home/jed/usr/lib/python2.5/site-packages/FIAT/shapes.pyc
# /home/jed/usr/lib/python2.5/site-packages/FIAT/factorial.pyc matches /home/jed/usr/lib/python2.5/site-packages/FIAT/factorial.py
import FIAT.factorial # precompiled from /home/jed/usr/lib/python2.5/site-packages/FIAT/factorial.pyc
# /home/jed/usr/lib/python2.5/site-packages/FIAT/numbering.pyc matches /home/jed/usr/lib/python2.5/site-packages/FIAT/numbering.py
import FIAT.numbering # precompiled from /home/jed/usr/lib/python2.5/site-packages/FIAT/numbering.pyc
# /home/jed/usr/lib/python2.5/site-packages/FIAT/reference.pyc matches /home/jed/usr/lib/python2.5/site-packages/FIAT/reference.py
import FIAT.reference # precompiled from /home/jed/usr/lib/python2.5/site-packages/FIAT/reference.pyc
# /home/jed/usr/lib/python2.5/site-packages/FIAT/Lagrange.pyc matches /home/jed/usr/lib/python2.5/site-packages/FIAT/Lagrange.py
import FIAT.Lagrange # precompiled from /home/jed/usr/lib/python2.5/site-packages/FIAT/Lagrange.pyc
# /home/jed/usr/lib/python2.5/site-packages/FIAT/dualbasis.pyc matches /home/jed/usr/lib/python2.5/site-packages/FIAT/dualbasis.py
import FIAT.dualbasis # precompiled from /home/jed/usr/lib/python2.5/site-packages/FIAT/dualbasis.pyc
# /home/jed/usr/lib/python2.5/site-packages/FIAT/functional.pyc matches /home/jed/usr/lib/python2.5/site-packages/FIAT/functional.py
import FIAT.functional # precompiled from /home/jed/usr/lib/python2.5/site-packages/FIAT/functional.pyc
# /home/jed/usr/lib/python2.5/site-packages/FIAT/quadrature.pyc matches /home/jed/usr/lib/python2.5/site-packages/FIAT/quadrature.py
import FIAT.quadrature # precompiled from /home/jed/usr/lib/python2.5/site-packages/FIAT/quadrature.pyc
# /home/jed/usr/lib/python2.5/site-packages/FIAT/jacobi.pyc matches /home/jed/usr/lib/python2.5/site-packages/FIAT/jacobi.py
import FIAT.jacobi # precompiled from /home/jed/usr/lib/python2.5/site-packages/FIAT/jacobi.pyc
# /home/jed/usr/lib/python2.5/site-packages/FIAT/gamma.pyc matches /home/jed/usr/lib/python2.5/site-packages/FIAT/gamma.py
import FIAT.gamma # precompiled from /home/jed/usr/lib/python2.5/site-packages/FIAT/gamma.pyc
# /home/jed/usr/lib/python2.5/site-packages/FIAT/polynomial.pyc matches /home/jed/usr/lib/python2.5/site-packages/FIAT/polynomial.py
import FIAT.polynomial # precompiled from /home/jed/usr/lib/python2.5/site-packages/FIAT/polynomial.pyc
# /home/jed/usr/lib/python2.5/site-packages/FIAT/expansions.pyc matches /home/jed/usr/lib/python2.5/site-packages/FIAT/expansions.py
import FIAT.expansions # precompiled from /home/jed/usr/lib/python2.5/site-packages/FIAT/expansions.pyc
# /home/jed/usr/lib/python2.5/site-packages/FIAT/functionaltype.pyc matches /home/jed/usr/lib/python2.5/site-packages/FIAT/functionaltype.py
import FIAT.functionaltype # precompiled from /home/jed/usr/lib/python2.5/site-packages/FIAT/functionaltype.pyc
# /home/jed/usr/lib/python2.5/site-packages/FIAT/functionalset.pyc matches /home/jed/usr/lib/python2.5/site-packages/FIAT/functionalset.py
import FIAT.functionalset # precompiled from /home/jed/usr/lib/python2.5/site-packages/FIAT/functionalset.pyc
>>> exi[K[K[K
# clear __builtin__._
# clear sys.path
# clear sys.argv
# clear sys.ps1
# clear sys.ps2
# clear sys.exitfunc
# clear sys.exc_type
# clear sys.exc_value
# clear sys.exc_traceback
# clear sys.last_type
# clear sys.last_value
# clear sys.last_traceback
# clear sys.path_hooks
# clear sys.path_importer_cache
# clear sys.meta_path
# restore sys.stdin
# restore sys.stdout
# restore sys.stderr
# cleanup __main__
# cleanup[1] random
# cleanup[1] _bisect
# cleanup[1] _curses
# cleanup[1] struct
# cleanup[1] zipimport
# cleanup[1] signal
# cleanup[1] token
# cleanup[1] cStringIO
# cleanup[1] encodings
# cleanup[1] FIAT
# cleanup[1] numpy.distutils.__version__
# cleanup[1] _ctypes
# cleanup[1] numpy.lib.info
# cleanup[1] numpy.core.memmap
# cleanup[1] itertools
# cleanup[1] opcode
# cleanup[1] FIAT.Lagrange
# cleanup[1] _heapq
# cleanup[1] binascii
# cleanup[1] sre_constants
# cleanup[1] cPickle
# cleanup[1] _codecs
# cleanup[1] curses.wrapper
# cleanup[1] _struct
# cleanup[1] _types
# cleanup[1] posix
# cleanup[1] encodings.aliases
# cleanup[1] _random
# cleanup[1] site
# cleanup[1] strop
# cleanup[1] readline
# cleanup[1] mmap
# cleanup[1] encodings.utf_8
# cleanup[1] FIAT.functionalset
# cleanup[1] FIAT.dualbasis
# cleanup[1] curses
# cleanup[1] codecs
# cleanup[1] FIAT.functional
# cleanup[1] FIAT.quadrature
# cleanup[1] FIAT.gamma
# cleanup[1] FIAT.functionaltype
# cleanup[1] FIAT.factorial
# cleanup[1] FIAT.polynomial
# cleanup[1] FIAT.expansions
# cleanup[1] FIAT.jacobi
# cleanup[1] FIAT.shapes
# cleanup[1] exceptions
# cleanup[1] FIAT.numbering
# cleanup[1] FIAT.reference
# cleanup[2] numpy.distutils.misc_util
# cleanup[2] heapq
# cleanup[2] numpy.core.info
# cleanup[2] distutils
# cleanup[2] numpy.core.defchararray
# cleanup[2] distutils.sysconfig
# cleanup[2] ctypes._endian
# cleanup[2] numpy.core.numerictypes
# cleanup[2] numpy.random.mtrand
# cleanup[2] distutils.dep_util
# cleanup[2] numpy.random.info
# cleanup[2] tempfile
# cleanup[2] numpy.linalg
# cleanup[2] numpy.testing
# cleanup[2] numpy.core.umath
# cleanup[2] numpy.distutils.ccompiler
# cleanup[2] numpy.distutils.exec_command
# cleanup[2] numpy.core.scalarmath
# cleanup[2] string
# cleanup[2] numpy.core.fromnumeric
# cleanup[2] numpy.lib.arraysetops
# cleanup[2] numpy.version
# cleanup[2] numpy.distutils.info
# cleanup[2] numpy.lib.type_check
# cleanup[2] numpy.lib.twodim_base
# cleanup[2] numpy.core._internal
# cleanup[2] bisect
# cleanup[2] numpy.fft.fftpack_lite
# cleanup[2] math
# cleanup[2] numpy.core.multiarray
# cleanup[2] distutils.log
# cleanup[2] distutils.version
# cleanup[2] numpy.distutils
# cleanup[2] numpy.add_newdocs
# cleanup[2] numpy.lib.getlimits
# cleanup[2] atexit
# cleanup[2] numpy.core.ma
# cleanup[2] re
# cleanup[2] numpy.lib._compiled_base
# cleanup[2] new
# cleanup[2] numpy.fft.helper
# cleanup[2] fcntl
# cleanup[2] UserDict
# cleanup[2] inspect
# cleanup[2] ctypes
# cleanup[2] imp
# cleanup[2] numpy.core._sort
# cleanup[2] distutils.ccompiler
# cleanup[2] thread
# cleanup[2] numpy.lib.ufunclike
# cleanup[2] traceback
# cleanup[2] distutils.spawn
# cleanup[2] numpy.linalg.lapack_lite
# cleanup[2] os
# cleanup[2] _sre
# cleanup[2] unittest
# cleanup[2] numpy.random
# cleanup[2] distutils.dir_util
# cleanup[2] numpy.distutils.unixccompiler
# cleanup[2] operator
# cleanup[2] distutils.util
# cleanup[2] numpy.core.arrayprint
# cleanup[2] posixpath
# cleanup[2] errno
# cleanup[2] types
# cleanup[2] tokenize
# cleanup[2] numpy
# cleanup[2] numpy.core.defmatrix
# cleanup[2] dis
# cleanup[2] numpy.__config__
# cleanup[2] numpy.testing.parametric
# cleanup[2] numpy.testing.utils
# cleanup[2] copy
# cleanup[2] numpy.ctypeslib
# cleanup[2] numpy.lib.scimath
# cleanup[2] numpy.fft
# cleanup[2] numpy.lib
# cleanup[2] numpy.lib.function_base
# cleanup[2] fnmatch
# cleanup[2] sre_parse
# cleanup[2] numpy.distutils.__config__
# cleanup[2] copy_reg
# cleanup[2] sre_compile
# cleanup[2] numpy.lib.polynomial
# cleanup[2] numpy._import_tools
# cleanup[2] numpy.fft.info
# cleanup[2] numpy.core.records
# cleanup[2] numpy.core._dotblas
# cleanup[2] numpy.testing.numpytest
# cleanup[2] numpy.core.numeric
# cleanup[2] numpy.linalg.info
# cleanup[2] distutils.unixccompiler
# cleanup[2] numpy.fft.fftpack
# cleanup[2] numpy.core
# cleanup[2] numpy.testing.info
# cleanup[2] numpy.distutils.log
# cleanup[2] stat
# cleanup[2] numpy.lib.utils
# cleanup[2] numpy.lib.index_tricks
# cleanup[2] warnings
# cleanup[2] glob
# cleanup[2] numpy.lib.shape_base
# cleanup[2] distutils.file_util
# cleanup[2] os.path
# cleanup[2] difflib
# cleanup[2] distutils.errors
# cleanup[2] linecache
# cleanup[2] time
# cleanup[2] numpy.lib.machar
# cleanup[2] numpy.linalg.linalg
# cleanup sys
# cleanup __builtin__
# cleanup ints: 57 unfreed ints in 9 out of 17 blocks
# cleanup floats: 76 unfreed floats in 8 out of 10 blocks
k\14:45[;1m[35m[;0m [33mjed[31mbrakk[36m10 [32m~[0m$ exit

Script done on Tue 25 Mar 2008 02:45:45 PM CET
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