Mailman 3 November 2011 - SciPy-User

Installing numpy on ironpython 2.7
by Evert Amador 03 Nov '11

03 Nov '11

Hello, I'm following the instruction on this page http://www.enthought.com/repo/.iron/ to install SciPy on IronPython 2.7. I'm stuck on step 3.) ironpkg I downloaded the ironpkg-1.0.0.py (save target file as" option) to the same IronPython directory, but when I type >ipy ironpkg-1.0.0.py --install the command prompt responds that the file doesn't exist. Could you please explain to me how do I get the ironpkg command available to continue the installation? Many thanks for your help. regards Evert Amador

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Derivative in scipy?
by François Boulogne 03 Nov '11

03 Nov '11

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear all, I was wondering if a piece of code has been developped for derivative calculations, espacially for a sample (array of points) like for integration: http://docs.scipy.org/doc/scipy/reference/tutorial/integrate.html with different methods (right or left first derivatives, second derivatives...) I didn't succeed in finding this in the documentation. Does it exist? If not, is it planned by someone? Thanks. Cheers, - -- François Boulogne. Membre de l'April - Promouvoir et défendre le logiciel libre http://www.april.org -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) iQIcBAEBAgAGBQJOrXHDAAoJEKkn15fZnrRLxbYP/3/NUzU5metNhGc4tw6Uo0mw kIlAxf1cvtopbJ+JTXrmKkJpyYUI1bMsqVKpPniW073dgPAfAX3Bajymysh5Hgnd 5+0hh7v8JmsIvKm9HrEePSrENYrIVTfFyvRV+tBLhkfHJ9Vj7uUy7a3/lyRS6s7v FEItXLhkNYtqEir8h2eZ7uW178mwq6nBl6Zi5UOjOXq7u0SxcnusKkYyiL+CirSN KafcrU+rUdHw6khE1exj435GMSKx+N3+rV/kDAQWWQc0ncWmdX2Jr7PapT1DQbNN b3UK2NjYGDZE2NMRuZmRmeTIk2S+PVPqRxEu0x62CS4Y4JnTaZx1xSiPGP0d9cZC NG4/9h0LFM8rxj/kxYjBakbIs6LhwPnS1ZvYf00o3eaY4+tLGx3UozoLpEWSCOuQ GrONTWvdUlfVWsd3qOhwCj+NORkz9yXJNqJHulgz6T8fKnMyPL+R80XfRuS1alxj m166ySHxrPDzwiSlV5vWR/1ajrEMAI/GYev55dtzlIx6hxfLVCOryFei/LNtlrN+ lYK48QqateqvLDs+NUq+7azmCAkc8fW5UeD7bBLdoGwlXvYaOEZh8+lzxU2sc0T4 93kNZAzOzv/CdcI1uhnp2NP8ODGEyRLx5cUlcKqmF/iAqtM2zc5Zca9YiygR2w83 XQsGdZYw4rkVMnUTk6Ep =/Nlz -----END PGP SIGNATURE-----

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ANN: Spyder v2.1
by Pierre Raybaut 03 Nov '11

03 Nov '11

Hi all, On the behalf of Spyder's development team (http://code.google.com/p/spyderlib/people/list), I'm pleased to announce that Spyder v2.1 has been released and is available for Windows XP/Vista/7, GNU/Linux and MacOS X: http://code.google.com/p/spyderlib/ Spyder is a free, open-source (MIT license) interactive development environment for the Python language with advanced editing, interactive testing, debugging and introspection features. Originally designed to provide MATLAB-like features (integrated help, interactive console, variable explorer with GUI-based editors for dictionaries, NumPy arrays, ...), it is strongly oriented towards scientific computing and software development. Thanks to the `spyderlib` library, Spyder also provides powerful ready-to-use widgets: embedded Python console (example: http://packages.python.org/guiqwt/_images/sift3.png), NumPy array editor (example: http://packages.python.org/guiqwt/_images/sift2.png), dictionary editor, source code editor, etc. Description of key features with tasty screenshots can be found at: http://code.google.com/p/spyderlib/wiki/Features This release represents a year of development since v2.0 and introduces major enhancements and new features: * Large performance and stability improvements * PySide support (PyQt is no longer exclusively required) * New profiler plugin (thanks to Santiago Jaramillo, a new contributor) * Experimental support for IPython v0.11+ * And many other changes: http://code.google.com/p/spyderlib/wiki/ChangeLog On Windows platforms, Spyder is also available as a stand-alone executable (don't forget to disable UAC on Vista/7). This all-in-one portable version is still experimental (for example, it does not embed sphinx -- meaning no rich text mode for the object inspector) but it should provide a working version of Spyder for Windows platforms without having to install anything else (except Python 2.x itself, of course). Don't forget to follow Spyder updates/news: * on the project website: http://code.google.com/p/spyderlib/ * and on our official blog: http://spyder-ide.blogspot.com/ Last, but not least, we welcome any contribution that helps making Spyder an efficient scientific development/computing environment. Join us to help creating your favourite environment! (http://code.google.com/p/spyderlib/wiki/NoteForContributors) Enjoy! -Pierre

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numpy with nose
by akshar bhosale 03 Nov '11

03 Nov '11

Hi, i am using mkl 10.1, intel cluster toolkit 11/069, os rhel 5.2 x86_64, python 2.6, processor is intel xeon numpy version is 1.6.0 my numpy.test hanging at below point : Test whether equivalent subarray dtypes hash the same. ... ok Test whether different subarray dtypes hash differently. ... ok Test some data types that are equal ... ok Test some more complicated cases that shouldn't be equal ... ok Test some simple cases that shouldn't be equal ... ok test_single_subarray (test_dtype.TestSubarray) ... ok test_einsum_errors (test_einsum.TestEinSum) ... ok test_einsum_sums_cfloat128 (test_einsum.TestEinSum) ... any pointers for this?

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mask array by shapefile
by questions anon 02 Nov '11

02 Nov '11

Hi All, Is there a way to select only the values within a particular shapefile to analyse. I would like to do something like: array=numpyarraycoveringtemperatureofwholestate shapefile=forestedregions.shp newarray=ma.masked_values(array, shapefile) meantemperatureofforestedregions=MA.mean(newarray) print meantemperatureofforestedregions Any ideas of functions I could use, examples I could follow? thanks

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SciPy version 0.9.0
by Mo Zhang 02 Nov '11

02 Nov '11

Hello, I installed scipy version 0.9.0 with Intel compiler, however, when I import a module in scipy, I get the following error: File "/opt/../scipy/0.9.0/lib/python2.7/site-packages/scipy/stats/__init__.py", line 7, in <module> from stats import * File "/opt/../scipy/0.9.0/lib/python2.7/site-packages/scipy/stats/stats.py", line 193, in <module> import scipy.special as special File "/opt/../scipy/0.9.0/lib/python2.7/site-packages/scipy/special/__init__.py", line 9, in <module> from _cephes import * ImportError: /opt/../scipy/0.9.0/lib/python2.7/site-packages/scipy/special/_cephes.so: undefined symbol: s_stop Please let me know how I can fix the problem. Thanks Mo Zhang

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Re: [SciPy-User] [Numpy-discussion] numpy error with mkl 10.1
by akshar bhosale 02 Nov '11

02 Nov '11

Hi, ldd _dotblas.so libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00002b12f0692000) libmkl_def.so => /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_def.so (0x00002b12f099c000) libmkl_intel_lp64.so => /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_intel_lp64.so (0x00002b12f14f1000) libmkl_intel_thread.so => /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_intel_thread.so (0x00002b12f184c000) libmkl_core.so => /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_core.so (0x00002b12f2575000) libmkl_mc.so => /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_mc.so (0x00002b12f2769000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b12f34bf000) libimf.so => /opt/intel/Compiler/11.0/069/lib/intel64/libimf.so (0x00002b12f36db000) libsvml.so => /opt/intel/Compiler/11.0/069/lib/intel64/libsvml.so (0x00002b12f3a32000) libm.so.6 => /lib64/libm.so.6 (0x00002b12f3bef000) libiomp5.so => /opt/intel/Compiler/11.0/069/lib/intel64/libiomp5.so (0x00002b12f3e74000) libintlc.so.5 => /opt/intel/Compiler/11.0/069/lib/intel64/libintlc.so.5 (0x00002b12f4005000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b12f4142000) libc.so.6 => /lib64/libc.so.6 (0x00002b12f4350000) libdl.so.2 => /lib64/libdl.so.2 (0x00002b12f46c7000) /lib64/ld-linux-x86-64.so.2 (0x0000003fb8000000) On Wed, Nov 2, 2011 at 10:14 PM, Olivier Delalleau <shish(a)keba.be> wrote: > Ok, can you print the output of ldd numpy/core/_dotblas.so? > > > -=- Olivier > > 2011/11/2 akshar bhosale <akshar.bhosale(a)gmail.com> > >> HI, >> It is already added in the LD_LIBRARY_PATH, thenalso it is generating the >> same error. >> >> >> On Wed, Nov 2, 2011 at 10:01 PM, Olivier Delalleau <shish(a)keba.be> wrote: >> >>> Locate your libmkl_lapack.so and try to add the directory that contains >>> it to your LD_LIBRARY_PATH environment variable. >>> >>> -=- Olivier >>> >>> 2011/11/2 akshar bhosale <akshar.bhosale(a)gmail.com> >>> >>>> Hi, >>>> >>>> i am getting following error. >>>> python -c 'import numpy;numpy.matrix([[1, 5, 10], [1.0, 3j, 4]], >>>> numpy.complex128).T.I.H' >>>> MKL FATAL ERROR: Cannot load libmkl_lapack.so >>>> >>>> have installed numpy 1.6.0 with python 2.6. >>>> i have intel cluster toolkit installed on my system. (11/069 version >>>> and mlk=10.1). i have machine having intel xeon processor and rhel 5.2 >>>> x86_64 >>>> platform. >>>> Kindly help >>>> >>>> _______________________________________________ >>>> NumPy-Discussion mailing list >>>> NumPy-Discussion(a)scipy.org >>>> http://mail.scipy.org/mailman/listinfo/numpy-discussion >>>> >>>> >>> >>> _______________________________________________ >>> NumPy-Discussion mailing list >>> NumPy-Discussion(a)scipy.org >>> http://mail.scipy.org/mailman/listinfo/numpy-discussion >>> >>> >> >> _______________________________________________ >> NumPy-Discussion mailing list >> NumPy-Discussion(a)scipy.org >> http://mail.scipy.org/mailman/listinfo/numpy-discussion >> >> > > _______________________________________________ > NumPy-Discussion mailing list > NumPy-Discussion(a)scipy.org > http://mail.scipy.org/mailman/listinfo/numpy-discussion > >

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numpy error with mkl 10.1
by akshar bhosale 02 Nov '11

02 Nov '11

Hi, i am getting following error. python -c 'import numpy;numpy.matrix([[1, 5, 10], [1.0, 3j, 4]], numpy.complex128).T.I.H' MKL FATAL ERROR: Cannot load libmkl_lapack.so have installed numpy 1.6.0 with python 2.6. i have intel cluster toolkit installed on my system. (11/069 version and mlk=10.1). i have machine having intel xeon processor and rhel 5.2 x86_64 platform. Kindly help

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ImportError: *.so: cannot open shared object file: No such file or directory
by Pundurs, Mark 02 Nov '11

02 Nov '11

I want to use the function stats.norm.isf, but no matter how I try to import it I end up with the error "ImportError: <libname>.so: cannot open shared object file: No such file or directory". The .so files cited do exist in /usr/lib (as symbolic links to other .so files that also exist in that directory). From what I've read, that's where they're supposed to be - but I think the Python installation is in a nonstandard location. Is that the problem? How can I work around it? Is there some way I can stitch together pieces of Scipy code in my script to directly access stats.norm.isf functionality and bypass these problems? I'm running Scipy 0.8.0/Python 2.6.3 under Red Hat Enterprise Linux ES release 4 (Nahant Update 5) on a Dell PowerEdge 1950. Traceback (most recent call last): File "/disk1/hadoop/tmp/taskTracker/jobcache/job_201109081055_6643/attempt_201109081055_6643_r_000000_0/work/./ExpandAndAverageFinal_ReducerB_pc.py", line 13, in <module> from scipy.stats import norm File "/tools/python/2.6.3_3/linux_x86_64/lib/python2.6/site-packages/scipy/stats/__init__.py", line 7, in <module> from stats import * File "/tools/python/2.6.3_3/linux_x86_64/lib/python2.6/site-packages/scipy/stats/stats.py", line 203, in <module> import scipy.linalg as linalg File "/tools/python/2.6.3_3/linux_x86_64/lib/python2.6/site-packages/scipy/linalg/__init__.py", line 9, in <module> from basic import * File "/tools/python/2.6.3_3/linux_x86_64/lib/python2.6/site-packages/scipy/linalg/basic.py", line 16, in <module> from lapack import get_lapack_funcs File "/tools/python/2.6.3_3/linux_x86_64/lib/python2.6/site-packages/scipy/linalg/lapack.py", line 14, in <module> from scipy.linalg import flapack ImportError: liblapack.so: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/disk1/hadoop/tmp/taskTracker/jobcache/job_201109081055_6658/attempt_201109081055_6658_r_000000_0/work/./ExpandAndAverageFinal_ReducerB_pc.py", line 13, in <module> from scipy.stats.norm import isf File "/tools/python/2.6.3_3/linux_x86_64/lib/python2.6/site-packages/scipy/stats/__init__.py", line 7, in <module> from stats import * File "/tools/python/2.6.3_3/linux_x86_64/lib/python2.6/site-packages/scipy/stats/stats.py", line 202, in <module> import scipy.special as special File "/tools/python/2.6.3_3/linux_x86_64/lib/python2.6/site-packages/scipy/special/__init__.py", line 8, in <module> from basic import * File "/tools/python/2.6.3_3/linux_x86_64/lib/python2.6/site-packages/scipy/special/basic.py", line 6, in <module> from _cephes import * ImportError: libgfortran.so.1: cannot open shared object file: No such file or directory Thanks, Mark Pundurs Data Analyst - Traffic Nokia Location & Commerce, Chicago The information contained in this communication may be CONFIDENTIAL and is intended only for the use of the recipient(s) named above. If you are not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication, or any of its contents, is strictly prohibited. If you have received this communication in error, please notify the sender and delete/destroy the original message and any copy of it from your computer or paper files.

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Lerch transcendent function
by josef.pktd＠gmail.com 01 Nov '11

01 Nov '11

Is the Lerch transcendent function available in scipy or python? http://en.wikipedia.org/wiki/Lerch_zeta_function#Definition capital phi http://mathworld.wolfram.com/LerchTranscendent.html (used for moments of Weibull-geometric distribution) Josef

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