Mailman 3 November 2009 - NumPy-Discussion

Compact way of performing array math with specified result type?
by Russell E. Owen Feb. 8, 2010

Feb. 8, 2010

I often find myself doing simple math on sequences of numbers (which might or might not be numpy arrays) where I want the result (and thus the inputs) coerced to a particular data type. I'd like to be able to say: numpy.divide(seq1, seq2, dtype=float) but ufuncs don't allow on to specify a result type. So I do this instead: numpy.array(seq1, dtype=float) / numpy.array(seq2, dtype=float) Is there a more compact solution (without having to create the result array first and supply it as an argument)? -- Russell

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MKL with 64bit crashes
by Kashyap Ashwin Jan. 21, 2010

Jan. 21, 2010

Hello, I compiled numpy-1.3.0 from sources on Ubuntu-hardy, x86-64 (Intel) with MKL. This is my site.cfg: [mkl] # library_dirs = /opt/intel/mkl/10.0.1.014/lib/32/ library_dirs = /opt/intel/mkl/10.2.2.025/lib/em64t include_dirs = /opt/intel/mkl/10.2.2.025/include lapack_libs = mkl_lapack #mkl_libs = mkl_core, guide, mkl_gf_ilp64, mkl_def, mkl_gnu_thread, iomp5, mkl_vml_mc3 mkl_libs = guide, mkl_core, mkl_gnu_thread, iomp5, mkl_gf_ilp64, mkl_mc3, mkl_def In [2]: numpy.test() Running unit tests for numpy NumPy version 1.3.0 NumPy is installed in /opt/********************* Python version 2.5.2 (r252:60911, Jul 22 2009, 15:33:10) [GCC 4.2.4 (Ubuntu 4.2.4-1ubuntu3)] nose version 0.11.0 .......... MKL ERROR: Parameter 4 was incorrect on entry to DGESV MKL ERROR: Parameter 4 was incorrect on entry to DGESV MKL ERROR: Parameter 4 was incorrect on entry to DGESV MKL ERROR: Parameter 4 was incorrect on entry to DGESV MKL ERROR: Parameter 4 was incorrect on entry to DGESV MKL ERROR: Parameter 4 was incorrect on entry to DGESV .. MKL ERROR: Parameter 4 was incorrect on entry to DGESV FSegmentation fault I am using gcc: gcc -v Using built-in specs. Target: x86_64-linux-gnu Configured with: ../src/configure -v --enable-languages=c,c++,fortran,objc,obj-c++,treelang --prefix=/usr --enable-shared --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --enable-nls --with-gxx-include-dir=/usr/include/c++/4.2 --program-suffix=-4.2 --enable-clocale=gnu --enable-libstdcxx-debug --enable-objc-gc --enable-mpfr --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu Thread model: posix gcc version 4.2.4 (Ubuntu 4.2.4-1ubuntu4) Anyone having the same issues? Do I have the mkl_libs correctly configured (this seems like a black art!) Thanks, Ashwin

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Import error in builds of 7726
by Chris Dec. 21, 2009

Dec. 21, 2009

I am building Numpy on OSX 10.6 using a recent update from SVN (r7726). Though I was able to build the package successfully, the resulting package generates an ImportError: import umath ImportError: dlopen(/Library/Python/2.6/site-packages/ numpy-1.4.0.dev7726-py2.6-macosx-10.6- universal.egg/numpy/core/umath.so, 2): Symbol not found : _npy_cexp Referenced from: /Library/Python/2.6/site-packages/ numpy-1.4.0.dev7726-py2.6-macosx-10.6-universal.egg/ numpy/core/umath.so Expected in: flat namespace in /Library/Python/2.6/site-packages/ numpy-1.4.0.dev7726-py2.6-macosx-10.6-universal.egg /numpy/core/umath.so Note that this did not occur previously (r7542). For some reason umath is not being built properly.

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non-standard standard deviation
by Dr. Phillip M. Feldman Dec. 11, 2009

Dec. 11, 2009

All of the statistical packages that I am currently using and have used in the past (Matlab, Minitab, R, S-plus) calculate standard deviation using the sqrt(1/(n-1)) normalization, which gives a result that is unbiased when sampling from a normally-distributed population. NumPy uses the sqrt(1/n) normalization. I'm currently using the following code to calculate standard deviations, but would much prefer if this could be fixed in NumPy itself: def mystd(x=numpy.array([]), axis=None): """This function calculates the standard deviation of the input using the definition of standard deviation that gives an unbiased result for samples from a normally-distributed population.""" -- View this message in context: http://old.nabble.com/non-standard-standard-deviation-tp26566808p26566808.h… Sent from the Numpy-discussion mailing list archive at Nabble.com.

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Assigning complex values to a real array
by Stéfan van der Walt Dec. 10, 2009

Dec. 10, 2009

Hi all, The following code succeeds, while I thought it should fail: a = np.zeros(6) # real b= np.arange(6)*(2+3j) # complex a[1] = b[1] # shouldn't this break? What is the rationale behind this behaviour? Cheers Stéfan

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Bytes vs. Unicode in Python3
by Pauli Virtanen Dec. 9, 2009

Dec. 9, 2009

Hi, The Python 3 porting needs some decisions on what is Bytes and what is Unicode. I'm currently taking the following approach. Comments? *** dtype field names Either Bytes or Unicode. But 'a' and b'a' are *different* fields. The issue is that: Python 2: {'a': 2}[u'a'] == 2, {u'a': 2}['a'] == 2 Python 3: {'a': 2}[b'a'], {b'a': 2}['a'] raise exceptions so the current assumptions in the C code of u'a' == b'a' cease to hold. dtype titles If Bytes or Unicode, work similarly as field names. dtype format strings, datetime tuple, and any other "protocol" strings Bytes. User can pass in Unicode, but it's converted using UTF8 codec. This will likely change repr() of various objects. Acceptable? -- Pauli Virtanen

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non-standard standard deviation
by Dr. Phillip M. Feldman Dec. 6, 2009

Dec. 6, 2009

All of the statistical packages that I am currently using and have used in the past (Matlab, Minitab, R, S-plus) calculate standard deviation using the sqrt(1/(n-1)) normalization, which gives a result that is unbiased when sampling from a normally-distributed population. NumPy uses the sqrt(1/n) normalization. I'm currently using the following code to calculate standard deviations, but would much prefer if this could be fixed in NumPy itself: def mystd(x=numpy.array([]), axis=None): """This function calculates the standard deviation of the input using the definition of standard deviation that gives an unbiased result for samples from a normally-distributed population.""" xd= x - x.mean(axis=axis) return sqrt( (xd*xd).sum(axis=axis) / (numpy.size(x,axis=axis)-1.0) ) -- View this message in context: http://old.nabble.com/non-standard-standard-deviation-tp26566843p26566843.h… Sent from the Numpy-discussion mailing list archive at Nabble.com.

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another numpy/ATLAS problem
by David Warde-Farley Dec. 6, 2009

Dec. 6, 2009

It seems like I've done this enough times on enough machines but I'm still running into problems... After installing what I'm pretty sure is a complete ATLAS+LAPACK and building numpy against it (appropriately editing site.cfg, etc.) I'm faced with this when building numpy-1.3.0: dwf@mirage:~/tmp$ python Python 2.6.4 (r264:75706, Nov 2 2009, 14:44:17) [GCC 4.4.1] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import numpy Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/dwf/virtualenv/stable/lib/python2.6/site-packages/numpy/ __init__.py", line 130, in <module> import add_newdocs File "/home/dwf/virtualenv/stable/lib/python2.6/site-packages/numpy/ add_newdocs.py", line 9, in <module> from lib import add_newdoc File "/home/dwf/virtualenv/stable/lib/python2.6/site-packages/numpy/ lib/__init__.py", line 13, in <module> from polynomial import * File "/home/dwf/virtualenv/stable/lib/python2.6/site-packages/numpy/ lib/polynomial.py", line 18, in <module> from numpy.linalg import eigvals, lstsq File "/home/dwf/virtualenv/stable/lib/python2.6/site-packages/numpy/ linalg/__init__.py", line 47, in <module> from linalg import * File "/home/dwf/virtualenv/stable/lib/python2.6/site-packages/numpy/ linalg/linalg.py", line 22, in <module> from numpy.linalg import lapack_lite ImportError: /home/dwf/virtualenv/stable/lib/python2.6/site-packages/ numpy/linalg/lapack_lite.so: undefined symbol: dlamc3_ FWIW these are the files that ATLAS has installed: dwf@mirage:~/Downloads$ ls /opt/sw/ATLAS/lib/ -al total 23472 drwxr-xr-x 2 root root 4096 2009-11-26 20:36 . drwxr-xr-x 4 root root 4096 2009-11-26 20:36 .. -rw-r--r-- 1 root root 12963138 2009-11-26 20:36 libatlas.a -rw-r--r-- 1 root root 466244 2009-11-26 20:36 libcblas.a -rw-r--r-- 1 root root 572812 2009-11-26 20:36 libf77blas.a -rw-r--r-- 1 root root 8979016 2009-11-26 20:36 liblapack.a -rw-r--r-- 1 root root 466678 2009-11-26 20:36 libptcblas.a -rw-r--r-- 1 root root 573196 2009-11-26 20:36 libptf77blas.a liblapack.a looks big enough for it to be a complete LAPACK. ATLAS (3.9.17) was configured with the following: ../configure -Ss kern /usr/bin/gcc-4.2 --prefix=/opt/sw/ATLAS --with- netlib-lapack-tarfile=/home/dwf/tmp/lapack-lite-3.1.1.tgz -Fa alg - fPIC -D c -DPentiumCPS=2668 -t 4 -b 64 I tried a few different things, including building dylibs, in which case I get an undefined symbol error for ATL__zttrsm. Any help would be appreciated. To be honest I'm not sure why lapack_lite is getting involved at all; I thought that was what got used in case of no detected LAPACK, but config definitely does detect ATLAS/LAPACK. David

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Python 3K merge
by Charles R Harris Dec. 3, 2009

Dec. 3, 2009

Hi Pauli, It looks like you doing great stuff with the py3k transition. Do you and David have any sort of merge schedule in mind? Chuck

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numpy 1.3.0 eggs with python2.6 seem broken on osx, and linux
by René Dudfield Dec. 2, 2009

Dec. 2, 2009

Hi, the other day I tried installing numpy with easy_install, and did not have much luck with python2.6. To reproduce, try installing with easy_install-2.6, or with buildout. The work around is to just install it in another way (eg, dmg or with setup.py install). cheers,

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