Release of SciPy Core 0.4 (Beta)
This is to announce the release of SciPy Core 0.4.X (beta) It is available at sourceforge which you can access by going to http://numeric.scipy.org Thanks to all who helped me with this release, especially Robert Kern Pearu Peterson Now, let's start getting this stable.... -Travis Oliphant
"Travis" == Travis Oliphant <oliphant@ee.byu.edu> writes:
Travis> This is to announce the release of SciPy Core 0.4.X (beta) Travis> http://numeric.scipy.org Many thanks! I just read your presentation for SciPy05 and the new core looks very impressive. Thanks for all the hard work! regards, prabhu
Prabhu is right: Great, that we can start using it now. Thanks a lot! Just two questions: - The presentation lets my PowerPoint always crash (OS X 10.3). Apparently it works elsewhere, but could you check whether it's broken, please? - And this is the reason why I'm writing to the whole list and not to Travis: I'd like to purchase the pre-version and think supporting SciPy is worth a few bucks. Just I'm sitting in Europe now and don't have a credit card (what for?). Is there an other way to purchase the book? (The sample looks really impressive.) Cheers Christian On 30 Sep 2005, at 10:40, Prabhu Ramachandran wrote:
"Travis" == Travis Oliphant <oliphant@ee.byu.edu> writes:
Travis> This is to announce the release of SciPy Core 0.4.X (beta)
Travis> http://numeric.scipy.org
Many thanks! I just read your presentation for SciPy05 and the new core looks very impressive. Thanks for all the hard work!
regards, prabhu
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Hi Travis, Does the new scipy core means that, at least on unix, we won't have to build and install Numeric anymore ? Regards, Christophe
christophe grimault wrote:
Hi Travis,
Does the new scipy core means that, at least on unix, we won't have to build and install Numeric anymore ?
Regards, Christophe
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The cvs entry http://www.scipy.org/cvs/ is obsolete and should be replaced by some user friendly comments on svn. What is really needed to install scipy via svn ? Nils
christophe grimault wrote:
Hi Travis,
Does the new scipy core means that, at least on unix, we won't have to build and install Numeric anymore ?
Right, scipy core replaces Numeric. Now, you still need to get scipy core built and installed. Which version of UNIX are you running? -Travis
Le vendredi 30 septembre 2005 à 08:32 -0600, Travis Oliphant a écrit :
christophe grimault wrote:
Hi Travis,
Does the new scipy core means that, at least on unix, we won't have to build and install Numeric anymore ?
Right, scipy core replaces Numeric.
Now, you still need to get scipy core built and installed. Which version of UNIX are you running?
-Travis
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I use linux Fedora Core3, with python 2.4, Scipy 0.3.2 and boost_1_33. Chris
OK, I am giving this a go. I seem to be not setting a flag about some math functions availability. Here are the details (aorry about the length of it but I snipped a lot!): OSX 10.3.9, Python 2.4.1 Installed g77v3.4-bin.tar.gz from http://hpc.sourceforge.net/ as described into /usr/local/... Installed fftw-3.0.1-fma.tar.gz from http://www.fftw.org/download.html into ~/Documents/local/... where I have other libraries I have installed. Got scipy_core-0.4.1.tar.gz from http://sourceforge.net/project/showfiles.php?group_id=1369&package_id=6222, wanted to try out the new replacement for Numeric tar -zxvf scipy_core-0.4.1.tar.gz cd scipy_core-0.4.1 python setup.py build Assuming default configuration (scipy/distutils/command/{setup_command,setup}.py was not found) Appending scipy.distutils.command configuration to scipy.distutils Assuming default configuration (scipy/distutils/fcompiler/{setup_fcompiler,setup}.py was not found) ... Appending scipy.base configuration to scipy 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'] lapack_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-faltivec'] Appending scipy.lib configuration to scipy Assuming default configuration (scipy/fftpack/{setup_fftpack,setup}.py was not found) ... scipy_core version 0.4.1 running build running config_fc running build_src building extension "scipy.base.multiarray" sources creating build creating build/src creating build/src/scipy creating build/src/scipy/base Generating build/src/scipy/base/config.h customize NAGFCompiler customize AbsoftFCompiler customize IbmFCompiler Could not locate executable f77 customize GnuFCompiler customize GnuFCompiler ... compiling C sources gcc options: '-fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd -fno-common -dynamic -DNDEBUG -g -O3 -Wall -Wstrict-prototypes' creating build/temp.darwin-7.9.0-Power_Macintosh-2.4/build creating build/temp.darwin-7.9.0-Power_Macintosh-2.4/build/src creating build/temp.darwin-7.9.0-Power_Macintosh-2.4/build/src/scipy creating build/temp.darwin-7.9.0-Power_Macintosh-2.4/build/src/scipy/base creating build/temp.darwin-7.9.0-Power_Macintosh-2.4/build/src/scipy/base/src compile options: '-Ibuild/src/scipy/base/src -Iscipy/base/include -Ibuild/src/scipy/base -Iscipy/base/src -I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 -c' gcc: build/src/scipy/base/src/umathmodule.c In file included from build/src/scipy/base/src/umathmodule.c:8: scipy/base/include/scipy/arrayobject.h:84: warning: redefinition of `ushort' /usr/include/sys/types.h:82: warning: `ushort' previously declared here scipy/base/include/scipy/arrayobject.h:85: warning: redefinition of `uint' /usr/include/sys/types.h:83: warning: `uint' previously declared here build/src/scipy/base/src/umathmodule.c: In function `nc_floor_quotl': build/src/scipy/base/src/umathmodule.c:1257: warning: implicit declaration of function `floorl' build/src/scipy/base/src/umathmodule.c: In function `nc_sqrtl': build/src/scipy/base/src/umathmodule.c:1269: warning: implicit declaration of function `sqrtl' ... build/src/scipy/base/__umath_generated.c:171: error: initializer element is not constant build/src/scipy/base/__umath_generated.c:171: error: (near initialization for `arccosh_data[2]') error: Command "gcc -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd -fno-common -dy namic -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -Ibuild/src/scipy/base/src -Iscipy/base/include -Ibuild/s rc/scipy/base -Iscipy/base/src -I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 -c b uild/src/scipy/base/src/umathmodule.c -o build/temp.darwin-7.9.0-Power_Macintosh-2.4/build/src/scipy/base /src/umathmodule.o" failed with exit status 1 At 12:59 AM -0600 9/30/05, Travis Oliphant wrote:
This is to announce the release of SciPy Core 0.4.X (beta)
It is available at sourceforge which you can access by going to
Thanks to all who helped me with this release, especially
Robert Kern Pearu Peterson
Now, let's start getting this stable....
-Travis Oliphant
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-- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- Rob Managan email managan at llnl.gov LLNL phone: 925-423-0903 P.O. Box 808, L-095 FAX: 925-422-3389 Livermore, CA 94551-0808
"python setup.py install" for scipy_core 0.4.1 fails to build with: error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -DNO_ATLAS_INFO=1 -Iscipy/base/include -Ibuild/src/scipy/base -Iscipy/base/src -I/usr/local/include/python2.4 -c scipy/corelib/blasdot/_dotblas.c -o build/temp.linux-i686-2.4/scipy/corelib/blasdot/_dotblas.o" failed with exit status 1 Red Hat 9.0, gcc 3.2.2, Python 2.4.2 Any hints? Regards, Steve Travis Oliphant wrote:
This is to announce the release of SciPy Core 0.4.X (beta)
It is available at sourceforge which you can access by going to
Thanks to all who helped me with this release, especially
Robert Kern Pearu Peterson
Now, let's start getting this stable....
-Travis Oliphant
_______________________________________________ SciPy-user mailing list SciPy-user@scipy.net http://www.scipy.net/mailman/listinfo/scipy-user
-- Steven H. Rogers, Ph.D., steve@shrogers.com Weblog: http://shrogers.com/weblog "He who refuses to do arithmetic is doomed to talk nonsense." -- John McCarthy
Steven H. Rogers wrote:
"python setup.py install" for scipy_core 0.4.1 fails to build with:
error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -DNO_ATLAS_INFO=1 -Iscipy/base/include -Ibuild/src/scipy/base -Iscipy/base/src -I/usr/local/include/python2.4 -c scipy/corelib/blasdot/_dotblas.c -o build/temp.linux-i686-2.4/scipy/corelib/blasdot/_dotblas.o" failed with exit status 1
Hmm. This is definitely a blas-related problem. What other errors do you see. A quick fix is to uncomment the blas_info=0 (line 15 of scipy/corelib/setup.py) and rerun setup (this will not try to build _dotblas.c I'd like to track down what the real problem is though. Do you see any output below blas_opt_info: when you run setup.py For example, my system shows. blas_opt_info: atlas_blas_threads_info: Setting PTATLAS=ATLAS NOT AVAILABLE atlas_blas_info: FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib/atlas'] language = c include_dirs = ['/usr/include/atlas'] These include_dirs are needed to pick up cblas.h -Travis
Looks like I have BLAS but not ATLAS. Here's the entire output from running setup.py: root@sojourner:/home/steve/dl/python/scipy/scipy_core-0.4.1# python setup.py install Assuming default configuration (scipy/distutils/command/{setup_command,setup}.py was not found) Appending scipy.distutils.command configuration to scipy.distutils Assuming default configuration (scipy/distutils/fcompiler/{setup_fcompiler,setup}.py was not found) Appending scipy.distutils.fcompiler configuration to scipy.distutils Appending scipy.distutils configuration to scipy Assuming default configuration (scipy/weave/{setup_weave,setup}.py was not found) Appending scipy.weave configuration to scipy Assuming default configuration (scipy/test/{setup_test,setup}.py was not found) Appending scipy.test configuration to scipy F2PY Version 2_1126 Appending scipy.f2py configuration to scipy Appending scipy.base configuration to scipy blas_opt_info: atlas_blas_threads_info: Setting PTATLAS=ATLAS NOT AVAILABLE atlas_blas_info: NOT AVAILABLE /home/steve/dl/python/scipy/scipy_core-0.4.1/scipy/distutils/system_info.py:1046: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the scipy_distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) blas_info: FOUND: libraries = ['blas'] library_dirs = ['/usr/lib'] language = f77 FOUND: libraries = ['blas'] library_dirs = ['/usr/lib'] define_macros = [('NO_ATLAS_INFO', 1)] language = f77 lapack_opt_info: atlas_threads_info: Setting PTATLAS=ATLAS scipy.distutils.system_info.atlas_threads_info NOT AVAILABLE atlas_info: scipy.distutils.system_info.atlas_info NOT AVAILABLE /home/steve/dl/python/scipy/scipy_core-0.4.1/scipy/distutils/system_info.py:970: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the scipy_distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) lapack_info: FOUND: libraries = ['lapack'] library_dirs = ['/usr/lib'] language = f77 FOUND: libraries = ['lapack', 'blas'] library_dirs = ['/usr/lib'] define_macros = [('NO_ATLAS_INFO', 1)] language = f77 Appending scipy.lib configuration to scipy Assuming default configuration (scipy/fftpack/{setup_fftpack,setup}.py was not found) Appending scipy.fftpack configuration to scipy Assuming default configuration (scipy/linalg/{setup_linalg,setup}.py was not found) Appending scipy.linalg configuration to scipy Assuming default configuration (scipy/stats/{setup_stats,setup}.py was not found) Appending scipy.stats configuration to scipy Appending scipy configuration to scipy_core version 0.4.1 running install running build running config_fc running build_src building extension "scipy.base.multiarray" sources adding 'build/src/scipy/base/config.h' to sources. adding 'build/src/scipy/base/__multiarray_api.h' to sources. adding 'build/src/scipy/base/src' to include_dirs. building extension "scipy.base.umath" sources adding 'build/src/scipy/base/config.h' to sources. adding 'build/src/scipy/base/__ufunc_api.h' to sources. adding 'build/src/scipy/base/src' to include_dirs. building extension "scipy.base._compiled_base" sources adding 'build/src/scipy/base/config.h' to sources. adding 'build/src/scipy/base/__multiarray_api.h' to sources. building extension "scipy.lib._dotblas" sources building extension "scipy.lib.fftpack_lite" sources building extension "scipy.lib.mtrand" sources building extension "scipy.lib.lapack_lite" sources running build_py running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using build_ext building 'scipy.lib._dotblas' extension compiling C sources gcc options: '-pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC' compile options: '-DNO_ATLAS_INFO=1 -Iscipy/base/include -Ibuild/src/scipy/base -Iscipy/base/src -I/usr/local/include/python2.4 -c' gcc: scipy/corelib/blasdot/_dotblas.c In file included from scipy/corelib/blasdot/_dotblas.c:6: scipy/base/include/scipy/arrayobject.h:84: warning: redefinition of `ushort' /usr/include/sys/types.h:152: warning: `ushort' previously declared here scipy/base/include/scipy/arrayobject.h:85: warning: redefinition of `uint' /usr/include/sys/types.h:153: warning: `uint' previously declared here scipy/base/include/scipy/arrayobject.h:86: warning: redefinition of `ulong' /usr/include/sys/types.h:151: warning: `ulong' previously declared here scipy/corelib/blasdot/_dotblas.c:10:22: cblas.h: No such file or directory scipy/corelib/blasdot/_dotblas.c: In function `FLOAT_dot': scipy/corelib/blasdot/_dotblas.c:21: warning: implicit declaration of function `cblas_sdot' scipy/corelib/blasdot/_dotblas.c: In function `DOUBLE_dot': scipy/corelib/blasdot/_dotblas.c:31: warning: implicit declaration of function `cblas_ddot' scipy/corelib/blasdot/_dotblas.c: In function `CFLOAT_dot': scipy/corelib/blasdot/_dotblas.c:42: warning: implicit declaration of function `cblas_cdotu_sub' scipy/corelib/blasdot/_dotblas.c: In function `CDOUBLE_dot': scipy/corelib/blasdot/_dotblas.c:52: warning: implicit declaration of function `cblas_zdotu_sub' scipy/corelib/blasdot/_dotblas.c: In function `dotblas_matrixproduct': scipy/corelib/blasdot/_dotblas.c:235: warning: implicit declaration of function `cblas_daxpy' scipy/corelib/blasdot/_dotblas.c:239: warning: implicit declaration of function `cblas_saxpy' scipy/corelib/blasdot/_dotblas.c:243: warning: implicit declaration of function `cblas_zaxpy' scipy/corelib/blasdot/_dotblas.c:247: warning: implicit declaration of function `cblas_caxpy' scipy/corelib/blasdot/_dotblas.c:277: warning: implicit declaration of function `cblas_dgemv' scipy/corelib/blasdot/_dotblas.c:277: `CblasRowMajor' undeclared (first use in this function) scipy/corelib/blasdot/_dotblas.c:277: (Each undeclared identifier is reported only once scipy/corelib/blasdot/_dotblas.c:277: for each function it appears in.) scipy/corelib/blasdot/_dotblas.c:278: `CblasNoTrans' undeclared (first use in this function) scipy/corelib/blasdot/_dotblas.c:283: warning: implicit declaration of function `cblas_sgemv' scipy/corelib/blasdot/_dotblas.c:289: warning: implicit declaration of function `cblas_zgemv' scipy/corelib/blasdot/_dotblas.c:295: warning: implicit declaration of function `cblas_cgemv' scipy/corelib/blasdot/_dotblas.c:306: `CblasTrans' undeclared (first use in this function) scipy/corelib/blasdot/_dotblas.c:334: warning: implicit declaration of function `cblas_dgemm' scipy/corelib/blasdot/_dotblas.c:341: warning: implicit declaration of function `cblas_sgemm' scipy/corelib/blasdot/_dotblas.c:348: warning: implicit declaration of function `cblas_zgemm' scipy/corelib/blasdot/_dotblas.c:355: warning: implicit declaration of function `cblas_cgemm' scipy/corelib/blasdot/_dotblas.c: In function `dotblas_innerproduct': scipy/corelib/blasdot/_dotblas.c:522: `CblasRowMajor' undeclared (first use in this function) scipy/corelib/blasdot/_dotblas.c:523: `CblasNoTrans' undeclared (first use in this function) scipy/corelib/blasdot/_dotblas.c:579: `CblasTrans' undeclared (first use in this function) scipy/corelib/blasdot/_dotblas.c: In function `dotblas_vdot': scipy/corelib/blasdot/_dotblas.c:699: warning: implicit declaration of function `cblas_zdotc_sub' scipy/corelib/blasdot/_dotblas.c:703: warning: implicit declaration of function `cblas_cdotc_sub' In file included from scipy/corelib/blasdot/_dotblas.c:6: scipy/base/include/scipy/arrayobject.h:84: warning: redefinition of `ushort' /usr/include/sys/types.h:152: warning: `ushort' previously declared here scipy/base/include/scipy/arrayobject.h:85: warning: redefinition of `uint' /usr/include/sys/types.h:153: warning: `uint' previously declared here scipy/base/include/scipy/arrayobject.h:86: warning: redefinition of `ulong' /usr/include/sys/types.h:151: warning: `ulong' previously declared here scipy/corelib/blasdot/_dotblas.c:10:22: cblas.h: No such file or directory scipy/corelib/blasdot/_dotblas.c: In function `FLOAT_dot': scipy/corelib/blasdot/_dotblas.c:21: warning: implicit declaration of function `cblas_sdot' scipy/corelib/blasdot/_dotblas.c: In function `DOUBLE_dot': scipy/corelib/blasdot/_dotblas.c:31: warning: implicit declaration of function `cblas_ddot' scipy/corelib/blasdot/_dotblas.c: In function `CFLOAT_dot': scipy/corelib/blasdot/_dotblas.c:42: warning: implicit declaration of function `cblas_cdotu_sub' scipy/corelib/blasdot/_dotblas.c: In function `CDOUBLE_dot': scipy/corelib/blasdot/_dotblas.c:52: warning: implicit declaration of function `cblas_zdotu_sub' scipy/corelib/blasdot/_dotblas.c: In function `dotblas_matrixproduct': scipy/corelib/blasdot/_dotblas.c:235: warning: implicit declaration of function `cblas_daxpy' scipy/corelib/blasdot/_dotblas.c:239: warning: implicit declaration of function `cblas_saxpy' scipy/corelib/blasdot/_dotblas.c:243: warning: implicit declaration of function `cblas_zaxpy' scipy/corelib/blasdot/_dotblas.c:247: warning: implicit declaration of function `cblas_caxpy' scipy/corelib/blasdot/_dotblas.c:277: warning: implicit declaration of function `cblas_dgemv' scipy/corelib/blasdot/_dotblas.c:277: `CblasRowMajor' undeclared (first use in this function) scipy/corelib/blasdot/_dotblas.c:277: (Each undeclared identifier is reported only once scipy/corelib/blasdot/_dotblas.c:277: for each function it appears in.) scipy/corelib/blasdot/_dotblas.c:278: `CblasNoTrans' undeclared (first use in this function) scipy/corelib/blasdot/_dotblas.c:283: warning: implicit declaration of function `cblas_sgemv' scipy/corelib/blasdot/_dotblas.c:289: warning: implicit declaration of function `cblas_zgemv' scipy/corelib/blasdot/_dotblas.c:295: warning: implicit declaration of function `cblas_cgemv' scipy/corelib/blasdot/_dotblas.c:306: `CblasTrans' undeclared (first use in this function) scipy/corelib/blasdot/_dotblas.c:334: warning: implicit declaration of function `cblas_dgemm' scipy/corelib/blasdot/_dotblas.c:341: warning: implicit declaration of function `cblas_sgemm' scipy/corelib/blasdot/_dotblas.c:348: warning: implicit declaration of function `cblas_zgemm' scipy/corelib/blasdot/_dotblas.c:355: warning: implicit declaration of function `cblas_cgemm' scipy/corelib/blasdot/_dotblas.c: In function `dotblas_innerproduct': scipy/corelib/blasdot/_dotblas.c:522: `CblasRowMajor' undeclared (first use in this function) scipy/corelib/blasdot/_dotblas.c:523: `CblasNoTrans' undeclared (first use in this function) scipy/corelib/blasdot/_dotblas.c:579: `CblasTrans' undeclared (first use in this function) scipy/corelib/blasdot/_dotblas.c: In function `dotblas_vdot': scipy/corelib/blasdot/_dotblas.c:699: warning: implicit declaration of function `cblas_zdotc_sub' scipy/corelib/blasdot/_dotblas.c:703: warning: implicit declaration of function `cblas_cdotc_sub' error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -DNO_ATLAS_INFO=1 -Iscipy/base/include -Ibuild/src/scipy/base -Iscipy/base/src -I/usr/local/include/python2.4 -c scipy/corelib/blasdot/_dotblas.c -o build/temp.linux-i686-2.4/scipy/corelib/blasdot/_dotblas.o" failed with exit status 1 Thanks, Steve Travis Oliphant wrote:
Steven H. Rogers wrote:
"python setup.py install" for scipy_core 0.4.1 fails to build with:
error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -DNO_ATLAS_INFO=1 -Iscipy/base/include -Ibuild/src/scipy/base -Iscipy/base/src -I/usr/local/include/python2.4 -c scipy/corelib/blasdot/_dotblas.c -o build/temp.linux-i686-2.4/scipy/corelib/blasdot/_dotblas.o" failed with exit status 1
Hmm. This is definitely a blas-related problem. What other errors do you see.
A quick fix is to uncomment the blas_info=0 (line 15 of scipy/corelib/setup.py) and rerun setup (this will not try to build _dotblas.c
I'd like to track down what the real problem is though.
Do you see any output below blas_opt_info: when you run setup.py
For example, my system shows.
blas_opt_info: atlas_blas_threads_info: Setting PTATLAS=ATLAS NOT AVAILABLE
atlas_blas_info: FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib/atlas'] language = c include_dirs = ['/usr/include/atlas']
These include_dirs are needed to pick up cblas.h
-Travis
_______________________________________________ SciPy-user mailing list SciPy-user@scipy.net http://www.scipy.net/mailman/listinfo/scipy-user
-- Steven H. Rogers, Ph.D., steve@shrogers.com Weblog: http://shrogers.com/weblog "He who refuses to do arithmetic is doomed to talk nonsense." -- John McCarthy
On Mon, 3 Oct 2005, Travis Oliphant wrote:
Steven H. Rogers wrote:
"python setup.py install" for scipy_core 0.4.1 fails to build with:
error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -DNO_ATLAS_INFO=1 -Iscipy/base/include -Ibuild/src/scipy/base -Iscipy/base/src -I/usr/local/include/python2.4 -c scipy/corelib/blasdot/_dotblas.c -o build/temp.linux-i686-2.4/scipy/corelib/blasdot/_dotblas.o" failed with exit status 1
Hmm. This is definitely a blas-related problem. What other errors do you see.
A quick fix is to uncomment the blas_info=0 (line 15 of scipy/corelib/setup.py) and rerun setup (this will not try to build _dotblas.c
I'd like to track down what the real problem is though.
The problem is that cblas.h was missing that _dotblas.c includes (see previous message in this thread). In newcore svn I have included cblas.h to scipy/corelib/blasdot to workaround this problem. Pearu
Pearu Peterson wrote:
On Mon, 3 Oct 2005, Travis Oliphant wrote:
Steven H. Rogers wrote:
"python setup.py install" for scipy_core 0.4.1 fails to build with:
error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -DNO_ATLAS_INFO=1 -Iscipy/base/include -Ibuild/src/scipy/base -Iscipy/base/src -I/usr/local/include/python2.4 -c scipy/corelib/blasdot/_dotblas.c -o build/temp.linux-i686-2.4/scipy/corelib/blasdot/_dotblas.o" failed with exit status 1
Hmm. This is definitely a blas-related problem. What other errors do you see.
A quick fix is to uncomment the blas_info=0 (line 15 of scipy/corelib/setup.py) and rerun setup (this will not try to build _dotblas.c
I'd like to track down what the real problem is though.
The problem is that cblas.h was missing that _dotblas.c includes (see previous message in this thread). In newcore svn I have included cblas.h to scipy/corelib/blasdot to workaround this problem.
Pearu
Ucommenting the blas_info=0 line allowed scipy_core to build and install. "import scipy" and "from scipy import *" seem to work, but scipy_core function names are not recognized. Also, README is an empty file. Is this expected? Steve -- Steven H. Rogers, Ph.D., steve@shrogers.com Weblog: http://shrogers.com/weblog "He who refuses to do arithmetic is doomed to talk nonsense." -- John McCarthy
Steven H. Rogers wrote:
Ucommenting the blas_info=0 line allowed scipy_core to build and install. "import scipy" and "from scipy import *" seem to work, but scipy_core function names are not recognized.
Could you show some code that fails and the error that results? Are you sure that you don't have an older version of scipy installed?
Also, README is an empty file. Is this expected?
Yes, we haven't gotten around to writing one, yet. -- Robert Kern rkern@ucsd.edu "In the fields of hell where the grass grows high Are the graves of dreams allowed to die." -- Richard Harter
I had trouble compiling the release candidate, it was not locating my external LAPACK, BLAS and ATLAS libraries. It turned out that site.cfg and sample_site.cfg are not present in the distutils directory of the release candidate. I copied site.cfg over from my SciPy-0.3.2 build and then compilation was successful. It might be useful to note in the README. Darren On Tuesday 04 October 2005 8:13 am, Robert Kern wrote:
Steven H. Rogers wrote:
Ucommenting the blas_info=0 line allowed scipy_core to build and install. "import scipy" and "from scipy import *" seem to work, but scipy_core function names are not recognized.
Could you show some code that fails and the error that results? Are you sure that you don't have an older version of scipy installed?
Also, README is an empty file. Is this expected?
Yes, we haven't gotten around to writing one, yet.
Robert Kern wrote:
Steven H. Rogers wrote:
Ucommenting the blas_info=0 line allowed scipy_core to build and install. "import scipy" and "from scipy import *" seem to work, but scipy_core function names are not recognized.
Could you show some code that fails and the error that results? Are you sure that you don't have an older version of scipy installed?
When I wrote the previous post nothing seemed to work. Things are looking better now. steve@sojourner:~$ python Python 2.4.2 (#1, Sep 30 2005, 18:34:48) [GCC 3.2.2 20030222 (Red Hat Linux 3.2.2-5)] on linux2 Type "help", "copyright", "credits" or "license" for more information.
from scipy import * a = array([[1,2,3],[4,5,6]]) print a [[1 2 3] [4 5 6]] a[1,1] 5 a.shape (2, 3) a.dtype Traceback (most recent call last): File "<stdin>", line 1, in ? AttributeError: dtype
-- Steven H. Rogers, Ph.D., steve@shrogers.com Weblog: http://shrogers.com/weblog "He who refuses to do arithmetic is doomed to talk nonsense." -- John McCarthy
Steven H. Rogers wrote:
Robert Kern wrote:
Could you show some code that fails and the error that results? Are you sure that you don't have an older version of scipy installed?
When I wrote the previous post nothing seemed to work. Things are looking better now.
steve@sojourner:~$ python Python 2.4.2 (#1, Sep 30 2005, 18:34:48) [GCC 3.2.2 20030222 (Red Hat Linux 3.2.2-5)] on linux2 Type "help", "copyright", "credits" or "license" for more information.
from scipy import * a = array([[1,2,3],[4,5,6]]) print a [[1 2 3] [4 5 6]] a[1,1] 5 a.shape (2, 3) a.dtype Traceback (most recent call last): File "<stdin>", line 1, in ? AttributeError: dtype
Are you sure that you don't have an older version of scipy installed? It should have a version number 0.4.x, not 0.3.x: In [6]: scipy.__version__ Out[6]: '0.4.2' -- Robert Kern rkern@ucsd.edu "In the fields of hell where the grass grows high Are the graves of dreams allowed to die." -- Richard Harter
Didn't think so, but I did have an old version in my PYTHONPATH. With that corrected, my 0.4.1 installation seems to be working. Thanks, Steve ////////////////// Robert Kern wrote:
Steven H. Rogers wrote:
Robert Kern wrote:
Could you show some code that fails and the error that results? Are you sure that you don't have an older version of scipy installed?
When I wrote the previous post nothing seemed to work. Things are looking better now.
steve@sojourner:~$ python Python 2.4.2 (#1, Sep 30 2005, 18:34:48) [GCC 3.2.2 20030222 (Red Hat Linux 3.2.2-5)] on linux2 Type "help", "copyright", "credits" or "license" for more information.
from scipy import * a = array([[1,2,3],[4,5,6]]) print a
[[1 2 3] [4 5 6]]
a[1,1]
5
a.shape
(2, 3)
a.dtype
Traceback (most recent call last): File "<stdin>", line 1, in ? AttributeError: dtype
Are you sure that you don't have an older version of scipy installed? It should have a version number 0.4.x, not 0.3.x:
In [6]: scipy.__version__ Out[6]: '0.4.2'
-- Steven H. Rogers, Ph.D., steve@shrogers.com Weblog: http://shrogers.com/weblog "He who refuses to do arithmetic is doomed to talk nonsense." -- John McCarthy
Steven H. Rogers wrote:
Robert Kern wrote:
Steven H. Rogers wrote:
Ucommenting the blas_info=0 line allowed scipy_core to build and install. "import scipy" and "from scipy import *" seem to work, but scipy_core function names are not recognized.
When I wrote the previous post nothing seemed to work. Things are looking better now.
steve@sojourner:~$ python Python 2.4.2 (#1, Sep 30 2005, 18:34:48) [GCC 3.2.2 20030222 (Red Hat Linux 3.2.2-5)] on linux2 Type "help", "copyright", "credits" or "license" for more information.
from scipy import * a = array([[1,2,3],[4,5,6]]) print a [[1 2 3] [4 5 6]] a[1,1] 5 a.shape (2, 3) a.dtype Traceback (most recent call last): File "<stdin>", line 1, in ? AttributeError: dtype
You are picking up an older version of scipy. Do you have scipy installed already? If so, we are working quickly on getting a replacement so that scipy can build on top of scipy_core. For now, you probably need to delete your scipy installation, and re-install scipy_core. Again, Old scipy and new scipy core do not work together yet. We are trying to fix this, but have not done so yet. -Travis
Travis Oliphant wrote:
Steven H. Rogers wrote:
Robert Kern wrote:
Steven H. Rogers wrote:
Ucommenting the blas_info=0 line allowed scipy_core to build and install. "import scipy" and "from scipy import *" seem to work, but scipy_core function names are not recognized.
When I wrote the previous post nothing seemed to work. Things are looking better now.
steve@sojourner:~$ python Python 2.4.2 (#1, Sep 30 2005, 18:34:48) [GCC 3.2.2 20030222 (Red Hat Linux 3.2.2-5)] on linux2 Type "help", "copyright", "credits" or "license" for more information.
from scipy import * a = array([[1,2,3],[4,5,6]]) print a [[1 2 3] [4 5 6]] a[1,1] 5 a.shape (2, 3) a.dtype Traceback (most recent call last): File "<stdin>", line 1, in ? AttributeError: dtype
You are picking up an older version of scipy. Do you have scipy installed already? If so, we are working quickly on getting a replacement so that scipy can build on top of scipy_core. For now, you probably need to delete your scipy installation, and re-install scipy_core.
Again,
Old scipy and new scipy core do not work together yet.
We are trying to fix this, but have not done so yet.
-Travis
_______________________________________________ SciPy-user mailing list SciPy-user@scipy.net http://www.scipy.net/mailman/listinfo/scipy-user Hi all,
I have installed an old version of scipy via svn. cd /var/tmp/svn svn co http://svn.scipy.org/svn/scipy/trunk scipy cd /var/tmp/svn/scipy svn co http://svn.scipy.org/svn/scipy_core/trunk/ scipy_core python setup.py build python setup.py install (as root) Now I would like to install new scipy. What should be done prior to a new installation since old scipy and new scipy core do not work together rm -rf /usr/local/lib/python2.4/site-packages/scipy_base/ rm -rf /usr/local/lib/python2.4/site-packages/scipy rm -rf /usr/local/lib/python2.4/site-packages/scipy_distutils/ And how do I get the new scipy ? svn co http://svn.scipy.org/svn/scipy/trunk scipy svn ??? Nils
Nils Wagner wrote:
Now I would like to install new scipy.
What should be done prior to a new installation since old scipy and new scipy core do not work together
rm -rf /usr/local/lib/python2.4/site-packages/scipy_base/ rm -rf /usr/local/lib/python2.4/site-packages/scipy rm -rf /usr/local/lib/python2.4/site-packages/scipy_distutils/
You will also want to remove the f2py package and its script as scipy.f2py replaces it. weave, too, although that is less likely to get in the way.
And how do I get the new scipy ?
svn co http://svn.scipy.org/svn/scipy/trunk scipy svn ???
No, that's still the old scipy. The new scipy_core and scipy in general are being developed on branches at the moment. As has been explained in the various announcement emails: # for scipy_core: svn co http://svn.scipy.org/svn/scipy_core/branches/newcore/ cd newcore python setup.py install cd .. # for the new scipy: svn co http://svn.scipy.org/svn/scipy/branches/newscipy/ We are in the process of porting the rest of scipy to the new scipy_core, so the latter tree doesn't build anything useful, yet. Contributions are welcome. In another email, Pearu has briefly outlined some basic information one needs to know about the new scipy.distutils, and there's more documentation on its way. There is a file TOCHANGE.txt that contains a list of things that need to be done to complete the port. -- Robert Kern rkern@ucsd.edu "In the fields of hell where the grass grows high Are the graves of dreams allowed to die." -- Richard Harter
Robert Kern wrote:
Nils Wagner wrote:
Now I would like to install new scipy.
What should be done prior to a new installation since old scipy and new scipy core do not work together
rm -rf /usr/local/lib/python2.4/site-packages/scipy_base/ rm -rf /usr/local/lib/python2.4/site-packages/scipy rm -rf /usr/local/lib/python2.4/site-packages/scipy_distutils/
You will also want to remove the f2py package and its script as scipy.f2py replaces it. weave, too, although that is less likely to get in the way.
And how do I get the new scipy ?
svn co http://svn.scipy.org/svn/scipy/trunk scipy svn ???
No, that's still the old scipy. The new scipy_core and scipy in general are being developed on branches at the moment. As has been explained in the various announcement emails:
# for scipy_core: svn co http://svn.scipy.org/svn/scipy_core/branches/newcore/ cd newcore python setup.py install cd ..
# for the new scipy: svn co http://svn.scipy.org/svn/scipy/branches/newscipy/
We are in the process of porting the rest of scipy to the new scipy_core, so the latter tree doesn't build anything useful, yet. Contributions are welcome. In another email, Pearu has briefly outlined some basic information one needs to know about the new scipy.distutils, and there's more documentation on its way. There is a file TOCHANGE.txt that contains a list of things that need to be done to complete the port.
Robert, Thank you very much for your helpful comments. How about /usr/local/include/python2.4/scipy/ ? Nils
Nils Wagner wrote:
How about
/usr/local/include/python2.4/scipy/ ?
That looks like a leftover from an older installation of the new scipy_core. You should remove it. -- Robert Kern rkern@ucsd.edu "In the fields of hell where the grass grows high Are the graves of dreams allowed to die." -- Richard Harter
Steven H. Rogers wrote:
Pearu Peterson wrote:
On Mon, 3 Oct 2005, Travis Oliphant wrote:
Steven H. Rogers wrote:
"python setup.py install" for scipy_core 0.4.1 fails to build with:
error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -DNO_ATLAS_INFO=1 -Iscipy/base/include -Ibuild/src/scipy/base -Iscipy/base/src -I/usr/local/include/python2.4 -c scipy/corelib/blasdot/_dotblas.c -o build/temp.linux-i686-2.4/scipy/corelib/blasdot/_dotblas.o" failed with exit status 1
Hmm. This is definitely a blas-related problem. What other errors do you see.
A quick fix is to uncomment the blas_info=0 (line 15 of scipy/corelib/setup.py) and rerun setup (this will not try to build _dotblas.c
I'd like to track down what the real problem is though.
The problem is that cblas.h was missing that _dotblas.c includes (see previous message in this thread). In newcore svn I have included cblas.h to scipy/corelib/blasdot to workaround this problem.
Pearu
Ucommenting the blas_info=0 line allowed scipy_core to build and install. "import scipy" and "from scipy import *" seem to work, but scipy_core function names are not recognized.
Which ones are you missing? -Travis
Pearu Peterson wrote:
The problem is that cblas.h was missing that _dotblas.c includes (see previous message in this thread). In newcore svn I have included cblas.h to scipy/corelib/blasdot to workaround this problem.
Thanks, I think this is a good idea. -Travis
Does the new scipy_core support the Numeric function PyArray_FromDimsAndData? I use that to create a front end to a stand alone program that generates a lot of arrays that I want to be able to query. Not the best approach maybe but it works! -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- Rob Managan email managan at llnl.gov LLNL phone: 925-423-0903 P.O. Box 808, L-095 FAX: 925-422-3389 Livermore, CA 94551-0808
Rob Managan wrote:
Does the new scipy_core support the Numeric function PyArray_FromDimsAndData?
I use that to create a front end to a stand alone program that generates a lot of arrays that I want to be able to query. Not the best approach maybe but it works!
Yes, All of the old Numeric C-API is available (I believe...). Direct access to descr->one and descr->zero does not work anymore, though (it's replaced with a function call). If you look at the source, you will see that these older calls are all special cases of the call to PyArray_New() -Travis
As of version 0.4.2 it appears to install on Mac OSX 10.3.9. However, scipy.test() gives a bus error Here is the end of scipy.test(verbosity=2) Found 4 tests for scipy.base.index_tricks Found 0 tests for __main__ check_basic (scipy.base.function_base.test_function_base.test_all) ... ok check_nd (scipy.base.function_base.test_function_base.test_all) ... BUFFER...3 BUFFER...3 ok check_basic (scipy.base.function_base.test_function_base.test_amax) ... ok check_basic (scipy.base.function_base.test_function_base.test_amin) ... ok check_basic (scipy.base.function_base.test_function_base.test_angle) ... ok check_basic (scipy.base.function_base.test_function_base.test_any) ... ok check_nd (scipy.base.function_base.test_function_base.test_any) ... BUFFER...3 BUFFER...3 ok check_basic (scipy.base.function_base.test_function_base.test_cumprod) ... ok check_basic (scipy.base.function_base.test_function_base.test_cumsum) ... ok check_basic (scipy.base.function_base.test_function_base.test_diff) ... ok check_nd (scipy.base.function_base.test_function_base.test_diff) ... NOBUFFER...200 NOBUFFER...200 NOBUFFER...200 NOBUFFER...200 NOBUFFER...200 ok check_basic (scipy.base.function_base.test_function_base.test_extins) ... ok check_both (scipy.base.function_base.test_function_base.test_extins) ... Bus error if I add some prints into sciy/base/tests/test_function_base.py: test_extins def check_both(self): print ' ' a = rand(10) print 'a',a mask = a > 0.5 print 'mask',mask ac = a.copy() print 'ac',ac c = extract(mask, a) print 'c',c insert(a,mask,0) print 'a',a insert(a,mask,c) print 'c',c assert_array_equal(a,ac) I get a [ 0.24629164 0.1397958 0.56355685 0.53457765 0.45035916 0.05456988 0.18843402 0.057217 0.48848317 0.89830088] mask [False False True True False False False False False True] ac [ 0.24629164 0.1397958 0.56355685 0.53457765 0.45035916 0.05456988 0.18843402 0.057217 0.48848317 0.89830088] c [ 0.56355685 0.53457765 0.89830088] Bus error which implies that the insert function fails. Any ideas as to what would cause this?? Thanks!! -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- Rob Managan email managan at llnl.gov LLNL phone: 925-423-0903 P.O. Box 808, L-095 FAX: 925-422-3389 Livermore, CA 94551-0808
participants (10)
-
Christian Meesters -
christophe grimault -
Darren Dale -
Nils Wagner -
Pearu Peterson -
Prabhu Ramachandran -
Rob Managan -
Robert Kern -
Steven H. Rogers -
Travis Oliphant