and uncomment the tests that you commented out. The tests that you cut and pasted are failing due to scipy not being installed. This isn't strictly necessary for fipy so don't worry about it at this stage.
Cheers On Thu, Dec 3, 2009 at 3:20 PM, Daniel Wheeler <[email protected]> wrote: > 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 > -- Daniel Wheeler
