Mailman 3 July 2011 - NumPy-Discussion

Multi-taper spectral analysis code available
by martin smith 22 Jul '11

22 Jul '11

This is the initial release of a module that implements Thomson's multi-taper spectral analysis algorithms. The code is based on a subroutine from Lees and Park and has, of course, a python interface. References are provided in the readme file. The code has seen substantial usage and should be fairly reliable. Examples are included. It's available at http://code.google.com/p/pymutt/. Martin L. Smith Blindgoat Geophysics

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Setup failure on Max OS X Lion
by Mark Higgins 22 Jul '11

22 Jul '11

I just tried to set up numpy on a new laptop with Mac OS X Lion (10.7) and am running into some problems. The laptop came with python 2.7 installed, but when I downloaded the dmg for numpy from the sourceforge side, it refused to install it saying that it couldn't find python 2.7. Odd, but maybe it was installed in some place numpy didn't expect. So I went to python.org and got the official 2.7 installer dmg and stuck that in. Seemed okay. Then I installed numpy using the dmg. Seemed okay. Now, though, when I start python at the terminal (or through Wing IDE) and import numpy, I get Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/__init__.py", line 78, in <module> from numpy import show_config as show_numpy_config File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/__init__.py", line 137, in <module> import add_newdocs File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/add_newdocs.py", line 9, in <module> from numpy.lib import add_newdoc File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/lib/__init__.py", line 4, in <module> from type_check import * File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/lib/type_check.py", line 8, in <module> import numpy.core.numeric as _nx File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/__init__.py", line 5, in <module> import multiarray ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/multiarray.so, 2): no suitable image found. Did find: /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/multiarray.so: no matching architecture in universal wrapper I'm not sure whether this is a problem with where the python 2.7 install is located, or whether it's something bespoke about the new Mac OS. I'm pretty sure I followed a similar route on an older laptop (which was OS X 10.6 and has python 2.6 installed by default) and it worked fine; but it was a while ago and I don't really remember. Any suggestions?

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ANN: NumPy 1.6.1 release
by Ralf Gommers 21 Jul '11

21 Jul '11

Hi, I am pleased to announce the availability of NumPy 1.6.1. This is a bugfix release for the 1.6.x series; the list of fixed bugs is given below. Sources and binaries can be found at http://sourceforge.net/projects/numpy/files/NumPy/1.6.1/ Thanks to anyone who contributed to this release. Enjoy, The NumPy developers Bug fixes for NumPy 1.6.1 ------------------------- #1834 einsum fails for specific shapes #1837 einsum throws nan or freezes python for specific array shapes #1838 object <-> structured type arrays regression #1851 regression for SWIG based code in 1.6.0 #1863 Buggy results when operating on array copied with astype() #1870 Fix corner case of object array assignment #1843 Py3k: fix error with recarray #1885 nditer: Error in detecting double reduction loop #1874 f2py: fix --include_paths bug #1749 Fix ctypes.load_library() #1895/1896 iter: writeonly operands weren't always being buffered correctly

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Re: [Numpy-discussion] f2py and openmp on mac os x with gfortran
by Brandt Belson 21 Jul '11

21 Jul '11

Hi all, As Juan said, I didn't include the -lgomp flag for f2py. Once I use that, the f2py module works with openMP as expected. Thanks, Brandt > > Message: 1 > Date: Thu, 21 Jul 2011 11:34:13 +0200 > From: Juan <fiolj(a)yahoo.com> > Subject: Re: [Numpy-discussion] f2py and openmp on mac os x with > gfortran > To: numpy-discussion(a)scipy.org > Message-ID: <4E27F295.8050305(a)yahoo.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Brandt, I am on linux and see the same problem. It is solved (at least > here) > if you add at the end the library libgomp, i.e: > f2py -c -m play play.f90 --fcompiler=gfortran --f90flags="-fopenmp" -lgomp > Hope it helps, > Juan > > > Hello, > > I'm struggling to create openmp subroutines. I've simplified the problem > > down to the subroutine below. > > > > -- play.f90 -- > > subroutine step(soln,n) > > implicit none > > integer n,i > > real*8 soln(n) > > > > !f2py intent(in) n > > !f2py intent(out) soln > > !f2py depend(n) soln > > > > !$OMP PARALLEL DO > > do i=1,n > > soln(i) = .1 > > end do > > !$OMP END PARALLEL DO > > end subroutine step > > > > > > I compile this with the command: > > > > f2py -c -m play play.f90 --fcompiler=gfortran --f90flags="-fopenmp" > > > > This completes successfully. When I import the module, I get the > following > > error message. > > > > $ python -c 'import play' > > Traceback (most recent call last): > > File "<string>", line 1, in <module> > > ImportError: dlopen(./play.so, 2): Symbol not found: _GOMP_parallel_end > > Referenced from: /home/bbelson/Desktop/SOR/play.so > > Expected in: flat namespace > > in /home/bbelson/Desktop/SOR/play.so > > > > It seems to me that the linking step is broken, however I did not see any > > other options in the f2py documentation to change the linking step. Did I > > miss something? > > > > Thanks, > > Brandt > > >

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X11 system info
by Darren Dale 21 Jul '11

21 Jul '11

In numpy.distutils.system info: default_x11_lib_dirs = libpaths(['/usr/X11R6/lib','/usr/X11/lib', '/usr/lib'], platform_bits) default_x11_include_dirs = ['/usr/X11R6/include','/usr/X11/include', '/usr/include'] These defaults won't work on the forthcoming Ubuntu 11.10, which installs X into /usr/lib/X11 and /usr/include/X11. Darren

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Re: [Numpy-discussion] f2py and openmp on mac os x with gfortran
by Juan 21 Jul '11

21 Jul '11

Hi Brandt, I am on linux and see the same problem. It is solved (at least here) if you add at the end the library libgomp, i.e: f2py -c -m play play.f90 --fcompiler=gfortran --f90flags="-fopenmp" -lgomp Hope it helps, Juan > Hello, > I'm struggling to create openmp subroutines. I've simplified the problem > down to the subroutine below. > > -- play.f90 -- > subroutine step(soln,n) > implicit none > integer n,i > real*8 soln(n) > > !f2py intent(in) n > !f2py intent(out) soln > !f2py depend(n) soln > > !$OMP PARALLEL DO > do i=1,n > soln(i) = .1 > end do > !$OMP END PARALLEL DO > end subroutine step > > > I compile this with the command: > > f2py -c -m play play.f90 --fcompiler=gfortran --f90flags="-fopenmp" > > This completes successfully. When I import the module, I get the following > error message. > > $ python -c 'import play' > Traceback (most recent call last): > File "<string>", line 1, in <module> > ImportError: dlopen(./play.so, 2): Symbol not found: _GOMP_parallel_end > Referenced from: /home/bbelson/Desktop/SOR/play.so > Expected in: flat namespace > in /home/bbelson/Desktop/SOR/play.so > > It seems to me that the linking step is broken, however I did not see any > other options in the f2py documentation to change the linking step. Did I > miss something? > > Thanks, > Brandt

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f2py and openmp on mac os x with gfortran
by Brandt Belson 21 Jul '11

21 Jul '11

Hello, I'm struggling to create openmp subroutines. I've simplified the problem down to the subroutine below. -- play.f90 -- subroutine step(soln,n) implicit none integer n,i real*8 soln(n) !f2py intent(in) n !f2py intent(out) soln !f2py depend(n) soln !$OMP PARALLEL DO do i=1,n soln(i) = .1 end do !$OMP END PARALLEL DO end subroutine step I compile this with the command: f2py -c -m play play.f90 --fcompiler=gfortran --f90flags="-fopenmp" This completes successfully. When I import the module, I get the following error message. $ python -c 'import play' Traceback (most recent call last): File "<string>", line 1, in <module> ImportError: dlopen(./play.so, 2): Symbol not found: _GOMP_parallel_end Referenced from: /home/bbelson/Desktop/SOR/play.so Expected in: flat namespace in /home/bbelson/Desktop/SOR/play.so It seems to me that the linking step is broken, however I did not see any other options in the f2py documentation to change the linking step. Did I miss something? Thanks, Brandt

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Alternative to boolean array
by Andrea Cimatoribus 20 Jul '11

20 Jul '11

Dear all, I would like to avoid the use of a boolean array (mask) in the following statement: mask = (A != 0.) B = A[mask] in order to be able to move this bit of code in a cython script (boolean arrays are not yet implemented there, and they slow down execution a lot as they can't be defined explicitely). Any idea of an efficient alternative? Thanks

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Difference between frompyfunc and vectorize?
by Olivier Verdier 20 Jul '11

20 Jul '11

Dear NumPy gurus, I don't get the difference between frompyfunc and vectorize. What is their respective use cases? Thanks! == Olivier

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pull request review: deprecating PyArrayObject* direct field access
by Mark Wiebe 19 Jul '11

19 Jul '11

https://github.com/numpy/numpy/pull/116 This pull request deprecates direct access to PyArrayObject fields. This direct access has been discouraged for a while through comments in the header file and documentation, but up till now, there was no way to disable it. I've created such a mechanism, and C extensions can test that they don't use deprecated C API by #defining NPY_NO_DEPRECATED_API at the top of the C file. I've confirmed that scipy master builds against this branch, and its test failures look unrelated to these changes (iterative methods failures). Additional testing of different versions and platforms would be appreciated! This also includes a few other miscellaneous changes: - improve error message in PyArray_FromArray - some missingdata NEP changes - allow comma-separated dtype strings to include datetime metadata - http://projects.scipy.org/numpy/ticket/466 -Mark

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