Mailman 3 August 2009 - NumPy-Discussion

ImportError: No module named multiarray
by Reckoner 17 Aug '09

17 Aug '09

Hi, I created a pickled file on my Windows PC, uploaded to a Linux machine and then received the following error: Python 2.5.4 (r254:67916, Feb 5 2009, 19:52:35) [GCC 4.1.2 20071124 (Red Hat 4.1.2-42)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import cPickle >>> cPickle.load(open('tst.pkl')) Traceback (most recent call last): File "<stdin>", line 1, in <module> ImportError: No module named multiarray Obviously, the pickled file loads fine on the Windows PC. the following is the result of numpy.test() >>> numpy.test() Running unit tests for numpy NumPy version 1.2.1 NumPy is installed in /nfs/02/reckoner/Starburst/lib/python2.5/site-packages/numpy Python version 2.5.4 (r254:67916, Feb 5 2009, 19:52:35) [GCC 4.1.2 20071124 (Red Hat 4.1.2-42)] nose version 0.10.3 ..........................................................................................................................................................................................................................................................................................................................................................................................................................................F................K................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ ====================================================================== FAIL: test_umath.TestComplexFunctions.test_against_cmath ---------------------------------------------------------------------- Traceback (most recent call last): File "/nfs/02/reckoner/Starburst/lib/python2.5/site-packages/nose-0.10.3-py2.5.egg/nose/case.py", line 182, in runTest self.test(*self.arg) File "/nfs/02/reckoner/Starburst/lib/python2.5/site-packages/numpy/core/tests/test_umath.py", line 268, in test_against_cmath assert abs(a - b) < atol, "%s %s: %s; cmath: %s"%(fname,p,a,b) AssertionError: arcsinh -2j: (-1.31695789692-1.57079632679j); cmath: (1.31695789692-1.57079632679j) ---------------------------------------------------------------------- Ran 1740 tests in 10.493s FAILED (KNOWNFAIL=1, failures=1) <nose.result.TextTestResult run=1740 errors=0 failures=1> Any help appreciated.

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is there a better way to do this array repeat?
by Chris Colbert 17 Aug '09

17 Aug '09

I don't think np.repeat will do what I want because the order needs to be preserved. I have a 1x3 array that I want to repeat n times and form an nx3 array where each row is a copy of the original array. So far I have this: >>> import numpy as np >>> a = np.arange(3) >>> b = np.asarray([a]*10) >>> b array([[0, 1, 2], [0, 1, 2], [0, 1, 2], [0, 1, 2], [0, 1, 2], [0, 1, 2], [0, 1, 2], [0, 1, 2], [0, 1, 2], [0, 1, 2]]) >>> b.shape (10, 3) the issue is that my n may be very large and I'd rather not make that list if I don't have to. Cheers, Chris

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IndexExpression bug?
by Michael McNeil Forbes 17 Aug '09

17 Aug '09

>>> np.array([0,1,2,3])[1:-1] array([1, 2]) but >>> np.array([0,1,2,3])[np.s_[1:-1]] array([1, 2, 3]) >>> np.array([0,1,2,3])[np.index_exp[1:-1]] array([1, 2, 3]) Possible fix: class IndexExpression(object): ... def __len__(self): return 0 (Presently this returns sys.maxint) Does this break anything (I can't find any coverage tests)? If not, I will submit a ticket. Michael.

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Specifying Index Programmatically
by T J 17 Aug '09

17 Aug '09

I have an array, and I need to index it like so: z[...,x,:] How can I write code which will index z, as above, when x is not known ahead of time. For that matter, the particular dimension I am querying is not known either. In case this is still confusing, I am looking for the NumPy way to do: z[("...",5,":")] z[(":", 3, ":", 5, "...")] z[(1, "...", 5)] Basically, I want to be able to pre-construct what should appear inside the []. The numbers are no problem, but I'm having trouble with the ellipsis and colon.

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memory address of array data?
by Robert 17 Aug '09

17 Aug '09

Is there a function to get the memory address (int) of (contigious) ndarray data on Python level - like array.array.buffer_info() ? I'd need it to pass it to a camera function.

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Cython BOF
by Dag Sverre Seljebotn 15 Aug '09

15 Aug '09

There's been some discussion earlier about how starting to write bigger parts of the NumPy/SciPy codebase in Cython could potentially lower the barrier of entry. Some topics: * Move towards PEP3118 as the primary scientific "data container" rather than ndarray? * Cython templates? * Native SIMD in Cython -- good or bad? (I don't know myself, to be honest.) * Future direction in general I'll add a Cython BOF to the wiki if somebody express interest. -- Dag Sverre

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Re: [Numpy-discussion] Can't import numpy - problem with lapack?
by Bent 15 Aug '09

15 Aug '09

Charles R Harris wrote: > > That's probably due to the ATLAS library you have installed, SuSe has a history of problems in that area. > Have you checked the ATLAS versions also? Is the hardware the same? > You certainly got something there. It turned out that the PCs, on which import numpy works, does not have anything named 'atlas' installed (apart from a kernel module named atlas_btns) whereas my workstation had a package named libatlas3-sse installed. When I removed this package, everything fell into place and import numpy now works. Thanks for the help Bent

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Can't import numpy - problem with lapack?
by Bent 15 Aug '09

15 Aug '09

Hi list I want to use Numpy with Gnuradio but I cannot make it work. The problem, which turns out to have nothing with Gnuradio to do, is an undefined symbol as witnessed by these messages: bent@yosie:~> python Python 2.6 (r26:66714, Feb 3 2009, 20:52:03) [GCC 4.3.2 [gcc-4_3-branch revision 141291]] 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 "/usr/lib/python2.6/site-packages/numpy/__init__.py", line 138, in <module> import linalg File "/usr/lib/python2.6/site-packages/numpy/linalg/__init__.py", line 47, in <module> from linalg import * File "/usr/lib/python2.6/site-packages/numpy/linalg/linalg.py", line 29, in <module> from numpy.linalg import lapack_lite ImportError: /usr/lib/python2.6/site-packages/numpy/linalg/lapack_lite.so: undefined symbol: zgesdd_ >>> quit() bent@yosie:~> My distribution is openSUSE 11.1 and what really bugs me is that the exact same setup works as expected on another PC also running openSUSE 11.1. As far as I can tell, the installed packages are exactly the same, version numbers, build dates, etc, all are the same... The only difference between the two PCs is that the one (the one that fails) is a new install and the other is an upgrade from an older release. I have googled high and low but not found anything that could bring me further. I hope that this (collectively) all-knowledgeable list can give me some pointers. Kind regards, Bent

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build_clib error during Enable 3_2_1 installation
by Gökhan Sever 14 Aug '09

14 Aug '09

For some unknown reason, ets develop can't pass the following compilation point: g++: enthought/kiva/agg/src/kiva_rect.cpp ar: adding 8 object files to build/temp.linux-i686-2.6/libkiva_src.a running build_ext build_clib already run, it is too late to ensure in-place build of build_clib Traceback (most recent call last): File "setup.py", line 327, in <module> **config File "/home/gsever/Desktop/python-repo/numpy/numpy/distutils/core.py", line 186, in setup return old_setup(**new_attr) File "/usr/lib/python2.6/distutils/core.py", line 152, in setup dist.run_commands() File "/usr/lib/python2.6/distutils/dist.py", line 975, in run_commands self.run_command(cmd) File "/usr/lib/python2.6/distutils/dist.py", line 995, in run_command cmd_obj.run() File "/home/gsever/Desktop/python-repo/numpy/numpy/distutils/command/build_ext.py", line 74, in run self.library_dirs.append(build_clib.build_clib) UnboundLocalError: local variable 'build_clib' referenced before assignment Traceback (most recent call last): File "/usr/bin/ets", line 8, in <module> load_entry_point('ETSProjectTools==0.6.0.dev-r24434', 'console_scripts', 'ets')() File "/usr/lib/python2.6/site-packages/ETSProjectTools-0.5.1-py2.6.egg/enthought/ets/ets.py", line 152, in main args.func(args, cfg) File "/usr/lib/python2.6/site-packages/ETSProjectTools-0.5.1-py2.6.egg/enthought/ets/develop.py", line 76, in main checkouts.perform(command, dry_run=args.dry_run) File "/usr/lib/python2.6/site-packages/ETSProjectTools-0.5.1-py2.6.egg/enthought/ets/tools/checkouts.py", line 126, in perform '%s' % project) RuntimeError: Unable to complete command for project: /home/gsever/Desktop/python-repo/ETS_3.3.1/Enable_3.2.1 Any suggestions? ################################################################## [gsever@ccn Desktop]$ python -c 'from numpy.f2py.diagnose import run; run()' ################################################################## ------ os.name='posix' ------ sys.platform='linux2' ------ sys.version: 2.6 (r26:66714, Jun 8 2009, 16:07:26) [GCC 4.4.0 20090506 (Red Hat 4.4.0-4)] ------ sys.prefix: /usr ------ sys.path=':/usr/lib/python2.6/site-packages/foolscap-0.4.2-py2.6.egg:/usr/lib/python2.6/site-packages/Twisted-8.2.0-py2.6-linux-i686.egg:/home/gsever/Desktop/python-repo/ipython:/home/gsever/Desktop/python-repo/numpy:/home/gsever/Desktop/python-repo/matplotlib/lib:/usr/lib/python2.6/site-packages/Sphinx-0.6.2-py2.6.egg:/usr/lib/python2.6/site-packages/docutils-0.5-py2.6.egg:/usr/lib/python2.6/site-packages/Jinja2-2.1.1-py2.6-linux-i686.egg:/usr/lib/python2.6/site-packages/Pygments-1.0-py2.6.egg:/usr/lib/python2.6/site-packages/xlwt-0.7.2-py2.6.egg:/usr/lib/python2.6/site-packages/spyder-1.0.0beta1-py2.6.egg:/usr/lib/python2.6/site-packages/PyOpenGL-3.0.0c1-py2.6.egg:/home/gsever/Desktop/python-repo/ETS_3.3.1/EnthoughtBase_3.0.4:/home/gsever/Desktop/python-repo/ETS_3.3.1/TraitsBackendWX_3.2.1:/home/gsever/Desktop/python-repo/ETS_3.3.1/ETSProjectTools_0.6.0:/home/gsever/Desktop/python-repo/ETS_3.3.1/Chaco_3.2.1:/home/gsever/Desktop/python-repo/ETS_3.3.1/ETS_3.3.1:/home/gsever/Desktop/python-repo/ETS_3.3.1/TraitsGUI_3.1.1:/home/gsever/Desktop/python-repo/ETS_3.3.1/Traits_3.2.1:/home/gsever/Desktop/python-repo/ETS_3.3.1/BlockCanvas_3.1.1:/usr/lib/python26.zip:/usr/lib/python2.6:/usr/lib/python2.6/plat-linux2:/usr/lib/python2.6/lib-tk:/usr/lib/python2.6/lib-old:/usr/lib/python2.6/lib-dynload:/usr/lib/python2.6/site-packages:/usr/lib/python2.6/site-packages/Numeric:/usr/lib/python2.6/site-packages/PIL:/usr/lib/python2.6/site-packages/gst-0.10:/usr/lib/python2.6/site-packages/gtk-2.0:/usr/lib/python2.6/site-packages:/usr/lib/python2.6/site-packages/wx-2.8-gtk2-unicode' ------ Failed to import numarray: No module named numarray Found Numeric version '24.2' in /usr/lib/python2.6/site-packages/Numeric/Numeric.pyc Found new numpy version '1.4.0.dev' in /home/gsever/Desktop/python-repo/numpy/numpy/__init__.pyc Found f2py2e version '2' in /home/gsever/Desktop/python-repo/numpy/numpy/f2py/f2py2e.pyc Found numpy.distutils version '0.4.0' in '/home/gsever/Desktop/python-repo/numpy/numpy/distutils/__init__.pyc' ------ Importing numpy.distutils.fcompiler ... ok ------ Checking availability of supported Fortran compilers: GnuFCompiler instance properties: archiver = ['/usr/bin/g77', '-cr'] compile_switch = '-c' compiler_f77 = ['/usr/bin/g77', '-g', '-Wall', '-fno-second- underscore', '-fPIC', '-O3', '-funroll-loops'] compiler_f90 = None compiler_fix = None libraries = ['g2c'] library_dirs = [] linker_exe = ['/usr/bin/g77', '-g', '-Wall', '-g', '-Wall'] linker_so = ['/usr/bin/g77', '-g', '-Wall', '-g', '-Wall', '- shared'] object_switch = '-o ' ranlib = ['/usr/bin/g77'] version = LooseVersion ('3.4.6') version_cmd = ['/usr/bin/g77', '--version'] Gnu95FCompiler instance properties: archiver = ['/usr/bin/gfortran', '-cr'] compile_switch = '-c' compiler_f77 = ['/usr/bin/gfortran', '-Wall', '-ffixed-form', '-fno- second-underscore', '-fPIC', '-O3', '-funroll-loops'] compiler_f90 = ['/usr/bin/gfortran', '-Wall', '-fno-second-underscore', '-fPIC', '-O3', '-funroll-loops'] compiler_fix = ['/usr/bin/gfortran', '-Wall', '-ffixed-form', '-fno- second-underscore', '-Wall', '-fno-second-underscore', '- fPIC', '-O3', '-funroll-loops'] libraries = ['gfortran'] library_dirs = [] linker_exe = ['/usr/bin/gfortran', '-Wall', '-Wall'] linker_so = ['/usr/bin/gfortran', '-Wall', '-Wall', '-shared'] object_switch = '-o ' ranlib = ['/usr/bin/gfortran'] version = LooseVersion ('4.4.0') version_cmd = ['/usr/bin/gfortran', '--version'] Fortran compilers found: --fcompiler=gnu GNU Fortran 77 compiler (3.4.6) --fcompiler=gnu95 GNU Fortran 95 compiler (4.4.0) Compilers available for this platform, but not found: --fcompiler=absoft Absoft Corp Fortran Compiler --fcompiler=compaq Compaq Fortran Compiler --fcompiler=g95 G95 Fortran Compiler --fcompiler=intel Intel Fortran Compiler for 32-bit apps --fcompiler=intele Intel Fortran Compiler for Itanium apps --fcompiler=intelem Intel Fortran Compiler for EM64T-based apps --fcompiler=lahey Lahey/Fujitsu Fortran 95 Compiler --fcompiler=nag NAGWare Fortran 95 Compiler --fcompiler=pg Portland Group Fortran Compiler --fcompiler=vast Pacific-Sierra Research Fortran 90 Compiler Compilers not available on this platform: --fcompiler=hpux HP Fortran 90 Compiler --fcompiler=ibm IBM XL Fortran Compiler --fcompiler=intelev Intel Visual Fortran Compiler for Itanium apps --fcompiler=intelv Intel Visual Fortran Compiler for 32-bit apps --fcompiler=mips MIPSpro Fortran Compiler --fcompiler=none Fake Fortran compiler --fcompiler=sun Sun or Forte Fortran 95 Compiler For compiler details, run 'config_fc --verbose' setup command. ------ Importing numpy.distutils.cpuinfo ... ok ------ CPU information: CPUInfoBase__get_nbits getNCPUs has_mmx has_sse has_sse2 has_sse3 has_ssse3 is_32bit is_Intel is_i686 ------ -- Gökhan

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passing "import numpy as np" as python command arg in 'doze
by David Goldsmith 14 Aug '09

14 Aug '09

Hi! Please remind: running python in the Windows Terminal (DOS command prompt), how does one pass the command "import numpy as np"? I tried 'python "import numpy as np"', to no avail. DG

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