Mailman 3 February 2009 - SciPy-Dev

Problem with weave and blitz and gcc 4.3 (SciPy 0.7.0)
by Lars Bittrich Feb. 12, 2009

Feb. 12, 2009

Hi all, on Ubuntu intrepid using gcc 4.3 I have problems using weave together with blitz converters. There is already an old ticket: http://www.scipy.org/scipy/scipy/ticket/739 Here is a minimal example to reproduce the problem (even with SciPy 0.7.0): from scipy.weave import inline, converters from numpy import array a = array([1]) code = "return_val = a(0);" print inline(code, ['a'], type_converters=converters.blitz) For the complete error output look at the ticket. The essential part is: /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/funcs.h:530: error: 'labs' is not a member of 'std' ... /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/mathfunc.h:45: error: 'labs' is not a member of 'std' As a workaround I should use gcc 4.2 but the also in the ticket mentioned patch from debian: http://bugs.debian.org/cgi-bin/bugreport.cgi?msg=10;filename=blitz%2B%2B.pa… seems much easier to apply. It is only two includes (both #include <cstdlib>). The patch workes well and all tests scipy.weave.test('full') are ok. Is there any reason why the patch is not applied in SciPy? I have even tested the patch with Ubuntu hardy (SciPy 0.6.0) and gcc 4.2. There at least the number of errors and failures does not change with or without the patch. Best regards, Lars

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scikits learn
by Nils Wagner Feb. 12, 2009

Feb. 12, 2009

Hi all, The installation of learn failed with compile options: '-I/home/nwagner/local/lib64/python2.6/site-packages/numpy/core/include -I/usr/include/python2.6 -c' gcc: _lk.c gcc: _lk.c: Datei oder Verzeichnis nicht gefunden gcc: no input files gcc: _lk.c: Datei oder Verzeichnis nicht gefunden gcc: no input files error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -fwrapv -fPIC -I/home/nwagner/local/lib64/python2.6/site-packages/numpy/core/include -I/usr/include/python2.6 -c _lk.c -o build/temp.linux-x86_64-2.6/_lk.o" failed with exit status 1 Any idea ? Nils

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scikits umfpack
by Nils Wagner Feb. 11, 2009

Feb. 11, 2009

python test_umfpack.py Traceback (most recent call last): File "test_umfpack.py", line 195, in <module> nose.run(argv=['', __file__]) NameError: name 'nose' is not defined #!/usr/bin/env python # """ Test functions for UMFPACK solver. The solver is accessed via spsolve(), so the built-in SuperLU solver is tested too, in single precision. """ import warnings import nose An "import nose" works for me. Another issue python try_umfpack.py /home/nwagner/local/lib64/python2.6/site-packages/scipy/linsolve/__init__.py:4: DeprecationWarning: scipy.linsolve has moved to scipy.sparse.linalg.dsolve warn('scipy.linsolve has moved to scipy.sparse.linalg.dsolve', DeprecationWarning) Traceback (most recent call last): File "try_umfpack.py", line 7, in <module> import scipy.linsolve.umfpack as um ImportError: No module named umfpack nwagner@linux-mogv:~/svn/umfpack/tests> python Python 2.6 (r26:66714, Feb 3 2009, 20:49:49) [GCC 4.3.2 [gcc-4_3-branch revision 141291]] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from scikits import umfpack as um The corresponding line in try_umfpack.py should be replaced by #import scipy.linsolve.umfpack as um from scikits import umfpack as um Nils

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ANN: SciPy 0.7.0
by Jarrod Millman Feb. 11, 2009

Feb. 11, 2009

I'm pleased to announce SciPy 0.7.0. SciPy is a package of tools for science and engineering for Python. It includes modules for statistics, optimization, integration, linear algebra, Fourier transforms, signal and image processing, ODE solvers, and more. This release comes sixteen months after the 0.6.0 release and contains many new features, numerous bug-fixes, improved test coverage, and better documentation. Please note that SciPy 0.7.0 requires Python 2.4 or greater (but not Python 3) and NumPy 1.2.0 or greater. For information, please see the release notes: https://sourceforge.net/project/shownotes.php?release_id=660191&group_id=27… You can download the release from here: https://sourceforge.net/project/showfiles.php?group_id=27747&package_id=195… Thank you to everybody who contributed to this release. Enjoy, Jarrod Millman

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0.7 release
by jason-sage＠creativetrax.com Feb. 10, 2009

Feb. 10, 2009

I am curious about the status of the 0.7 release. IIRC, there was a scipy 0.7rc2 tagged about two weeks ago. Thanks, Jason

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SciLAB
by Miroslav.Houdek＠esa.int Feb. 10, 2009

Feb. 10, 2009

I needed to read MatLAB and SciLAB files and found only MatLAB support in Numpy/Scipy, so I developed the support for SciLAB files. Now it's working with basic data types, so it works allright for the task I needed. Would anyone be interested in including it in Scipy.Io? It would need some extra effort to include more obscure data types and stuff like that. If so, what should I do? Best regards, Miroslav -------------------------------------------------------- Bla, bla, bla, something deep as usual in mailing lists, nothing is as it seems, this and that sucks while other things rule.

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DCT naming conventions ?
by David Cournapeau Feb. 10, 2009

Feb. 10, 2009

Hi, I needed DCT transforms, so I finished implementing them in scipy (both single and double prec): http://projects.scipy.org/scipy/scipy/browser/trunk/scipy/fftpack/realtrans… I followed the definitions of wikipedia/fftw, using the fftpack implementations. I am not sure about naming conventions: - dct2 is the type II DCT, not the 2dimension DCT (multidimensional dcts are not implemented - I don't need them myself) - dct3 and dct2 are inverse from each other (compared to dct/idct notation of matlab; dct2(x, norm=ortho) is the same as matlab dct(x), and dct3(x, norm='ortho') is the same as matlab idct. Unless someone has a better idea/suggestion, I will put those definitions in scipy.fftpack namespace in a couple of days, cheers, David

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some scipy.interpolate functions appear to be inaccessible
by Tom Grydeland Feb. 9, 2009

Feb. 9, 2009

Hi developers, I tried figuring out how to use scipy.interpolate to create cubic splines with "natural" boundary conditions (i.e. y'' = 0 at the end points), but failed. When I look in the source file for scipy/interpolate/interpolate.py it certainly looks like there is code to create the tridiagonal system to solve for such splines ( _get_spline3_Bb()), but this function appears to be orphaned. There are a number of functions _find_xxx() that do nothing except raise NotImplementedError, although these should be called from splmake(), from the looks of it. Does anyone know the intended structure of these functions? I could try to make them work, given a roadmap. Regards, -- Tom Grydeland <Tom.Grydeland(a)(gmail.com)>

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Distutils: incorrect inference of cpu type on Ubuntu Intrepid
by anand.prabhakar.patil Feb. 5, 2009

Feb. 5, 2009

Hi all, I just installed numpy from the debian packages on a virtual machine in a 'cloud' to do some multiprocessing. The numpy version is 1.1.1, but the problem (I think) would happen with 1.3.0.dev6034 as well. While trying to build a package that incorporates Fortran sources, I ran into the following: gfortran:f77: mbgw/st_cov_fun/fst_cov_fun.f f951: error: CPU you selected does not support x86-64 instruction set f951: error: CPU you selected does not support x86-64 instruction set f951: error: CPU you selected does not support x86-64 instruction set f951: error: CPU you selected does not support x86-64 instruction set error: Command "/usr/bin/gfortran -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops -march=k6-2 -mmmx -msse2 -msse -msse3 -Ibuild/src.linux-x86_64-2.5 -I/usr/lib/python2.5/site-packages/numpy/core/include -I/usr/include/python2.5 -c -c mbgw/st_cov_fun/fst_cov_fun.f -o build/temp.linux-x86_64-2.5/mbgw/st_cov_fun/fst_cov_fun.o" failed with exit status 1 The problem seems to be the -march=k6-2 flag, which is not right because the chip is a 64-bit Opteron. The flag was set because the method numpy.distutils.cpuinfo.cpu._is_AthlonK6_2 returned True: def _is_AthlonK6_2(self): return self._is_AMD() and self.info[0]['model'] == '2' def _is_AMD(self): return self.info[0]['vendor_id']=='AuthenticAMD' which is understandable given the machine's /proc/cpuinfo, which follows... but the chip is a 64-bit Opteron, as I said. Should I file a bug report? Thanks, Anand 0# cat /proc/cpuinfo processor : 0 vendor_id : AuthenticAMD cpu family : 16 model : 2 model name : Quad-Core AMD Opteron(tm) Processor 2352 stepping : 3 cpu MHz : 2109.267 cache size : 512 KB physical id : 0 siblings : 4 core id : 0 cpu cores : 4 apicid : 0 initial apicid : 0 fpu : yes fpu_exception : yes cpuid level : 5 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm 3dnowext 3dnow constant_tsc rep_good pni monitor cx16 lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs bogomips : 4218.52 TLB size : 1024 4K pages clflush size : 64 cache_alignment : 64 address sizes : 48 bits physical, 48 bits virtual power management: ts ttp tm stc 100mhzsteps hwpstate [...]

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scipy.org is down again
by Nils Wagner Feb. 5, 2009

Feb. 5, 2009

Hi all, I cannot access http://www.scipy.org Nils

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