Mailman 3 August 2010 - NumPy-Discussion

set operation
by gerardob Aug. 17, 2010

Aug. 17, 2010

I would like to create a set composed of the numbers 2,3,4,...49,50,51. How do i do? Thanks. -- View this message in context: http://old.nabble.com/set-operation-tp29449267p29449267.html Sent from the Numpy-discussion mailing list archive at Nabble.com.

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ANN: NumPy 1.5.0 beta 1
by Ralf Gommers Aug. 17, 2010

Aug. 17, 2010

I am pleased to announce the availability of the first beta of NumPy 1.5.0. This will be the first NumPy release to include support for Python 3, as well as for Python 2.7. Please try this beta and report any problems on the NumPy mailing list. Binaries, sources and release notes can be found at https://sourceforge.net/projects/numpy/files/ Please note that binaries for Python 3.1 are not yet up, they will follow as soon as a minor issue with building them is resolved. Building from source with Python 3.1 should work without problems. Enjoy, Ralf

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Building f2py extensions on AMD64 with Python 2.7 Numpy 1.5, MSVC 2008 Pro and gfortran
by Åsmund Hjulstad Aug. 17, 2010

Aug. 17, 2010

Hi all, Are there any success stories in building f2py extensions on AMD64 with latest versions? Building the same extension on 32 bit works like a charm. I am having trouble finding documentation or examples, is it supposed to be working? Compiling (with distutils) works like a charm, but that does not help when I'm stuck figuring out link dependencies. It seems to me that the gfortran library depends on a mingw that is in conflict with some CRT library. I have to admit, I'm probably in way too deep waters, and should really be satisfied with 32 bit, but still, it would be fun to get it working. GFortran is from MinGW-w64 project on sourceforge, version 4.5.1 prerelease. Any pointers or other experiences? Regards, Åsmund Hjulstad

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f2py performance question from a rookie
by Vasileios Gkinis Aug. 16, 2010

Aug. 16, 2010

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basic question about numpy arrays
by gerardob Aug. 16, 2010

Aug. 16, 2010

I have a numpy array A , such that when i print A it appears: [[ 10.] [ 20.]] I would like to have a one dimensional array B (obtained from A) such that B[0] = 10 and B[1]=20. It could be seen as the transpose of A. How can i obtain B = [10,20] from A? I tried transpose(1,0) but it doesn't seem to be useful. Thanks. -- View this message in context: http://old.nabble.com/basic-question-about-numpy-arrays-tp29449184p29449184… Sent from the Numpy-discussion mailing list archive at Nabble.com.

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save data to csv with column names
by Guillaume Chérel Aug. 16, 2010

Aug. 16, 2010

Hello, I'd like to know if there is an easy way to save a list of 1D arrays to a csv file, with the first line of the file being the column names. I found the following, but I can't get to save the column names: data = rec.array([X1,X2,X3,X4], names=[n1,n2,n3,n4]) savetxt("filename", data, delimiter=",", fmt=["%i","%d", "%f","%f"]) Thank you, Guillaume

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Building numpy on Mac OS X 10.6, i386 (no ppc) 32/64bit: Error in Fortran tests due to ppc64
by Samuel John Aug. 16, 2010

Aug. 16, 2010

Hello! At first, I'd like to say thanks to the numpy/scipy team and all contributors. Great software! On Snow Leopard, aka Mac OS X 10.6.4 (server) I managed to build numpy 2.0.0.dev8636 (and scipy 0.9.0.dev6646) for arch i386 in combined 32/64bit against MacPorts python27 (No ppc here!). All tests pass (yeha!), except for the fortran related ones. I think there is an issue with detecting the right arch. My numpy and python are both i386 32/64 bit but now ppc. Only these tests fail, all others pass: test_callback.TestF77Callback.test_all ... ERROR test_mixed.TestMixed.test_all ... ERROR test_return_character.TestF77ReturnCharacter.test_all ... ERROR test_return_character.TestF90ReturnCharacter.test_all ... ERROR test_return_complex.TestF77ReturnComplex.test_all ... ERROR test_return_complex.TestF90ReturnComplex.test_all ... ERROR test_return_integer.TestF77ReturnInteger.test_all ... ERROR test_return_integer.TestF90ReturnInteger.test_all ... ERROR test_return_logical.TestF77ReturnLogical.test_all ... ERROR test_return_logical.TestF90ReturnLogical.test_all ... ERROR test_return_real.TestCReturnReal.test_all ... ok test_return_real.TestF77ReturnReal.test_all ... ERROR test_return_real.TestF90ReturnReal.test_all ... ERROR [...] ---------------------------------------------------------------------- Ran 2989 tests in 47.008s FAILED (KNOWNFAIL=4, SKIP=1, errors=12) Some more information (Perhaps I did some known mistake in those steps? Details at the end of this mail): o Mac OS X 10.6.4 (intel Core 2 duo) o Python 2.7 (r27:82500, Aug 15 2010, 12:19:40) [GCC 4.2.1 (Apple Inc. build 5659) + GF 4.2.4] on darwin o gcc --version i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5664) o gfortran --version GNU Fortran (GCC) 4.2.1 (Apple Inc. build 5659) + GF 4.2.4 from gfortran from http://r.research.att.com/tools/ o I used the BLAS/LAPACK that is provided by Apple's Accelerate framework. o environment: export CFLAGS="-arch i386 -arch x86_64" export FFLAGS="-m32 -m64" export LDFLAGS="-Wall -undefined dynamic_lookup -bundle -arch i386 -arch x86_64 -framework Accelerate" o bulid: python setup.py build --fcompiler=gnu95 I have not found a matching ticket in trac. Should I open one or did I something very stupid during the build process? Thanks! Samuel PS: I failed to succeed in the first shot with python.org's official fat precompiled .dmg-file release (ppc/i386 32/64 bit), so I used MacPorts. Later today, I'll try again to compile against python.org because I think numpy/scipy recommends that version. For completeness, here are my build steps: o Building numpy/scipy from source: http://scipy.org/Installing_SciPy/Mac_OS_X: - Make sure XCode is installed with the Development target 10.4 SDK - Download and install gfortran from http://r.research.att.com/tools/ - svn co http://svn.scipy.org/svn/numpy/trunk numpy - svn co http://svn.scipy.org/svn/scipy/trunk scipy - sudo port install fftw-3 - sudo port install suitesparse - sudo port install swig-python - mkdir scipy_numpy; cd scipy_numpy - cd numpy - cp site.cfg.example site.cfg - You may want to copy the site.cfg to ~/.numpy-site.cfg - Edit site.cfg to contain only the following: [DEFAULT] library_dirs = /opt/local/lib include_dirs = /opt/local/include [amd] amd_libs = amd [umfpack] umfpack_libs = umfpack [fftw] libraries = fftw3 - export MACOSX_DEPLOYMENT_TARGET=10.6 - export CFLAGS="-arch i386 -arch x86_64" - export FFLAGS="-m32 -m64" - export LDFLAGS="-Wall -undefined dynamic_lookup -bundle -arch i386 -arch x86_64 -framework Accelerate" - export PYTHONPATH="/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/" - python setup.py build --fcompiler=gnu95 - sudo python setup.py install - cd .. - cd scipy - sed 's|include <\(umfpack[^\.]*\.h\)>|include </opt/local/include/ufsparse/\1>|g' <scipy/sparse/linalg/dsolve/umfpack/umfpack.i >scipy/sparse/linalg/dsolve/umfpack/___tmp.i - mv scipy/sparse/linalg/dsolve/umfpack/umfpack.i scipy/sparse/linalg/dsolve/umfpack/umfpack.old - mv scipy/sparse/linalg/dsolve/umfpack/___tmp.i scipy/sparse/linalg/dsolve/umfpack/umfpack.i - python setup.py build --fcompiler=gnu95 - cd - python import numpy; numpy.test() import scipy; scipy.test() A short excerpt of numpy.test()'s output: ====================================================================== ERROR: test_return_real.TestF90ReturnReal.test_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.4-py2.7.egg/nose/case.py", line 367, in setUp try_run(self.inst, ('setup', 'setUp')) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose-0.11.4-py2.7.egg/nose/util.py", line 491, in try_run return func() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 341, in setUp module_name=self.module_name) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 156, in build_code module_name=module_name) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 73, in wrapper memo[key] = func(*a, **kw) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/tests/util.py", line 128, in build_module % (cmd[4:], asstr(out))) RuntimeError: Running f2py failed: ['-m', '_test_ext_module_5403', '/var/folders/sy/syxH3HBVEUyeFZOejvLLp+++-+2/-Tmp-/tmpJVSKpT/tmpHRbp1O.f90'] running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building extension "_test_ext_module_5403" sources f2py options: [] f2py:> /var/folders/sy/syxH3HBVEUyeFZOejvLLp+++-+2/-Tmp-/tmpOAl6fb/src.macosx-10.6-x86_64-2.7/_test_ext_module_5403module.c […snip…] build_src: building npy-pkg config files running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize NAGFCompiler Could not locate executable f95 customize AbsoftFCompiler Could not locate executable f90 Could not locate executable f77 customize IBMFCompiler Could not locate executable xlf90 Could not locate executable xlf customize IntelFCompiler Could not locate executable ifort Could not locate executable ifc customize GnuFCompiler Could not locate executable g77 customize Gnu95FCompiler Found executable /usr/bin/gfortran customize Gnu95FCompiler customize Gnu95FCompiler using build_ext building '_test_ext_module_5403' extension compiling C sources C compiler: /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -pipe -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes ortran f77 compiler: /usr/bin/gfortran […snip…] Fortran f90 compiler: /usr/bin/gfortran […snip…] Fortran fix compiler: /usr/bin/gfortran […snip…] […snip…] ld: warning: in /var/folders/xxx/src.macosx-10.6-x86_64-2.7/_test_ext_module_5403module.o, file was built for unsupported file format which is not the architecture being linked (i386) […snip…] ld: warning: in /usr/lib/libSystem.dylib, missing required architecture ppc64 in file ld: in /usr/lib/libSystem.B.dylib, missing required architecture ppc64 in file for architecture ppc64 collect2: ld returned 1 exit status lipo: can't open input file: /var/folders/sy/syxH3HBVEUyeFZOejvLLp+++-+2/-Tmp-//ccXwmeM6.out (No such file or directory) error: Command "/usr/bin/gfortran -Wall -arch ppc -arch i686 -arch x86_64 -arch ppc64 -Wall -undefined dynamic_lookup -bundle /var/folders/xxx/src.macosx-10.6-x86_64-2.7/_test_ext_module_5403module.o /var/folders/xxx/src.macosx-10.6-x86_64-2.7/fortranobject.o /var/folders/sy/syxH3HBVEUyeFZOejvLLp+++-+2/-Tmp-/tmpOAl6fb/var/folders/sy/syxH3HBVEUyeFZOejvLLp+++-+2/-Tmp-/tmpJVSKpT/tmpHRbp1O.o /var/folders/xxx/src.macosx-10.6-x86_64-2.7/_test_ext_module_5403-f2pywrappers2.o -lgfortran -o ./_test_ext_module_5403.so" failed with exit status 1 [Note, i replace a long temp path by xxx just in this mail to make it more readable.] ---------------------------------------------------------------------- Ran 2989 tests in 47.008s FAILED (KNOWNFAIL=4, SKIP=1, errors=12) Btw: scipy.test(): Ran 5340 tests in 711.401s FAILED (KNOWNFAIL=14, SKIP=31, errors=3, failures=3)

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Re: [Numpy-discussion] [SciPy-Dev] Good-bye, sort of (John Hunter)
by Joe Harrington Aug. 16, 2010

Aug. 16, 2010

While this thread is super off-topic (and long enough that I'm not going to quote it), I'm actually finding it very interesting, as a non-MATLAB person, to find out what I need to say to the MATLAB mafia here to demonstrate that MATLAB has sufficient flaws and non-followers "out in the real world" that perhaps certain classes could allow their students to use other languages, like Python. Could those contributing here put up a Cookbook page of "reasons why we've moved on from MATLAB", to be used as a resource by people trying to convince supervisors/professors/sponsors/clients that they should be allowed to use Python? It would be important for such a page to be polite and not offensive to those readers, who may like MATLAB. A similar page for IDL would be great....and did anyone notice that IDL 8.0 has a number of language enhancements, all designed to make it more like Python? Sadly, they fall well short. --jh--

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Re: [Numpy-discussion] Matlab vs. Python (Was: Re: [SciPy-Dev] Good-bye, sort of (John Hunter)) (Sturla Molden)
by Ioan-Alexandru Lazar Aug. 15, 2010

Aug. 15, 2010

Hi everyone, I've been pretty happy with how Spider went along when I tried it. I use Emacs but I think Spyder is perfectly usable for someone used to Matlab. A few HPC-centric of my reasons (I've shamelessly copy-pasted this because I'm lazy right now): 1. Python is an expressive, full-fledged, general-purpose application language. There is slightly more boilerplate for doing math-related operations (i.e. creating a matrix is not as simple as A=[[1, 2, 3]; [4, 5, 6]] but rather A=numpy.array([[1,2,3],[4,5,6]])). On the other hand, everything other than math can be expressed without causing severe nausea and vomiting to the user. 2. The package-module structure of Python allows me to obtain a significantly less cluttered workspace. 3. Theres built-in support for automatically generating meaningful and useful documentation 4. The wonderful FFI support allows me to easily work with external C code. Writing MEX functions is a total mess, I hate that. On the other hand, its easy for me to integrate Python with a custom-compiled version of UMFPACK or any other solver, and wrappers can be automatically generated with SWIG for a minimal amount of effort. 5. There is a Matlab wrapper called mlabwrap, so legacy code written in Matlab is not lost effort. 6. I can use Emacs for my development rather than choosing between a) working in half-assed environment without code completion or b) working with Matlabs incredibly slow and sloppy user interface on Unix systems. 7. I have built-in support for primitives like linked lists, queues, stacks and tuples 8. I have standards-compliant support for MPI that does not look alien in Python (theres support for that in Matlab too, but it feels like youre coding on Mars in a library written somewhere in the Andromeda galaxy). This is extremely important to me right now because the algorithm were implementing will be presented in a conference in September, and I want to have an implementation that uses standard tools, available to every HPC developer. On the other hand, I will be able to further optimize communication (if this will seem to be required) by using a good distributed-object library like PyRO. Some details about what exactly it is that I am using it for are on my blog at http://zencoding.org/archives/137#more-137, although it's rather sketchy -- I plan to write a slightly more detailed document about my experience with Python for HPC and how it compares against Matlab's PCS and DCS. I've been banging my head against Matlab for a while so I'll gladly write a thing or two on the wiki if you think this sort of use case is relevant. One other observation -- Matlab does have some support for parallel processing via PCS, but you have to pay for that, and it's not too flexible. There's also DCS for distributed computing. Some of my colleagues have been using those and aren't too happy about their flexibility just yet. MathWorks is also not too verbose about what particular parts of Matlab are parallelized and not, so we've been randomly stumbling upon parts that were actually parallelized (e.g. UMFPACK is linked against a multithreaded BLAS) even though we thought they weren't. Their documentation is detailed, but as far as careful details about under-the-hood issues and optimization methods, it's a bad joke. If you need it as a glorified handheld calculator or as a prototyping tool, it's great, but writing full-fledged apps in it is painful. Best regards, Alexandru Lazar, Numerical Modeling Laboratory, Politehnica University of Bucharest

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review request
by Ralf Gommers Aug. 14, 2010

Aug. 14, 2010

Hi, I'd appreciate a review of these changes: http://github.com/rgommers/numpy/tree/changes-for-1.5 http://github.com/rgommers/numpy/tree/deprecations Thanks, Ralf

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