Mailman 3 March 2009 - NumPy-Discussion

Normalization of ifft
by Lutz Maibaum March 27, 2009

March 27, 2009

Hello, I just started to use python and numpy for some numerical analysis. I have a question about the definition of the inverse Fourier transform. The user gives the formula (p.180) x[m] = Sum_k X[k] exp(j 2pi k m / n) where X[k] are the Fourier coefficients, and n is the length of the arrays. The online documentation (http://docs.scipy.org/doc/numpy/reference/routines.fft.html), on the other hand, states that there is an additional factor of 1/n, which is required to make ifft() the inverse of fft(). Is this a misprint in the user guide? Lutz

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Moved python install, import errors
by David Warde-Farley March 27, 2009

March 27, 2009

Hi all, I built ATLAS, Python 2.5 and NumPy on the local disk of a cluster node, so that disk access would be faster than over NFS, and then moved it back. I made sure to modify all the relevant paths in __config__.py but when importing I receive this error, which I can't make heads or tails of, since core/ does contain an __init__.py. Has anyone seen anything like this before? Thanks, David In [1]: import numpy --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) /home/dwf/<ipython console> in <module>() /home/dwf/software/Python-2.5.4/lib/python2.5/site-packages/numpy/ __init__.py in <module>() 128 return loader(*packages, **options) 129 --> 130 import add_newdocs 131 __all__ = ['add_newdocs'] 132 /home/dwf/software/Python-2.5.4/lib/python2.5/site-packages/numpy/ add_newdocs.py in <module>() 7 # core/fromnumeric.py, core/defmatrix.py up-to-date. 8 ----> 9 from lib import add_newdoc 10 11 ############################################################################### /home/dwf/software/Python-2.5.4/lib/python2.5/site-packages/numpy/lib/ __init__.py in <module>() 11 12 import scimath as emath ---> 13 from polynomial import * 14 from machar import * 15 from getlimits import * /home/dwf/software/Python-2.5.4/lib/python2.5/site-packages/numpy/lib/ polynomial.py in <module>() 9 import re 10 import warnings ---> 11 import numpy.core.numeric as NX 12 13 from numpy.core import isscalar, abs AttributeError: 'module' object has no attribute 'core'

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Re: [Numpy-discussion] Numpy v1.3.0b1 on Linux w/ Intel compilers - unknown file type
by Christian Marquardt March 27, 2009

March 27, 2009

Hmm. I downloaded the beta tar file and started from the untarred contents plus a patch for the Intel compilers (some changes of the command line arguments for the compiler and a added setup.cfg file specifying the paths to the Intel MKL libraries) which applied cleanly. I then ran python setup.py config --compiler=intel config_fc --fcompiler=intel build_clib --compiler=intel build_ext --compiler=intel install which failed. After playing around a bit, I found that it seems that the build_clib --compiler=intel subcommand which causes the trouble; after disabling it, that is with python setup.py config --compiler=intel config_fc --fcompiler=intel build_ext --compiler=intel install things compile fine - and all but four of the unit tests fail (test_linalg.TestEigh and test_linalg.TestEigvalsh in both test_csingle and test_cdouble - should I be worried?) How are the .src files converted? Many thanks, Christian. ----- "Charles R Harris" <charlesr.harris(a)gmail.com> wrote: > > > > On Thu, Mar 26, 2009 at 6:25 PM, Christian Marquardt < christian(a)marquardt.sc > wrote: > Hello, > > I tried to compile and install numpy 1.3.0b1 on a Suse Linux 10.3 with Python > 2.5.x and an Intel C and Fortran compilers 10.1 as well as the MKL 10.0. The > distutils do find the compilers and the MKL (when using similar settings as I > used successfully for all previous numpy versions sonce 1.0.4 or so), but then > bail out with the following error: > > ...>python setup.py install > > [...] > > running config > running config_fc > unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options > running build_clib > Found executable /opt/intel/cc/10.1.018/bin/icc > Could not locate executable ecc > customize IntelCCompiler > customize IntelCCompiler using build_clib > building 'npymath' library > compiling C sources > C compiler: icc > > error: unknown file type '.src' (from 'numpy/core/src/npy_math.c.src') > > I think the error message does not even come from the compiler... > > I'm lost... What does it mean, and why are there source files named ...c.src? > > That file should be preprocessed to produce npy_math.c which ends up in the build directory. I don't know what is going on here, but you might first try deleting the build directory just to see what happens. There might be some setup file that is screwy/outdated also. Did you download the beta and do a clean extract? > > Chuck > > > > _______________________________________________ Numpy-discussion mailing list Numpy-discussion(a)scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion -- Dr. Christian Marquardt Email: christian(a)marquardt.sc Wilhelm-Leuschner-Str. 27 Tel.: +49 (0) 6151 95 13 776 64293 Darmstadt Mobile: +49 (0) 179 290 84 74 Germany Fax: +49 (0) 6151 95 13 885

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Re: [Numpy-discussion] Numpy v1.3.0b1 on Linux w/ Intel compilers - unknown file type
by Christian Marquardt March 27, 2009

March 27, 2009

Oh sorry - you are right (too late in the night here in Europe). The output is similar in all four cases - it looks like AssertionError: Arrays are not almost equal (mismatch 100.0%) x: array([ 4.60555124+0.j, -2.60555124+0.j], dtype=complex64) y: array([-2.60555124 +1.11022302e-16j, 4.60555124 -1.11022302e-16j], dtype=complex64) Are x and y the expected and actual results? That would just show that there are small rounding errors in the imaginary part, and that MKL returns the results in another order, no? ----- "Charles R Harris" <charlesr.harris(a)gmail.com> wrote: > > > > 2009/3/26 Christian Marquardt < christian(a)marquardt.sc > > > > Hmm. > > I downloaded the beta tar file and started from the untarred contents plus a patch for the Intel compilers > (some changes of the command line arguments for the compiler and a added setup.cfg file specifying the > paths to the Intel MKL libraries) which applied cleanly. I then ran > > python setup.py config --compiler=intel config_fc --fcompiler=intel build_clib --compiler=intel build_ext --compiler=intel install > > which failed. > > After playing around a bit, I found that it seems that the build_clib --compiler=intel subcommand which > causes the trouble; after disabling it, that is with > > python setup.py config --compiler=intel config_fc --fcompiler=intel build_ext --compiler=intel install > > things compile fine - and all but four of the unit tests fail (test_linalg.TestEigh and test_linalg.TestEigvalsh > in both test_csingle and test_cdouble - should I be worried?) > > Four unit tests fail, or all fail except four? I assume you meant the former. I'm not sure what the failures mean, can you check if they are really bad or just some numbers a little bit off. I'm guessing these routines are calling into MKL. > > > > > How are the .src files converted? > > The *.xxx.src files are templates that are processed by numpy/distutils/conv_template.py to produce *.xxx files. When you have to repeat basically the same code with umpteen different types a bit of automation helps. The actual conversion is controlled by the setup/scons files, I don't remember exactly where. > > Chuck > > > > _______________________________________________ Numpy-discussion mailing list Numpy-discussion(a)scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion -- Dr. Christian Marquardt Email: christian(a)marquardt.sc Wilhelm-Leuschner-Str. 27 Tel.: +49 (0) 6151 95 13 776 64293 Darmstadt Mobile: +49 (0) 179 290 84 74 Germany Fax: +49 (0) 6151 95 13 885

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Re: [Numpy-discussion] numpy v1.2.0 vs 1.2.1 and setup_tools
by Christian Marquardt March 27, 2009

March 27, 2009

v1.3.0b1 has the same problem - setup_tools doesn't seem to recognize that numpy is already installed in the system's site-packages directory. Maybe I should add that I'm using virtualenv to generate a test environment which includes the systems site-packages; setup_tools does seem recognize other packages which are only available there (e.g., scipy or netCDF4 if specified as a requirement for the install... strange. It also doesn't seem to work for tables (2.1, so not the newest version)). Any ideas on what might be going on? Thanks a lot, Christian. ----- "Christian Marquardt" <christian(a)marquardt.sc> wrote: > Hello! > > I ran into the following problem: > > I have easy_installable packages which list numpy as a dependency. > numpy itself is installed in the system's site-packages directory and > works fine. > > When running a python setup.py install of the package with numpy > v1.2.0 installed, everything works fine. When running the same command > with numpy 1.2.1 installed, it tries to download a numpy tar file from > Pypi and to compile and install it again. It looks as if v1.2.1 isn't > providing the relevant information to the setup tools, but 1.2.0 did. > > I don't know about v1.3.0b1 yet - I have difficulties to compile that > currently (another email). I'd be more than willing to track this > down, but is there anybody who could give me a starting point where I > should start to look? > > Many thanks, > > Christian. > _______________________________________________ > Numpy-discussion mailing list > Numpy-discussion(a)scipy.org > http://mail.scipy.org/mailman/listinfo/numpy-discussion -- Dr. Christian Marquardt Email: christian(a)marquardt.sc Wilhelm-Leuschner-Str. 27 Tel.: +49 (0) 6151 95 13 776 64293 Darmstadt Mobile: +49 (0) 179 290 84 74 Germany Fax: +49 (0) 6151 95 13 885

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Numpy v1.3.0b1 on Linux w/ Intel compilers - unknown file type
by Christian Marquardt March 27, 2009

March 27, 2009

Hello, I tried to compile and install numpy 1.3.0b1 on a Suse Linux 10.3 with Python 2.5.x and an Intel C and Fortran compilers 10.1 as well as the MKL 10.0. The distutils do find the compilers and the MKL (when using similar settings as I used successfully for all previous numpy versions sonce 1.0.4 or so), but then bail out with the following error: ...>python setup.py install [...] running config running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_clib Found executable /opt/intel/cc/10.1.018/bin/icc Could not locate executable ecc customize IntelCCompiler customize IntelCCompiler using build_clib building 'npymath' library compiling C sources C compiler: icc error: unknown file type '.src' (from 'numpy/core/src/npy_math.c.src') I think the error message does not even come from the compiler... I'm lost... What does it mean, and why are there source files named ...c.src? Many thanks, Christian

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numpy v1.2.0 vs 1.2.1 and setup_tools
by Christian Marquardt March 27, 2009

March 27, 2009

Hello! I ran into the following problem: I have easy_installable packages which list numpy as a dependency. numpy itself is installed in the system's site-packages directory and works fine. When running a python setup.py install of the package with numpy v1.2.0 installed, everything works fine. When running the same command with numpy 1.2.1 installed, it tries to download a numpy tar file from Pypi and to compile and install it again. It looks as if v1.2.1 isn't providing the relevant information to the setup tools, but 1.2.0 did. I don't know about v1.3.0b1 yet - I have difficulties to compile that currently (another email). I'd be more than willing to track this down, but is there anybody who could give me a starting point where I should start to look? Many thanks, Christian.

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Numpy 1.3.0b1 with Intel compiler
by Christian Marquardt March 27, 2009

March 27, 2009

Hello, I tried to compile and install numpy 1.3.0b1 on a Suse Linux 10.3 with Python 2.5.x and an Intel C and Fortran compilers 10.1 as well as the MKL 10.0. The distutils do find the compilers and the MKL (when using similar settings as I used successfully for all previous numpy versions sonce 1.0.4 or so), but then bail out with the following error: ...>python setup.py install [...] running config running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_clib Found executable /opt/intel/cc/10.1.018/bin/icc Could not locate executable ecc customize IntelCCompiler customize IntelCCompiler using build_clib building 'npymath' library compiling C sources C compiler: icc error: unknown file type '.src' (from 'numpy/core/src/npy_math.c.src') I think the error message does not even come from the compiler... I'm lost... WHat does it mean, and why are there source files named ...c.src? Many thanks, Christian

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Re: [Numpy-discussion] Where is the instruction of installing numpy with Intel lib MKL?
by Ben Park March 27, 2009

March 27, 2009

BTW, this timing on a core 2 Duo 2.0GH laptop ,with the Enthought Python Distribution, is around 0.2 second. Ben Park wrote: > > I have spent many hours trying to do this, to no avail. The numpy > installation I got didn't seem to link to the MKL library. A 1000x1000 > matrix multiplication took 8 seconds. > > import numpy as N > import numpy.random as RN > import time > > m = 1000 > #m = 2000 > #m = 10000 > #m = 30000 > #m = 40000 > > X = N.zeros((m,m),'f') > for i in range(m): > X[i,:] = RN.random((m,)).astype('f') > #X = RN.random((m, m)).astype('f') > > t1 = time.time() > Y = N.dot(X, X) > t2 = time.time() > print 'dt = %f' %(t2-t1) > > The result is about 8 seconds on a Intel Core 2 Duo 2.0GH laptop. > Certainly not fast. > -- View this message in context: http://www.nabble.com/Where-is-the-instruction-of-installing-numpy-with-Int… Sent from the Numpy-discussion mailing list archive at Nabble.com.

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Using loadtxt() twice on same file freezes python
by Sander de Kievit March 26, 2009

March 26, 2009

Hi, On my PC the following code freezes python: [code] import numpy as np from StringIO import StringIO c = StringIO("0 1\n2 3") np.loadtxt(c) np.loadtxt(c) [/code] Is this intentional behaviour or should I report this as a bug? Regards, Sander

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