Mailman 3 December 2005 - SciPy-User

Failed Build from SVN
by Frank 16 Dec '05

16 Dec '05

Hi All, After a successful (?) core installation, I get the following (see below for full log) during the scipy build: "AttributeError: Configuration instance has no attribute 'make_config_py" Any ideas? Thanks, Frank Assuming default configuration (Lib/utils/{setup_utils,setup}.py was not found) Appending scipy.utils configuration to scipy Appending scipy.io configuration to scipy fftw_info: FOUND: libraries = ['rfftw', 'fftw'] library_dirs = ['/usr/local/lib'] define_macros = [('SCIPY_FFTW_H', None)] include_dirs = ['/usr/local/include'] djbfft_info: NOT AVAILABLE DJBFFT (http://cr.yp.to/djbfft.html) libraries not found. Directories to search for the libraries can be specified in the scipy_distutils/site.cfg file (section [djbfft]) or by setting the DJBFFT environment variable. Appending scipy.fftpack configuration to scipy Appending scipy.signal configuration to scipy blas_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-faltivec', '-I/System/Library/Frameworks/ vecLib.framework/Headers'] Appending scipy.integrate configuration to scipy lapack_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-faltivec'] Appending scipy.linalg configuration to scipy Appending scipy.special configuration to scipy Appending scipy.optimize configuration to scipy Appending scipy.stats configuration to scipy Appending scipy.interpolate configuration to scipy Appending scipy.sparse configuration to scipy Appending scipy.cluster configuration to scipy Appending scipy.lib.blas configuration to scipy.lib Appending scipy.lib.lapack configuration to scipy.lib Appending scipy.lib configuration to scipy Traceback (most recent call last): File "setup.py", line 42, in ? setup_package() File "setup.py", line 28, in setup_package config.add_subpackage('Lib') File "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ python2.3/site-packages/scipy/distutils/misc_util.py", line 395, in add_subpackage config = self.get_subpackage(subpackage_name,subpackage_path) File "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ python2.3/site-packages/scipy/distutils/misc_util.py", line 385, in get_subpackage config = setup_module.configuration(*args) File "/Users/fjbrooks/installme/scipy/Lib/setup.py", line 20, in configuration config.make_config_py('__scipy_config__') AttributeError: Configuration instance has no attribute 'make_config_py'

2 8

unexpected matrix behavior
by Alan G Isaac 16 Dec '05

16 Dec '05

I would like to understand the behavior of matrices, as shown below. Is it expected? If so, what is the general principle? Thank you, Alan Isaac >>> scipy.base.__version__ '0.8.4' >>> x = [[1,2],[3,4]] >>> y = scipy.array(x) >>> z = scipy.mat(x) >>> xz = zip(*x) >>> yz = zip(*y) >>> zz = zip(*z) >>> xz [(1, 3), (2, 4)] >>> yz [(1, 3), (2, 4)] >>> zz [(matrix([[1, 2]]), matrix([[3, 4]]))]

2 2

New named fields in scipy core --- possible uses in color images
by Travis E. Oliphant 16 Dec '05

16 Dec '05

I know that many people are not aware of the new named fields that are now an integral part of scipy_core. So, here is a simple example of their use. First of all, named fields can be constructed from any data type, not just records. The only thing the recarray subclass does is to make construction a bit cleaner, perhaps, and to allow attribute access to fields. Consider the following code (works with recent SVN): image = zeros((256,256),dtype=(uint32, [('r','u1'),('g','u1'),('b','u1'),('a','u1')])) This creates an array of zeros (which for math operations can be interpreted as an unsigned 32-bit integer) but which has named fields 'r', 'g', 'b', and 'a'. These fields can be accessed (as unsigned 8-bit integers) using image['r'] image['g'] image['b'] image['a'] or the whole image can be accessed at one time using the image array. I'm not sure, aside from perhaps code readibility, if there is any benefit from this approach over the standard representation as image = zeros((256,256,4), dtype=uint8) but, it's kind of interesting that such things are now possible. Note, however, that one thing the records.py module provides over this simple approach is an "array-scalar" that also can have fields. In our example: image['r'][10,20] would work and return a uint8 scalar, but image[10,20]['r'] would not because image[10,20] is a uint32 scalar (no fields). image[10,20].getfield(*image.dtypedescr.fields['r']) would work though. Have fun... -Travis

3 2

Bug in FFTPACK wrappers
by Rob Managan 15 Dec '05

15 Dec '05

I am still getting errors on mac OSX 10.3.9, python 2.4.1 in the ifft(fft(sin(x))) when the fftpack routine is used. The routines in the basic package work properly. Does anyone have them working properly? Any pointers on how to find out where the problem is? I think fftpack is using fftw-3.x libraries. I have attached a simple script that shows the difference between the basic and fftpack results. -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- Rob Managan email managan at llnl.gov LLNL phone: 925-423-0903 P.O. Box 808, L-095 FAX: 925-422-3389 Livermore, CA 94551-0808

2 1

Benchmark data
by Travis Oliphant 15 Dec '05

15 Dec '05

I'd like people to try out scipy core in SVN. I made improvements to the buffered ufunc section of code that I think will make a big difference in the recently published benchmarks. Here are some results that I get now (I've got a debug build with no optimizations). Optimization flags: -g -Wall -Wstrict-prototypes CPU info: getNCPUs has_3dnow has_3dnowext has_mmx is_32bit is_AMD is_singleCPU Numeric-24.2 numarray-1.5.1 scipy-core-0.8.1.1614 benchmark size = 4 (vectors of length 256) label Numeric numarray scipy.base 1 0.0001121 0.002115 9.108e-05 2 0.0001349 0.0008631 0.000133 3 7.105e-05 0.000989 8.202e-05 4 0.0001509 0.003712 0.0001481 5 6.39e-05 0.04328 6.986e-05 6 6.008e-05 5.412e-05 9.012e-05 7 0.0001211 0.0003929 0.000129 8 4.292e-05 0.000118 3.004e-05 9 0.0005081 0.00541 0.0006039 10 0.0004249 0.0006261 0.00056 11 0.000329 0.000932 0.000422 TOTAL 0.002019 0.0585 0.002359 Optimization flags: -g -Wall -Wstrict-prototypes CPU info: getNCPUs has_3dnow has_3dnowext has_mmx is_32bit is_AMD is_singleCPU Numeric-24.2 numarray-1.5.1 scipy-core-0.8.1.1614 benchmark size = 6 (vectors of length 4096) label Numeric numarray scipy.base 1 0.000401 0.002003 0.0003419 2 0.0003641 0.001114 0.0004022 3 0.000263 0.001245 0.000315 4 0.0005591 0.004512 0.000577 5 0.000298 0.001587 0.000283 6 0.000268 0.000284 0.0002999 7 0.000464 0.000725 0.0004301 8 0.0002861 0.000536 0.0001659 9 0.004739 0.0104 0.004864 10 0.04717 0.004666 0.004523 11 0.003594 0.004486 0.003582 TOTAL 0.0584 0.03156 0.01578 Optimization flags: -g -Wall -Wstrict-prototypes CPU info: getNCPUs has_3dnow has_3dnowext has_mmx is_32bit is_AMD is_singleCPU Numeric-24.2 numarray-1.5.1 scipy-core-0.8.1.1614 benchmark size = 11 (vectors of length 4194304) label Numeric numarray scipy.base 1 0.414 0.231 0.3357 2 0.3932 0.509 0.4095 3 0.2833 0.3737 0.3759 4 1.157 1.118 0.6301 5 0.4359 0.4895 0.3693 6 0.2868 0.3933 0.3205 7 1.211 1.354 0.6187 8 0.7242 0.8617 0.4587 9 8.506 12.46 7.865 10 9.726 13.13 6.891 11 7.518 10.44 8.416 TOTAL 30.66 41.35 26.69 I think these benchmarks are showing that scipy base is at least doing better than it was -Travis

7 14

Re: [SciPy-user] weave issue NEVER MIND
by Chris Fonnesbeck 15 Dec '05

15 Dec '05

I'm an idiot. Sorry. On 12/15/05, Chris Fonnesbeck <fonnesbeck(a)gmail.com> wrote: > I am trying to use weave inline to help me calculate the gamma function: > > def gamma_function(xx): > > # Returns the value ln[gamma(xx)] for xx > 0 > gammln = """ > # Line 10 "likelihood_plots.py" > double x,y,tmp,ser; > static double cof[6]={76.18009172947146,-86.50532032941677, > 24.01409824083091,-1.231739572450155, > 0.1208650973866179e-2,-0.5395239384953e-5}; > int j; > y=x=xx; > tmp=x+5.5; > tmp -= (x+0.5)*log(tmp); > ser=1.000000000190015; > for (j=0;j<=5;j++) ser += cof[j]/++y; > return_val = -tmp+log(2.5066282746310005*ser/x); > """ > > return weave.inline(gammln,['xx'],headers=['math.h'],compiler='gcc') > > As far as I can tell this looks valid. However, it fails: > > <weave: compiling> > /Users/chris/.python24_compiled/sc_2ced629c1dae7b8a8d767dfb199392380.cpp:17:10: > #include expects "FILENAME" or <FILENAME> > /Users/chris/.python24_compiled/sc_2ced629c1dae7b8a8d767dfb199392380.cpp:660:23: > invalid preprocessing directive #Line > /Users/chris/.python24_compiled/sc_2ced629c1dae7b8a8d767dfb199392380.cpp:17:10: > #include expects "FILENAME" or <FILENAME> > /Users/chris/.python24_compiled/sc_2ced629c1dae7b8a8d767dfb199392380.cpp:660:23: > invalid preprocessing directive #Line > --------------------------------------------------------------------------- > scipy.weave.build_tools.CompileError > Traceback (most recent call last) > > /Users/chris/<console> > > /Users/chris/likelihood_plots.py in gamma_function(xx=4.0) > 22 """ > 23 > ---> 24 return weave.inline(gammln,['xx'],headers=['math.h'],compiler='gcc') > global weave.inline = <function inline at 0x26aec30> > gammln = ' \n # Line 10 "likelihood_plots.py"\n > double x,y,tmp,ser; \n static double > cof[6]={76.18009172947146,-86.50532032941677, \n > 24.01409824083091,-1.231739572450155, \n > 0.1208650973866179e-2,-0.5395239384953e-5}; \n int j; \n > y=x=xx; \n tmp=x+5.5; \n tmp -= > (x+0.5)*log(tmp); \n ser=1.000000000190015; \n > for (j=0;j<=5;j++) ser += cof[j]/++y; \n return_val = > -tmp+log(2.5066282746310005*ser/x); \n ' > global headers = undefined > global compiler = undefined > 25 > 26 def factln(x): > > /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave/inline_tools.py > in inline(code=' \n # Line 10 "likelihood_plots.py"\n > ...n_val = -tmp+log(2.5066282746310005*ser/x); \n ', > arg_names=['xx'], local_dict={'__builtins__': {'ArithmeticError': > <class exceptions.ArithmeticError at 0x7ba0>, 'AssertionError': <class > exceptions.AssertionError at 0x7ab0>, 'AttributeError': <class > exceptions.AttributeError at 0x7960>, 'DeprecationWarning': <class > exceptions.DeprecationWarning at 0x1e120>, 'EOFError': <class > exceptions.EOFError at 0x7750>, 'Ellipsis': Ellipsis, > 'EnvironmentError': <class exceptions.EnvironmentError at 0x7630>, > 'Exception': <class exceptions.Exception at 0x7480>, 'False': False, > 'FloatingPointError': <class exceptions.FloatingPointError at 0x7cc0>, > ...}, 'gammln': ' \n # Line 10 "likelihood_plots.py"\n > ...n_val = -tmp+log(2.5066282746310005*ser/x); \n ', 'xx': 4.0}, > global_dict={'ArrayType': <type 'scipy.ndarray'>, 'Character': 'S1', > 'Complex': 'D', 'Complex0': 'D', 'Complex128': 'G', 'Complex32': 'F', > 'Complex64': 'D', 'ERR_CALL': 3, 'ERR_DEFAULT': 0, 'ERR_IGNORE': 0, > ...}, force=0, compiler='gcc', verbose=0, support_code=None, > headers=['math.h'], customize=None, type_converters=None, > auto_downcast=1, **kw={}) > 332 customize=customize, > 333 type_converters = type_converters, > --> 334 auto_downcast = auto_downcast, > auto_downcast = 1 > 335 **kw) > 336 > > /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave/inline_tools.py > in compile_function(code=' \n # Line 10 > "likelihood_plots.py"\n ...n_val = > -tmp+log(2.5066282746310005*ser/x); \n ', arg_names=['xx'], > local_dict={'__builtins__': {'ArithmeticError': <class > exceptions.ArithmeticError at 0x7ba0>, 'AssertionError': <class > exceptions.AssertionError at 0x7ab0>, 'AttributeError': <class > exceptions.AttributeError at 0x7960>, 'DeprecationWarning': <class > exceptions.DeprecationWarning at 0x1e120>, 'EOFError': <class > exceptions.EOFError at 0x7750>, 'Ellipsis': Ellipsis, > 'EnvironmentError': <class exceptions.EnvironmentError at 0x7630>, > 'Exception': <class exceptions.Exception at 0x7480>, 'False': False, > 'FloatingPointError': <class exceptions.FloatingPointError at 0x7cc0>, > ...}, 'gammln': ' \n # Line 10 "likelihood_plots.py"\n > ...n_val = -tmp+log(2.5066282746310005*ser/x); \n ', 'xx': 4.0}, > global_dict={'ArrayType': <type 'scipy.ndarray'>, 'Character': 'S1', > 'Complex': 'D', 'Complex0': 'D', 'Complex128': 'G', 'Complex32': 'F', > 'Complex64': 'D', 'ERR_CALL': 3, 'ERR_DEFAULT': 0, 'ERR_IGNORE': 0, > ...}, module_dir='likelihood_plots.py', compiler='gcc', verbose=0, > support_code=None, headers=['math.h'], customize=None, > type_converters=None, auto_downcast=1, **kw={}) > 440 # setting. All input keywords are passed through to distutils > 441 mod.compile(location=storage_dir,compiler=compiler, > --> 442 verbose=verbose, **kw) > verbose = 0 > kw = {} > 443 > 444 # import the module and return the function. Make sure > > /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave/ext_tools.py > in compile(self=<scipy.weave.inline_tools.inline_ext_module instance > at 0x4610260>, location='/Users/chris/.python24_compiled', > compiler='gcc', verbose=0, **kw={'define_macros': [], > 'extra_compile_args': [], 'extra_link_args': [], 'include_dirs': > ['/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave', > '/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave/scxx'], > 'libraries': [], 'library_dirs': [], 'sources': > ['/Library/Frameworks/Python.framework/Versions/2....n2.4/site-packages/scipy/weave/scxx/weave_imp.cpp']}) > 351 success = build_tools.build_extension(file, temp_dir = temp, > 352 compiler_name = compiler, > --> 353 verbose = verbose, **kw) > verbose = 0 > kw = {'extra_link_args': [], 'define_macros': [], 'libraries': > [], 'sources': ['/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave/scxx/weave_imp.cpp'], > 'extra_compile_args': [], 'library_dirs': [], 'include_dirs': > ['/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave', > '/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave/scxx']} > 354 if not success: > 355 raise SystemError, 'Compilation failed' > > /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave/build_tools.py > in build_extension(module_path='/Users/chris/.python24_compiled/sc_2ced629c1dae7b8a8d767dfb199392380.cpp', > compiler_name='unix', build_dir='/Users/chris/.python24_compiled', > temp_dir='/tmp/chris/python24_intermediate/compiler_d8b3562b82bb4cfa4fea7b37ec5ea6ce', > verbose=0, **kw={'define_macros': [], 'extra_compile_args': [], > 'extra_link_args': [], 'include_dirs': > ['/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave', > '/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave/scxx'], > 'libraries': [], 'library_dirs': [], 'sources': > ['/Library/Frameworks/Python.framework/Versions/2....n2.4/site-packages/scipy/weave/scxx/weave_imp.cpp']}) > 272 environ = copy.deepcopy(os.environ) > 273 try: > --> 274 setup(name = module_name, ext_modules = [ext],verbose=verb) > setup = <function setup at 0x2932530> > global name = undefined > module_name = 'sc_2ced629c1dae7b8a8d767dfb199392380' > global ext_modules = undefined > ext = <scipy.distutils.extension.Extension instance at 0x4620b48> > verbose = 0 > verb = 0 > 275 finally: > 276 # restore state > > /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/distutils/core.py > in setup(**attr={'ext_modules': [<scipy.distutils.extension.Extension > instance at 0x4620b48>], 'name': > 'sc_2ced629c1dae7b8a8d767dfb199392380', 'verbose': 0}) > 91 new_attr['data_files'] = new_data_files > 92 > ---> 93 return old_setup(**new_attr) > global old_setup = <function setup at 0x28a37b0> > new_attr = {'cmdclass': {'bdist_rpm': <class > scipy.distutils.command.bdist_rpm.bdist_rpm at 0x292fc00>, 'sdist': > <class scipy.distutils.command.sdist.sdist at 0x29182d0>, 'build_src': > <class scipy.distutils.command.build_src.build_src at 0x290ef00>, > 'config_fc': <class scipy.distutils.command.config_compiler.config_fc > at 0x28fe360>, 'build_clib': <class > scipy.distutils.command.build_clib.build_clib at 0x28fea50>, > 'build_scripts': <class > scipy.distutils.command.build_scripts.build_scripts at 0x290ef60>, > 'build_ext': <class scipy.distutils.command.build_ext.build_ext at > 0x28fe690>, 'develop': <class setuptools.command.develop.develop at > 0x292fed0>, 'build_py': <class > scipy.distutils.command.build_py.build_py at 0x28fe330>, > 'install_data': <class > scipy.distutils.command.install_data.install_data at 0x29186f0>, > 'egg_info': <class setuptools.command.egg_info.egg_info at 0x2b2a8a0>, > 'install_headers': <class > scipy.distutils.command.install_headers.install_headers at 0x292f6f0>, > 'easy_install': <class setuptools.command.easy_install.easy_install at > 0x295ec90>, 'bdist_egg': <class setuptools.command.bdist_egg.bdist_egg > at 0x28dffc0>, 'install': <class > scipy.distutils.command.install.install at 0x292f720>, 'config': > <class scipy.distutils.command.config.config at 0x28f7f90>, 'build': > <class scipy.distutils.command.build.build at 0x28fe240>}, 'headers': > [], 'ext_modules': [<scipy.distutils.extension.Extension instance at > 0x4620b48>], 'name': 'sc_2ced629c1dae7b8a8d767dfb199392380', > 'verbose': 0} > 94 > 95 def _check_append_library(libraries, item): > > /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/distutils/core.py > in setup(**attrs={'cmdclass': {'bdist_egg': <class > setuptools.command.bdist_egg.bdist_egg at 0x28dffc0>, 'bdist_rpm': > <class scipy.distutils.command.bdist_rpm.bdist_rpm at 0x292fc00>, > 'build': <class scipy.distutils.command.build.build at 0x28fe240>, > 'build_clib': <class scipy.distutils.command.build_clib.build_clib at > 0x28fea50>, 'build_ext': <class > scipy.distutils.command.build_ext.build_ext at 0x28fe690>, 'build_py': > <class scipy.distutils.command.build_py.build_py at 0x28fe330>, > 'build_scripts': <class > scipy.distutils.command.build_scripts.build_scripts at 0x290ef60>, > 'build_src': <class scipy.distutils.command.build_src.build_src at > 0x290ef00>, 'config': <class scipy.distutils.command.config.config at > 0x28f7f90>, 'config_fc': <class > scipy.distutils.command.config_compiler.config_fc at 0x28fe360>, ...}, > 'ext_modules': [<scipy.distutils.extension.Extension instance at > 0x4620b48>], 'headers': [], 'name': > 'sc_2ced629c1dae7b8a8d767dfb199392380', 'script_args': ['build_ext', > '--compiler=unix', '--build-lib', '/Users/chris/.python24_compiled', > '--build-temp', > '/tmp/chris/python24_intermediate/compiler_d8b3562b82bb4cfa4fea7b37ec5ea6ce'], > 'script_name': '', 'verbose': 0}) > 164 raise > 165 else: > --> 166 raise SystemExit, "error: " + str(msg) > global SystemExit = undefined > global str = undefined > msg = <distutils.errors.CompileError instance at 0x4625058> > 167 > 168 return dist > > CompileError: error: Command "c++ -fno-strict-aliasing > -Wno-long-double -no-cpp-precomp -mno-fused-madd -fPIC -fno-common > -dynamic -DNDEBUG -g -O3 -Wstrict-prototypes > -I/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave > -I/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave/scxx > -I/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/base/include > -I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 > -c /Users/chris/.python24_compiled/sc_2ced629c1dae7b8a8d767dfb199392380.cpp > -o /tmp/chris/python24_intermediate/compiler_d8b3562b82bb4cfa4fea7b37ec5ea6ce/Users/chris/.python24_compiled/sc_2ced629c1dae7b8a8d767dfb199392380.o" > failed with exit status 1 > > > -- > Chris Fonnesbeck > Atlanta, GA > -- Chris Fonnesbeck Atlanta, GA

1 0

weave issue
by Chris Fonnesbeck 15 Dec '05

15 Dec '05

I am trying to use weave inline to help me calculate the gamma function: def gamma_function(xx): # Returns the value ln[gamma(xx)] for xx > 0 gammln = """ # Line 10 "likelihood_plots.py" double x,y,tmp,ser; static double cof[6]={76.18009172947146,-86.50532032941677, 24.01409824083091,-1.231739572450155, 0.1208650973866179e-2,-0.5395239384953e-5}; int j; y=x=xx; tmp=x+5.5; tmp -= (x+0.5)*log(tmp); ser=1.000000000190015; for (j=0;j<=5;j++) ser += cof[j]/++y; return_val = -tmp+log(2.5066282746310005*ser/x); """ return weave.inline(gammln,['xx'],headers=['math.h'],compiler='gcc') As far as I can tell this looks valid. However, it fails: <weave: compiling> /Users/chris/.python24_compiled/sc_2ced629c1dae7b8a8d767dfb199392380.cpp:17:10: #include expects "FILENAME" or <FILENAME> /Users/chris/.python24_compiled/sc_2ced629c1dae7b8a8d767dfb199392380.cpp:660:23: invalid preprocessing directive #Line /Users/chris/.python24_compiled/sc_2ced629c1dae7b8a8d767dfb199392380.cpp:17:10: #include expects "FILENAME" or <FILENAME> /Users/chris/.python24_compiled/sc_2ced629c1dae7b8a8d767dfb199392380.cpp:660:23: invalid preprocessing directive #Line --------------------------------------------------------------------------- scipy.weave.build_tools.CompileError Traceback (most recent call last) /Users/chris/<console> /Users/chris/likelihood_plots.py in gamma_function(xx=4.0) 22 """ 23 ---> 24 return weave.inline(gammln,['xx'],headers=['math.h'],compiler='gcc') global weave.inline = <function inline at 0x26aec30> gammln = ' \n # Line 10 "likelihood_plots.py"\n double x,y,tmp,ser; \n static double cof[6]={76.18009172947146,-86.50532032941677, \n 24.01409824083091,-1.231739572450155, \n 0.1208650973866179e-2,-0.5395239384953e-5}; \n int j; \n y=x=xx; \n tmp=x+5.5; \n tmp -= (x+0.5)*log(tmp); \n ser=1.000000000190015; \n for (j=0;j<=5;j++) ser += cof[j]/++y; \n return_val = -tmp+log(2.5066282746310005*ser/x); \n ' global headers = undefined global compiler = undefined 25 26 def factln(x): /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave/inline_tools.py in inline(code=' \n # Line 10 "likelihood_plots.py"\n ...n_val = -tmp+log(2.5066282746310005*ser/x); \n ', arg_names=['xx'], local_dict={'__builtins__': {'ArithmeticError': <class exceptions.ArithmeticError at 0x7ba0>, 'AssertionError': <class exceptions.AssertionError at 0x7ab0>, 'AttributeError': <class exceptions.AttributeError at 0x7960>, 'DeprecationWarning': <class exceptions.DeprecationWarning at 0x1e120>, 'EOFError': <class exceptions.EOFError at 0x7750>, 'Ellipsis': Ellipsis, 'EnvironmentError': <class exceptions.EnvironmentError at 0x7630>, 'Exception': <class exceptions.Exception at 0x7480>, 'False': False, 'FloatingPointError': <class exceptions.FloatingPointError at 0x7cc0>, ...}, 'gammln': ' \n # Line 10 "likelihood_plots.py"\n ...n_val = -tmp+log(2.5066282746310005*ser/x); \n ', 'xx': 4.0}, global_dict={'ArrayType': <type 'scipy.ndarray'>, 'Character': 'S1', 'Complex': 'D', 'Complex0': 'D', 'Complex128': 'G', 'Complex32': 'F', 'Complex64': 'D', 'ERR_CALL': 3, 'ERR_DEFAULT': 0, 'ERR_IGNORE': 0, ...}, force=0, compiler='gcc', verbose=0, support_code=None, headers=['math.h'], customize=None, type_converters=None, auto_downcast=1, **kw={}) 332 customize=customize, 333 type_converters = type_converters, --> 334 auto_downcast = auto_downcast, auto_downcast = 1 335 **kw) 336 /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave/inline_tools.py in compile_function(code=' \n # Line 10 "likelihood_plots.py"\n ...n_val = -tmp+log(2.5066282746310005*ser/x); \n ', arg_names=['xx'], local_dict={'__builtins__': {'ArithmeticError': <class exceptions.ArithmeticError at 0x7ba0>, 'AssertionError': <class exceptions.AssertionError at 0x7ab0>, 'AttributeError': <class exceptions.AttributeError at 0x7960>, 'DeprecationWarning': <class exceptions.DeprecationWarning at 0x1e120>, 'EOFError': <class exceptions.EOFError at 0x7750>, 'Ellipsis': Ellipsis, 'EnvironmentError': <class exceptions.EnvironmentError at 0x7630>, 'Exception': <class exceptions.Exception at 0x7480>, 'False': False, 'FloatingPointError': <class exceptions.FloatingPointError at 0x7cc0>, ...}, 'gammln': ' \n # Line 10 "likelihood_plots.py"\n ...n_val = -tmp+log(2.5066282746310005*ser/x); \n ', 'xx': 4.0}, global_dict={'ArrayType': <type 'scipy.ndarray'>, 'Character': 'S1', 'Complex': 'D', 'Complex0': 'D', 'Complex128': 'G', 'Complex32': 'F', 'Complex64': 'D', 'ERR_CALL': 3, 'ERR_DEFAULT': 0, 'ERR_IGNORE': 0, ...}, module_dir='likelihood_plots.py', compiler='gcc', verbose=0, support_code=None, headers=['math.h'], customize=None, type_converters=None, auto_downcast=1, **kw={}) 440 # setting. All input keywords are passed through to distutils 441 mod.compile(location=storage_dir,compiler=compiler, --> 442 verbose=verbose, **kw) verbose = 0 kw = {} 443 444 # import the module and return the function. Make sure /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave/ext_tools.py in compile(self=<scipy.weave.inline_tools.inline_ext_module instance at 0x4610260>, location='/Users/chris/.python24_compiled', compiler='gcc', verbose=0, **kw={'define_macros': [], 'extra_compile_args': [], 'extra_link_args': [], 'include_dirs': ['/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave', '/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave/scxx'], 'libraries': [], 'library_dirs': [], 'sources': ['/Library/Frameworks/Python.framework/Versions/2....n2.4/site-packages/scipy/weave/scxx/weave_imp.cpp']}) 351 success = build_tools.build_extension(file, temp_dir = temp, 352 compiler_name = compiler, --> 353 verbose = verbose, **kw) verbose = 0 kw = {'extra_link_args': [], 'define_macros': [], 'libraries': [], 'sources': ['/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave/scxx/weave_imp.cpp'], 'extra_compile_args': [], 'library_dirs': [], 'include_dirs': ['/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave', '/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave/scxx']} 354 if not success: 355 raise SystemError, 'Compilation failed' /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave/build_tools.py in build_extension(module_path='/Users/chris/.python24_compiled/sc_2ced629c1dae7b8a8d767dfb199392380.cpp', compiler_name='unix', build_dir='/Users/chris/.python24_compiled', temp_dir='/tmp/chris/python24_intermediate/compiler_d8b3562b82bb4cfa4fea7b37ec5ea6ce', verbose=0, **kw={'define_macros': [], 'extra_compile_args': [], 'extra_link_args': [], 'include_dirs': ['/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave', '/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave/scxx'], 'libraries': [], 'library_dirs': [], 'sources': ['/Library/Frameworks/Python.framework/Versions/2....n2.4/site-packages/scipy/weave/scxx/weave_imp.cpp']}) 272 environ = copy.deepcopy(os.environ) 273 try: --> 274 setup(name = module_name, ext_modules = [ext],verbose=verb) setup = <function setup at 0x2932530> global name = undefined module_name = 'sc_2ced629c1dae7b8a8d767dfb199392380' global ext_modules = undefined ext = <scipy.distutils.extension.Extension instance at 0x4620b48> verbose = 0 verb = 0 275 finally: 276 # restore state /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/distutils/core.py in setup(**attr={'ext_modules': [<scipy.distutils.extension.Extension instance at 0x4620b48>], 'name': 'sc_2ced629c1dae7b8a8d767dfb199392380', 'verbose': 0}) 91 new_attr['data_files'] = new_data_files 92 ---> 93 return old_setup(**new_attr) global old_setup = <function setup at 0x28a37b0> new_attr = {'cmdclass': {'bdist_rpm': <class scipy.distutils.command.bdist_rpm.bdist_rpm at 0x292fc00>, 'sdist': <class scipy.distutils.command.sdist.sdist at 0x29182d0>, 'build_src': <class scipy.distutils.command.build_src.build_src at 0x290ef00>, 'config_fc': <class scipy.distutils.command.config_compiler.config_fc at 0x28fe360>, 'build_clib': <class scipy.distutils.command.build_clib.build_clib at 0x28fea50>, 'build_scripts': <class scipy.distutils.command.build_scripts.build_scripts at 0x290ef60>, 'build_ext': <class scipy.distutils.command.build_ext.build_ext at 0x28fe690>, 'develop': <class setuptools.command.develop.develop at 0x292fed0>, 'build_py': <class scipy.distutils.command.build_py.build_py at 0x28fe330>, 'install_data': <class scipy.distutils.command.install_data.install_data at 0x29186f0>, 'egg_info': <class setuptools.command.egg_info.egg_info at 0x2b2a8a0>, 'install_headers': <class scipy.distutils.command.install_headers.install_headers at 0x292f6f0>, 'easy_install': <class setuptools.command.easy_install.easy_install at 0x295ec90>, 'bdist_egg': <class setuptools.command.bdist_egg.bdist_egg at 0x28dffc0>, 'install': <class scipy.distutils.command.install.install at 0x292f720>, 'config': <class scipy.distutils.command.config.config at 0x28f7f90>, 'build': <class scipy.distutils.command.build.build at 0x28fe240>}, 'headers': [], 'ext_modules': [<scipy.distutils.extension.Extension instance at 0x4620b48>], 'name': 'sc_2ced629c1dae7b8a8d767dfb199392380', 'verbose': 0} 94 95 def _check_append_library(libraries, item): /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/distutils/core.py in setup(**attrs={'cmdclass': {'bdist_egg': <class setuptools.command.bdist_egg.bdist_egg at 0x28dffc0>, 'bdist_rpm': <class scipy.distutils.command.bdist_rpm.bdist_rpm at 0x292fc00>, 'build': <class scipy.distutils.command.build.build at 0x28fe240>, 'build_clib': <class scipy.distutils.command.build_clib.build_clib at 0x28fea50>, 'build_ext': <class scipy.distutils.command.build_ext.build_ext at 0x28fe690>, 'build_py': <class scipy.distutils.command.build_py.build_py at 0x28fe330>, 'build_scripts': <class scipy.distutils.command.build_scripts.build_scripts at 0x290ef60>, 'build_src': <class scipy.distutils.command.build_src.build_src at 0x290ef00>, 'config': <class scipy.distutils.command.config.config at 0x28f7f90>, 'config_fc': <class scipy.distutils.command.config_compiler.config_fc at 0x28fe360>, ...}, 'ext_modules': [<scipy.distutils.extension.Extension instance at 0x4620b48>], 'headers': [], 'name': 'sc_2ced629c1dae7b8a8d767dfb199392380', 'script_args': ['build_ext', '--compiler=unix', '--build-lib', '/Users/chris/.python24_compiled', '--build-temp', '/tmp/chris/python24_intermediate/compiler_d8b3562b82bb4cfa4fea7b37ec5ea6ce'], 'script_name': '', 'verbose': 0}) 164 raise 165 else: --> 166 raise SystemExit, "error: " + str(msg) global SystemExit = undefined global str = undefined msg = <distutils.errors.CompileError instance at 0x4625058> 167 168 return dist CompileError: error: Command "c++ -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd -fPIC -fno-common -dynamic -DNDEBUG -g -O3 -Wstrict-prototypes -I/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave -I/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/weave/scxx -I/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/base/include -I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 -c /Users/chris/.python24_compiled/sc_2ced629c1dae7b8a8d767dfb199392380.cpp -o /tmp/chris/python24_intermediate/compiler_d8b3562b82bb4cfa4fea7b37ec5ea6ce/Users/chris/.python24_compiled/sc_2ced629c1dae7b8a8d767dfb199392380.o" failed with exit status 1 -- Chris Fonnesbeck Atlanta, GA

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interpolate subpackage
by Frank 15 Dec '05

15 Dec '05

Does anyone know why certain subpackages such as interpolate and integrate are not defined while others such as linalg and fft work fine? For example: Python 2.3.5 (#1, Mar 20 2005, 20:38:20) [GCC 3.3 20030304 (Apple Computer, Inc. build 1809)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> from scipy import * >>> interpolate Traceback (most recent call last): File "<stdin>", line 1, in ? NameError: name 'interpolate' is not defined >>> linalg <module 'scipy.basic.linalg' from '/System/Library/Frameworks/ Python.framework/Versions/2.3/lib/python2.3/site-packages/scipy/basic/ linalg.pyc'> >>>

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Bug in inverse matrix calculation for "scipy_core-0.8.4.win32-py2.3.exe"
by Randewijk P-J <pjrandew＠sun.ac.za> 15 Dec '05

15 Dec '05

Dear Travis, Thank-you for the "silent" version (0.8.4) of scipy_core. Unfortunately when trying to invert a singular matrix using scipy_core 0.8.4, python "crashes" instead of issuing the usual error message: ... >>> m.I Traceback (most recent call last): File "<interactive input>", line 1, in ? File "C:\Python\Lib\site-packages\scipy\base\matrix.py", line 197, in getI return matrix(linalg.inv(self)) File "C:\Python\Lib\site-packages\scipy\linalg\basic.py", line 221, in inv if info>0: raise LinAlgError, "singular matrix" LinAlgError: singular matrix >>> ... On this note. Is there a way of determining before hand in scipy if a matrix is singular, say by calculating its rank, e.g.: ... >>> if matrix_rank(my_matrix) < max(my_matrix.shape): ... And then if the matrix is singular, is there a way in scipy to calculate the reduced row-echelon form (RREF) for a linear system of equation, a.k.a. linalg.solve, e.g. ... >>> linalg.rref(a,b) ... http://en.wikipedia.org/wiki/Gauss-Jordan_elimination shows a "formal algorithm" to calculate reduced row-echelon matrix. Its looks easy to implement in ("high level") python, but a "low level" implementation in scipy would be "nice"... (for lazy people like myself) Regards, Peter-Jan

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Re: [SciPy-user] Bug in inversematrixcalculation for "scipy_core-0.8.4.win32-py2.3.exe"
by Randewijk P-J <pjrandew＠sun.ac.za> 15 Dec '05

15 Dec '05

Oops, My platform is winXP, py2.3 using the following binaries: scipy_core-0.8.4.win32-py2.3.exe and scipy-0.4.3.win32-py2.3.exe The "older" scipy_core binary file: scipy_core-0.6.1.win32-py2.3.exe and scipy-0.4.3.win32-py2.3.exe does works fine together... > -----Original Message----- > From: scipy-user-bounces(a)scipy.net > [mailto:scipy-user-bounces@scipy.net] On Behalf Of Randewijk > P-J <pjrandew(a)sun.ac.za> > Sent: 15 December 2005 09:39 > To: SciPy Users List > Subject: Re: [SciPy-user] Bug in inversematrixcalculation for > "scipy_core-0.8.4.win32-py2.3.exe" > > > Dear Travis, > > ... > >>> os.environ['NO_SCIPY_IMPORT']='True' > >>> from scipy import * > Skip importing scipy packages (NO_SCIPY_IMPORT=True) > >>> k > matrix([[ 400. , 400. , 0. , 0. ], > [ 0. , 0. , 400. , 400. ], > [ 0. , 346.41016151, 0. , 173.20508076], > [ 346.41016151, 0. , 173.20508076, 0. ]]) > >>> k.I > Traceback (most recent call last): > File "<pyshell#5>", line 1, in ? > k.I > File "C:\Python\Lib\site-packages\scipy\base\matrix.py", > line 204, in getI > return matrix(linalg.inv(self)) > File > "C:\Python\Lib\site-packages\scipy\basic\basic_lite.py", line > 103, in inverse > return solve_linear_equations(a, Numeric.identity(a.shape[0])) > File > "C:\Python\Lib\site-packages\scipy\basic\basic_lite.py", line > 93, in solve_linear_equations > raise LinAlgError, 'Singular matrix' > LinAlgError: Singular matrix > >>> > ... > > Further to Nils & Fernando's comments, for the following > singular matrix k, and with 'NO_SCIPY_IMPORT'='True' > > ... > >>> k > matrix([[ 391.69663728, 407.81602433, 0. , 0. ], > [ 0. , 0. , 391.69663728, 407.81602433], > [ 0. , 346.1991378 , 0. , 183.56941791], > [ 346.1991378 , 0. , 183.56941791, 0. ]]) > >>> k.I > matrix([[ -1.64892268e+13, -8.74328513e+12, 1.94239968e+13, > 1.86562414e+13], > [ 1.58374716e+13, 8.39769695e+12, -1.86562414e+13, > -1.79188325e+13], > [ 3.10975335e+13, 1.64892268e+13, -3.66323052e+13, > -3.51843721e+13], > [ -2.98683685e+13, -1.58374716e+13, 3.51843721e+13, > 3.37936702e+13]]) > >>> > ... > > Both k matrixes fail however in full scipy... and shows the > annoying message, "pythonw.exe has encountered a problem and > needs to close. We are sorry for the inconvenience." > > My platform is winXP, py2.3 using the following binaries: > scipy_core-0.8.4.win32-py2.3.exe scipy-0.4.3.win32-py2.3.exe > > scipy_core-0.6.1.win32-py2.3.exe > and > scipy-0.4.3.win32-py2.3.exe > > Doesn't works fine together... > > PJR > > P.S. How does the 'NO_SCIPY_IMPORT' environment variable work? > > with > > ... > >>> os.environ['NO_SCIPY_IMPORT']=1 > > Traceback (most recent call last): > File "<pyshell#1>", line 1, in ? > os.environ['NO_SCIPY_IMPORT']=1 # this will not import > full scipy but > File "C:\Python\Lib\os.py", line 414, in __setitem__ > putenv(key, item) > TypeError: putenv() argument 2 must be string, not int > ... > > "os.environ['NO_SCIPY_IMPORT']='True'" works, as shown at the > top, but > > ... > >>> os.environ['NO_SCIPY_IMPORT']='False' > >>> from scipy import * > Skip importing scipy packages (NO_SCIPY_IMPORT=False) > >>> > ... > > Doesn't work as I would have expect it... > > > > -----Original Message----- > > From: scipy-user-bounces(a)scipy.net > > [mailto:scipy-user-bounces@scipy.net] On Behalf Of Travis Oliphant > > Sent: 15 December 2005 00:27 > > To: SciPy Users List > > Subject: Re: [SciPy-user] Bug in inverse matrixcalculation > > for "scipy_core-0.8.4.win32-py2.3.exe" > > > > > > Randewijk P-J <pjrandew(a)sun.ac.za> wrote: > > > > > Dear Travis, > > > > > > Thank-you for the "silent" version (0.8.4) of scipy_core. > > > > > > Unfortunately when trying to invert a singular matrix using > > scipy_core > > > 0.8.4, python "crashes" instead of issuing the usual > error message: > > > > I'm not seeing this. I'm getting the proper error message. > > Can you show > > us the matrix you are using and give more information about > > the platform. > > > > Also, try it when the environment variable NO_SCIPY_IMPORT=1 > > > > import os > > os.environ['NO_SCIPY_IMPORT']=1 # this will not import full > > scipy but > > use only scipy_core\ > > import scipy > > > > Full scipy installs its own (hopefully better) matrix > > inverse. We need > > to figure out which one is giving you trouble. > > > > -Travis > > > > > > _______________________________________________ > > SciPy-user mailing list > > SciPy-user(a)scipy.net > http://www.scipy.net/mailman/listinfo/scipy-user > > > > _______________________________________________ > SciPy-user mailing list > SciPy-user(a)scipy.net http://www.scipy.net/mailman/listinfo/scipy-user >

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