Mailman 3 August 2009 - SciPy-User

Memory usage of scipy.io.loadmat
by Ariel Rokem 17 Aug '09

17 Aug '09

Hi everyone, I have stumbled on some interesting behavior of scipy.io.loadmat. The short of it - it looks like loadmat is gobbling up memory in some unjustified manner and releasing it under some strange circumstances. Here's the long story. This is all happening on a Mac OS 10.5.7, running EPD 4.0.30001 (Python 2.5.2), but with a relatively new version of scipy (see below). I start ipython -pylab in one terminal and run 'top' in another, in order to monitor the memory usage. Here's what I get initially: PhysMem: 417M wired, 449M active, 183M inactive, 1055M used, 3041M free. Then: In [1]: import scipy In [2]: scipy.__version__ Out[2]: '0.8.0.dev5606' In [3]: import scipy.io as sio Here's what it looks like now: PhysMem: 418M wired, 450M active, 183M inactive, 1058M used, 3038M free. So far, so good. I read in a large matfile with tons of data in it: In [4]: a = sio.loadmat('/Users/arokem/Projects/SchizoSpread/Scans/SMR033109_MC/Gray/Original/TSeries/Scan1/tSeries1.mat') PhysMem: 419M wired, 1024M active, 183M inactive, 1632M used, 2464M free. So - about 600 MB of memory is taken up by this new variable. Now to the wierdness: In [5]: b --------------------------------------------------------------------------- NameError Traceback (most recent call last) /Users/arokem/<ipython console> in <module>() NameError: name 'b' is not defined Of course - 'b' doesn't exist! But now, the memory usage has dramatically gone down: PhysMem: 420M wired, 740M active, 183M inactive, 1350M used, 2746M free. So - just invoking an error in the ipython command line has freed up 300 MB. Where did they come from? I tried different things - assigning other variables doesn't seem to free up this memory. Neither do calls to other functions. Except "plot()", which does seem to do the trick for some reason. Interestingly, when I run all this in a python interactive session (and not ipython), I get a similar memory usage initially. Calling a non-existent variable does not free up the memory, but other things do. For example, import matplotlib.pylab into the namespace did the trick. Does anyone have any idea what is going on? Thanks -- Ariel -- Ariel Rokem Helen Wills Neuroscience Institute University of California, Berkeley http://argentum.ucbso.berkeley.edu/ariel

9 14

Tutorial Prep: one IntroTest Failure after Python(x, y) install
by David Goldsmith 17 Aug '09

17 Aug '09

Hi! I installed Python(x,y) (successfully, I believe) but when I run the Intro Test script I get: Running tests: __main__.test_imports('setuptools', None) ... MOD: setuptools, version: 0.6c9 ok __main__.test_imports('IPython', None) ... MOD: IPython, version: 0.9.1 ok __main__.test_imports('numpy', None) ... MOD: numpy, version: 1.3.0 ok <snip> Plots with math ... ok ====================================================================== ERROR: __main__.test_imports('enthought.mayavi.api', None) ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\lib\site-packages\nose\case.py", line 183, in runTest self.test(*self.arg) File "IntroTests.py", line 91, in check_import exec "import %s as m" % mnames File "<string>", line 1, in <module> ImportError: No module named enthought.mayavi.api ---------------------------------------------------------------------- Ran 14 tests in 6.198s FAILED (errors=1) So at: http://code.enthought.com/projects/mayavi/docs/development/html/mayavi/inst… I read: "Under Window [sic] the best way to install Mayavi is to install a full Python distribution, such as EPD or Pythonxy. Note that Pythonxy has a special download which provides a complete installer for Mayavi and all its dependencies and is a much smaller download than EPD or the full Pythonxy install." OK, so I click on "special download" and run that. No (reported) problems. I try the Intro Tests again and get: ====================================================================== ERROR: __main__.test_imports('enthought.mayavi.api', None) ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python25\lib\site-packages\nose\case.py", line 183, in runTest self.test(*self.arg) File "IntroTests.py", line 91, in check_import exec "import %s as m" % mnames File "<string>", line 1, in <module> File "c:\python25\lib\site-packages\Mayavi-3.0.2-py2.5-win32.egg\enthought\mayavi\api.py", line 2, in <module> from enthought.mayavi.core.engine import Engine File "c:\python25\lib\site-packages\Mayavi-3.0.2-py2.5-win32.egg\enthought\mayavi\core\engine.py", line 24, in <module> from enthought.traits.ui.api import View, Item File "c:\python25\lib\site-packages\Traits-3.0.2-py2.5-win32.egg\enthought\traits\ui\api.py", line 104, in <module> _constants = toolkit().constants() File "c:\python25\lib\site-packages\Traits-3.0.2-py2.5-win32.egg\enthought\traits\ui\toolkit.py", line 369, in constants raise NotImplementedError NotImplementedError ---------------------------------------------------------------------- Ran 14 tests in 8.628s FAILED (errors=1) I guess that's progress, but I'm not sure what to do next. DG

2 1

How to build simulation software like Simulink using SciPy?
by loretta 17 Aug '09

17 Aug '09

I wonder how simulation software could be built using SciPy. I tried to do so, but get into troubles as soon as feedback pathes are involved. What I want to achieve is a package, that can be called periodically every T seconds, where all blocks (which are connected to each other) are calculated and results are recorded in blocks that can display signals (scopes). Between the coarse grained T seconds, I create a time vector for odeint, to calculate state vectors between the coarse grained i*T. Without odeint I would have to choose a very small T to approach continuous time situation. I want odeint to do that (and it does), because it's so much faster than some homebrew ode solver. The rule I've implemented to solve a net of blocks is: A block may be calculated as soon as all its predecessors have been calculated. Everything works as expected, if I don't create loops. If I create loops, I only get at the output results of each block at i*T. What I need is a method to get at the output results of each blocks at the times j*Tau (where Tau < T and j = range( T/Tau)) odeint is solving the 1st order differential eq. While having all these difficulties to get at proper results, I really wonder how Simulink is doing all this. Anyone willing to shed some light on this? Kind regards Loretta

3 2

Re: [SciPy-User] Some updates on the tutorial test scripts and versions of tools needed
by Tom Kuiper 17 Aug '09

17 Aug '09

Fernando Perez wrote: > here are some notes regarding the tutorial requirements. I am sending this to > all of you, though some of it may only apply to those attending the advanced > track. > > - If you had troubles with the testing scripts, please note that I've fixed a > few small issues. The current versions are (intro, advanced and > pycuda-specific): > > https://cirl.berkeley.edu/fperez/tmp/intro_tut_checklist.py > https://cirl.berkeley.edu/fperez/tmp/adv_tut_checklist.py > https://cirl.berkeley.edu/fperez/tmp/pycuda_tut_checklist.py > ... The stable Debian version of cython is 0.9.8. I just downloaded it. "AssertionError: Cython version (0, 9, 8) found, at least (0, 11, 2) required" It seems that 0.11.2 is in the unstable Debian distribution. Can someone suggest how to get that package without having to upgrade to unstable? Thanks Tom

7 7

Scipy Test failures
by McCully, Dwayne (NIH/NLM/LHC) [C] 16 Aug '09

16 Aug '09

Hello Everyone, This is my first time sending e-mail to the scipy user community. I have a small problem and I would like some help from anyone: Why does the scipy.test() fail to find omp_set_lock when its compiled into ATLAS? My ATLAS variable is set correctly. See below Dwayne [root@niamssolexa lib]# env | grep ATLAS ATLAS=/usr/local/atlas/lib [root@niamssolexa lib]# ls libatlas.a libatlas.so libcblas.a libcblas.so libf77blas.a libf77blas.so liblapack.a liblapack.so libptcblas.a libptcblas.so libptf77blas.a libptf77blas.so [root@niamssolexa lib]# strings libatlas.a | grep omp_set_lock omp_set_lock omp_set_lock omp_set_lock omp_set_lock omp_set_lock [root@niamssolexa lib]# strings libatlas.so | grep omp_set_lock omp_set_lock [root@niamssolexa ~]# python Python 2.5.2 (r252:60911, Mar 5 2008, 20:59:51) [GCC 4.1.2 20070626 (Red Hat 4.1.2-14)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import scipy >>> scipy.test() Running unit tests for scipy NumPy version 1.2.1 NumPy is installed in /usr/local/lib/python2.5/site-packages/numpy SciPy version 0.7.1 SciPy is installed in /usr/local/lib/python2.5/site-packages/scipy Python version 2.5.2 (r252:60911, Mar 5 2008, 20:59:51) [GCC 4.1.2 20070626 (Red Hat 4.1.2-14)] nose version 0.11.0 /usr/local/lib/python2.5/site-packages/scipy/linsolve/__init__.py:4: DeprecationWarning: scipy.linsolve has moved to scipy.sparse.linalg.dsolve warn('scipy.linsolve has moved to scipy.sparse.linalg.dsolve', DeprecationWarning) ............................................................................................................................................................................................................EE......................../usr/local/lib/python2.5/site-packages/scipy/io/matlab/mio.py:111: Warning: Unreadable variable "testfunc", because "Cannot read matlab functions" matfile_dict = MR.get_variables() ........../usr/local/lib/python2.5/site-packages/scipy/io/matlab/mio.py:165: FutureWarning: Using oned_as default value ('column') This will change to 'row' in future versions oned_as=oned_as) ........................./usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:438: FutureWarning: Using oned_as default value ('column') This will change to 'row' in future versions mfw = MatFile5Writer(StringIO()) ......../usr/local/lib/python2.5/site-packages/scipy/io/matlab/mio.py:84: FutureWarning: Using struct_as_record default value (False) This will change to True in future versions return MatFile5Reader(byte_stream, **kwargs) ...............................Warning: 1000000 bytes requested, 20 bytes read. ./usr/local/lib/python2.5/site-packages/numpy/lib/utils.py:110: DeprecationWarning: write_array is deprecated warnings.warn(str1, DeprecationWarning) /usr/local/lib/python2.5/site-packages/numpy/lib/utils.py:110: DeprecationWarning: read_array is deprecated warnings.warn(str1, DeprecationWarning) ..E..................../usr/local/lib/python2.5/site-packages/numpy/lib/utils.py:110: DeprecationWarning: npfile is deprecated warnings.warn(str1, DeprecationWarning) .........EEEEE.................................................................................................................................................................................................................................................................................................................................................................................................................................EEEEE............................................................................................................................................................................................................................................................................................................................................K.K................................................................................................................................................................................................................................................................................................................E...warning: specified build_dir '_bad_path_' does not exist or is not writable. Trying default locations .....warning: specified build_dir '_bad_path_' does not exist or is not writable. Trying default locations ...............................building extensions here: /root/.python25_compiled/m15 ................................................................................................ ====================================================================== ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName addr.filename, addr.module) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/local/lib/python2.5/site-packages/scipy/integrate/__init__.py", line 10, in <module> from odepack import * File "/usr/local/lib/python2.5/site-packages/scipy/integrate/odepack.py", line 7, in <module> import _odepack ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock ====================================================================== ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName addr.filename, addr.module) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/local/lib/python2.5/site-packages/scipy/interpolate/__init__.py", line 13, in <module> from rbf import Rbf File "/usr/local/lib/python2.5/site-packages/scipy/interpolate/rbf.py", line 47, in <module> from scipy import linalg File "/usr/local/lib/python2.5/site-packages/scipy/linalg/__init__.py", line 8, in <module> from basic import * File "/usr/local/lib/python2.5/site-packages/scipy/linalg/basic.py", line 17, in <module> from lapack import get_lapack_funcs File "/usr/local/lib/python2.5/site-packages/scipy/linalg/lapack.py", line 17, in <module> from scipy.linalg import flapack ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock ====================================================================== ERROR: test_integer (test_array_import.TestReadArray) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.5/site-packages/scipy/io/tests/test_array_import.py", line 52, in test_integer from scipy import stats File "/usr/local/lib/python2.5/site-packages/scipy/stats/__init__.py", line 7, in <module> from stats import * File "/usr/local/lib/python2.5/site-packages/scipy/stats/stats.py", line 199, in <module> import scipy.linalg as linalg File "/usr/local/lib/python2.5/site-packages/scipy/linalg/__init__.py", line 8, in <module> from basic import * File "/usr/local/lib/python2.5/site-packages/scipy/linalg/basic.py", line 17, in <module> from lapack import get_lapack_funcs File "/usr/local/lib/python2.5/site-packages/scipy/linalg/lapack.py", line 17, in <module> from scipy.linalg import flapack ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock ====================================================================== ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName addr.filename, addr.module) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/local/lib/python2.5/site-packages/scipy/lib/blas/__init__.py", line 9, in <module> import fblas ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock ====================================================================== ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName addr.filename, addr.module) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/local/lib/python2.5/site-packages/scipy/lib/lapack/__init__.py", line 9, in <module> import calc_lwork ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock ====================================================================== ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName addr.filename, addr.module) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/local/lib/python2.5/site-packages/scipy/linalg/__init__.py", line 8, in <module> from basic import * File "/usr/local/lib/python2.5/site-packages/scipy/linalg/basic.py", line 17, in <module> from lapack import get_lapack_funcs File "/usr/local/lib/python2.5/site-packages/scipy/linalg/lapack.py", line 17, in <module> from scipy.linalg import flapack ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock ====================================================================== ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName addr.filename, addr.module) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/local/lib/python2.5/site-packages/scipy/linsolve/__init__.py", line 6, in <module> from scipy.sparse.linalg.dsolve import * File "/usr/local/lib/python2.5/site-packages/scipy/sparse/linalg/__init__.py", line 5, in <module> from isolve import * File "/usr/local/lib/python2.5/site-packages/scipy/sparse/linalg/isolve/__init__.py", line 4, in <module> from iterative import * File "/usr/local/lib/python2.5/site-packages/scipy/sparse/linalg/isolve/iterative.py", line 5, in <module> import _iterative ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock ====================================================================== ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName addr.filename, addr.module) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/local/lib/python2.5/site-packages/scipy/maxentropy/__init__.py", line 9, in <module> from maxentropy import * File "/usr/local/lib/python2.5/site-packages/scipy/maxentropy/maxentropy.py", line 74, in <module> from scipy import optimize File "/usr/local/lib/python2.5/site-packages/scipy/optimize/__init__.py", line 11, in <module> from lbfgsb import fmin_l_bfgs_b File "/usr/local/lib/python2.5/site-packages/scipy/optimize/lbfgsb.py", line 30, in <module> import _lbfgsb ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock ====================================================================== ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName addr.filename, addr.module) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/local/lib/python2.5/site-packages/scipy/odr/__init__.py", line 11, in <module> import odrpack File "/usr/local/lib/python2.5/site-packages/scipy/odr/odrpack.py", line 103, in <module> from scipy.odr import __odrpack ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock ====================================================================== ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName addr.filename, addr.module) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/local/lib/python2.5/site-packages/scipy/optimize/__init__.py", line 11, in <module> from lbfgsb import fmin_l_bfgs_b File "/usr/local/lib/python2.5/site-packages/scipy/optimize/lbfgsb.py", line 30, in <module> import _lbfgsb ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock ====================================================================== ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName addr.filename, addr.module) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/local/lib/python2.5/site-packages/scipy/signal/__init__.py", line 10, in <module> from filter_design import * File "/usr/local/lib/python2.5/site-packages/scipy/signal/filter_design.py", line 12, in <module> from scipy import special, optimize File "/usr/local/lib/python2.5/site-packages/scipy/optimize/__init__.py", line 11, in <module> from lbfgsb import fmin_l_bfgs_b File "/usr/local/lib/python2.5/site-packages/scipy/optimize/lbfgsb.py", line 30, in <module> import _lbfgsb ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock ====================================================================== ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName addr.filename, addr.module) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/local/lib/python2.5/site-packages/scipy/sparse/linalg/__init__.py", line 5, in <module> from isolve import * File "/usr/local/lib/python2.5/site-packages/scipy/sparse/linalg/isolve/__init__.py", line 4, in <module> from iterative import * File "/usr/local/lib/python2.5/site-packages/scipy/sparse/linalg/isolve/iterative.py", line 5, in <module> import _iterative ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock ====================================================================== ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName addr.filename, addr.module) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/local/lib/python2.5/site-packages/scipy/sparse/tests/test_base.py", line 31, in <module> from scipy.sparse.linalg import splu File "/usr/local/lib/python2.5/site-packages/scipy/sparse/linalg/__init__.py", line 5, in <module> from isolve import * File "/usr/local/lib/python2.5/site-packages/scipy/sparse/linalg/isolve/__init__.py", line 4, in <module> from iterative import * File "/usr/local/lib/python2.5/site-packages/scipy/sparse/linalg/isolve/iterative.py", line 5, in <module> import _iterative ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock ====================================================================== ERROR: Failure: ImportError (/usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.5/site-packages/nose/loader.py", line 379, in loadTestsFromName addr.filename, addr.module) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/usr/local/lib/python2.5/site-packages/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/local/lib/python2.5/site-packages/scipy/stats/__init__.py", line 7, in <module> from stats import * File "/usr/local/lib/python2.5/site-packages/scipy/stats/stats.py", line 199, in <module> import scipy.linalg as linalg File "/usr/local/lib/python2.5/site-packages/scipy/linalg/__init__.py", line 8, in <module> from basic import * File "/usr/local/lib/python2.5/site-packages/scipy/linalg/basic.py", line 17, in <module> from lapack import get_lapack_funcs File "/usr/local/lib/python2.5/site-packages/scipy/linalg/lapack.py", line 17, in <module> from scipy.linalg import flapack ImportError: /usr/local/atlas/lib/libatlas.so: undefined symbol: omp_set_lock ---------------------------------------------------------------------- Ran 1539 tests in 27.082s FAILED (KNOWNFAIL=2, errors=14) <nose.result.TextTestResult run=1539 errors=14 failures=0> >>>

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Additional Pearu-fication of zunzun.com (spline curves and surfaces)
by James Phillips 16 Aug '09

16 Aug '09

Added 2d spline curves: http://zunzun.com/Equation/2/Spline/Spline/ and 3D spline surfaces: http://zunzun.com/Equation/3/Spline/Spline/ to http://zunzun.com - the automatically generated Python spline curve and surface evaluation code was partially based on: http://svn.scipy.org/svn/scipy/trunk/scipy/interpolate/fitpack/splev.f http://svn.scipy.org/svn/scipy/trunk/scipy/interpolate/fitpack/fpbisp.f http://svn.scipy.org/svn/scipy/trunk/scipy/interpolate/fitpack/fpbspl.f as noted in the evaluation output source code comments. I plan to use the existing Python output code to generate C++, Java, C#, etc. later on - at least end users have something for now if they require evaluation code in those languages in the immediate future. My 2D source code browsable at: http://code.google.com/p/pythonequations/source/browse/trunk/pythonequation… My 3D source code browsable at: http://code.google.com/p/pythonequations/source/browse/trunk/pythonequation… Pearu, thank you very much for the Fortran work that allowed me to automatically generate the Python evaluation code for end users. Now on to parallel processing for Robert Kern's DE code! James

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Re: [SciPy-User] FAIL: __main__.test_loadtxt(array([('M', 21, 72.0), ('F', 35, 58.0)],
by Fernando Perez 16 Aug '09

16 Aug '09

Hi Egill, On Sun, Aug 16, 2009 at 10:58 AM, Egill Hauksson<ehauksson(a)gmail.com> wrote: > To all, > > Any ideas -- see below for one FAIL. > > Thanks > Egill > > In [13]: %run intro.py [...] > AssertionError: > Arrays are not equal > > (mismatch 100.0%) > x: array([('M', 21, 72.0), ('F', 35, 58.0)], > dtype=[('gender', '|S1'), ('age', '>i4'), ('weight', '>f4')]) > y: array([('M', 21, 72.0), ('F', 35, 58.0)], > dtype=[('gender', '|S1'), ('age', '<i4'), ('weight', '<f4')]) Ah, don't worry. You must be on a power PC Mac instead of an Intel one, and the mismatch is simply in the endianness of the data. I just failed to account for the possibility of a Big Endian chip in the tests. So the failure is just in my test, your setup is OK. Sorry about that! Cheers, f

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Chinese scipy user group needs help
by Steve Han 16 Aug '09

16 Aug '09

Hi list, We are a numpy/scipy user group in Shandong Province ,China.Our interest is at using Numpy/Scipy and Python multiprocessing to leverage scientifc and engineering computing in day to day work.We need the help from the community of Scipy,first we mean establish a local scipy community,then the other.Any suggestion? Thanks a lot! -- Best Regards, Steve Han

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Re: [SciPy-User] scipy in google wave (screenshot attached)
by Paul Böhm 16 Aug '09

16 Aug '09

>Interesting -- is the python code run the the wave to generate the >figure? If so, how did you get around the problem that only pure >python code can run in the appengine, so presumably numpy and mpl >would not work? Are you passing the python code to another server >which serves up the png? we ported the waveapi to ec2 (or just any machine), and then wrote an appengine app that bridges the data out to us :p if someone was seriously interested in developing a collaborative scipy notebook, i'd love to help get that started. i think Wave would work fabulously as a UI to scipy. (i don't think i'll be the one to do it though, since other projects occupy my time usually) paul

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numpy: loadtxt with default value
by Andreas Matthias 15 Aug '09

15 Aug '09

The documentation of numpy.loadtxt says that the `converters' parameter can be used to provide a default value for missing data. However the following doesn't work. import numpy as np from StringIO import StringIO s = StringIO('111 222') a = np.loadtxt(s, dtype = {'names': ('a', 'b', 'c'), 'formats': (float, float, float)}, converters = {2: lambda s: float(s or 0)} ) What's wrong with this code? Ciao Andreas

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