Mailman 3 December 2006 - SciPy-User

Wow, Python much faster than MatLab
by Stef Mientki 30 Dec '06

30 Dec '06

hi All, instead of questions, my first success story: I converted my first MatLab algorithm into Python (using SciPy), and it not only works perfectly, but also runs much faster: MatLab: 14 msec Python: 2 msec After taking the first difficult steps into Python, all kind of small problems as you already know, it nows seems a piece of cake to convert from MatLab to Python. (the final programs of MatLab and Python can almost only be distinguished by the comment character ;-) Especially I like: - more relaxed behavior of exceeded the upper limit of a (1-dimensional) array - much more functions available, like a simple "mean" - reducing datatype if it's allowed (booleans of 1 byte) thanks for all your help, probably need some more in the future, cheers, Stef Mientki

2 2

C API issue
by belinda thom 29 Dec '06

29 Dec '06

Hi, I'm beginning to play around w/scipy, and have some problems when doing "from scipy import *" that don't occur when just doing "import scipy" (appended below). Is there an explanation for this behavior? The version of scipy I'm using came from http://pythonmac.org/ packages/py24-fat/index.html. Thanks, --b 8 % python Python 2.4.4 (#1, Oct 18 2006, 10:34:39) [GCC 4.0.1 (Apple Computer, Inc. build 5341)] on darwin Type "help", "copyright", "credits" or "license" for more information. history mechanism set up >>> from scipy import * RuntimeError: module compiled against version 1000002 of C-API but this version of numpy is 1000009 Traceback (most recent call last): File "<stdin>", line 1, in ? File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/io/__init__.py", line 8, in ? from numpyio import packbits, unpackbits, bswap, fread, fwrite, \ ImportError: numpy.core.multiarray failed to import >>> 9 % python Python 2.4.4 (#1, Oct 18 2006, 10:34:39) [GCC 4.0.1 (Apple Computer, Inc. build 5341)] on darwin Type "help", "copyright", "credits" or "license" for more information. history mechanism set up >>> import scipy >>> from scipy import * RuntimeError: module compiled against version 1000002 of C-API but this version of numpy is 1000009 Traceback (most recent call last): File "<stdin>", line 1, in ? File "/Library/Frameworks/Python.framework/Versions/2.4/lib/ python2.4/site-packages/scipy/io/__init__.py", line 8, in ? from numpyio import packbits, unpackbits, bswap, fread, fwrite, \ ImportError: numpy.core.multiarray failed to import

1 0

missing fopen?
by J Oishi 29 Dec '06

29 Dec '06

Hi, I am just getting started with scipy (using 0.5.2), and I need to read large amounts of fortran77 unformatted data that comes out of our simulation code. Searching the web, it appears there used to be a class called fopen which had some fort_read methods which would do what I need. However, the source for this info is several years old. If I do a import scipy.io help(scipy.io) I get a hopeful message about fopen, but it doesn't seem to exist: In [2]: test = scipy.io.fopen('test.dat') ------------------------------------------------------------------------ --- exceptions.AttributeError Traceback (most recent call last) /Users/joishi/<ipython console> AttributeError: 'module' object has no attribute 'fopen' Additionally, grepping through Lib/io/numpyiomodule.c seems to reveal nothing about fopen. Has it been expunged from scipy? If so, is there any way to read f77 unformatted binary? thanks, j

1 0

probably a stupid question: MatLab equivalent of "diff" ?
by Stef Mientki 29 Dec '06

29 Dec '06

Does anyone know the equivalent of the MatLab "diff" function. The "diff" functions calculates the difference between 2 succeeding elements of an array. I need to detect (fast) the falling edge of a binary signal. There's derivate function in Python diff, but when you use an binary (true/false) input, it also detects rising edges. Probably a stupid question, but I still have troubles, digging to huge amount of information about Python. thanks, Stef Mientki

4 9

moving average, moving standard deviation, etc...
by Matt Knox 27 Dec '06

27 Dec '06

Does anyone know of a slick way to calculate a simple moving average and/or moving standard deviation? And when I say slick, I mean loop-free way, because it would be fairly easy to code a looping way of doing it, it would just be really slow. To be more specific, when I say moving standard deviation, I mean for example... if A is a 1-dimensional array with 100 elements, and I'm using a window size of 10, then the result at index 10 would be A[0:10].std(), the result at index 11 would be A[1:11].std() , etc... And similarly for moving average, and so forth. Is their a general way to do these kind of things? Or would it have to be a special case for each type of calculation to avoid looping? Any help is greatly appreciated. Thanks in advance, - Matt

6 10

accumulate with custom functions
by Matt Knox 26 Dec '06

26 Dec '06

I work quite a bit with another language called FAME, which is very vector based. In FAME I calculate exponentially weighted moving averages (exp mave) in the following way: suppose X is a 1 dimensional array, then to Calculate an exp mave I would do: myExpMave = X Case firstvalue(X)+1 to lastvalue(X) #sets global operating range set myExpMave[N] = myExpMave[N-1] + k * (myExpMave[N]-myExpMave[N-1]) #where k is some constant smoothing factor, N is an index placeholder recognized by FAME essentially, what this does in numpy terms is accumulate with a function defined as "def mycalc(a, b, k): return a + k * (b - a)" So, getting to the topic of my post, is their anyway to accomplish this kind of accumulation swiftly without resorting to writing a new ufunc in C? Or what would be the best way to do this kind of thing generally? Ie. accumulate with some kind of arbitrary, but still simple, function. Thanks in advance for any help you can provide. - Matt

2 2

(newbie) IIR, is there a MatLab "filter" equivalent ?
by Stef Mientki 23 Dec '06

23 Dec '06

hello, this might be a dumb question, if so, sorry for my ignorance, but my math is rusted, and I'm a completly newbie (to Python), I haven't even installed Python on my computer yet ;-) I'm evaluating some packages for easy data-acquisition and (real-time) data-analysis, specific for bio-physical signals (e.g. ECG, EOG, etc). I've seen LabView and threw it in the recycle bin. I've seen MatLab and decided it needed a user friendly wrapper, after which it looks quit powerfull. After my positive experiences with MatLab scripting (didn't realize scripting could be so fast), I searched for more and found 2 other interesting packages (both open source), - SciLab : almost identical to MatLab, and with an equivalent Simulation module - Python + huge collection of tools : suited for a wide range of platforms, even for small PIC micro controllers I quickly read some documents about NumPy and SciPy, and most functions I need are there, even the clip function which is missing in MatLab. But I couldn't find the equivalent of the MatLab "filter" function: y = filter(b,a,X) The filter function is implemented as a direct form II transposed structure, y(n) = b(1)*x(n) + b(2)*x(n-1) + ... + b(nb+1)*x(n-nb) - a(2)*y(n-1) - ... - a(na+1)*y(n-na) Is there a Python equivalent to this filter function ? I tried to look in the archives of this mailinglist, but that's not a job for humans. (btw, does anyone has the complete list archive in Thunderbird format ?) What I also couldn't find ( I do admit that Python information is overwhelming, but maybe that's the problem for newbies) is there a toolbox to generate the filter polynomes ? thanks, Stef Mientki

3 4

desactivating R
by Joshua Petterson 20 Dec '06

20 Dec '06

Hi all, it's certainely a stupid question, but how can I desactivate the use of R when I do a "from scipy import *" or "from scipy.stats import stats", because I have some trouble with it (random segfault)? Do I have to uninstall "rpy"? Another question: is it possible to save a session from ipython, like we can do with R? thanks

3 10

Installing scipy-5.2 on fedora 64 bit: cannot import name flapack
by Niels L Ellegaard 20 Dec '06

20 Dec '06

Dear masters I am trying to install scipy 5.2 on a fedora 64 bit machine with numpy 1.0.1. When I try to run scipy.test() i get the following error from scipy.linalg import flapack ImportError: cannot import name flapack I must be doing something wrong, but I cannot see what, so I would be grateful for some hints (Details below.. sorry about the flood) Thanks in advance Niels ***************** Output from scipy.test() ************ python -c 'import scipy; scipy.test()' Found 4 tests for scipy.io.array_import Found 397 tests for scipy.ndimage Found 96 tests for scipy.sparse.sparse Found 20 tests for scipy.fftpack.pseudo_diffs Found 6 tests for scipy.optimize.optimize Found 6 tests for scipy.interpolate.fitpack Found 6 tests for scipy.interpolate Found 12 tests for scipy.io.mmio Found 18 tests for scipy.fftpack.basic Found 4 tests for scipy.io.recaster Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack' from '.../linsolve/umfpack/__init__.pyc'> /usr/lib64/python2.4/site-packages/scipy/linsolve/umfpack/tests/ test_umfpack.py:17: AttributeError: 'module' object has no attribute 'umfpack' (in ?) Found 4 tests for scipy.optimize.zeros Found 28 tests for scipy.io.mio Warning: FAILURE importing tests for <module 'scipy.special.basic' from '...ckages/scipy/special/basic.pyc'> /usr/lib64/python2.4/site-packages/scipy/linalg/lapack.py:17: ImportError: cannot import name flapack (in ?) Warning: FAILURE importing tests for <module 'scipy.lib.blas.fblas' from '...ckages/scipy/lib/blas/fblas.so'> /usr/lib64/python2.4/site-packages/scipy/lib/blas/__init__.py:10: ImportError: /usr/lib64/python2.4/site-packages/scipy/lib/blas/cblas.so: undefined symbol: cblas_saxpy (in ?) Warning: FAILURE importing tests for <module 'scipy.linsolve.umfpack.umfpack' from '...y/linsolve/umfpack/umfpack.pyc'> /usr/lib64/python2.4/site-packages/scipy/linsolve/umfpack/tests/test_ mfpack.py:17: AttributeError: 'module' object has no attribute 'umfpack' (in ?) Found 1 tests for scipy.optimize.cobyla Found 4 tests for scipy.fftpack.helper Found 0 tests for __main__ Don't worry about a warning regarding the number of bytes read. Warning: 1000000 bytes requested, 20 bytes read. ...E......................................................................... ............................................................................ ............................................................................. ............................................................................. ............................................................................. ..........................Resizing... 16 17 24 Resizing... 20 7 35 Resizing... 23 7 47 Resizing... 24 25 58 Resizing... 28 7 68 Resizing... 28 27 73 .....Use minimum degree ordering on A'+A. ........................Use minimum degree ordering on A'+A. ...................Resizing... 16 17 24 Resizing... 20 7 35 Resizing... 23 7 47 Resizing... 24 25 58 Resizing... 28 7 68 Resizing... 28 27 73 .....Use minimum degree ordering on A'+A. .................Resizing... 16 17 24 Resizing... 20 7 35 Resizing... 23 7 47 Resizing... 24 25 58 Resizing... 28 7 68 Resizing... 28 27 73 .....Use minimum degree ordering on A'+A. ...................................... /usr/lib64/python2.4/site-packages/scipy/interpolate/fitpack2.py:457: UserWarning: The coefficients of the spline returned have been computed as the minimal norm least-squares solution of a (numerically) rank deficient system (deficiency=7). If deficiency is large, the results may be inaccurate. Deficiency may strongly depend on the value of eps. warnings.warn(message) ....................................................................... ............ ====================================================================== ERROR: check_integer (scipy.io.tests.test_array_import.test_read_array) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python2.4/site-packages/scipy/io/tests/test_array_import.py", line 55, in check_integer from scipy import stats File "/usr/lib64/python2.4/site-packages/scipy/stats/__init__.py", line 7, in ? from stats import * File "/usr/lib64/python2.4/site-packages/scipy/stats/stats.py", line 190, in ? import scipy.special as special File "/usr/lib64/python2.4/site-packages/scipy/special/__init__.py", line 10, in ? import orthogonal File "/usr/lib64/python2.4/site-packages/scipy/special/orthogonal.py", line 65, in ? from scipy.linalg import eig File "/usr/lib64/python2.4/site-packages/scipy/linalg/__init__.py", line 8, in ? from basic import * File "/usr/lib64/python2.4/site-packages/scipy/linalg/basic.py", line 17, in ? from lapack import get_lapack_funcs File "/usr/lib64/python2.4/site-packages/scipy/linalg/lapack.py", line 17, in ? from scipy.linalg import flapack ImportError: cannot import name flapack ---------------------------------------------------------------------- Ran 606 tests in 2.998s FAILED (errors=1) *************** Site.cfg ************* [lapack] library_dirs = /usr/lib64 [atlas] library_dirs = /usr/lib64:/usr/lib64/atlas [blas] library_dirs = /usr/lib64:/usr/lib64/atlas [umfpack] library_dirs = /usr/lib64 include_dirs = /usr/include/ufsparse/ [amd] library_dirs = /usr/lib64 [fftw] library_dirs = /usr/lib64/ [fftw2] library_dirs = /usr/lib64/ [fftw3] library_dirs = /usr/lib64/ **************** Output from installation ******* python setup.py install > log.0 Warning: Subpackage 'Lib' configuration returned as 'scipy' cat log.0 mkl_info: libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE fftw3_info: FOUND: libraries = ['fftw3'] library_dirs = ['/usr/lib64/'] define_macros = [('SCIPY_FFTW3_H', None)] include_dirs = ['/usr/include'] djbfft_info: NOT AVAILABLE blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS Setting PTATLAS=ATLAS Setting PTATLAS=ATLAS FOUND: libraries = ['lapack', 'blas'] library_dirs = ['/usr/lib64/atlas'] language = c include_dirs = ['/usr/include/atlas'] customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using config compiling '_configtest.c': /* This file is generated from numpy_distutils/system_info.py */ void ATL_buildinfo(void); int main(void) { ATL_buildinfo(); return 0; } C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fPIC compile options: '-c' gcc: _configtest.c gcc -pthread _configtest.o -L/usr/lib64/atlas -llapack -lblas -o _configtest ATLAS version 3.6.0 built by root on Thu Jun 3 21:13:07 UTC 2004: UNAME : Linux ravel 2.6.5 #3 SMP Tue Apr 13 13:41:54 UTC 2004 x86_64 GNU/Linux INSTFLG : MMDEF : /home/camm/atlas3-3.6.0/CONFIG/ARCHS/HAMMER64SSE2/gcc/gemm ARCHDEF : /home/camm/atlas3-3.6.0/CONFIG/ARCHS/HAMMER64SSE2/gcc/misc F2CDEFS : -DAdd__ -DStringSunStyle CACHEEDGE: 720896 F77 : /home/camm/usr/bin/g77, version GNU Fortran (GCC) 3.3.3 (Debian 20040422) F77FLAGS : -fomit-frame-pointer -O -m64 CC : /usr/bin/gcc, version gcc (GCC) 3.3.3 (Debian 20040422) CC FLAGS : -fomit-frame-pointer -O -mfpmath=387 -m64 MCC : /usr/bin/gcc, version gcc (GCC) 3.3.3 (Debian 20040422) MCCFLAGS : -fomit-frame-pointer -O -mfpmath=387 -m64 success! removing: _configtest.c _configtest.o _configtest FOUND: libraries = ['lapack', 'blas'] library_dirs = ['/usr/lib64/atlas'] language = c define_macros = [('ATLAS_INFO', '"\\"3.6.0\\""')] include_dirs = ['/usr/include/atlas'] ATLAS version 3.6.0 lapack_opt_info: lapack_mkl_info: NOT AVAILABLE atlas_threads_info: Setting PTATLAS=ATLAS numpy.distutils.system_info.atlas_threads_info Setting PTATLAS=ATLAS Setting PTATLAS=ATLAS FOUND: libraries = ['lapack', 'lapack', 'blas'] library_dirs = ['/usr/lib64/atlas'] language = f77 include_dirs = ['/usr/include/atlas'] customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using config compiling '_configtest.c': /* This file is generated from numpy_distutils/system_info.py */ void ATL_buildinfo(void); int main(void) { ATL_buildinfo(); return 0; } C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fPIC compile options: '-c' gcc: _configtest.c gcc -pthread _configtest.o -L/usr/lib64/atlas -llapack -llapack -lblas -o _configtest ATLAS version 3.6.0 built by root on Thu Jun 3 21:13:07 UTC 2004: UNAME : Linux ravel 2.6.5 #3 SMP Tue Apr 13 13:41:54 UTC 2004 x86_64 GNU/Linux INSTFLG : MMDEF : /home/camm/atlas3-3.6.0/CONFIG/ARCHS/HAMMER64SSE2/gcc/gemm ARCHDEF : /home/camm/atlas3-3.6.0/CONFIG/ARCHS/HAMMER64SSE2/gcc/misc F2CDEFS : -DAdd__ -DStringSunStyle CACHEEDGE: 720896 F77 : /home/camm/usr/bin/g77, version GNU Fortran (GCC) 3.3.3 (Debian 20040422) F77FLAGS : -fomit-frame-pointer -O -m64 CC : /usr/bin/gcc, version gcc (GCC) 3.3.3 (Debian 20040422) CC FLAGS : -fomit-frame-pointer -O -mfpmath=387 -m64 MCC : /usr/bin/gcc, version gcc (GCC) 3.3.3 (Debian 20040422) MCCFLAGS : -fomit-frame-pointer -O -mfpmath=387 -m64 success! removing: _configtest.c _configtest.o _configtest FOUND: libraries = ['lapack', 'lapack', 'blas'] library_dirs = ['/usr/lib64/atlas'] language = f77 define_macros = [('ATLAS_INFO', '"\\"3.6.0\\""')] include_dirs = ['/usr/include/atlas'] ATLAS version 3.6.0 ATLAS version 3.6.0 non-existing path in 'Lib/linsolve': 'tests' umfpack_info: amd_info: FOUND: libraries = ['amd'] library_dirs = ['/usr/lib64'] FOUND: libraries = ['umfpack', 'amd'] library_dirs = ['/usr/lib64'] swig_opts = ['-I/usr/include/ufsparse'] define_macros = [('SCIPY_UMFPACK_H', None)] include_dirs = ['/usr/include/ufsparse'] non-existing path in 'Lib/maxentropy': 'doc' running install running build running config_fc running build_src building py_modules sources building library "dfftpack" sources building library "linpack_lite" sources building library "mach" sources building library "quadpack" sources building library "odepack" sources building library "fitpack" sources building library "superlu_src" sources building library "odrpack" sources building library "minpack" sources building library "rootfind" sources building library "c_misc" sources building library "cephes" sources building library "mach" sources building library "toms" sources building library "amos" sources building library "cdf" sources building library "specfun" sources building library "statlib" sources building extension "scipy.cluster._vq" sources building extension "scipy.fftpack._fftpack" sources f2py options: [] adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.4' to include_dirs. building extension "scipy.fftpack.convolve" sources f2py options: [] adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.4' to include_dirs. building extension "scipy.integrate._quadpack" sources building extension "scipy.integrate._odepack" sources building extension "scipy.integrate.vode" sources f2py options: [] adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.4' to include_dirs. building extension "scipy.interpolate._fitpack" sources building extension "scipy.interpolate.dfitpack" sources f2py options: [] adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.4' to include_dirs. adding 'build/src.linux-x86_64-2.4/Lib/interpolate/dfitpack- f2pywrappers.f' to sources. building extension "scipy.io.numpyio" sources building extension "scipy.lib.blas.fblas" sources f2py options: ['skip:', ':'] adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.4' to include_dirs. adding 'build/src.linux-x86_64-2.4/build/src.linux-x86_64-2.4/Lib/lib/blas/fblas- f2pywrappers.f' to sources. building extension "scipy.lib.blas.cblas" sources adding 'Lib/lib/blas/cblas.pyf.src' to sources. f2py options: ['skip:', ':'] adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.4' to include_dirs. building extension "scipy.lib.lapack.flapack" sources f2py options: ['skip:', ':'] adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.4' to include_dirs. building extension "scipy.lib.lapack.clapack" sources adding 'Lib/lib/lapack/clapack.pyf.src' to sources. f2py options: ['skip:', ':'] adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.4' to include_dirs. building extension "scipy.lib.lapack.calc_lwork" sources f2py options: [] adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.4' to include_dirs. building extension "scipy.lib.lapack.atlas_version" sources building extension "scipy.linalg.fblas" sources adding 'build/src.linux-x86_64-2.4/scipy/linalg/fblas.pyf' to sources. f2py options: [] adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.4' to include_dirs. adding 'build/src.linux-x86_64-2.4/build/src.linux-x86_64-2.4/scipy/linalg/fblas- f2pywrappers.f' to sources. building extension "scipy.linalg.cblas" sources adding 'build/src.linux-x86_64-2.4/scipy/linalg/cblas.pyf' to sources. f2py options: [] adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.4' to include_dirs. building extension "scipy.linalg.flapack" sources adding 'build/src.linux-x86_64-2.4/scipy/linalg/flapack.pyf' to sources. f2py options: [] adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.4' to include_dirs. adding 'build/src.linux-x86_64-2.4/build/src.linux-x86_64-2.4/scipy/linalg/flapack- f2pywrappers.f' to sources. building extension "scipy.linalg.clapack" sources adding 'build/src.linux-x86_64-2.4/scipy/linalg/clapack.pyf' to sources. f2py options: [] adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.4' to include_dirs. building extension "scipy.linalg._flinalg" sources f2py options: [] adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.4' to include_dirs. building extension "scipy.linalg.calc_lwork" sources f2py options: [] adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.4' to include_dirs. building extension "scipy.linalg.atlas_version" sources building extension "scipy.linalg._iterative" sources f2py options: [] adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.4' to include_dirs. building extension "scipy.linsolve._zsuperlu" sources building extension "scipy.linsolve._dsuperlu" sources building extension "scipy.linsolve._csuperlu" sources building extension "scipy.linsolve._ssuperlu" sources building extension "scipy.linsolve.umfpack.__umfpack" sources adding 'Lib/linsolve/umfpack/umfpack.i' to sources. building extension "scipy.odr.__odrpack" sources building extension "scipy.optimize._minpack" sources building extension "scipy.optimize._zeros" sources building extension "scipy.optimize._lbfgsb" sources f2py options: [] adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.4' to include_dirs. building extension "scipy.optimize.moduleTNC" sources building extension "scipy.optimize._cobyla" sources f2py options: [] adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.4' to include_dirs. building extension "scipy.optimize.minpack2" sources f2py options: [] adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.4' to include_dirs. building extension "scipy.signal.sigtools" sources building extension "scipy.signal.spline" sources building extension "scipy.sparse.sparsetools" sources f2py options: [] adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.4' to include_dirs. building extension "scipy.special._cephes" sources building extension "scipy.special.specfun" sources f2py options: ['--no-wrap-functions'] adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.4' to include_dirs. building extension "scipy.stats.statlib" sources f2py options: ['--no-wrap-functions'] adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.4' to include_dirs. building extension "scipy.stats.futil" sources f2py options: [] adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.4' to include_dirs. building extension "scipy.stats.mvn" sources f2py options: [] adding 'build/src.linux-x86_64-2.4/fortranobject.c' to sources. adding 'build/src.linux-x86_64-2.4' to include_dirs. adding 'build/src.linux-x86_64-2.4/Lib/stats/mvn-f2pywrappers.f' to sources. building extension "scipy.ndimage._nd_image" sources building data_files sources running build_py copying build/src.linux-x86_64-2.4/scipy/__config__.py -> build/lib.linux-x86_64-2.4/scipy running build_clib customize UnixCCompiler customize UnixCCompiler using build_clib customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using build_clib running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using build_ext running install_lib copying build/lib.linux-x86_64-2.4/scipy/__config__.py -> /usr/lib64/python2.4/site-packages/scipy byte-compiling /usr/lib64/python2.4/site-packages/scipy/__config__.py to __config__.pyc running install_data

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Errors compiling scipy with icc and intel mkl
by Tom Denniston 18 Dec '06

18 Dec '06

I get a recurrent error no matter what i seem to try compiling scipy. The latest attempt I used the intel compiler and the intel mkl following the instructions on the wiki. I keep getting these undefined references to __MAIN. I am sure this is something really obvious that I am missing but I'm using intel mkl version 8.0.1 and icc version 8.1 and g77 from gcc version GCC 3.2.3. Does anyone know what this error means. I know the g77 is rather old but I am unfortunately stuck with it: compile options: '-DSCIPY_MKL_H -DSCIPY_MKL_H -I/local/intel/mkl/8.0.1/include -I/usr/local/include -I/usr/include -I/local/include -Ibuild/src.linux-i686-2.5 -I/local/lib/python2.5/site-packages/numpy/core/include -I/local/include/python2.5 -c' /local/tools/gcc/3.2.3/bin/g77 -L/local/lib -L/lib -L/usr/lib -L/usr/X11R6/lib -L/local/intel/mkl/8.0.1/lib/32/ build/temp.linux-i686-2.5/build/src.linux-i686-2.5/Lib/fftpack/_fftpackmodule.o build/temp.linux-i686-2.5/Lib/fftpack/src/zfft.o build/temp.linux-i686-2.5/Lib/fftpack/src/drfft.o build/temp.linux-i686-2.5/Lib/fftpack/src/zrfft.o build/temp.linux-i686-2.5/Lib/fftpack/src/zfftnd.o build/temp.linux-i686-2.5/build/src.linux-i686-2.5/fortranobject.o -L/local/intel/mkl/8.0.1/lib/32 -L/local/lib/python2.5/config -Lbuild/temp.linux-i686-2.5 -ldfftpack -lmkl -lvml -lpthread -lpython2.5 -lg2c -o build/lib.linux-i686-2.5/scipy/fftpack/_fftpack.so build/temp.linux-i686-2.5/Lib/fftpack/src/zfftnd.o(.text+0x215): In function `get_cache_id_zmklfftnd': : undefined reference to `_intel_fast_memcpy' build/temp.linux-i686-2.5/build/src.linux-i686-2.5/fortranobject.o(.text+0xa7e): In function `fortran_setattr': : undefined reference to `_intel_fast_memcpy' build/temp.linux-i686-2.5/build/src.linux-i686-2.5/fortranobject.o(.text+0xb0b): In function `fortran_setattr': : undefined reference to `_intel_fast_memcpy' build/temp.linux-i686-2.5/build/src.linux-i686-2.5/fortranobject.o(.text+0xf76): In function `array_from_pyobj': : undefined reference to `_intel_fast_memset' /local/tools/gcc/3.2.3/bin/../lib/gcc-lib/i686-pc-linux-gnu/3.2.3/../../../libfrtbegin.a(frtbegin.o)(.text+0x32): In function `main': : undefined reference to `MAIN__' collect2: ld returned 1 exit status build/temp.linux-i686-2.5/Lib/fftpack/src/zfftnd.o(.text+0x215): In function `get_cache_id_zmklfftnd': : undefined reference to `_intel_fast_memcpy' build/temp.linux-i686-2.5/build/src.linux-i686-2.5/fortranobject.o(.text+0xa7e): In function `fortran_setattr': : undefined reference to `_intel_fast_memcpy' build/temp.linux-i686-2.5/build/src.linux-i686-2.5/fortranobject.o(.text+0xb0b): In function `fortran_setattr': : undefined reference to `_intel_fast_memcpy' build/temp.linux-i686-2.5/build/src.linux-i686-2.5/fortranobject.o(.text+0xf76): In function `array_from_pyobj': : undefined reference to `_intel_fast_memset' /local/tools/gcc/3.2.3/bin/../lib/gcc-lib/i686-pc-linux-gnu/3.2.3/../../../libfrtbegin.a(frtbegin.o)(.text+0x32): In function `main': : undefined reference to `MAIN__' collect2: ld returned 1 exit status

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