From relja.ljubobratovic at 3lateral.com Wed Dec 3 09:15:24 2014 From: relja.ljubobratovic at 3lateral.com (Relja Ljubobratovic) Date: Wed, 3 Dec 2014 15:15:24 +0100 Subject: [SciPy-User] NumPy/SciPy compilation VC10/Intel Fortran/MKL Message-ID: Hello, I need to compile NumPy and SciPy in Windows 7 x64, with Microsoft Visual Compiler 2010, and Intel Fortran compiler 2015, using Intel MKL. I'm compiling against Python 2.7.6 x64, which is compiled using same C/C++ compiler (I've downloaded compiled version from http://p-nand-q.com/python/building-python-27-with-vs2010.html). I need these packages for Autodesk Maya 2014, which has integrated Python 2.7.3 x64, compiled with VC10. Here is my NumPy site.cfg: [DEFAULT] library_dirs = C:\Program Files (x86)\Microsoft Visual Studio 10.0\VC\lib\amd64 include_dirs = C:\Program Files (x86)\Microsoft Visual Studio 10.0\VC\include [mkl] library_dirs = C:\Program Files (x86)\Intel\Composer XE 2015\mkl\lib\intel64 include_dirs = C:\Program Files (x86)\Intel\Composer XE 2015\mkl\include mkl_libs = mkl_rt,mkl_intel_lp64,mkl_intel_thread,mkl_core lapack_libs = mkl_lapack95_lp64 blas_libs = mkl_blas95_lp64 ---------------------------------------------- NumPy compilation shows strange linking errors and failures on _configtests - linking errors are evident in the numpy build log that I've provided. It seems that linker has no access to stdc++ libs? (unresolved external symbol strtoull, strtoll etc.) But at the end it compiles fine, and the installation and nose tests pass with no errors. I cannot understand if so much testing failures could be normal during the compilation? But during the SciPy compilation fatal linking errors occur while linking compiled .lib files to .pyd. I'm not completely sure to which package these unresolved externals belong ? I've tried examining libs for externals that are not found, but I'm failing to figure this out. I'm not so familiar with MKL, and I can't figure out if I'm missing some linking in NumPy site.cfg? Linking error is at the end of the scipy build log. I'm using msvccompiler.py configuration from the downloaded Python's distutils. I have inspected it, and it seems ok to me - could the reason for numpy linking errors come from here? And visual fortran configuration is present in numpy's distutils. Command I'm using for setup.py is: python setup.py config --compiler=msvc --fcompiler=intelvem build_clib --compiler=msvc --fcompiler=intelvem build_ext --compiler=msvc --fcompiler=intelvem install I'm trying to compile numpy-1.9.1 with scipy-0.14.0, but I've also tried with few older versions of both, and had the same outcome. I've also tried with git master versions, but again the same errors occur. Complete build logs are added as attachments. I'd be grateful if anyone can point out the solution to the errors I'm having. Thanks, Relja Ljubobratovic -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: numpy_build.log Type: application/octet-stream Size: 325914 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: scipy_build.log Type: application/octet-stream Size: 359146 bytes Desc: not available URL: From cournape at gmail.com Wed Dec 3 10:58:07 2014 From: cournape at gmail.com (David Cournapeau) Date: Wed, 3 Dec 2014 15:58:07 +0000 Subject: [SciPy-User] NumPy/SciPy compilation VC10/Intel Fortran/MKL In-Reply-To: References: Message-ID: On Wed, Dec 3, 2014 at 2:15 PM, Relja Ljubobratovic < relja.ljubobratovic at 3lateral.com> wrote: > Hello, > > I need to compile NumPy and SciPy in Windows 7 x64, with Microsoft Visual > Compiler 2010, and Intel Fortran compiler 2015, using Intel MKL. I'm > compiling against Python 2.7.6 x64, which is compiled using same C/C++ > compiler (I've downloaded compiled version from > http://p-nand-q.com/python/building-python-27-with-vs2010.html). I need > these packages for Autodesk Maya 2014, which has integrated Python 2.7.3 > x64, compiled with VC10. > > Here is my NumPy site.cfg: > [DEFAULT] > library_dirs = C:\Program Files (x86)\Microsoft Visual Studio > 10.0\VC\lib\amd64 > include_dirs = C:\Program Files (x86)\Microsoft Visual Studio > 10.0\VC\include > > [mkl] > library_dirs = C:\Program Files (x86)\Intel\Composer XE > 2015\mkl\lib\intel64 > include_dirs = C:\Program Files (x86)\Intel\Composer XE 2015\mkl\include > mkl_libs = mkl_rt,mkl_intel_lp64,mkl_intel_thread,mkl_core > lapack_libs = mkl_lapack95_lp64 > blas_libs = mkl_blas95_lp64 > > ---------------------------------------------- > > NumPy compilation shows strange linking errors and failures on > _configtests - linking errors are evident in the numpy build log that I've > provided. It seems that linker has no access to stdc++ libs? (unresolved > external symbol strtoull, strtoll etc.) But at the end it compiles fine, > and the installation and nose tests pass with no errors. I cannot > understand if so much testing failures could be normal during the > compilation? > Those are configuration tests. You should ignore those > > But during the SciPy compilation fatal linking errors occur while linking > compiled .lib files to .pyd. I'm not completely sure to which package these > unresolved externals belong ? I've tried examining libs for externals that > are not found, but I'm failing to figure this out. I'm not so familiar with > MKL, and I can't figure out if I'm missing some linking in NumPy site.cfg? > Linking error is at the end of the scipy build log. > The first thing I would look at is ensureing all the .lib/.obj linked together in the failed linking step are at the same architecture. It seems that you are using the correct ifort and cl compilers, but you never know. THe missing symbols are supposed to be in the fftpack.lib being linked, so I would check the symbols in fftpack.lib as well. David > > I'm using msvccompiler.py configuration from the downloaded Python's > distutils. I have inspected it, and it seems ok to me - could the reason > for numpy linking errors come from here? And visual fortran configuration > is present in numpy's distutils. Command I'm using for setup.py is: > python setup.py config --compiler=msvc --fcompiler=intelvem > build_clib --compiler=msvc --fcompiler=intelvem build_ext --compiler=msvc > --fcompiler=intelvem install > > > I'm trying to compile numpy-1.9.1 with scipy-0.14.0, but I've also tried > with few older versions of both, and had the same outcome. I've also tried > with git master versions, but again the same errors occur. > > Complete build logs are added as attachments. I'd be grateful if anyone > can point out the solution to the errors I'm having. > > Thanks, > Relja Ljubobratovic > > > > _______________________________________________ > SciPy-User mailing list > SciPy-User at scipy.org > http://mail.scipy.org/mailman/listinfo/scipy-user > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ccordoba12 at gmail.com Wed Dec 3 16:31:13 2014 From: ccordoba12 at gmail.com (=?UTF-8?B?Q2FybG9zIEPDs3Jkb2Jh?=) Date: Wed, 03 Dec 2014 16:31:13 -0500 Subject: [SciPy-User] ANN: Spyder 2.3.2 is released! Message-ID: <547F8121.80808@gmail.com> Hi all, On the behalf of Spyder's development team (http://code.google.com/p/spyderlib/people/list), I'm pleased to announce that Spyder 2.3.2 has been released and is available for Windows XP/Vista/7/8, GNU/Linux and MacOS X: https://bitbucket.org/spyder-ide/spyderlib/downloads This release represents more than 2 months of development since 2.3.1 and introduces major enhancements and new features: * Editor - Improve cells visualization - Add support for drag selection and improve look of line number area - Open on it any text file present in the Variable Explorer - View and edit IPython notebooks as Json files - Syntax highlighting for Json and Yaml files * Variable Explorer: - Import csv files as Pandas DataFrames - Improve browsing speed for NumPy arrays and DataFrames with more than 1e5 elements * IPython Console - Add a stop button to easily stop computations We fixed almost 40 bugs, merged 13 pull requests from 8 authors and added about 150 commits between these two releases. This is a very important bugfix release which solved a lot of unicode problems in our consoles, the variable explorer and the main interface, so everyone is encouraged to update. For a full list of fixes see our changelog: https://code.google.com/p/spyderlib/wiki/ChangeLog Spyder is a free, open-source (MIT license) interactive development environment for the Python language with advanced editing, interactive testing, debugging and introspection features. Originally designed to provide MATLAB-like features (integrated help, interactive console, variable explorer with GUI-based editors for dictionaries, NumPy arrays, ...), it is strongly oriented towards scientific computing and software development. Enjoy! -Carlos From relja.ljubobratovic at 3lateral.com Thu Dec 4 04:38:20 2014 From: relja.ljubobratovic at 3lateral.com (Relja Ljubobratovic) Date: Thu, 4 Dec 2014 10:38:20 +0100 Subject: [SciPy-User] SciPy-User Digest, Vol 136, Issue 2 In-Reply-To: References: Message-ID: > > The first thing I would look at is ensureing all the .lib/.obj linked > together in the failed linking step are at the same architecture. It seems > that you are using the correct ifort and cl compilers, but you never know. Thank you, David, for providing these informations and advices. I did thorough inspection of all libraries and objects that are involved in failed linking and it seems that they are all compiled using same architecture setup (x64). Although I found that missing symbols needed for linking of object files dct.obj and dst.obj. What troubles me now, is that these external symbols used here, are named with the underscore (e.g. dsinqb_), but those symbols are present in fftpack.lib as without the underscore. This is my first encounter with fortran compilation, so I'm unsure of this, but I've read that fortran functions that are wrapped to c, receive the following underscore (like lapacke functions, but I'm only guessing). Is it possible that some sort of name mangling is needed for compilation or linking of those objects? -------------- next part -------------- An HTML attachment was scrubbed... URL: From relja.ljubobratovic at 3lateral.com Thu Dec 4 04:42:36 2014 From: relja.ljubobratovic at 3lateral.com (Relja Ljubobratovic) Date: Thu, 4 Dec 2014 10:42:36 +0100 Subject: [SciPy-User] NumPy/SciPy compilation VC10/Intel Fortran/MKL - Architecture question Message-ID: > > The first thing I would look at is ensureing all the .lib/.obj linked > together in the failed linking step are at the same architecture. It seems > that you are using the correct ifort and cl compilers, but you never know. Thank you, David, for providing information and advice. I did thorough inspection of all libraries and objects that are involved in failed linking and it seems that they are all compiled using same architecture setup (x64). Although I found that missing symbols needed for linking of object files dct.obj and dst.obj. What troubles me now, is that these external symbols used here, are named with the underscore (e.g. dsinqb_), but those symbols are present in fftpack.lib as without underscore. This is my first encounter with fortran compilation, so I'm unsure of this, but I've read that fortran functions that are wrapped to c, receive the following underscore (like lapacke functions, but I'm only guessing). Is it possible that some sort of name mangling is needed for compilation or linking of those objects? -------------- next part -------------- An HTML attachment was scrubbed... URL: From cournape at gmail.com Thu Dec 4 05:39:38 2014 From: cournape at gmail.com (David Cournapeau) Date: Thu, 4 Dec 2014 10:39:38 +0000 Subject: [SciPy-User] NumPy/SciPy compilation VC10/Intel Fortran/MKL - Architecture question In-Reply-To: References: Message-ID: On Thu, Dec 4, 2014 at 9:42 AM, Relja Ljubobratovic < relja.ljubobratovic at 3lateral.com> wrote: > The first thing I would look at is ensureing all the .lib/.obj linked >> together in the failed linking step are at the same architecture. It seems >> that you are using the correct ifort and cl compilers, but you never know. > > > Thank you, David, for providing information and advice. > > I did thorough inspection of all libraries and objects that are involved > in failed linking and it seems that they are all compiled using same > architecture setup (x64). Although I found that missing symbols needed for > linking of object files dct.obj and dst.obj. What troubles me now, is that > these external symbols used here, are named with the underscore (e.g. > dsinqb_), but those symbols are present in fftpack.lib as without > underscore. This is my first encounter with fortran compilation, so I'm > unsure of this, but I've read that fortran functions that are wrapped to c, > receive the following underscore (like lapacke functions, but I'm only > guessing). Is it possible that some sort of name mangling is needed for > compilation or linking of those objects? > Yes, that may be the cause. I suspect you are one of the first person to look into compiling with those tools. The fortran mangling is unfortunately compiler-dependent: either the mangling in recent version of ifort changed (unlikely), or we do not detect it correctly with this version of ifort in numpy/scipy (more likely). David -------------- next part -------------- An HTML attachment was scrubbed... URL: From rob.clewley at gmail.com Thu Dec 4 12:04:20 2014 From: rob.clewley at gmail.com (Rob Clewley) Date: Thu, 4 Dec 2014 12:04:20 -0500 Subject: [SciPy-User] [ANN] PyDSTool 0.90 major release: dynamical systems modeling tools Message-ID: I'm pleased to announce PyDSTool 0.90 has been released on PyPI and Sourceforge. PyDSTool provides a range of high- and low-level simulation and analysis tools for mathematical models that use dynamical systems (for instance, ordinary differential equations and discrete maps). It relies significantly on numpy, scipy, and matplotlib but has its own modern and fast ODE solvers as well as bifurcation and continuation analysis tools. Several scientific toolboxes are also included. The primary purpose of this release is to be fully compatible with Python 3.3+ and 2.6-2.7 (although further support of 2.6 has been dropped), and also better support for 64-bit systems. For the first time, it uses a fully-automatic installer and is available on PyPI: https://pypi.python.org/pypi/PyDSTool Bleeding edge versions and the latest full release can be found at https://github.com/robclewley/pydstool with a mirror of releases at Sourceforge, http://pydstool.sf.net. Installation instructions are provided in the README.rst that's visible at the repo sites. The majority of these developments are due to the hard work of Vladimir Zakharov in Moscow, which is greatly appreciated. As usual, there are also many minor fixes and improvements included in this version. Details are given in the github history. Please continue to use the sourceforge site for user help queries and discussion (please join the user mailing list at https://sourceforge.net/p/pydstool/mailman/), while the github site can be used if you want to contribute to code development directly. Contributions are very welcome! In an upcoming release, there will be better GUI support for simulating and analyzing models. Please let us know if you have any comments or problems with installation or use. -Rob From sturla.molden at gmail.com Fri Dec 5 04:29:25 2014 From: sturla.molden at gmail.com (Sturla Molden) Date: Fri, 05 Dec 2014 10:29:25 +0100 Subject: [SciPy-User] ANN: Spyder 2.3.2 is released! In-Reply-To: <547F8121.80808@gmail.com> References: <547F8121.80808@gmail.com> Message-ID: I cannot use Spyder because of the narrow vertical line spacing that hurts my eyes. I am not sure if it is due to the retina screen or not, but it is really atrocious. Any decent editor allows this to be adjusted. Sturla On 03/12/14 22:31, Carlos C?rdoba wrote: > Hi all, > > On the behalf of Spyder's development team > (http://code.google.com/p/spyderlib/people/list), I'm pleased to > announce that Spyder 2.3.2 has been released and is available for > Windows XP/Vista/7/8, GNU/Linux and MacOS X: > https://bitbucket.org/spyder-ide/spyderlib/downloads > > This release represents more than 2 months of development since 2.3.1 > and introduces major enhancements and new features: > > * Editor > - Improve cells visualization > - Add support for drag selection and improve look of line number area > - Open on it any text file present in the Variable Explorer > - View and edit IPython notebooks as Json files > - Syntax highlighting for Json and Yaml files > > * Variable Explorer: > - Import csv files as Pandas DataFrames > - Improve browsing speed for NumPy arrays and DataFrames with more > than 1e5 elements > > * IPython Console > - Add a stop button to easily stop computations > > We fixed almost 40 bugs, merged 13 pull requests from 8 authors and > added about 150 commits between these two releases. This is a very > important bugfix release which solved a lot of unicode problems in our > consoles, the variable explorer and the main interface, so everyone is > encouraged to update. For a full list of fixes see our changelog: > https://code.google.com/p/spyderlib/wiki/ChangeLog > > Spyder is a free, open-source (MIT license) interactive development > environment for the Python language with advanced editing, interactive > testing, debugging and introspection features. Originally designed to > provide MATLAB-like features (integrated help, interactive console, > variable explorer with GUI-based editors for dictionaries, NumPy arrays, > ...), it is strongly oriented towards scientific computing and software > development. > > Enjoy! > -Carlos > From ccordoba12 at gmail.com Fri Dec 5 12:55:33 2014 From: ccordoba12 at gmail.com (=?UTF-8?B?Q2FybG9zIEPDs3Jkb2Jh?=) Date: Fri, 05 Dec 2014 12:55:33 -0500 Subject: [SciPy-User] ANN: Spyder 2.3.2 is released! In-Reply-To: References: <547F8121.80808@gmail.com> Message-ID: <5481F195.8070109@gmail.com> Between lines in the Editor you mean? Are you using Anaconda by any chance? El 05/12/14 a las 04:29, Sturla Molden escribi?: > I cannot use Spyder because of the narrow vertical line spacing that > hurts my eyes. I am not sure if it is due to the retina screen or not, > but it is really atrocious. Any decent editor allows this to be adjusted. > > Sturla > > > > On 03/12/14 22:31, Carlos C?rdoba wrote: >> Hi all, >> >> On the behalf of Spyder's development team >> (http://code.google.com/p/spyderlib/people/list), I'm pleased to >> announce that Spyder 2.3.2 has been released and is available for >> Windows XP/Vista/7/8, GNU/Linux and MacOS X: >> https://bitbucket.org/spyder-ide/spyderlib/downloads >> >> This release represents more than 2 months of development since 2.3.1 >> and introduces major enhancements and new features: >> >> * Editor >> - Improve cells visualization >> - Add support for drag selection and improve look of line number area >> - Open on it any text file present in the Variable Explorer >> - View and edit IPython notebooks as Json files >> - Syntax highlighting for Json and Yaml files >> >> * Variable Explorer: >> - Import csv files as Pandas DataFrames >> - Improve browsing speed for NumPy arrays and DataFrames with more >> than 1e5 elements >> >> * IPython Console >> - Add a stop button to easily stop computations >> >> We fixed almost 40 bugs, merged 13 pull requests from 8 authors and >> added about 150 commits between these two releases. This is a very >> important bugfix release which solved a lot of unicode problems in our >> consoles, the variable explorer and the main interface, so everyone is >> encouraged to update. For a full list of fixes see our changelog: >> https://code.google.com/p/spyderlib/wiki/ChangeLog >> >> Spyder is a free, open-source (MIT license) interactive development >> environment for the Python language with advanced editing, interactive >> testing, debugging and introspection features. Originally designed to >> provide MATLAB-like features (integrated help, interactive console, >> variable explorer with GUI-based editors for dictionaries, NumPy arrays, >> ...), it is strongly oriented towards scientific computing and software >> development. >> >> Enjoy! >> -Carlos >> > > _______________________________________________ > SciPy-User mailing list > SciPy-User at scipy.org > http://mail.scipy.org/mailman/listinfo/scipy-user -------------- next part -------------- An HTML attachment was scrubbed... URL: From sturla.molden at gmail.com Fri Dec 5 13:53:26 2014 From: sturla.molden at gmail.com (Sturla Molden) Date: Fri, 05 Dec 2014 19:53:26 +0100 Subject: [SciPy-User] ANN: Spyder 2.3.2 is released! In-Reply-To: <5481F195.8070109@gmail.com> References: <547F8121.80808@gmail.com> <5481F195.8070109@gmail.com> Message-ID: On 05/12/14 18:55, Carlos C?rdoba wrote: > Between lines in the Editor you mean? Are you using Anaconda by any chance? Yes and yes :) Sturla From ccordoba12 at gmail.com Fri Dec 5 15:35:29 2014 From: ccordoba12 at gmail.com (=?UTF-8?B?Q2FybG9zIEPDs3Jkb2Jh?=) Date: Fri, 05 Dec 2014 15:35:29 -0500 Subject: [SciPy-User] ANN: Spyder 2.3.2 is released! In-Reply-To: References: <547F8121.80808@gmail.com> <5481F195.8070109@gmail.com> Message-ID: <54821711.7000201@gmail.com> I've also seen this issue but just with Anaconda. I think it's a problem with the way Continuum guys compile Qt (the graphical library used by Spyder). I'll try to work with them to solve it. Cheers, Carlos El 05/12/14 a las 13:53, Sturla Molden escribi?: > On 05/12/14 18:55, Carlos C?rdoba wrote: >> Between lines in the Editor you mean? Are you using Anaconda by any chance? > Yes and yes :) > > > Sturla > > > _______________________________________________ > SciPy-User mailing list > SciPy-User at scipy.org > http://mail.scipy.org/mailman/listinfo/scipy-user -------------- next part -------------- An HTML attachment was scrubbed... URL: From u.fechner at tudelft.nl Fri Dec 5 16:41:16 2014 From: u.fechner at tudelft.nl (Uwe Fechner) Date: Fri, 05 Dec 2014 22:41:16 +0100 Subject: [SciPy-User] ANN: Spyder 2.3.2 is released! In-Reply-To: <54821711.7000201@gmail.com> References: <547F8121.80808@gmail.com> <5481F195.8070109@gmail.com> <54821711.7000201@gmail.com> Message-ID: <5482267C.7010200@tudelft.nl> Hello, I am using Ubuntu 12.04, and I also have the impression that the line spacing of Spyder 2.3.2 is too small. It is significantly smaller than the line spacing in the IPython console and the project manager. Screen-shot: https://dl.dropboxusercontent.com/u/9075004/Spyder_2.3.2.png Any ideas? Uwe Fechner Am 05.12.2014 um 21:35 schrieb Carlos C?rdoba: > I've also seen this issue but just with Anaconda. I think it's a problem with the way Continuum guys > compile Qt (the graphical library used by Spyder). I'll try to work with them to solve it. > > Cheers, > Carlos > > El 05/12/14 a las 13:53, Sturla Molden escribi?: >> On 05/12/14 18:55, Carlos C?rdoba wrote: >>> Between lines in the Editor you mean? Are you using Anaconda by any chance? >> Yes and yes :) >> >> >> Sturla >> >> >> _______________________________________________ >> SciPy-User mailing list >> SciPy-User at scipy.org >> http://mail.scipy.org/mailman/listinfo/scipy-user > > > > _______________________________________________ > SciPy-User mailing list > SciPy-User at scipy.org > http://mail.scipy.org/mailman/listinfo/scipy-user > -- --------------------------------------------- Uwe Fechner, M.Sc. Delft University of Technology Faculty of Aerospace Engineering/ Wind Energy Kluyverweg 1, 2629 HS Delft, The Netherlands Phone: +31-15-27-88902 From ccordoba12 at gmail.com Fri Dec 5 17:29:18 2014 From: ccordoba12 at gmail.com (=?UTF-8?B?Q2FybG9zIEPDs3Jkb2Jh?=) Date: Fri, 05 Dec 2014 17:29:18 -0500 Subject: [SciPy-User] ANN: Spyder 2.3.2 is released! In-Reply-To: <5482267C.7010200@tudelft.nl> References: <547F8121.80808@gmail.com> <5481F195.8070109@gmail.com> <54821711.7000201@gmail.com> <5482267C.7010200@tudelft.nl> Message-ID: <548231BE.50104@gmail.com> Ok, I'll look into it for 2.3.3. Once I have something working I'll put a message here so you can test it. Cheers, Carlos El 05/12/14 a las 16:41, Uwe Fechner escribi?: > Hello, > > I am using Ubuntu 12.04, and I also have the impression that the line spacing of Spyder 2.3.2 is too > small. It is significantly smaller than the line spacing in the IPython console and the > project manager. > > Screen-shot: > https://dl.dropboxusercontent.com/u/9075004/Spyder_2.3.2.png > > Any ideas? > > Uwe Fechner > > > Am 05.12.2014 um 21:35 schrieb Carlos C?rdoba: >> I've also seen this issue but just with Anaconda. I think it's a problem with the way Continuum guys >> compile Qt (the graphical library used by Spyder). I'll try to work with them to solve it. >> >> Cheers, >> Carlos >> >> El 05/12/14 a las 13:53, Sturla Molden escribi?: >>> On 05/12/14 18:55, Carlos C?rdoba wrote: >>>> Between lines in the Editor you mean? Are you using Anaconda by any chance? >>> Yes and yes :) >>> >>> >>> Sturla >>> >>> >>> _______________________________________________ >>> SciPy-User mailing list >>> SciPy-User at scipy.org >>> http://mail.scipy.org/mailman/listinfo/scipy-user >> >> >> _______________________________________________ >> SciPy-User mailing list >> SciPy-User at scipy.org >> http://mail.scipy.org/mailman/listinfo/scipy-user >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From njs at pobox.com Wed Dec 10 12:09:41 2014 From: njs at pobox.com (Nathaniel Smith) Date: Wed, 10 Dec 2014 17:09:41 +0000 Subject: [SciPy-User] Fwd: [Python-Dev] Python 2.x and 3.x use survey, 2014 edition In-Reply-To: References: Message-ID: ---------- Forwarded message ---------- From: "Bruno Cauet" Date: 10 Dec 2014 17:07 Subject: [Python-Dev] Python 2.x and 3.x use survey, 2014 edition To: , Cc: "Dan Stromberg" Hi all, Last year a survey was conducted on python 2 and 3 usage. Here is the 2014 edition, slightly updated (from 9 to 11 questions). It should not take you more than 1 minute to fill. I would be pleased if you took that time. Here's the url: http://goo.gl/forms/tDTcm8UzB3 I'll publish the results around the end of the year. Last year results: https://wiki.python.org/moin/2.x-vs-3.x-survey Thank you Bruno _______________________________________________ Python-Dev mailing list Python-Dev at python.org https://mail.python.org/mailman/listinfo/python-dev Unsubscribe: https://mail.python.org/mailman/options/python-dev/njs%40pobox.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From relja.ljubobratovic at 3lateral.com Thu Dec 11 10:25:29 2014 From: relja.ljubobratovic at 3lateral.com (Relja Ljubobratovic) Date: Thu, 11 Dec 2014 16:25:29 +0100 Subject: [SciPy-User] NumPy/SciPy compilation VC10/Intel Fortran/MKL - Solution Message-ID: Thanks to coordination from David Cournapeau , I've managed to figure out the problem and compile SciPy. Fortran functions (or are they called subrutines? - sorry I'm not familiar with fortran) compiled with Intel Visual Fortran are named with uppercase letters, without any suffix underscores when linked to a c program. So I needed to add these two preprocessor options in distutils/msvccompiler.py file compilation flags: NO_APPEND_FORTRAN and UPPERCASE_FORTRAN. So compiler compile_options list would have these two more items: self.compile_options = [ ..., '/DNO_APPEND_FORTRAN', '/DUPPERCASE_FORTRAN'] These options are used in SciPy C header/source files as fortran extern symbol name switches. With these options, compilation and linking was successful. I don't know if this is the right, or the only way to do it, but it worked for me! Thank you David, and I hope this will be of help to others who encounter similar errors. Best regards, Relja -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeffreback at gmail.com Fri Dec 12 08:43:33 2014 From: jeffreback at gmail.com (Jeff Reback) Date: Fri, 12 Dec 2014 08:43:33 -0500 Subject: [SciPy-User] ANN: pandas v0.15.2 Message-ID: Hello, We are proud to announce v0.15.2 of pandas, a minor release from 0.15.1. This release includes a small number of API changes, several new features, enhancements, and performance improvements along with a large number of bug fixes. This was a short release of 4 weeks with 137 commits by 49 authors encompassing 75 issues. We recommend that all users upgrade to this version. For a more full description of Whatsnew for v0.15.2, see here: http://pandas.pydata.org/pandas-docs/stable/whatsnew.html *What is it:* *pandas* is a Python package providing fast, flexible, and expressive data structures designed to make working with ?relational? or ?labeled? data both easy and intuitive. It aims to be the fundamental high-level building block for doing practical, real world data analysis in Python. Additionally, it has the broader goal of becoming the most powerful and flexible open source data analysis / manipulation tool available in any language. Documentation: http://pandas.pydata.org/pandas-docs/stable/ Source tarballs, windows binaries are available on PyPI: https://pypi.python.org/pypi/pandas windows binaries are courtesy of Christoph Gohlke and are built on Numpy 1.8 macosx wheels are courtesy of Matthew Brett Please report any issues here: https://github.com/pydata/pandas/issues Thanks The Pandas Development Team Contributors to the 0.15.2 release - Aaron Staple - Angelos Evripiotis - Artemy Kolchinsky - Benoit Pointet - Brian Jacobowski - Charalampos Papaloizou - Chris Warth - David Stephens - Fabio Zanini - Francesc Via - Henry Kleynhans - Jake VanderPlas - Jan Schulz - Jeff Reback - Jeff Tratner - Joris Van den Bossche - Kevin Sheppard - Matt Suggit - Matthew Brett - Phillip Cloud - Rupert Thompson - Scott E Lasley - Stephan Hoyer - Stephen Simmons - Sylvain Corlay - Thomas Grainger - Tiago Antao - Trent Hauck - Victor Chaves - Victor Salgado - Vikram Bhandoh - WANG Aiyong - Will Holmgren - behzad nouri - broessli - charalampos papaloizou - immerrr - jnmclarty - jreback - mgilbert - onesandzeroes - peadarcoyle - rockg - seth-p - sinhrks - unutbu - wavedatalab - ?smund Hjulstad -------------- next part -------------- An HTML attachment was scrubbed... URL: From flying-sheep at web.de Sat Dec 13 09:40:26 2014 From: flying-sheep at web.de (Philipp A.) Date: Sat, 13 Dec 2014 15:40:26 +0100 Subject: [SciPy-User] Fwd: [Python-Dev] Python 2.x and 3.x use survey, 2014 edition In-Reply-To: References: Message-ID: for more insights this year, the raw data would be very useful. many statistics will be much more interesting using conditions, e.g.: - how large a fraction who never wrote something source compatible with both python 2+3 still write things in python 2? - how large a fraction who lack incentive to switch have never even tried python 3? - how many who have dependencies holding them back never ported anything? 2014-12-10 18:09 GMT+01:00 Nathaniel Smith : > > ---------- Forwarded message ---------- > From: "Bruno Cauet" > Date: 10 Dec 2014 17:07 > Subject: [Python-Dev] Python 2.x and 3.x use survey, 2014 edition > To: , > Cc: "Dan Stromberg" > > Hi all, > Last year a survey was conducted on python 2 and 3 usage. > Here is the 2014 edition, slightly updated (from 9 to 11 questions). > It should not take you more than 1 minute to fill. I would be pleased if > you took that time. > > Here's the url: http://goo.gl/forms/tDTcm8UzB3 > I'll publish the results around the end of the year. > > Last year results: https://wiki.python.org/moin/2.x-vs-3.x-survey > > Thank you > Bruno > > _______________________________________________ > Python-Dev mailing list > Python-Dev at python.org > https://mail.python.org/mailman/listinfo/python-dev > Unsubscribe: > https://mail.python.org/mailman/options/python-dev/njs%40pobox.com > > > _______________________________________________ > SciPy-User mailing list > SciPy-User at scipy.org > http://mail.scipy.org/mailman/listinfo/scipy-user > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sjr at sjrx.net Tue Dec 16 08:32:55 2014 From: sjr at sjrx.net (=?utf-8?Q?Steve_Ramage?=) Date: Tue, 16 Dec 2014 05:32:55 -0800 Subject: [SciPy-User] Mann-Whitney U Test Message-ID: Hello, I am wondering why the Mann-Whiney U Test always returns the smallu value in the source code, it seems like it should return the U statistic for x or y consistently. https://github.com/scipy/scipy/blob/v0.14.0/scipy/stats/stats.py#L3943 . I might be missing something, but it seems impossible to determine which distribution in the lower, Wikipedia gives an example of where the lower median is not correct, reproduced below: #!/usr/bin/env python import scipy.stats as stats import scipy.stats.mstats as mstats Hare = [ 1 , 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29] Tortoise = [ 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31, 32, 33, 34, 35, 36, 37, 38] print "Hare Median: %d, Tortoise Median: %d, U1: %d, U2: %d"%(mstats.mquantiles(Hare,[0.5])[0],mstats.mquantiles(Tortoise,[0.5])[0], stats.mannwhitneyu(Hare, Tortoise)[0], stats.mannwhitneyu(Tortoise,Hare)[0]) Hare Median: 20, Tortoise Median: 19, U1: 100, U2: 100 From josef.pktd at gmail.com Tue Dec 16 10:01:13 2014 From: josef.pktd at gmail.com (josef.pktd at gmail.com) Date: Tue, 16 Dec 2014 10:01:13 -0500 Subject: [SciPy-User] Mann-Whitney U Test In-Reply-To: References: Message-ID: On Tue, Dec 16, 2014 at 8:32 AM, Steve Ramage wrote: > Hello, > > I am wondering why the Mann-Whiney U Test always returns the smallu value > in the source code, it seems like it should return the U statistic for x or > y consistently. > https://github.com/scipy/scipy/blob/v0.14.0/scipy/stats/stats.py#L3943 . > > I might be missing something, but it seems impossible to determine which > distribution in the lower, smallu is returned because it is is the actual test statistic for comparison with tables (or the normal approximation) (see Wikipedia) However, except for inertia and backwards compatibility it would have been better to change this. Also, the function still returns the one-sided p-value which is inconsistent with returning a two-sided test statistic. In comparison, ttests return one-sided test statistic and two-sided p-values. > Wikipedia gives an example of where the lower median is not correct, > reproduced below: > > #!/usr/bin/env python > import scipy.stats as stats > import scipy.stats.mstats as mstats > > Hare = [ 1 , 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, > 26, 27, 28, 29] > Tortoise = [ 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31, 32, 33, 34, > 35, 36, 37, 38] > > print "Hare Median: %d, Tortoise Median: %d, U1: %d, U2: > %d"%(mstats.mquantiles(Hare,[0.5])[0],mstats.mquantiles(Tortoise,[0.5])[0], > stats.mannwhitneyu(Hare, Tortoise)[0], stats.mannwhitneyu(Tortoise,Hare)[0]) > > Hare Median: 20, Tortoise Median: 19, U1: 100, U2: 100 > What's your point? smallu is not directly related to the medians. We replicate the formulas and results of Wikipedia, so everything looks right to me. I don't really understand the example, since I don't remember the details of Mann-Whitney-U or cannot figure them out right now . Josef > _______________________________________________ > SciPy-User mailing list > SciPy-User at scipy.org > http://mail.scipy.org/mailman/listinfo/scipy-user > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sjr at sjrx.net Tue Dec 16 10:07:42 2014 From: sjr at sjrx.net (=?utf-8?Q?Steve_Ramage?=) Date: Tue, 16 Dec 2014 07:07:42 -0800 Subject: [SciPy-User] Mann-Whitney U Test Message-ID: Thanks, That makes sense, my point with the example was only to demonstrate that the lower median is not necessary the 'lower distribution'. Cheers, Steve Ramage -----Original message----- From: josef.pktd at gmail.com Sent: Tue 16-12-2014 16:03 Subject: Re: [SciPy-User] Mann-Whitney U Test To: SciPy Users List ; > On Tue, Dec 16, 2014 at 8:32 AM, Steve Ramage > wrote: > Hello, > > I am wondering why the Mann-Whiney U Test always returns the smallu value in > the source code, it seems like it should return the U statistic for x or y > consistently. > https://github.com/scipy/scipy/blob/v0.14.0/scipy/stats/stats.py#L3943 . > > I might be missing something, but it seems impossible to determine which > distribution in the lower, > > > smallu is returned because it is is the actual test statistic for comparison > with tables (or the normal approximation) ? (see Wikipedia) > > However, except for inertia and backwards compatibility it would have been > better to change this. > Also, the function still returns the one-sided p-value which is inconsistent > with returning a two-sided test statistic. > In comparison, ttests return one-sided test statistic and two-sided p-values. > > > ? > Wikipedia gives an example of where the lower median is not correct, reproduced > below: > > #!/usr/bin/env python > import scipy.stats as stats > import scipy.stats.mstats as mstats > > Hare =? ? ?[ 1 ,? 2,? 3,? 4,? 5,? 6,? 7,? 8,? 9, 20, 21, 22, 23, 24, 25, 26, > 27, 28, 29] > Tortoise = [ 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31, 32, 33, 34, 35, > 36, 37, 38] > > print "Hare Median: %d, Tortoise Median: %d, U1: %d, U2: > %d"%(mstats.mquantiles(Hare,[0.5])[0],mstats.mquantiles(Tortoise,[0.5])[0], > stats.mannwhitneyu(Hare, Tortoise)[0], stats.mannwhitneyu(Tortoise,Hare)[0]) > > Hare Median: 20, Tortoise Median: 19, U1: 100, U2: 100 > > What's your point? > > smallu is not directly related to the medians. > > We replicate the formulas and results of Wikipedia, so everything looks right > to me. > I don't really understand the example, since I don't remember the details of > Mann-Whitney-U or cannot figure them out right now . > > Josef > ? > _______________________________________________ > SciPy-User mailing list > SciPy-User at scipy.org > http://mail.scipy.org/mailman/listinfo/scipy-user > > > > _______________________________________________ > > SciPy-User mailing list > > SciPy-User at scipy.org > > http://mail.scipy.org/mailman/listinfo/scipy-user > > > > From opossumnano at gmail.com Wed Dec 17 07:34:36 2014 From: opossumnano at gmail.com (Tiziano Zito) Date: Wed, 17 Dec 2014 13:34:36 +0100 Subject: [SciPy-User] [ANN] Summer School "Advanced Scientific Programming in Python" in Munich, Germany Message-ID: <20141217123435.GC18021@eniac> Advanced Scientific Programming in Python ========================================= a Summer School by the G-Node, the Bernstein Center for Computational Neuroscience Munich and the Graduate School of Systemic Neurosciences Scientists spend more and more time writing, maintaining, and debugging software. While techniques for doing this efficiently have evolved, only few scientists have been trained to use them. As a result, instead of doing their research, they spend far too much time writing deficient code and reinventing the wheel. In this course we will present a selection of advanced programming techniques, incorporating theoretical lectures and practical exercises tailored to the needs of a programming scientist. New skills will be tested in a real programming project: we will team up to develop an entertaining scientific computer game. We use the Python programming language for the entire course. Python works as a simple programming language for beginners, but more importantly, it also works great in scientific simulations and data analysis. We show how clean language design, ease of extensibility, and the great wealth of open source libraries for scientific computing and data visualization are driving Python to become a standard tool for the programming scientist. This school is targeted at Master or PhD students and Post-docs from all areas of science. Competence in Python or in another language such as Java, C/C++, MATLAB, or Mathematica is absolutely required. Basic knowledge of Python is assumed. Participants without any prior experience with Python should work through the proposed introductory materials before the course. Date and Location ================= August 31?September 5, 2015. Munich, Germany. Preliminary Program =================== Day 0 (Mon Aug 31) ? Best Programming Practices ? Best Practices for Scientific Computing ? Version control with git and how to contribute to Open Source with github ? Object-oriented programming & design patterns Day 1 (Tue Sept 1) ? Software Carpentry ? Test-driven development, unit testing & quality assurance ? Debugging, profiling and benchmarking techniques ? Advanced Python: generators, decorators, and context managers Day 2 (Wed Sept 2) ? Scientific Tools for Python ? Advanced NumPy ? The Quest for Speed (intro): Interfacing to C with Cython ? Contributing to Open Source Software/Programming in teams Day 3 (Thu Sept 3) ? The Quest for Speed ? Writing parallel applications in Python ? Python 3: why should I care ? Programming project Day 4 (Fri Sept 4) ? Efficient Memory Management ? When parallelization does not help: the starving CPUs problem ? Programming project Day 5 (Sat Sept 5) ? Practical Software Development ? Programming project ? The Pelita Tournament Every evening we will have the tutors' consultation hour: Tutors will answer your questions and give suggestions for your own projects. Applications ============ You can apply on-line at https://python.g-node.org Applications must be submitted before 23:59 UTC, March 31, 2015. Notifications of acceptance will be sent by May 1, 2015. No fee is charged but participants should take care of travel, living, and accommodation expenses. Candidates will be selected on the basis of their profile. Places are limited: acceptance rate is usually around 20%. Prerequisites: You are supposed to know the basics of Python to participate in the lectures Preliminary Faculty =================== ? Francesc Alted, freelance developer, author of PyTables, Spain ? Pietro Berkes, Enthought Inc., UK ? Kathryn D. Huff, Department of Nuclear Engineering, University of California - Berkeley, USA ? Zbigniew J?drzejewski-Szmek, Krasnow Institute, George Mason University, USA ? Eilif Muller, Blue Brain Project, ?cole Polytechnique F?d?rale de Lausanne, Switzerland ? Rike-Benjamin Schuppner, Institute for Theoretical Biology, Humboldt-Universit?t zu Berlin, Germany ? Nelle Varoquaux, Centre for Computational Biology Mines ParisTech, Institut Curie, U900 INSERM, Paris, France ? St?fan van der Walt, Applied Mathematics, Stellenbosch University, South Africa ? Niko Wilbert, TNG Technology Consulting GmbH, Germany ? Tiziano Zito, Forschungszentrum J?lich GmbH, Germany Organized by Tiziano Zito (head) and Zbigniew J?drzejewski-Szmek for the German Neuroinformatics Node of the INCF Germany, Christopher Roppelt for the German Center for Vertigo and Balance Disorders (DSGZ) and the Graduate School of Systemic Neurosciences (GSN) of the Ludwig-Maximilians-Universit?t Munich Germany, Christoph Hartmann for the Frankfurt Institute for Advanced Studies (FIAS) and International Max Planck Research School (IMPRS) for Neural Circuits, Frankfurt Germany, and Jakob Jordan for the Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6), J?lich Research Centre and JARA. Additional funding provided by the Bernstein Center for Computational Neuroscience (BCCN) Munich. Website: https://python.g-node.org Contact: python-info at g-node.org From matthew.brett at gmail.com Wed Dec 17 16:32:45 2014 From: matthew.brett at gmail.com (Matthew Brett) Date: Wed, 17 Dec 2014 16:32:45 -0500 Subject: [SciPy-User] [SciPy-Dev] ANN: Scipy 0.15.0 release candidate 1 In-Reply-To: References: Message-ID: Hi, On Mon, Dec 15, 2014 at 2:47 PM, Pauli Virtanen wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear all, > > Scipy 0.15.0 release candidate 1 is now available. If no surprises > turn up, the final release is planned within two weeks. > > Source tarballs, full release notes etc. are available at > https://sourceforge.net/projects/scipy/files/scipy/0.15.0rc1/ OSX wheels at http://wheels.scipy.org/ (via https://travis-ci.org/MacPython/scipy-wheels). Scipy-stack tests running at https://travis-ci.org/MacPython/scipy-stack-osx-testing Cheers, Matthew From cournape at gmail.com Fri Dec 19 08:48:44 2014 From: cournape at gmail.com (David Cournapeau) Date: Fri, 19 Dec 2014 13:48:44 +0000 Subject: [SciPy-User] [SciPy-Dev] ANN: Scipy 0.14.1 release candidate 1 In-Reply-To: References: Message-ID: I built that rc on top of numpy 1.8.1 and MKL, and it worked on every platform we support @ Enthought. I saw a few test failures on linux and windows 64 bits, but those were there before or are precisions issues. I also tested when run on top of numpy 1.9.1 (but still built against 1.8.1), w/ similar results. Thanks for all the hard work, David On Sun, Dec 14, 2014 at 10:29 PM, Pauli Virtanen wrote: > > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear all, > > We have finished preparing the Scipy 0.14.1 release candidate 1. > If no regressions turn up, the final release is planned within the > following weeks. > > The 0.14.1 release will be a bugfix-only release, addressing the > following issues: > > - - gh-3630 NetCDF reading results in a segfault > - - gh-3631 SuperLU object not working as expected for complex matrices > - - gh-3733 Segfault from map_coordinates > - - gh-3780 Segfault when using CSR/CSC matrix and uint32/uint64 > - - gh-3781 Fix omitted types in sparsetools typemaps > - - gh-3802 0.14.0 API breakage: _gen generators are missing from > scipy.stats.distributions API > - - gh-3805 ndimge test failures with numpy 1.10 > - - gh-3812 == sometimes wrong on csr_matrix > - - gh-3853 Many scipy.sparse test errors/failures with numpy 1.9.0b2 > - - gh-4084 Fix exception declarations for Cython 0.21.1 compatibility > - - gh-4093 Avoid a memory error in splev(x, tck, der=k) > - - gh-4104 Workaround SGEMV segfault in Accelerate (maintenance 0.14.x) > - - gh-4143 Fix ndimage functions for large data > - - gh-4149 Bug in expm for integer arrays > - - gh-4154 Ensure that the 'size' argument of PIL's 'resize' method is > a tuple > - - gh-4163 ZeroDivisionError in scipy.sparse.linalg.lsqr > - - gh-4164 Remove use of deprecated numpy API in lib/lapack/ f2py wrapper > - - gh-4180 pil resize support tuple fix > - - gh-4168 Address arpack test failures on windows 32 bits with numpy > 1.9.1 > - - gh-4218 make ndimage interpolation compatible with numpy relaxed > strides > - - gh-4225 off-by-one error in PPoly shape checks > - - gh-4248 fix issue with incorrect use of closure for slsqp > > Source tarballs and binaries are available at > https://sourceforge.net/projects/scipy/files/scipy/0.14.1rc1/ > > Best regards, > Pauli Virtanen > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1 > > iEYEARECAAYFAlSOD0YACgkQ6BQxb7O0pWDO5ACfccLqMvZWfkHqSzDCkMSoRKAU > n7cAni6XhWJRy7oJ757rlGeIi0e34HTn > =9bB/ > -----END PGP SIGNATURE----- > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev at scipy.org > http://mail.scipy.org/mailman/listinfo/scipy-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From denis.akhiyarov at gmail.com Tue Dec 30 10:56:42 2014 From: denis.akhiyarov at gmail.com (Denis Akhiyarov) Date: Tue, 30 Dec 2014 09:56:42 -0600 Subject: [SciPy-User] SciPy-User Digest, Vol 136, Issue 2 In-Reply-To: References: Message-ID: You can get numpy linked with MKL here: http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy On Dec 3, 2014 12:00 PM, wrote: > Send SciPy-User mailing list submissions to > scipy-user at scipy.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://mail.scipy.org/mailman/listinfo/scipy-user > or, via email, send a message with subject or body 'help' to > scipy-user-request at scipy.org > > You can reach the person managing the list at > scipy-user-owner at scipy.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of SciPy-User digest..." > > > Today's Topics: > > 1. Re: NumPy/SciPy compilation VC10/Intel Fortran/MKL > (David Cournapeau) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 3 Dec 2014 15:58:07 +0000 > From: David Cournapeau > Subject: Re: [SciPy-User] NumPy/SciPy compilation VC10/Intel > Fortran/MKL > To: SciPy Users List > Message-ID: > 1i-XoHyEpXysPfmE3zOcQ at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > On Wed, Dec 3, 2014 at 2:15 PM, Relja Ljubobratovic < > relja.ljubobratovic at 3lateral.com> wrote: > > > Hello, > > > > I need to compile NumPy and SciPy in Windows 7 x64, with Microsoft Visual > > Compiler 2010, and Intel Fortran compiler 2015, using Intel MKL. I'm > > compiling against Python 2.7.6 x64, which is compiled using same C/C++ > > compiler (I've downloaded compiled version from > > http://p-nand-q.com/python/building-python-27-with-vs2010.html). I need > > these packages for Autodesk Maya 2014, which has integrated Python 2.7.3 > > x64, compiled with VC10. > > > > Here is my NumPy site.cfg: > > [DEFAULT] > > library_dirs = C:\Program Files (x86)\Microsoft Visual Studio > > 10.0\VC\lib\amd64 > > include_dirs = C:\Program Files (x86)\Microsoft Visual Studio > > 10.0\VC\include > > > > [mkl] > > library_dirs = C:\Program Files (x86)\Intel\Composer XE > > 2015\mkl\lib\intel64 > > include_dirs = C:\Program Files (x86)\Intel\Composer XE 2015\mkl\include > > mkl_libs = mkl_rt,mkl_intel_lp64,mkl_intel_thread,mkl_core > > lapack_libs = mkl_lapack95_lp64 > > blas_libs = mkl_blas95_lp64 > > > > ---------------------------------------------- > > > > NumPy compilation shows strange linking errors and failures on > > _configtests - linking errors are evident in the numpy build log that > I've > > provided. It seems that linker has no access to stdc++ libs? (unresolved > > external symbol strtoull, strtoll etc.) But at the end it compiles fine, > > and the installation and nose tests pass with no errors. I cannot > > understand if so much testing failures could be normal during the > > compilation? > > > > Those are configuration tests. You should ignore those > > > > > > But during the SciPy compilation fatal linking errors occur while linking > > compiled .lib files to .pyd. I'm not completely sure to which package > these > > unresolved externals belong ? I've tried examining libs for externals > that > > are not found, but I'm failing to figure this out. I'm not so familiar > with > > MKL, and I can't figure out if I'm missing some linking in NumPy > site.cfg? > > Linking error is at the end of the scipy build log. > > > > The first thing I would look at is ensureing all the .lib/.obj linked > together in the failed linking step are at the same architecture. It seems > that you are using the correct ifort and cl compilers, but you never know. > > THe missing symbols are supposed to be in the fftpack.lib being linked, so > I would check the symbols in fftpack.lib as well. > > David > > > > > > I'm using msvccompiler.py configuration from the downloaded Python's > > distutils. I have inspected it, and it seems ok to me - could the reason > > for numpy linking errors come from here? And visual fortran configuration > > is present in numpy's distutils. Command I'm using for setup.py is: > > python setup.py config --compiler=msvc --fcompiler=intelvem > > build_clib --compiler=msvc --fcompiler=intelvem build_ext --compiler=msvc > > --fcompiler=intelvem install > > > > > > I'm trying to compile numpy-1.9.1 with scipy-0.14.0, but I've also tried > > with few older versions of both, and had the same outcome. I've also > tried > > with git master versions, but again the same errors occur. > > > > Complete build logs are added as attachments. I'd be grateful if anyone > > can point out the solution to the errors I'm having. > > > > Thanks, > > Relja Ljubobratovic > > > > > > > > _______________________________________________ > > SciPy-User mailing list > > SciPy-User at scipy.org > > http://mail.scipy.org/mailman/listinfo/scipy-user > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.scipy.org/pipermail/scipy-user/attachments/20141203/0a2e30e2/attachment-0001.html > > ------------------------------ > > _______________________________________________ > SciPy-User mailing list > SciPy-User at scipy.org > http://mail.scipy.org/mailman/listinfo/scipy-user > > > End of SciPy-User Digest, Vol 136, Issue 2 > ****************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pav at iki.fi Tue Dec 30 15:23:34 2014 From: pav at iki.fi (Pauli Virtanen) Date: Tue, 30 Dec 2014 22:23:34 +0200 Subject: [SciPy-User] ANN: Scipy 0.14.1 release Message-ID: <54A309C6.3080504@iki.fi> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear all, We are pleased to announce the Scipy 0.14.1 release. The 0.14.1 release is a bugfix-only release, addressing the following issues: - - gh-3630 NetCDF reading results in a segfault - - gh-3631 SuperLU object not working as expected for complex matrices - - gh-3733 Segfault from map_coordinates - - gh-3780 Segfault when using CSR/CSC matrix and uint32/uint64 - - gh-3781 Fix omitted types in sparsetools typemaps - - gh-3802 0.14.0 API breakage: _gen generators are missing from scipy.stats.distributions API - - gh-3805 Ndimge test failures with numpy 1.10 - - gh-3812 == sometimes wrong on csr_matrix - - gh-3853 Many scipy.sparse test errors/failures with numpy 1.9.0b2 - - gh-4084 Fix exception declarations for Cython 0.21.1 compatibility - - gh-4093 Avoid a memory error in splev(x, tck, der=k) - - gh-4104 Workaround SGEMV segfault in Accelerate (maintenance 0.14.x) - - gh-4143 Fix ndimage functions for large data - - gh-4149 Bug in expm for integer arrays - - gh-4154 Ensure that the 'size' argument of PIL's 'resize' method is a tuple - - gh-4163 ZeroDivisionError in scipy.sparse.linalg.lsqr - - gh-4164 Remove use of deprecated numpy API in lib/lapack/ f2py wrapper - - gh-4180 PIL resize support tuple fix - - gh-4168 Address arpack test failures on windows 32 bits with numpy 1.9.1 - - gh-4203 Sparse matrix multiplication in 0.14.x slower compared to 0.13.x - - gh-4218 Make ndimage interpolation compatible with numpy relaxed strides - - gh-4225 Off-by-one error in PPoly shape checks - - gh-4248 Fix issue with incorrect use of closure for slsqp Source tarballs and binaries are available at https://sourceforge.net/projects/scipy/files/SciPy/0.14.1/ Best regards, Pauli Virtanen -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iEYEARECAAYFAlSjCcYACgkQ6BQxb7O0pWBxcwCfcnd4uva5hzMHQlHmWxlfbja3 T0AAn2QQmhcotDRB2c2p41Xzjb4MJ13f =yBxH -----END PGP SIGNATURE-----