Mailman 3 September 2009 - SciPy-Dev

SLSQP Constrained Optimizer Status
by Rob Falck 25 Nov '13

25 Nov '13

I'm currently implementing the Sequential Least Squares Quadratic Programming (SLSQP) optimizer, by Dieter Kraft, for use in Scipy. The Fortran code being wrapped with F2PY is here: http://www.netlib.org/toms/733 (its use within Scipy has been cleared) SLSQP provides for bounds on the independent variables, as well as equality and inequality constraint functions, which is a capability that doesn't exist in scipy.optimize. Currently the code works, although the constraint normals are being generated by approximation. I'm working on a way to pass these in. I think the most elegant way will be a single function that returns the matrix of constraint normals. For a demonstration of what the code can do, here is an optimization of f(x,y) = 2xy + 2x - x**2 - 2y**2 Example 14.2 in Chapra & Canale gives the maximum as x=2.0, y=1.0. The unbounded optimization tests find this solution. As expected, its faster when derivatives are provided rather than approximated. Unbounded optimization. Derivatives approximated. Elapsed time: 1.45792961121 ms Results [[1.9999999515712266, 0.99999996181577444], -1.9999999999999984, 4, 0, 'Optimization terminated successfully.'] Unbounded optimization. Derivatives provided. Elapsed time: 1.03211402893 ms Results [[1.9999999515712266, 0.99999996181577444], -1.9999999999999984, 4, 0, 'Optimization terminated successfully.'] The following example uses an equality constraint to find the optimal when x=y. Bound optimization. Derivatives approximated. Elapsed time: 1.384973526 ms Results [[0.99999996845920858, 0.99999996845920858], -0.99999999999999889, 4, 0, 'Optimization terminated successfully.'] I've tried to conform to the syntax used by the other optimizers in scipy.optimize. The function definition and doc string are below. If anyone is interested in testing it out, let me know. def fmin_slsqp( func, x0 , eqcons=[], f_eqcons=None, ieqcons=[], f_ieqcons=None, bounds = [], fprime = None, fprime_cons=None,args = (), iter = 100, acc = 1.0E-6, iprint = 1, full_output = 0, epsilon = _epsilon ): """ Minimize a function using Sequential Least SQuares Programming Description: Python interface function for the SLSQP Optimization subroutine originally implemented by Dieter Kraft. Inputs: func - Objective function (in the form func(x, *args)) x0 - Initial guess for the independent variable(s). eqcons - A list of functions of length n such that eqcons[j](x0,*args) == 0.0 in a successfully optimized problem f_eqcons - A function of the form f_eqcons(x, *args) that returns an array in which each element must equal 0.0 in a successfully optimized problem. If f_eqcons is specified, eqcons is ignored. ieqcons - A list of functions of length n such that ieqcons[j](x0,*args) >= 0.0 in a successfully optimized problem f_ieqcons - A function of the form f_ieqcons(x0, *args) that returns an array in which each element must be greater or equal to 0.0 in a successfully optimized problem. If f_ieqcons is specified, ieqcons is ignored. bounds - A list of tuples specifying the lower and upper bound for each independent variable [ (xl0, xu0), (xl1, xu1), ...] fprime - A function that evaluates the partial derivatives of func fprime_cons - A function of the form f(x, *args) that returns the m by n array of constraint normals. If not provided, the normals will be approximated. Equality constraint normals precede inequality constraint normals. args - A sequence of additional arguments passed to func and fprime iter - The maximum number of iterations (int) acc - Requested accuracy (float) iprint - The verbosity of fmin_slsqp. iprint <= 0 : Silent operation iprint == 1 : Print summary upon completion (default) iprint >= 2 : Print status of each iterate and summary full_output - If 0, return only the minimizer of func (default). Otherwise, output final objective function and summary information. epsilon - The step size for finite-difference derivative estimates. Outputs: ( x, { fx, gnorm, its, imode, smode }) x - The final minimizer of func. fx - The final value of the objective function. its - The number of iterations. imode - The exit mode from the optimizer, as an integer. smode - A string describing the exit mode from the optimizer. Exit modes are defined as follows: -1 : Gradient evaluation required (g & a) 0 : Optimization terminated successfully. 1 : Function evaluation required (f & c) 2 : Number of equality constraints larger than number of independent variables 3 : More than 3*n iterations in LSQ subproblem 4 : Inequality constraints incompatible 5 : Singular matrix E in LSQ subproblem 6 : Singular matrix C in LSQ subproblem 7 : Rank-deficient equality constraint subproblem HFTI 8 : Positive directional derivative for linesearch 9 : Iteration limit exceeded -- - Rob Falck

4 16

Continuous Wavelet Transform for SciPy
by Sean Arms 13 Nov '09

13 Nov '09

Greetings! My name is Sean Arms and I'm a graduate student at the University of Oklahoma in the School of Meteorology. As part of my PhD research, I'm studying coherent structures in atmospheric boundary layer turbulence, primarily using in-situ observations and, secondarily, Direct Numerical Simulation (DNS) output. One common approach for detecting coherent structures in observational datasets relies on the use of the global wavelet power spectrum as estimated from a continuous wavelet transform (CWT). I know SciPy has a DWT impementation, and I've already been in contact with Filip. He recommeded that I post my code in hopes that it would add some momentum to the python-cwt development and create some feedback (I'm currently looking for a good place to post my code). I've implemented the CWT using pure python (that is, I did not write any C extension code myself - nothing to build), along with one mother wavelet (second derivitive of a Gaussian, or the Mexican Hat) - I'll be adding more Mother wavelets as I go along. I've made it a point to (try to) design my MotherWavelet class to be easily extendable. I'm working on documentation and a few tests at the moment, but so far my code compares well with other wavelet routines. The point of this email is to introduce myself and let the SciPy dev community know that I am willing to help develop CWT support for SciPy - I'll already be doing the work for my research, so I might as well put in the extra effort to make is usable by the larger community! Cheers! Sean Arms Graduate Research Assistant School of Meteorology University of Oklahoma

4 7

Doc edit rights
by Michael Droettboom 03 Oct '09

03 Oct '09

I've been improving the chararray functionality (see this thread [1]). It would be helpful to get edit rights to the documentation editor so I can comment on and mark some docstrings for review. (FWIW, I think Travis O. is giving me SVN commit rights, so that's taken care of.) [1] http://www.nabble.com/Re%3A--SciPy-dev--Deprecate-chararray--was-Plea-for-h… Cheers, Mike -- Michael Droettboom Science Software Branch Operations and Engineering Division Space Telescope Science Institute Operated by AURA for NASA

3 3

Fast (O(n log(n)) ) implementation of Kendall Tau
by Enzo Michelangeli 01 Oct '09

01 Oct '09

Dear all, A few days ago I posted to http://projects.scipy.org/scipy/ticket/999 a drop-in replacement for scipy.stats.kendalltau. My code implements the algorithm with complexity O(n log()) described by William R. Knight in a paper of 1966 archived at http://www.jstor.org/pss/2282833 , whereas the function currently in SciPy has complexity O(n^2), which makes it unusable with large data sets. One potential issue here is that my code is in part derived from a Java implementation contained in the Java package called "Law" (http://law.dsi.unimi.it/software/law-1.4-src.tar.gz ). That code is GPL'd, but its authors (http://law.dsi.unimi.it/index.php?option=com_contact&catid=4&Itemid=3 ) have already informally confirmed to me by e-mail that they have no objections to the release of my Python code under a BSD-style license. Now my question is: exactly which steps should I take in order to clear the path to a possible inclusion in SciPy? All the best, Enzo Michelangeli

4 6

Viewing svn status (ready to merge, merged, etc.) at thenumpy trac site
by David Goldsmith 01 Oct '09

01 Oct '09

How does one do it? (Assuming it's possible.) DG

1 0

New Work Flow Diagram
by David Goldsmith 29 Sep '09

29 Sep '09

Hi! Can someone with the appropriate privilege please add the attached to http://mentat.za.net/numpy/? Thanks! DG

1 0

CS causes compiler error on solaris in cluster hierarchy
by John Hunter 26 Sep '09

26 Sep '09

When I try and compile scipy svn HEAD on solaris for python2.4 using gcc 3.4.3, I get the following compiler error. Apparently CS is reserved as a numeric constant: scipy/cluster/src/hierarchy.c:1082: error: subscripted value is neither array nor pointer scipy/cluster/src/hierarchy.c:1082: error: subscripted value is neither array nor pointer scipy/cluster/src/hierarchy.c:1086: error: subscripted value is neither array nor pointer scipy/cluster/src/hierarchy.c:1091: error: subscripted value is neither array nor pointer scipy/cluster/src/hierarchy.c:1091: error: subscripted value is neither array nor pointer scipy/cluster/src/hierarchy.c:1095: error: subscripted value is neither array nor pointer scipy/cluster/src/hierarchy.c: At top level: The attached patch (replace CS by CS_) allows scipy to compile on this platform johnh@udesktop191:scipy> gcc --version gcc (GCC) 3.4.3 (csl-sol210-3_4-branch+sol_rpath) Copyright (C) 2004 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. johnh@udesktop191:scipy> python -V Python 2.4.5 johnh@udesktop191:scipy> uname -a SunOS udesktop191 5.10 Generic_137138-09 i86pc i386 i86pc

2 1

Re: [SciPy-dev] Installing Numpy/Scipy with custom ATLAS [SOLVED]
by Skipper Seabold 25 Sep '09

25 Sep '09

On Thu, Sep 24, 2009 at 2:10 PM, Skipper Seabold <jsseabold(a)gmail.com> wrote: > On Thu, Sep 24, 2009 at 1:50 PM, Skipper Seabold <jsseabold(a)gmail.com> wrote: >> For some reason I thought it would be a good idea to install a custom >> ATLAS...again. >> >> I think I've built lapack 3.1.1 and atlas 3.8.0 correctly following >> the instructions here <http://www.scipy.org/Installing_SciPy/Linux> >> and the ones included with atlas, but we shall see...the checks pass >> at least. I installed the atlas libraries to ~/atlas and copied over >> the dynamic libraries by hand. >> >> I then edit my site.cfg >> >> [DEFAULT] >> library_dirs = /usr/local/lib:/usr/lib:/home/skipper/atlas/lib >> include_dirs = /usr/local/include:/usr/include:usr/include/suitesparse:/home/skipper/atlas/include >> [blas_opt] >> libraries = ptf77blas, ptcblas, atlas >> [lapack_opt] >> libraries = lapack, ptf77blas, ptcblas, atlas >> [amd] >> amd_libs = amd >> [umfpack] >> umfpack_libs = umfpack >> [fftw] >> libraries = fftw3 >> >> I then build and install numpy without error. But when I try to >> import numpy I get >> [...] >> /usr/local/lib/python2.6/dist-packages/numpy/linalg/linalg.py in <module>() >> 20 isfinite, size >> 21 from numpy.lib import triu >> ---> 22 from numpy.linalg import lapack_lite >> 23 from numpy.matrixlib.defmatrix import matrix_power >> 24 >> >> ImportError: /usr/local/lib/python2.6/dist-packages/numpy/linalg/lapack_lite.so: >> undefined symbol: ATL_dptsyrk >> >> >> Running ldd gives >> >> $ ldd /usr/local/lib/python2.6/dist-packages/numpy/linalg/lapack_lite.so >> linux-vdso.so.1 => (0x00007fff129fe000) >> liblapack.so => /usr/lib/atlas/liblapack.so (0x00007f4609c57000) >> libatlas.so => /usr/lib/libatlas.so (0x00007f4609615000) >> libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00007f4609338000) >> libm.so.6 => /lib/libm.so.6 (0x00007f46090b3000) >> libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f4608e9b000) >> libc.so.6 => /lib/libc.so.6 (0x00007f4608b28000) >> libblas.so.3gf => /usr/lib/atlas/libblas.so.3gf (0x00007f46084ad000) >> /lib64/ld-linux-x86-64.so.2 (0x00007f460a991000) >> >> I currently have atlas installed from David's repo as well >> (incidentally, David, where is your repo, I can't find it again, and >> wanted to add it to the wiki.) and am wondering if there is a conflict >> here. When I look at the build log it says, for example, >> >> FOUND: >> libraries = ['ptf77blas', 'ptcblas', 'atlas'] >> library_dirs = ['/home/skipper/atlas/lib'] >> language = c >> include_dirs = ['/usr/include'] >> >> Should include_dirs be '/home/skipper/atlas/include' ? I don't know. >> Any pointers would be appreciated, as I wasn't able to install numpy >> without trying to use the threaded libraries either now... I can >> provide anymore output as needed. Build log attached. >> >> Cheers, >> >> Skipper >> > > I figured the include directories in site.cfg were greedy, so I > changed the order to > > library_dirs = /usr/local/lib:/usr/lib:/home/skipper/atlas/lib > include_dirs = /home/skipper/atlas/include:/usr/local/include:/usr/include:/usr/include/suitesparse > > but I get the same import error in numpy. > > The correct include directory is listed in the build log, but I'm > wondering why it says atlas 3.8.3 when I installed 3.8.0 > > New build log attached. > > Skipper > I can't believe it, but I figured it out. I uninstalled the old atlas, then had to copy libatlas.so from the directory where I installed atlas to /usr/lib/ and everything went to plan. I now see all of my cores working when trying to invert a large matrix rather than one core getting overloaded and it taking forever. Sorry for the noise. Skipper

1 0

Installing Numpy/Scipy with custom ATLAS
by Skipper Seabold 25 Sep '09

25 Sep '09

For some reason I thought it would be a good idea to install a custom ATLAS...again. I think I've built lapack 3.1.1 and atlas 3.8.0 correctly following the instructions here <http://www.scipy.org/Installing_SciPy/Linux> and the ones included with atlas, but we shall see...the checks pass at least. I installed the atlas libraries to ~/atlas and copied over the dynamic libraries by hand. I then edit my site.cfg [DEFAULT] library_dirs = /usr/local/lib:/usr/lib:/home/skipper/atlas/lib include_dirs = /usr/local/include:/usr/include:usr/include/suitesparse:/home/skipper/atlas/include [blas_opt] libraries = ptf77blas, ptcblas, atlas [lapack_opt] libraries = lapack, ptf77blas, ptcblas, atlas [amd] amd_libs = amd [umfpack] umfpack_libs = umfpack [fftw] libraries = fftw3 I then build and install numpy without error. But when I try to import numpy I get [...] /usr/local/lib/python2.6/dist-packages/numpy/linalg/linalg.py in <module>() 20 isfinite, size 21 from numpy.lib import triu ---> 22 from numpy.linalg import lapack_lite 23 from numpy.matrixlib.defmatrix import matrix_power 24 ImportError: /usr/local/lib/python2.6/dist-packages/numpy/linalg/lapack_lite.so: undefined symbol: ATL_dptsyrk Running ldd gives $ ldd /usr/local/lib/python2.6/dist-packages/numpy/linalg/lapack_lite.so linux-vdso.so.1 => (0x00007fff129fe000) liblapack.so => /usr/lib/atlas/liblapack.so (0x00007f4609c57000) libatlas.so => /usr/lib/libatlas.so (0x00007f4609615000) libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00007f4609338000) libm.so.6 => /lib/libm.so.6 (0x00007f46090b3000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f4608e9b000) libc.so.6 => /lib/libc.so.6 (0x00007f4608b28000) libblas.so.3gf => /usr/lib/atlas/libblas.so.3gf (0x00007f46084ad000) /lib64/ld-linux-x86-64.so.2 (0x00007f460a991000) I currently have atlas installed from David's repo as well (incidentally, David, where is your repo, I can't find it again, and wanted to add it to the wiki.) and am wondering if there is a conflict here. When I look at the build log it says, for example, FOUND: libraries = ['ptf77blas', 'ptcblas', 'atlas'] library_dirs = ['/home/skipper/atlas/lib'] language = c include_dirs = ['/usr/include'] Should include_dirs be '/home/skipper/atlas/include' ? I don't know. Any pointers would be appreciated, as I wasn't able to install numpy without trying to use the threaded libraries either now... I can provide anymore output as needed. Build log attached. Cheers, Skipper

1 1

scipy-weave unit tests fail on KeyError
by Emmanuel Lambert 24 Sep '09

24 Sep '09

Hi, I compiled SciPy and Numpy on a machine with Scientific Linux (64bit). We detected a problem with Weave and after investigation, it turns out that some of the unit tests delivered with Scipy-Weave also fail ! Below is a list of tests that fail in for example the "test_c_spec" file. They all raise a KeyError. This is with SciPy 0.7.1 on Python 2.6. I also downloaded the latest Weave code again from the SVN repository (trunk), but the problem is not resolved. Any idea on how to tackle this problem? There are no posts that help me further. It looks like the compilation done by Weave works fine (see sample stdout also below), but afterwards, he cannot find the compiled code in the list. What could cause this? thanks for any help. Emmanuel ******************* SAMPLE OF STDOUT ****************** -------------------- >> begin captured stdout << --------------------- <weave: compiling> running build_ext running build_src building extension "sc_d133102ab45193e072f8dbb5a1f6848513" sources customize UnixCCompiler customize UnixCCompiler using build_ext customize UnixCCompiler customize UnixCCompiler using build_ext building 'sc_d133102ab45193e072f8dbb5a1f6848513' extension compiling C++ sources C compiler: g++ -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 - Wall -fPIC compile options: '-I/user/home/gent/vsc401/vsc40157/scipy-runtime/ scipy/weave -I/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/ weave/scxx -I/user/home/gent/vsc401/vsc40157/numpy-runtime/numpy/core/ include -I/apps/gent/gengar/harpertown/software/Python/2.6.2- gimkl-0.5.0/include/python2.6 -c' g++: /user/home/gent/vsc401/vsc40157/.python26_compiled/ sc_d133102ab45193e072f8dbb5a1f6848513.cpp g++ -pthread -shared /tmp/vsc40157/python26_intermediate/ compiler_c1b5f1b73f1ce7d0c836cdad4c7c5ded/user/home/gent/vsc401/ vsc40157/.python26_compiled/sc_d133102ab45193e072f8dbb5a1f6848513.o / tmp/vsc40157/python26_intermediate/ compiler_c1b5f1b73f1ce7d0c836cdad4c7c5ded/user/home/gent/vsc401/ vsc40157/scipy-runtime/scipy/weave/scxx/weave_imp.o -o /user/home/gent/ vsc401/vsc40157/.python26_compiled/ sc_d133102ab45193e072f8dbb5a1f6848513.so running scons --------------------- >> end captured stdout << ---------------------- ********************** TESTS THAT FAIL *********************** -bash-3.2$ python ./test_c_spec.py E..........EE.................EEEE......E..........EE.................EEEE.............. ====================================================================== ERROR: test_call_function (test_c_spec.CallableConverter) ---------------------------------------------------------------------- Traceback (most recent call last): File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ tests/test_c_spec.py", line 296, in test_call_function compiler=self.compiler,force=1) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ inline_tools.py", line 301, in inline function_catalog.add_function(code,func,module_dir) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 648, in add_function self.cache[code] = self.get_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 615, in get_functions function_list = self.get_cataloged_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 529, in get_cataloged_functions if cat is not None and code in cat: File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ lib/python2.6/shelve.py", line 110, in __contains__ return key in self.dict File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ dumbdbm_patched.py", line 73, in __getitem__ pos, siz = self._index[key] # may raise KeyError KeyError: 0 ====================================================================== ERROR: test_file_to_py (test_c_spec.FileConverter) ---------------------------------------------------------------------- Traceback (most recent call last): File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ tests/test_c_spec.py", line 262, in test_file_to_py force=1) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ inline_tools.py", line 301, in inline function_catalog.add_function(code,func,module_dir) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 648, in add_function self.cache[code] = self.get_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 615, in get_functions function_list = self.get_cataloged_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 529, in get_cataloged_functions if cat is not None and code in cat: File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ lib/python2.6/shelve.py", line 110, in __contains__ return key in self.dict File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ dumbdbm_patched.py", line 73, in __getitem__ pos, siz = self._index[key] # may raise KeyError KeyError: 0 ====================================================================== ERROR: test_py_to_file (test_c_spec.FileConverter) ---------------------------------------------------------------------- Traceback (most recent call last): File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ tests/test_c_spec.py", line 246, in test_py_to_file inline_tools.inline(code,['file'],compiler=self.compiler,force=1) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ inline_tools.py", line 301, in inline function_catalog.add_function(code,func,module_dir) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 648, in add_function self.cache[code] = self.get_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 615, in get_functions function_list = self.get_cataloged_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 529, in get_cataloged_functions if cat is not None and code in cat: File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ lib/python2.6/shelve.py", line 110, in __contains__ return key in self.dict File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ dumbdbm_patched.py", line 73, in __getitem__ pos, siz = self._index[key] # may raise KeyError KeyError: 0 ====================================================================== ERROR: test_convert_to_dict (test_c_spec.SequenceConverter) ---------------------------------------------------------------------- Traceback (most recent call last): File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ tests/test_c_spec.py", line 305, in test_convert_to_dict inline_tools.inline("",['d'],compiler=self.compiler,force=1) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ inline_tools.py", line 301, in inline function_catalog.add_function(code,func,module_dir) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 648, in add_function self.cache[code] = self.get_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 615, in get_functions function_list = self.get_cataloged_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 529, in get_cataloged_functions if cat is not None and code in cat: File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ lib/python2.6/shelve.py", line 110, in __contains__ return key in self.dict File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ dumbdbm_patched.py", line 73, in __getitem__ pos, siz = self._index[key] # may raise KeyError KeyError: 0 ====================================================================== ERROR: test_convert_to_list (test_c_spec.SequenceConverter) ---------------------------------------------------------------------- Traceback (most recent call last): File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ tests/test_c_spec.py", line 309, in test_convert_to_list inline_tools.inline("",['l'],compiler=self.compiler,force=1) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ inline_tools.py", line 301, in inline function_catalog.add_function(code,func,module_dir) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 648, in add_function self.cache[code] = self.get_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 615, in get_functions function_list = self.get_cataloged_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 529, in get_cataloged_functions if cat is not None and code in cat: File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ lib/python2.6/shelve.py", line 110, in __contains__ return key in self.dict File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ dumbdbm_patched.py", line 73, in __getitem__ pos, siz = self._index[key] # may raise KeyError KeyError: 0 ====================================================================== ERROR: test_convert_to_string (test_c_spec.SequenceConverter) ---------------------------------------------------------------------- Traceback (most recent call last): File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ tests/test_c_spec.py", line 313, in test_convert_to_string inline_tools.inline("",['s'],compiler=self.compiler,force=1) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ inline_tools.py", line 301, in inline function_catalog.add_function(code,func,module_dir) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 648, in add_function self.cache[code] = self.get_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 615, in get_functions function_list = self.get_cataloged_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 529, in get_cataloged_functions if cat is not None and code in cat: File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ lib/python2.6/shelve.py", line 110, in __contains__ return key in self.dict File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ dumbdbm_patched.py", line 73, in __getitem__ pos, siz = self._index[key] # may raise KeyError KeyError: 0 ====================================================================== ERROR: test_convert_to_tuple (test_c_spec.SequenceConverter) ---------------------------------------------------------------------- Traceback (most recent call last): File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ tests/test_c_spec.py", line 317, in test_convert_to_tuple inline_tools.inline("",['t'],compiler=self.compiler,force=1) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ inline_tools.py", line 301, in inline function_catalog.add_function(code,func,module_dir) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 648, in add_function self.cache[code] = self.get_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 615, in get_functions function_list = self.get_cataloged_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 529, in get_cataloged_functions if cat is not None and code in cat: File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ lib/python2.6/shelve.py", line 110, in __contains__ return key in self.dict File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ dumbdbm_patched.py", line 73, in __getitem__ pos, siz = self._index[key] # may raise KeyError KeyError: 0 ====================================================================== ERROR: test_call_function (test_c_spec.TestCallableConverterUnix) ---------------------------------------------------------------------- Traceback (most recent call last): File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ tests/test_c_spec.py", line 296, in test_call_function compiler=self.compiler,force=1) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ inline_tools.py", line 301, in inline function_catalog.add_function(code,func,module_dir) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 648, in add_function self.cache[code] = self.get_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 615, in get_functions function_list = self.get_cataloged_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 529, in get_cataloged_functions if cat is not None and code in cat: File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ lib/python2.6/shelve.py", line 110, in __contains__ return key in self.dict File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ dumbdbm_patched.py", line 73, in __getitem__ pos, siz = self._index[key] # may raise KeyError KeyError: 0 ====================================================================== ERROR: test_file_to_py (test_c_spec.TestFileConverterUnix) ---------------------------------------------------------------------- Traceback (most recent call last): File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ tests/test_c_spec.py", line 262, in test_file_to_py force=1) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ inline_tools.py", line 301, in inline function_catalog.add_function(code,func,module_dir) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 648, in add_function self.cache[code] = self.get_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 615, in get_functions function_list = self.get_cataloged_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 529, in get_cataloged_functions if cat is not None and code in cat: File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ lib/python2.6/shelve.py", line 110, in __contains__ return key in self.dict File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ dumbdbm_patched.py", line 73, in __getitem__ pos, siz = self._index[key] # may raise KeyError KeyError: 0 ====================================================================== ERROR: test_py_to_file (test_c_spec.TestFileConverterUnix) ---------------------------------------------------------------------- Traceback (most recent call last): File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ tests/test_c_spec.py", line 246, in test_py_to_file inline_tools.inline(code,['file'],compiler=self.compiler,force=1) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ inline_tools.py", line 301, in inline function_catalog.add_function(code,func,module_dir) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 648, in add_function self.cache[code] = self.get_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 615, in get_functions function_list = self.get_cataloged_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 529, in get_cataloged_functions if cat is not None and code in cat: File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ lib/python2.6/shelve.py", line 110, in __contains__ return key in self.dict File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ dumbdbm_patched.py", line 73, in __getitem__ pos, siz = self._index[key] # may raise KeyError KeyError: 0 ====================================================================== ERROR: test_convert_to_dict (test_c_spec.TestSequenceConverterUnix) ---------------------------------------------------------------------- Traceback (most recent call last): File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ tests/test_c_spec.py", line 305, in test_convert_to_dict inline_tools.inline("",['d'],compiler=self.compiler,force=1) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ inline_tools.py", line 301, in inline function_catalog.add_function(code,func,module_dir) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 648, in add_function self.cache[code] = self.get_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 615, in get_functions function_list = self.get_cataloged_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 529, in get_cataloged_functions if cat is not None and code in cat: File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ lib/python2.6/shelve.py", line 110, in __contains__ return key in self.dict File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ dumbdbm_patched.py", line 73, in __getitem__ pos, siz = self._index[key] # may raise KeyError KeyError: 0 ====================================================================== ERROR: test_convert_to_list (test_c_spec.TestSequenceConverterUnix) ---------------------------------------------------------------------- Traceback (most recent call last): File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ tests/test_c_spec.py", line 309, in test_convert_to_list inline_tools.inline("",['l'],compiler=self.compiler,force=1) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ inline_tools.py", line 301, in inline function_catalog.add_function(code,func,module_dir) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 648, in add_function self.cache[code] = self.get_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 615, in get_functions function_list = self.get_cataloged_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 529, in get_cataloged_functions if cat is not None and code in cat: File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ lib/python2.6/shelve.py", line 110, in __contains__ return key in self.dict File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ dumbdbm_patched.py", line 73, in __getitem__ pos, siz = self._index[key] # may raise KeyError KeyError: 0 ====================================================================== ERROR: test_convert_to_string (test_c_spec.TestSequenceConverterUnix) ---------------------------------------------------------------------- Traceback (most recent call last): File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ tests/test_c_spec.py", line 313, in test_convert_to_string inline_tools.inline("",['s'],compiler=self.compiler,force=1) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ inline_tools.py", line 301, in inline function_catalog.add_function(code,func,module_dir) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 648, in add_function self.cache[code] = self.get_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 615, in get_functions function_list = self.get_cataloged_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 529, in get_cataloged_functions if cat is not None and code in cat: File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ lib/python2.6/shelve.py", line 110, in __contains__ return key in self.dict File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ dumbdbm_patched.py", line 73, in __getitem__ pos, siz = self._index[key] # may raise KeyError KeyError: 0 ====================================================================== ERROR: test_convert_to_tuple (test_c_spec.TestSequenceConverterUnix) ---------------------------------------------------------------------- Traceback (most recent call last): File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ tests/test_c_spec.py", line 317, in test_convert_to_tuple inline_tools.inline("",['t'],compiler=self.compiler,force=1) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ inline_tools.py", line 301, in inline function_catalog.add_function(code,func,module_dir) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 648, in add_function self.cache[code] = self.get_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 615, in get_functions function_list = self.get_cataloged_functions(code) File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ catalog.py", line 529, in get_cataloged_functions if cat is not None and code in cat: File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ lib/python2.6/shelve.py", line 110, in __contains__ return key in self.dict File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ dumbdbm_patched.py", line 73, in __getitem__ pos, siz = self._index[key] # may raise KeyError KeyError: 0 ---------------------------------------------------------------------- Ran 88 tests in 32.581s FAILED (errors=14)

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