Try installing version 1.1 of pysparse from <http://sourceforge.net/projects/pysparse/files/>.
On Thu, Dec 3, 2009 at 3:08 PM, Qingshan Chen <[email protected]> wrote: > Hi, > Thanks to all the people who have responded to my message. Here is a bit > more information about my set-up: > OS: Debian lenny > CPU: Intel Pentium D duo core > Python: 2.5.2 > > I have followed the instructions in the guide as closely as possible, and > installed the following required packages: > Numpy: 1.1.0 (pre-built Debian package) > python-sparse: 1.0.1 (pre-built Debian package, pysparse in Debian, as far > as I know) > Python-matplotlib: 0.98.1 (pre-built Debian package) > > Following suggestions made by some of you, I commented out 'terms.test' in > fipy/test.py, and > 'phase.test', 'convection.test', 'diffusion.test', 'elphf.test', > 'levelSet.test' and 'cahnHilliard.test' in examples/test.py, because each > of them causes the mysterious segmentation fault. With all these commented > out, the test run to the end, and give me the following error messages: > > ************************************************Error messages > starts**************************************************************** > ====================================================================== > FAIL: Doctest: > fipy.tools.dimensions.physicalField.PhysicalField.__array_wrap__ > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/usr/lib/python2.5/doctest.py", line 2128, in runTest > raise self.failureException(self.format_failure(new.getvalue())) > AssertionError: Failed doctest test for > fipy.tools.dimensions.physicalField.PhysicalField.__array_wrap__ > File > "/home/qchen/Documents/FiPy-2.0.2/fipy/tools/dimensions/physicalField.py", > line 608, in __array_wrap__ > > ---------------------------------------------------------------------- > File > "/home/qchen/Documents/FiPy-2.0.2/fipy/tools/dimensions/physicalField.py", > line 623, in > fipy.tools.dimensions.physicalField.PhysicalField.__array_wrap__ > Failed example: > from scipy.special import gamma as Gamma > Exception raised: > Traceback (most recent call last): > File "/usr/lib/python2.5/doctest.py", line 1228, in __run > compileflags, 1) in test.globs > File "<doctest > fipy.tools.dimensions.physicalField.PhysicalField.__array_wrap__[2]>", line > 1, in <module> > from scipy.special import gamma as Gamma > ImportError: No module named scipy.special > ---------------------------------------------------------------------- > File > "/home/qchen/Documents/FiPy-2.0.2/fipy/tools/dimensions/physicalField.py", > line 624, in > fipy.tools.dimensions.physicalField.PhysicalField.__array_wrap__ > Failed example: > print type(Gamma(PhysicalField([1.0, 2.0]))) > Exception raised: > Traceback (most recent call last): > File "/usr/lib/python2.5/doctest.py", line 1228, in __run > compileflags, 1) in test.globs > File "<doctest > fipy.tools.dimensions.physicalField.PhysicalField.__array_wrap__[3]>", line > 1, in <module> > print type(Gamma(PhysicalField([1.0, 2.0]))) > NameError: name 'Gamma' is not defined > > > ====================================================================== > FAIL: Doctest: fipy.variables.variable.Variable.__array_wrap__ > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/usr/lib/python2.5/doctest.py", line 2128, in runTest > raise self.failureException(self.format_failure(new.getvalue())) > AssertionError: Failed doctest test for > fipy.variables.variable.Variable.__array_wrap__ > File "/home/qchen/Documents/FiPy-2.0.2/fipy/variables/variable.py", line > 135, in __array_wrap__ > > ---------------------------------------------------------------------- > File "/home/qchen/Documents/FiPy-2.0.2/fipy/variables/variable.py", line > 143, in fipy.variables.variable.Variable.__array_wrap__ > Failed example: > from scipy.special import gamma as Gamma > Exception raised: > Traceback (most recent call last): > File "/usr/lib/python2.5/doctest.py", line 1228, in __run > compileflags, 1) in test.globs > File "<doctest fipy.variables.variable.Variable.__array_wrap__[1]>", > line 1, in <module> > from scipy.special import gamma as Gamma > ImportError: No module named scipy.special > ---------------------------------------------------------------------- > File "/home/qchen/Documents/FiPy-2.0.2/fipy/variables/variable.py", line > 144, in fipy.variables.variable.Variable.__array_wrap__ > Failed example: > print type(Gamma(Variable([1.0, 2.0]))) > Exception raised: > Traceback (most recent call last): > File "/usr/lib/python2.5/doctest.py", line 1228, in __run > compileflags, 1) in test.globs > File "<doctest fipy.variables.variable.Variable.__array_wrap__[2]>", > line 1, in <module> > print type(Gamma(Variable([1.0, 2.0]))) > NameError: name 'Gamma' is not defined > > > ====================================================================== > FAIL: Doctest: fipy.variables.betaNoiseVariable.BetaNoiseVariable > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/usr/lib/python2.5/doctest.py", line 2128, in runTest > raise self.failureException(self.format_failure(new.getvalue())) > AssertionError: Failed doctest test for > fipy.variables.betaNoiseVariable.BetaNoiseVariable > File > "/home/qchen/Documents/FiPy-2.0.2/fipy/variables/betaNoiseVariable.py", line > 43, in BetaNoiseVariable > > ---------------------------------------------------------------------- > File "/home/qchen/Documents/FiPy-2.0.2/fipy/variables/betaNoiseVariable.py", > line 82, in fipy.variables.betaNoiseVariable.BetaNoiseVariable > Failed example: > from scipy.special import gamma as Gamma > Exception raised: > Traceback (most recent call last): > File "/usr/lib/python2.5/doctest.py", line 1228, in __run > compileflags, 1) in test.globs > File "<doctest fipy.variables.betaNoiseVariable.BetaNoiseVariable[12]>", > line 1, in <module> > from scipy.special import gamma as Gamma > ImportError: No module named scipy.special > ---------------------------------------------------------------------- > File "/home/qchen/Documents/FiPy-2.0.2/fipy/variables/betaNoiseVariable.py", > line 84, in fipy.variables.betaNoiseVariable.BetaNoiseVariable > Failed example: > for a in arange(0.5,5,0.5): > alpha.setValue(a) > for b in arange(0.5,5,0.5): > beta.setValue(b) > betadist.setValue((Gamma(alpha + beta) / (Gamma(alpha) * > Gamma(beta))) > * x**(alpha - 1) * (1 - x)**(beta - 1)) > if __name__ == '__main__': > import sys > print >>sys.stderr, "alpha: %g, beta: %g" % (alpha, beta) > viewer.plot() > histoplot.plot() > Exception raised: > Traceback (most recent call last): > File "/usr/lib/python2.5/doctest.py", line 1228, in __run > compileflags, 1) in test.globs > File "<doctest fipy.variables.betaNoiseVariable.BetaNoiseVariable[13]>", > line 6, in <module> > * x**(alpha - 1) * (1 - x)**(beta - 1)) > NameError: name 'Gamma' is not defined > > > ====================================================================== > FAIL: Doctest: fipy.variables.gammaNoiseVariable.GammaNoiseVariable > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/usr/lib/python2.5/doctest.py", line 2128, in runTest > raise self.failureException(self.format_failure(new.getvalue())) > AssertionError: Failed doctest test for > fipy.variables.gammaNoiseVariable.GammaNoiseVariable > File > "/home/qchen/Documents/FiPy-2.0.2/fipy/variables/gammaNoiseVariable.py", > line 41, in GammaNoiseVariable > > ---------------------------------------------------------------------- > File > "/home/qchen/Documents/FiPy-2.0.2/fipy/variables/gammaNoiseVariable.py", > line 80, in fipy.variables.gammaNoiseVariable.GammaNoiseVariable > Failed example: > from scipy.special import gamma as Gamma > Exception raised: > Traceback (most recent call last): > File "/usr/lib/python2.5/doctest.py", line 1228, in __run > compileflags, 1) in test.globs > File "<doctest > fipy.variables.gammaNoiseVariable.GammaNoiseVariable[12]>", line 1, in > <module> > from scipy.special import gamma as Gamma > ImportError: No module named scipy.special > ---------------------------------------------------------------------- > File > "/home/qchen/Documents/FiPy-2.0.2/fipy/variables/gammaNoiseVariable.py", > line 82, in fipy.variables.gammaNoiseVariable.GammaNoiseVariable > Failed example: > for shape in arange(1,8,1): > alpha.setValue(shape) > for rate in arange(0.5,2.5,0.5): > beta.setValue(rate) > gammadist.setValue(x**(alpha - 1) * (beta**alpha * exp(-beta * x)) > / Gamma(alpha)) > if __name__ == '__main__': > import sys > print >>sys.stderr, "alpha: %g, beta: %g" % (alpha, beta) > viewer.plot() > histoplot.plot() > Exception raised: > Traceback (most recent call last): > File "/usr/lib/python2.5/doctest.py", line 1228, in __run > compileflags, 1) in test.globs > File "<doctest > fipy.variables.gammaNoiseVariable.GammaNoiseVariable[13]>", line 5, in > <module> > gammadist.setValue(x**(alpha - 1) * (beta**alpha * exp(-beta * x)) / > Gamma(alpha)) > NameError: name 'Gamma' is not defined > > > ---------------------------------------------------------------------- > Ran 255 tests in 86.167s > > FAILED (failures=4) > ************************************************Error messages > ends**************************************************************** > > I know little about the python language (please don't kick me out because > of this. I am excited about this great piece of work, and want to be able to > use it). I would appreciate some hints about what might have caused the > errors, or how to fix them. We may later go back to fix the segmentation > faults. Thank you! > > Best regards, > Qingshan > > > Daniel Wheeler wrote: >> >> Hi Qingshan, >> >> As previously suggested commenting out some of the tests might shed >> some light on the issue. Try commenting out "'models.test'," in >> "fipy/test.py" and "'levelSet.test'," in "examples/test.py" and rerun, >> Some of the failures may be irrelevant for the problems you are >> interested in. >> >> Cheers >> >> On Wed, Dec 2, 2009 at 4:38 PM, Qingshan Chen <[email protected]> wrote: >> >>> >>> Hi, >>> I am trying to install fipy on my desktop running debian lenny, but it >>> failed at the testing stage. I have installed numpy, python-sparse >>> (pysparse >>> in debian) and python-matplotlib. Running the command python setup.py >>> test >>> gives me the following messages, with the error message at the end. >>> >>> ------------------------------------------------------Screen message >>> starts------------------------------------------------------------------ >>> running test >>> running egg_info >>> writing FiPy.egg-info/PKG-INFO >>> writing top-level names to FiPy.egg-info/top_level.txt >>> writing dependency_links to FiPy.egg-info/dependency_links.txt >>> writing entry points to FiPy.egg-info/entry_points.txt >>> reading manifest file 'FiPy.egg-info/SOURCES.txt' >>> reading manifest template 'MANIFEST.in' >>> writing manifest file 'FiPy.egg-info/SOURCES.txt' >>> running build_ext >>> import fipy.solvers.test ... ok >>> import fipy.models.test ... ok >>> import fipy.terms.test ... ok >>> import fipy.tools.test ... ok >>> import fipy.meshes.test ... ok >>> import fipy.variables.test ... ok >>> import fipy.viewers.test ... ok >>> import fipy.boundaryConditions.test ... ok >>> import fipy.models.levelSet.test ... ok >>> import fipy.models.levelSet.electroChem.test ... ok >>> import fipy.models.levelSet.advection.advectionTerm ... ok >>> import fipy.models.levelSet.advection.higherOrderAdvectionTerm ... ok >>> import fipy.models.levelSet.distanceFunction.distanceVariable ... ok >>> import fipy.models.levelSet.surfactant.surfactantVariable ... ok >>> import fipy.models.levelSet.distanceFunction.levelSetDiffusionVariable .. >>> ok >>> import fipy.models.levelSet.surfactant.adsorbingSurfactantEquation ... ok >>> import fipy.models.levelSet.surfactant.convectionCoeff ... ok >>> import fipy.models.levelSet.surfactant.lines ... ok >>> import fipy.models.levelSet.electroChem.metalIonSourceVariable ... ok >>> import fipy.models.levelSet.electroChem.metalIonDiffusionEquation ... ok >>> import fipy.models.levelSet.electroChem.gapFillMesh ... ok >>> Doctest: >>> >>> fipy.models.levelSet.electroChem.metalIonSourceVariable._MetalIonSourceVariable >>> .. ok >>> Doctest: >>> >>> fipy.models.levelSet.electroChem.metalIonDiffusionEquation.buildMetalIonDiffusionEquation >>> .. ok >>> Doctest: fipy.models.levelSet.electroChem.gapFillMesh.GapFillMesh ... sh: >>> gmsh: command not found >>> FAIL >>> Doctest: fipy.models.levelSet.electroChem.gapFillMesh.TrenchMesh ... sh: >>> gmsh: command not found >>> FAIL >>> Doctest: fipy.models.levelSet.advection.advectionTerm._AdvectionTerm ... >>> ok >>> Doctest: >>> >>> fipy.models.levelSet.advection.higherOrderAdvectionTerm._HigherOrderAdvectionTerm >>> .. ok >>> Doctest: >>> fipy.models.levelSet.distanceFunction.distanceVariable.DistanceVariable >>> .. >>> ok >>> Doctest: >>> >>> fipy.models.levelSet.distanceFunction.distanceVariable.DistanceVariable._getCellInterfaceFlag >>> .. ok >>> Doctest: >>> >>> fipy.models.levelSet.distanceFunction.distanceVariable.DistanceVariable._getCellInterfaceNormals >>> .. ok >>> Doctest: >>> >>> fipy.models.levelSet.distanceFunction.distanceVariable.DistanceVariable._getCellValueOverFaces >>> .. ok >>> Doctest: >>> >>> fipy.models.levelSet.distanceFunction.distanceVariable.DistanceVariable._getInterfaceFlag >>> .. ok >>> Doctest: >>> >>> fipy.models.levelSet.distanceFunction.distanceVariable.DistanceVariable._getInterfaceNormals >>> .. ok >>> Doctest: >>> >>> fipy.models.levelSet.distanceFunction.distanceVariable.DistanceVariable._getLevelSetNormals >>> .. ok >>> Doctest: >>> >>> fipy.models.levelSet.distanceFunction.distanceVariable.DistanceVariable.getCellInterfaceAreas >>> .. ok >>> Doctest: >>> >>> fipy.models.levelSet.surfactant.surfactantVariable.SurfactantVariable.__init__ >>> .. ok >>> Doctest: >>> >>> fipy.models.levelSet.distanceFunction.levelSetDiffusionVariable._LevelSetDiffusionVariable >>> .. ok >>> Doctest: >>> >>> fipy.models.levelSet.surfactant.adsorbingSurfactantEquation.AdsorbingSurfactantEquation >>> .. Segmentation fault >>> >>> >>> ------------------------------------------------------Screen message >>> ends------------------------------------------------------------------ >>> >>> Any input will be appreciated! >>> Qingshan >>> >>> >> >> >> >> > > -- Daniel Wheeler
