Mailman 3 July 2005 - SciPy-User

Building Scipy on Dell 64bit Xeon
by David Noriega July 14, 2005

July 14, 2005

Hello, I've been put in charge of setting up a Dell 64bit Xeon workstation and on the side I've been tring to get scipy to install, but I haven't had any luck. I compiled LAPACK, BLAS, and ATLAS sucsesfuly and scipy finds them. Its when I try to build scipy that I get problems. I try just plain "./setup.py build" and I get these errors: /usr/bin/ld: /usr/lib/gcc-lib/x86_64-redhat-linux/3.2.3/libg2c.a(s_stop.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib/gcc-lib/x86_64-redhat-linux/3.2.3/libg2c.a: could not read symbols: Bad value collect2: ld returned 1 exit status /usr/bin/ld: /usr/lib/gcc-lib/x86_64-redhat-linux/3.2.3/libg2c.a(s_stop.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib/gcc-lib/x86_64-redhat-linux/3.2.3/libg2c.a: could not read symbols: Bad value collect2: ld returned 1 exit status error: Command "/usr/bin/g77 -shared build/temp.linux-x86_64-2.4/Lib/special/cephesmodule.o build/temp.linux-x86_64-2.4/Lib/special/amos_wrappers.o build/temp.linux-x86_64-2.4/Lib/special/specfun_wrappers.o build/temp.linux-x86_64-2.4/Lib/special/toms_wrappers.o build/temp.linux-x86_64-2.4/Lib/special/cdf_wrappers.o build/temp.linux-x86_64-2.4/Lib/special/ufunc_extras.o -Lbuild/temp.linux-x86_64-2.4 -lamos -ltoms -lc_misc -lcephes -lmach -lcdf -lspecfun -lg2c -o build/lib.linux-x86_64-2.4/scipy/special/cephes.so" failed with exit status 1 I also installed Intel's compiler, but I get different errors: ld: skipping incompatible build/temp.linux-x86_64-2.4/libc_misc.a when searching for -lc_misc ld: cannot find -lc_misc ld: skipping incompatible build/temp.linux-x86_64-2.4/libc_misc.a when searching for -lc_misc ld: cannot find -lc_misc error: Command "/usr/local/intel/bin/ifort -shared -nofor_main build/temp.linux-x86_64-2.4/Lib/special/cephesmodule.o build/temp.linux-x86_64-2.4/Lib/special/amos_wrappers.o build/temp.linux-x86_64-2.4/Lib/special/specfun_wrappers.o build/temp.linux-x86_64-2.4/Lib/special/toms_wrappers.o build/temp.linux-x86_64-2.4/Lib/special/cdf_wrappers.o build/temp.linux-x86_64-2.4/Lib/special/ufunc_extras.o -Lbuild/temp.linux-x86_64-2.4 -lamos -ltoms -lc_misc -lcephes -lmach -lcdf -lspecfun -o build/lib.linux-x86_64-2.4/scipy/special/cephes.so" failed with exit status 1 In trying to figure out whats wrong, I changed some items in scipy_distutils. I'm running Fedora Core 4 x86_64, so I had scipy looking in /usr/lib64 and /usr/X11R6/lib64 for libraries. I also set scipy to use gcc32, just because when I compiled ATLAS Don't fear that philosophy's an impious way --superstition's more likely to lead folk astray. ~Lucretius, De rerum natura, Book One http://mindbender.deviantart.com __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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pyfits question: handling gzipped fits files
by Russell E. Owen July 14, 2005

July 14, 2005

Is there some reasonable way to get pyfits to read a gzipped fits file (in a way that works on Windows and unix)? I realize I can unzip the file first, but I was hoping to have it directly read (unzipped on the fly). I can't see any command that takes a file-like object (instead of a file path), so I can't see how to take advantage of Python's gzip module. I realize I can just edit the code and add this in, but, well...if there's a better way I'd love to know about it and if there isn't, I'd like to request that it be modified to handle gzipped files automatically. -- Russell P.S. I hope this isn't a duplicate. I tried posting before I was a member of the list -- I read it on gmane -- and that posting was held.

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RE: weird
by Howey, David A July 14, 2005

July 14, 2005

sorry - ignore me, I've figured it out. It's the indentation on 'elif' of course! Duh Dave -----Original Message----- From: Howey, David A Sent: 14 July 2005 10:44 To: 'SciPy Users List' Subject: weird I'm new to Python, so just working through the tutorials on python.org The question is, why doesn't this work: In [34]: if x<0: ....: print 'blah' ....: elif x == 0: ------------------------------------------------------------ File "<console>", line 3 elif x == 0: ^ SyntaxError: invalid syntax Surely this is the simplest thing? Does is have a problem with 'elif'? But it's in the tutorial!! Dave

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weird
by Howey, David A July 14, 2005

July 14, 2005

I'm new to Python, so just working through the tutorials on python.org The question is, why doesn't this work: In [34]: if x<0: ....: print 'blah' ....: elif x == 0: ------------------------------------------------------------ File "<console>", line 3 elif x == 0: ^ SyntaxError: invalid syntax Surely this is the simplest thing? Does is have a problem with 'elif'? But it's in the tutorial!! Dave

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RE: [SciPy-user] pycrust
by Howey, David A July 13, 2005

July 13, 2005

One last thing with crimson editor is that the autoindent doesn't seem to work for python .py files. Unless I'm missing something (it is switched on). Have you got it working? Dave -----Original Message----- From: scipy-user-bounces(a)scipy.net [mailto:scipy-user-bounces@scipy.net] On Behalf Of Ryan Krauss Sent: 13 July 2005 16:20 To: SciPy Users List Subject: Re: [SciPy-user] pycrust Add C:\Program Files\Crimson Editor to your windows path variable and then set the line in ipythonrc.ini to read editor cedt I just tried it and it worked.

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matplotlib, py2exe and import problems
by Noko Phala July 13, 2005

July 13, 2005

Not sure if this is the right list, but can someone tell mw how to successfully create an executable of a script that uses matplotlib? The example script in the documentation odes not appear to work. I keep missing modules, and everytime I add the missing module, a new one crops up. Much like the problems listed here: http://mail.python.org/pipermail/python-list/2005-February/267595.html My recent error message is: Traceback (most recent call last): File "Uranium_Leaching_ Modelv1.py", line 162, in ? File "pylab.pyc", line 1, in ? File "matplotlib\pylab.pyc", line 217, in ? File "matplotlib\backends\__init__.pyc", line 24, in pylab_setup ImportError: No module named backend_tkagg Thanks, Noko ------------------------------------------------------------------------------------------ This e-mail was checked by the e-Sweeper Service. For more information visit our website, Clearswift Corporation e-Sweeper : http://www.mimesweeper.com/products/esweeper/ ------------------------------------------------------------------------------------------

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RE: [SciPy-user] wxpython
by Howey, David A July 13, 2005

July 13, 2005

thanks. I'll try that. I'm currently coding in matlab to simulate 1D steady state fluid dynamics problems, and considering the switch to python/scipy. Key issues of concern: 1) can matrices/vectors be handled in the same way (this is the power of matlab of course). eg. the matlab 'dot' notation which operates element by element on matrices. using vectors greatly speeds up code over for loops and makes it more compact. 2) matlab has extremely powerful plotting facilities 3) object orientation. Actually I think python might excel here. I get a bit frustrated with matlab objects (no passing by reference, for example). 4) creation of executables/binaries-- should be okay Do you or anyone have any comments on these points? Dave ________________________________ From: scipy-user-bounces(a)scipy.net [mailto:scipy-user-bounces@scipy.net] On Behalf Of Ryan Krauss Sent: 13 July 2005 13:41 To: SciPy Users List Subject: Re: [SciPy-user] wxpython Dave, I actually get the same thing. I know it can be frustrating to try new software and have it not work completely out of the box. At this point in the installation, someone recommended to me to switch to Ipython and matplotlib. That is what I have done and I am quite happy with it. Ryan Howey, David A wrote: I've now installed wxpython, and sadly get: import gui_thread gui_thread.start() Traceback (most recent call last): File "<pyshell#1>", line 1, in -toplevel- gui_thread.start() File "C:\Python23\Lib\site-packages\gui_thread\__init__.py", line 73, in start wxPython_thread() File "C:\Python23\Lib\site-packages\gui_thread\wxPython_thread.py", line 160, in wxPython_thread sys.modules[name] = wrap_extmodule(module,call_holder) File "C:\Python23\Lib\site-packages\gui_thread\wxPython_thread.py", line 61, in wrap_extmodule raise NotImplementedError,`t` NotImplementedError: <type 'PyCObject'> Perhaps I've done something wrong? Dave -----Original Message----- From: scipy-user-bounces(a)scipy.net [mailto:scipy-user-bounces@scipy.net] On Behalf Of Brice Thurin Sent: 13 July 2005 13:12 To: SciPy Users List Subject: Re: [SciPy-user] wxpython Hi, I had some trouble in the past as well using gui_thread and someone recommend me to use matplotlib (http://matplotlib.sourceforge.net). Otherwise, wxpython allows you to play with gui and can be find here: (http://www.wxpython.org). Brice _______________________________________________ SciPy-user mailing list SciPy-user(a)scipy.net http://www.scipy.net/mailman/listinfo/scipy-user

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RE: [SciPy-user] pycrust
by Howey, David A July 13, 2005

July 13, 2005

Thanks - this is helpful. I am trying to get ipython to use an editor other than windows notepad. First I tried editing the 'ipythonrc' file. Didn't have any affect - still uses notepad. Then I tried a command line: ipython -editor C:\Program Files\Crimson Editor\cedt.exe It doesn't like that. I think it's something to do with the spaces in the path. Should I use \%20 ? Anyone else got this sorted on a win32 system? Thanks Dave -----Original Message----- From: scipy-user-bounces(a)scipy.net [mailto:scipy-user-bounces@scipy.net] On Behalf Of Ryan Krauss Sent: 13 July 2005 16:03 To: SciPy Users List Subject: Re: [SciPy-user] pycrust As long as you use the TkAgg backend, I was able to use matplotlib and scipy with pycrust: import pylab from scipy import * x=arange(0,1,0.1) y=sin(2*pi*x) pylab.plot(x,y) pylab.show() The only catch is that once you show() your plots, you have to close them all before you can do anything else in the command window (because gui_thread doesn't work). While pycrust and its variants form a nice environment, the editor associated with them is pretty plain and the history mechanism isn't persistant (i.e. it doesn't remember commands after you close it and restart it). Ryan

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RE: [SciPy-user] wxpython
by Howey, David A July 13, 2005

July 13, 2005

yeah, I've got it running in colour.. I just meant the 'inline' colour changes as you type also, what editor do you use with ipython? I quite liked the idle built in editor Dave ________________________________ From: scipy-user-bounces(a)scipy.net [mailto:scipy-user-bounces@scipy.net] On Behalf Of Ryan Krauss Sent: 13 July 2005 14:13 To: SciPy Users List Subject: Re: [SciPy-user] wxpython Ipython can be made to run in color if you follow the Windows install instructions. It will also suggest syntax when you hit the tab key. Howey, David A wrote: gui_thread is obsolete and has not been upgraded to handle the latest wxPython. ipython has up-to-date threading support. I've just installed ipython. Seems okay, although I was getting to quite like the look and feel of 'idle', particularly the way it hints at syntax (like excel does) and also uses colours in the interpreter, and links to its own editor. Dave _______________________________________________ SciPy-user mailing list SciPy-user(a)scipy.net http://www.scipy.net/mailman/listinfo/scipy-user

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RE: plotting and Py2exe
by Noko Phala July 13, 2005

July 13, 2005

Hi, Does anyone have any experience with making executables of a scipy-using python script that uses a plotting function like gplt or plt? I canot get the executable to plot. Other methods of solving scipy-related problems with py2exe did not work so far (e.g. scipy.gplt in includes, etc). Thanks, Noko ------------------------------------------------------------------------------------------ This e-mail was checked by the e-Sweeper Service. For more information visit our website, Clearswift Corporation e-Sweeper : http://www.mimesweeper.com/products/esweeper/ ------------------------------------------------------------------------------------------

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