Mailman 3 October 2004 - SciPy-User

Help required regding Eigenvectors
by Sudheer Phani 14 Mar '22

14 Mar '22

Hello All, I have been encountering some strange problems with the calculation of eigen vectors using python. The problem is with the sign of the eigen vectors calculated. On Very few occasions the eigen vectors calculated using python have an opposite sign than the actual eigenvectors, though the magnitude is correct. Can any one of you plz help me in this regard and suggest me some solution if you have encoutered similar problems . Any help in this regd is appreciated Thanks in Advace regds Sudheer

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eigenvalues of sparse matrix
by David Grant 17 Nov '04

17 Nov '04

Sorry, another sparse question: Is there anything is scipy which can find the eigenvalues and eigenvectors of a sparse matrix? -- David J. Grant Scientific Officer Intellectual Property D-Wave Systems Inc. tel: 604.732.6604 fax: 604.732.6614 ************************** CONFIDENTIAL COMMUNICATION This electronic transmission, and any documents attached hereto, is confidential. The information is intended only for use by the recipient named above. If you have received this electronic message in error, please notify the sender and delete the electronic message. Any disclosure, copying, distribution, or use of the contents of information received in error is strictly prohibited.

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lingalg.svd performance?
by Nick Arnett 11 Nov '04

11 Nov '04

What sort of performance should I expect using lingalg.svd on matrixes on the order of 500 x 15000? I'm using a 2 Ghz P4 system with 2 GB of memory and these are taking hours to complete. I previously was using an external SVD utility that was taking a couple of minutes, and I'm going to have to switch back to it unless there's some way to get Scipy to do this a lot faster. I'm using the pre-built binaries, with ATLAS and F2PY installed. I'm not eager to build my own, but if that is likely to speed things up a lot, I'll give it a shot. Any help will be gratefully appreciated. Nick

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C++ extensions
by David Grant 09 Nov '04

09 Nov '04

Hey guys (and girls, are there any???), I have some C++ code, it does a decomposition of a large matrix.. It has a bunch of objects. It is very black box though, you just declare an object, give it the matrix and it will give an output. I think it uses CLAPACK. I would like to call this from python. I looked at some Weave information, but that didn't help, because I obviously can't run this in-line since it is many files. Any help like web links is appreciated. David

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Derivative() usage?
by Francesc Alted 04 Nov '04

04 Nov '04

Hi, I'm trying to figure out how to compute the derivatives of a function with scipy, but the documentation is a bit terse for me: def derivative(func,x0,dx=1.0,n=1,args=(),order=3): """Given a function, use an N-point central differenece formula with spacing dx to compute the nth derivative at x0, where N is the value of order and must be odd. Warning: Decreasing the step size too small can result in round-off error. """ I would like to compute a derivative of an arbitrary order, but by reading the docs, I'm not sure what the n and order parameters exactly means. Someone smarter than me can help me? -- Francesc Alted

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Re: [SciPy-user] Undefined symbol "ATL_cpttrsm"
by Lee Harr 31 Oct '04

31 Oct '04

>atlas or atlas_r should be the last in library names list. So try changing >'atlas' to 'atlas_r' in calc_info method of atlas_info class and undo your >changes in atlas_threads_info, .. > Ok.. I changed ... def calc_info(self): lib_dirs = self.get_lib_dirs() info = {} atlas_libs = self.get_libs('atlas_libs', self._lib_names + ['atlas']) lapack_libs = self.get_libs('lapack_libs',['lapack']) to ... def calc_info(self): lib_dirs = self.get_lib_dirs() info = {} atlas_libs = self.get_libs('atlas_libs', self._lib_names + ['atlas_r']) lapack_libs = self.get_libs('lapack_libs',['lapack']) but I still get ... ImportError: /usr/local/lib/python2.3/site-packages/scipy/linalg/clapack.so: Undefined symbol "clapack_sgesv" _________________________________________________________________ FREE pop-up blocking with the new MSN Toolbar - get it now! http://toolbar.msn.com/

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Re: [SciPy-user] Undefined symbol "ATL_cpttrsm"
by Lee Harr 31 Oct '04

31 Oct '04

>>>>ImportError: /usr/local/lib/libptf77blas.so.1: Undefined symbol >>>>"ATL_cpttrsm" >>>> >>>> >>>>Any hints on how to fix this are appreciated ... >>> >>>Symbol "ATL_cpttrsm" should be defined in atlas library, try `nm >>>/usr/local/lib/libatlas.* | grep ATL_cpttrsm`. >> >> >>so... it looks like the threaded (_r) libs have the symbol, but not >>the unthreaded, but the threaded libs were not linked in ... > >This should be done in scipy_distutils/system_info.py. Look for >the definition of *atlas_threads* classes. If freebsd uses for _r-libraries >for threaded linking then pt{f77,c}blas should be replaced >with {f77,c}blas_r but I am not sure, the usage of _r-libraries looks odd >to me. Could anyone explain why freebsd introduces _r-libraries? > I tried changing: class atlas_threads_info(atlas_info): _lib_names = ['ptf77blas','ptcblas'] class atlas_blas_threads_info(atlas_blas_info): _lib_names = ['ptf77blas','ptcblas'] to: class atlas_threads_info(atlas_info): _lib_names = ['atlas_r','ptf77blas','ptcblas'] class atlas_blas_threads_info(atlas_blas_info): _lib_names = ['atlas_r','ptf77blas','ptcblas'] Now I get this .... >>>from scipy import * >>>linalg.solve Traceback (most recent call last): File "<stdin>", line 1, in ? File "/usr/local/lib/python2.3/site-packages/scipy_base/ppimport.py", line 270, in __getattr__ module = self._ppimport_importer() File "/usr/local/lib/python2.3/site-packages/scipy_base/ppimport.py", line 243, in _ppimport_importer module = __import__(name,None,None,['*']) File "/usr/local/lib/python2.3/site-packages/scipy/linalg/__init__.py", line 8, in ? from basic import * File "/usr/local/lib/python2.3/site-packages/scipy/linalg/basic.py", line 11, in ? from lapack import get_lapack_funcs File "/usr/local/lib/python2.3/site-packages/scipy/linalg/lapack.py", line 16, in ? import clapack ImportError: /usr/local/lib/python2.3/site-packages/scipy/linalg/clapack.so: Undefined symbol "clapack_sgesv" but I do not see that one defined anywhere... _________________________________________________________________ FREE pop-up blocking with the new MSN Toolbar - get it now! http://toolbar.msn.com/

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Re: [SciPy-user] Undefined symbol "ATL_cpttrsm"
by Lee Harr 31 Oct '04

31 Oct '04

>>ImportError: /usr/local/lib/libptf77blas.so.1: Undefined symbol >>"ATL_cpttrsm" >> >> >>Any hints on how to fix this are appreciated ... > >Symbol "ATL_cpttrsm" should be defined in atlas library, try `nm >/usr/local/lib/libatlas.* | grep ATL_cpttrsm`. $nm /usr/local/lib/libatlas.so.1 | grep ATL_cpttrsm $nm /usr/local/lib/libatlas.a | grep ATL_cpttrsm $nm /usr/local/lib/libatlas_r.so.1 | grep ATL_cpttrsm 005cfeb8 T ATL_cpttrsm 005cfc48 T ATL_cpttrsm0 005cfca8 T ATL_cpttrsm_nt $nm /usr/local/lib/libatlas_r.a | grep ATL_cpttrsm U ATL_cpttrsm0 ATL_cpttrsm.o: 00000244 T ATL_cpttrsm 00000000 T ATL_cpttrsm0 00000054 T ATL_cpttrsm_nt >So it looks like atlas library was not used during the linking of flapack >extension module or -lptf77blas was specified after -latlas. > >What is the output (both stdout and stderr) of > >>>>from scipy_distutils.system_info import get_info >>>>get_info('lapack_opt') > >>>get_info('lapack_opt') lapack_opt_info: atlas_threads_info: scipy_distutils.system_info.atlas_threads_info FOUND: libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas'] library_dirs = ['/usr/local/lib'] language = f77 include_dirs = ['/usr/local/include'] running build_src building extension "atlas_version" sources creating build creating build/src adding 'build/src/atlas_version_0x3987e8cd.c' to sources. running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext Could not locate executable g77 customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using build_ext building 'atlas_version' extension compling C sources cc options: '-fno-strict-aliasing -DNDEBUG -O -pipe -D_THREAD_SAFE -DTHREAD_STACK_SIZE=0x20000 -fPIC' creating build/temp.freebsd-4.10-STABLE-i386-2.3 creating build/temp.freebsd-4.10-STABLE-i386-2.3/build creating build/temp.freebsd-4.10-STABLE-i386-2.3/build/src compile options: '-I/usr/local/include -I/usr/local/include/python2.3 -c' cc: build/src/atlas_version_0x3987e8cd.c creating build/lib.freebsd-4.10-STABLE-i386-2.3 /usr/bin/f77 -shared build/temp.freebsd-4.10-STABLE-i386-2.3/build/src/atlas_version_0x3987e8cd.o -L/usr/local/lib -L/usr/lib -latlas -lg2c -o build/lib.freebsd-4.10-STABLE-i386-2.3/atlas_version.so FOUND: libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas'] library_dirs = ['/usr/local/lib'] language = f77 define_macros = [('ATLAS_INFO', '"\\"3.6.0\\""')] include_dirs = ['/usr/local/include'] {'libraries': ['lapack', 'ptf77blas', 'ptcblas', 'atlas'], 'library_dirs': ['/usr/local/lib'], 'language': 'f77', 'define_macros': [('ATLAS_INFO', '"\\"3.6.0\\""')], 'include_dirs': ['/usr/local/include']} so... it looks like the threaded (_r) libs have the symbol, but not the unthreaded, but the threaded libs were not linked in ... I am looking around (through ...Lib/linalg/...) but I do not see where I might point the build to the correct lib. Thanks for your time. _________________________________________________________________ Don't just search. Find. Check out the new MSN Search! http://search.msn.com/

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Undefined symbol "ATL_cpttrsm"
by Lee Harr 31 Oct '04

31 Oct '04

I am running scipy on FreeBSD 4.10 built from ports. Most things seem to work fine, but ... >>>from scipy import * >>>linalg.solve Traceback (most recent call last): File "<stdin>", line 1, in ? File "/usr/local/lib/python2.3/site-packages/scipy_base/ppimport.py", line 270, in __getattr__ module = self._ppimport_importer() File "/usr/local/lib/python2.3/site-packages/scipy_base/ppimport.py", line 243, in _ppimport_importer module = __import__(name,None,None,['*']) File "/usr/local/lib/python2.3/site-packages/scipy/linalg/__init__.py", line 8, in ? from basic import * File "/usr/local/lib/python2.3/site-packages/scipy/linalg/basic.py", line 11, in ? from lapack import get_lapack_funcs File "/usr/local/lib/python2.3/site-packages/scipy/linalg/lapack.py", line 15, in ? import flapack ImportError: /usr/local/lib/libptf77blas.so.1: Undefined symbol "ATL_cpttrsm" Any hints on how to fix this are appreciated ... _________________________________________________________________ Don't just search. Find. Check out the new MSN Search! http://search.msn.com/

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High-Performance BLAS by Kazushige Goto
by Nils Wagner 29 Oct '04

29 Oct '04

Hi all, Is it possible to use the High-Performance BLAS by Kazushige Goto http://www.cs.utexas.edu/users/flame/goto/ instead of ATLAS ? Any pointer would be appreciated. Nils

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