Mailman 3 May 2012 - SciPy-User

Problem with Installation of Scipy on Macbook
by manisha pujari 21 Nov '12

21 Nov '12

Hello everyone, This is the first time I am using scipy and I am having much trouble to just install it on my macbook. I am using Python 2.6 and numpy 1.6.0. I downloaded scipy0.9.0 tar.gz file from the web link http://sourceforge.net/projects/scipy/files/scipy/ and tried to install it from the source. But on giving the command scipy-0.9.0$ python setup.py build it is always giving the following problem : Warning: No configuration returned, assuming unavailable.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'] non-existing path in 'scipy/io': 'docs' lapack_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-faltivec'] umfpack_info: libraries umfpack not found in /System/Library/Frameworks/Python.framework/Versions/2.6/lib libraries umfpack not found in /usr/local/lib libraries umfpack not found in /usr/lib /Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/system_info.py:463: UserWarning: UMFPACK sparse solver (http://www.cise.ufl.edu/research/sparse/umfpack/) not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [umfpack]) or by setting the UMFPACK environment variable. warnings.warn(self.notfounderror.__doc__) NOT AVAILABLE Traceback (most recent call last): File "setup.py", line 181, in <module> setup_package() File "setup.py", line 173, in setup_package configuration=configuration ) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/core.py", line 152, in setup config = configuration() File "setup.py", line 122, in configuration config.add_subpackage('scipy') File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/misc_util.py", line 972, in add_subpackage caller_level = 2) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/misc_util.py", line 941, in get_subpackage caller_level = caller_level + 1) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/misc_util.py", line 878, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/setup.py", line 20, in configuration config.add_subpackage('special') File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/misc_util.py", line 972, in add_subpackage caller_level = 2) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/misc_util.py", line 941, in get_subpackage caller_level = caller_level + 1) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/misc_util.py", line 878, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/special/setup.py", line 54, in configuration extra_info=get_info("npymath") File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/misc_util.py", line 2184, in get_info pkg_info = get_pkg_info(pkgname, dirs) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/misc_util.py", line 2136, in get_pkg_info return read_config(pkgname, dirs) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/npy_pkg_config.py", line 390, in read_config v = _read_config_imp(pkg_to_filename(pkgname), dirs) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/npy_pkg_config.py", line 326, in _read_config_imp meta, vars, sections, reqs = _read_config(filenames) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/npy_pkg_config.py", line 309, in _read_config meta, vars, sections, reqs = parse_config(f, dirs) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/npy_pkg_config.py", line 281, in parse_config raise PkgNotFound("Could not find file(s) %s" % str(filenames)) numpy.distutils.npy_pkg_config.PkgNotFound: Could not find file(s) ['/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/core/lib/npy-pkg-config/npymath.ini'] I am unable to understand where and what exactly the problem is. Can anyone please help me? I will be really thankful for a response. -- Regards, Manisha

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Installing issue with python 2.7, numpy 1.5.0b1 in my Mac
by Markus Hubig 05 Sep '12

05 Sep '12

Hi @all, maybe this is a known issue but I didn't find any useful information out there. When I try to install scipy-0.8.0 with pip I get this strange error about missing files ... File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/npy_pkg_config.py", line 276, in parse_config raise PkgNotFound("Could not find file(s) %s" % str(filenames)) numpy.distutils.npy_pkg_config.PkgNotFound: Could not find file(s) ['/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/lib/npy-pkg-config/npymath.ini'] The complete error can be found here: http://gist.github.com/527697 Is there a known solution for this? Any help would be nice ... - Markus -- Can't read my mail? Just don't hold it that way!

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[SciPy-user] adaptive simulated annealing (ASA)
by Dieter Werthmüller 14 Jul '12

14 Jul '12

Hi there, The message 'adaptive simulated annealing (ASA)' is over four years old now, asking for a python implementation of ASA (http://www.ingber.com/#ASA). I was wondering if such an implementation is around today? Kind regards, Dieter -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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linalg.eigh hangs only after importing sparse module
by Nicolas Pinto 25 Jun '12

25 Jun '12

Hello, The following simple code hangs only when sparse has been imported: ``` from scipy import sparse # <<<<<<< BUG import numpy as np from scipy import linalg N = 1000 np.random.seed(42) X = np.random.random((N, N)) print X.mean() v, Q = linalg.eigh(X) print v.mean() ``` Do you think this may be related to other arpack/umfpack/etc. known failures ? Please let us know how can we help fix this issue. Thanks for your help. Regards, -- Nicolas Pinto http://web.mit.edu/pinto

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Re: [SciPy-User] sinc interpolation
by Travis Oliphant 07 Jun '12

07 Jun '12

On Nov 20, 2009, at 2:26 PM, David Trem wrote: > Hello, > > Is sinc interpolation available in Scipy ? Yes, use scipy.signal.resample which uses a Fourier method to downsample or upsample a signal: from scipy.signal import resample from numpy import r_, sin from pylab import plot x = r_[0:10] y = sin(x) yy = resample(x, 100) # This is a bit tricky to get the x-samples right xx = r_[0:10:101j][:-1] plot(x,y,'ro', xx, yy) -Travis

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Re: [SciPy-User] 2-D data interpolation
by Nadav Horesh 06 Jun '12

06 Jun '12

You can try also scipy.interpolate.griddata (not the pylab's griddata!) Nadav

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Re: [SciPy-User] 2-D data interpolation
by David Baddeley 31 May '12

31 May '12

It's a bit of a special case, but if your starting values are already on a regular grid scipy.ndimage.map_coordinates is what you're after. Cheers, David ------------------------------ On Fri, Jun 1, 2012 1:18 AM NZST Darcoux Christine wrote: >Hi, > >I am converting a matlab code to python and I am looking for a >function like interp2 [1] for 2-D data interpolation. > >My matlab code has calls like > >M = interp2(x,y,z, xi,yi, 'cubic') > >where x, y and z describe a surface function. The interp2 function >returns a matrix M corresponding to the elements of xi and yi and >determined by cubic interpolation. > >Any help would be greatly appreciated, > >[1] http://www.mathworks.com/help/techdoc/ref/interp2.html >_______________________________________________ >SciPy-User mailing list >SciPy-User(a)scipy.org >http://mail.scipy.org/mailman/listinfo/scipy-user

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2-D data interpolation
by Darcoux Christine 31 May '12

31 May '12

Hi, I am converting a matlab code to python and I am looking for a function like interp2 [1] for 2-D data interpolation. My matlab code has calls like M = interp2(x,y,z, xi,yi, 'cubic') where x, y and z describe a surface function. The interp2 function returns a matrix M corresponding to the elements of xi and yi and determined by cubic interpolation. Any help would be greatly appreciated, [1] http://www.mathworks.com/help/techdoc/ref/interp2.html

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SciPy Install on Cygwin (Successful Once)
by Greg Mosby 30 May '12

30 May '12

Hi, I'm installing SciPy on my Win7 machine using Cygwin and its Python 2.6.7 version. I actually managed to successfully install Scipy not to long ago, but I had some rebasing issues that ended with me having to reinstall cygwin and those directories. I followed the basic outline of installing ATLAS plus LAPACK. I have Numpy. I made a site.cfg for my unzipped scipy-0.10.1 directory to make sure it would look in the right spots for the lapack, atlas, etc libraries. It's the same as the one I used for my successful install. But when I run: python setup.py config_fc --fcompiler=gnu95 install I get undefined reference errors. I can tell they are somehow due to the install script not including a clapack.h file. The location of the file is in my environment path, but perhaps not my python sys.path. However, it's in one of the include directories I place in the site.cfg too, so I'm not sure why the install is missing it. The last of the undefined references is: "build/temp.cygwin-1.7.15-i686-2.6/build/src.cygwin-1.7.15-i686-2.6/build/src.cygwin-1.7.15-i686-2.6/scipy/lib/lapack/clapackmodule.o:clapackmodule.c:(.data+0x1414): undefined reference to `_clapack_ztrtri' collect2: ld returned 1 exit status error: Command "/usr/bin/gfortran -Wall -Wall -shared build/temp.cygwin-1.7.15-i686-2.6/build/src.cygwin-1.7.15-i686-2.6/build/src.cygwin-1.7.15-i686-2.6/scipy/lib/lapack/clapackmodule.o build/temp.cygwin-1.7.15-i686-2.6/build/src.cygwin-1.7.15-i686-2.6/fortranobject.o -L/usr/local/atlas/lib -L/usr/lib/gcc/i686-pc-cygwin/4.5.3 -L/usr/lib/python2.6/config -Lbuild/temp.cygwin-1.7.15-i686-2.6 -llapack -lptf77blas -lptcblas -latlas -lpython2.6 -lgfortran -o build/lib.cygwin-1.7.15-i686-2.6/scipy/lib/lapack/clapack.dll" failed with exit status 1" I'll attach a copy of the results from: python -c 'from numpy.f2py.diagnose import run; run()'. Thanks in advance. -- Best, Greg

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Scientific Software and Web Developer Needed
by Chris Barker 30 May '12

30 May '12

Scientific Software and Web Developer Needed NOAA Emergency Response Division Help us develop our next-generation oil spill transport model. Background: The Emergency Response Division (ERD) of NOAA's Office of Response and Restoration (OR&R) provides scientific expertise to support the response to oil and chemical spills in the coastal environment. We played a major role in the recent Deepwater Horizon oil spill in the Gulf of Mexico. In order to fulfill our mission, we develop many of the software tools and models required to support a response to hazardous material spills. We are currently in the middle of a program to develop our next-generation oil spill transport model, taking into account lessons learned from years of response and recent major incidents. There are currently two positions available: one will focus on on the computational code in C++, Pyhton and Cython, and the other on a new web front end (Python, HTML, CSS, Javascript). General Characteristics: The incumbents in this position will provide software development services to support the mission of the Emergency Response Division of NOAA's Office of Response and Restoration. As part of his/her efforts, independent evaluation and application of development techniques, algorithms, software architecture, and programming patterns will be required. The incumbent will work with the staff of ERD to provide analysis on user needs and software, GUI, and library design. He/she will be expect to work primarily on site at NOAA's facility in Seattle. Knowledge: The incumbent must be able to apply modern concepts of software engineering and design to the development of computational code, web applications, and libraries. The incumbent will need to be able to design, write, refactor, and implement code for a complex web application and/or computational library. The incumbent will work with a multi-disciplinary team including scientists, users, and other developers, utilizing software development practices such as usability design, version control, bug and issue tracking, and unit testing. Good communication skills and the knowledge of working as part of a team are required. Direction received: The incumbent will participate on various research and development teams. While endpoints will be identified through Division management and some direct supervision will be provided, the incumbent will be responsible for progressively being able to take input from team meetings and design objectives and propose strategies for reaching endpoints. Typical duties and responsibilities: The incumbent will work with the oil and chemical spill modeling team to improve and develop new tools and models used in fate and transport forecasting. Different components of the project will be written in C++, Python, and Javascript. Education requirement, minimum: Bachelor's degree in a technical discipline. Experience requirement, minimum: One to five years experience in development of complex software systems in one or more full-featured programming languages (C, C++, Java, Python, Javaascript, Ruby, Fortran, etc.) The team requires experience in the following languages/disciplines. Each incumbent will need experience in some subset: * Computational/Scientific programming * Numerical Analysis/Methods * Parallel processing * Desktop GUI * Web services * Web clients: HTML/CSS/Javascript * Python * C/C++ * Python--C/C++ integration * Software development team leadership While the incumbent will work on-site at NOAA, directly with the NOAA team, this is a contract position with General Dynamics Information Technology: http://www.gdit.com/default.aspx For more information and to apply, use the GDIT web site: http://www.resumeware.net/gdns_rw/gdns_web/job_detail.cfm?recnum=1&totalrec… If that long url doesn't work, try: http://www.resumeware.net/gdns_rw/gdns_web/job_search.cfm and search for job ID: 199765 You can also send questions about employment issues to: Susan Bowley: susan.bowley(a)gdit.com And questions about the nature of the work to: Chris Barker: Chris.Barker(a)noaa.gov -- Christopher Barker, Ph.D. Oceanographer Emergency Response Division NOAA/NOS/OR&R (206) 526-6959 voice 7600 Sand Point Way NE (206) 526-6329 fax Seattle, WA 98115 (206) 526-6317 main reception Chris.Barker(a)noaa.gov

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