Mailman 3 June 2007 - SciPy-User

problems with _fitpack module
by dmitrey June 19, 2007

June 19, 2007

hi all, I try to use scipy.sandbox.spline module, but it yields >>> from scipy.sandbox import spline Traceback (innermost last): File "<stdin>", line 1, in <module> File "/usr/lib/python2.5/site-packages/scipy/sandbox/spline/__init__.py", line 7, in <module> from fitpack import * File "/usr/lib/python2.5/site-packages/scipy/sandbox/spline/fitpack.py", line 35, in <module> import _fitpack ImportError: No module named _fitpack scipy 0.5.2 had been installed from ubuntu packages website (for Ubuntu Feisty Linux). Any suggestions? Thank you in advance, Dmitrey.

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question splines
by dmitrey June 19, 2007

June 19, 2007

hi all, I need a func from scipy or other Python free software that provides quickly 1-variable interpolation of some funcs (I mean vectoriezed form) by 2nd-order splines. for example, I have (x from R) func1(x) = sin(x) func2(x) = cos(x) func3(x) = x^2 + x + 2*atan(x) (the number of the funcs may be very great, up to ~ 1000) So I have several points x = 0.1, 0.2, 0.3, 0.4 and I want to obtain func1(x), func2(x), func3(x) values from any point within the [0.1; 0.4] region. Also, it would be very nice if 1) the interpolation function would provide a value outside the region, interpolated by linear or quadratic or any other way; 2) I have possibility to do binary insert of new points. I.e., initially I have values of func1, func2, func3 in x=0.1 and x=0.3. Then I got values in x=0.4. Then - in x = 0.2, etc, etc . I know that sorted x-arrays allow to obtain interpolated values more quickly, like interp1() vs interp() in MATLAB. Can I somewhow take advantages in my case? Thank you in advance, Dmitrey.

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lagrange multipliers in python
by fdu.xiaojf＠gmail.com June 19, 2007

June 19, 2007

Hi all, Sorry for the cross-posting. I'm trying to find the minimum of a multivariate function F(x1, x2, ..., xn) subject to multiple constraints G1(x1, x2, ..., xn) = 0, G2(...) = 0, ..., Gm(...) = 0. The conventional way is to construct a dummy function Q, $$Q(X, \Lambda) = F(X) + \lambda_1 G1(X) + \lambda_2 G2(X) + ... + \lambda_m Gm(X)$$ and then calculate the value of X and \Lambda when the gradient of function Q equals 0. I think this is a routine work, so I want to know if there are available functions in python(mainly scipy) to do this? Or maybe there is already a better way in python? I have googled but haven't found helpful pages. Thanks a lot. Xiao Jianfeng

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How to determine if a function is convex or not ?
by fdu.xiaojf＠gmail.com June 18, 2007

June 18, 2007

Hi all, CVXOPT(http://abel.ee.ucla.edu/cvxopt) can handle both equality and inequality constraints, but it can only deal with convex functions. So I want to know how to determine if a function is convex or not. Are there some rules for this? Or I have to calculate the derivatives ? Thanks. Xiao Jianfeng

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sparse least squares problem
by Bryan Cole June 18, 2007

June 18, 2007

Hi, I've got a sparse (complex) least-squares problem to solve. Can anyone suggest the most appropriate scipy routines to apply to this (i.e. do the sparse solvers do least squares, for example?). scipy.linalg.lstsq works OK for small datasets but it. doesn't seem to scale up well. Maybe an iterative approach would be better. Any pointers would be much appreciated. I'm no linalg expert. cheers, Bryan

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Problems compiling scipy on SuSE 10.2
by Karl Edler June 17, 2007

June 17, 2007

Hello, Recently I tried installing scipy from rpm packages on SuSE 10.2 (64bit) and failed. Now I have tried compiling scipy and have run into some problems. I compiled atlas successfully and copied its *.a files to /usr/lib64/atlas I ran "python setup.py build" in the scipy directory and the build failed since it couldn't find the -lgcc_s library. I made a symbolic link from /lib64/libgcc_s.so.1 -> /lib64/libgcc_s.so and the build was able to proceed. Now the build fails with something about -fPIC which I don't understand. Here is the last bit of the output from "python setup.py build" (notice : relocation R_X86_64_PC32 against `atl_f77wrap_dscal__' can not be used when making a shared object; recompile with -fPIC): customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using build_ext building 'scipy.integrate._odepack' extension compiling C sources C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -fmessage-length=0 -Wall -D_FORTIFY_SOURCE=2 -g -fPIC compile options: '-DATLAS_INFO="\"3.6.0\"" -I/usr/local/lib64/atlas -I/usr/lib64/python2.5/site-packages/numpy/core/include -I/usr/include/python2.5 -c' /usr/bin/g77 -g -Wall -shared build/temp.linux-x86_64-2.5/Lib/integrate/_odepackmodule.o -L/usr/local/lib64/atlas -L/usr/lib/python2.5/config -Lbuild/temp.linux-x86_64-2.5 -lodepack -llinpack_lite -lmach -lptf77blas -lptcblas -latlas -lpython2.5 -lg2c -o build/lib.linux-x86_64-2.5/scipy/integrate/_odepack.so /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../../x86_64-suse-linux/bin/ld: /usr/local/lib64/atlas/libptf77blas.a(dscal.o): relocation R_X86_64_PC32 against `atl_f77wrap_dscal__' can not be used when making a shared object; recompile with -fPIC /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../../x86_64-suse-linux/bin/ld: final link failed: Bad value /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../../x86_64-suse-linux/bin/ld: /usr/local/lib64/atlas/libptf77blas.a(dscal.o): relocation R_X86_64_PC32 against `atl_f77wrap_dscal__' can not be used when making a shared object; recompile with -fPIC /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../../x86_64-suse-linux/bin/ld: final link failed: Bad value error: Command "/usr/bin/g77 -g -Wall -shared build/temp.linux-x86_64-2.5/Lib/integrate/_odepackmodule.o -L/usr/local/lib64/atlas -L/usr/lib/python2.5/config -Lbuild/temp.linux-x86_64-2.5 -lodepack -llinpack_lite -lmach -lptf77blas -lptcblas -latlas -lpython2.5 -lg2c -o build/lib.linux-x86_64-2.5/scipy/integrate/_odepack.so" failed with exit status 1 ---------------------------------------------------------------------------------------------------------------- Does anyone know what this means or how to fix it? Thanks, Karl Edler

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svn checkout question
by william ratcliff June 17, 2007

June 17, 2007

I work under windows xp and recently was using tortoise svn to try to check out scipy with the hopes of building it from source. I was prompted for a user name and password. Is this supposed to happen? Also, do I need to do anything special to get files from the sandbox? Thanks, William

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numpy r3871 broken
by Nils Wagner June 16, 2007

June 16, 2007

gnu: no Fortran 90 compiler found Traceback (most recent call last): File "setup.py", line 90, in <module> setup_package() File "setup.py", line 83, in setup_package configuration=configuration ) File "/home/nwagner/svn/numpy/numpy/distutils/core.py", line 176, in setup return old_setup(**new_attr) File "/usr/lib64/python2.5/distutils/core.py", line 151, in setup dist.run_commands() File "/usr/lib64/python2.5/distutils/dist.py", line 974, in run_commands self.run_command(cmd) File "/usr/lib64/python2.5/distutils/dist.py", line 994, in run_command cmd_obj.run() File "/home/nwagner/svn/numpy/numpy/distutils/command/install.py", line 16, in run r = old_install.run(self) File "/usr/lib64/python2.5/distutils/command/install.py", line 511, in run self.run_command('build') File "/usr/lib64/python2.5/distutils/cmd.py", line 333, in run_command self.distribution.run_command(command) File "/usr/lib64/python2.5/distutils/dist.py", line 994, in run_command cmd_obj.run() File "/usr/lib64/python2.5/distutils/command/build.py", line 112, in run self.run_command(cmd_name) File "/usr/lib64/python2.5/distutils/cmd.py", line 333, in run_command self.distribution.run_command(command) File "/usr/lib64/python2.5/distutils/dist.py", line 994, in run_command cmd_obj.run() File "/home/nwagner/svn/numpy/numpy/distutils/command/build_src.py", line 130, in run self.build_sources() File "/home/nwagner/svn/numpy/numpy/distutils/command/build_src.py", line 147, in build_sources self.build_extension_sources(ext) File "/home/nwagner/svn/numpy/numpy/distutils/command/build_src.py", line 250, in build_extension_sources sources = self.generate_sources(sources, ext) File "/home/nwagner/svn/numpy/numpy/distutils/command/build_src.py", line 307, in generate_sources source = func(extension, build_dir) File "numpy/core/setup.py", line 51, in generate_config_h library_dirs = default_lib_dirs) File "/usr/lib64/python2.5/distutils/command/config.py", line 278, in try_run self._check_compiler() File "/home/nwagner/svn/numpy/numpy/distutils/command/config.py", line 30, in _check_compiler dry_run=self.dry_run, force=1) File "/home/nwagner/svn/numpy/numpy/distutils/fcompiler/__init__.py", line 787, in new_fcompiler compiler = get_default_fcompiler(plat, requiref90=requiref90) File "/home/nwagner/svn/numpy/numpy/distutils/fcompiler/__init__.py", line 771, in get_default_fcompiler requiref90=requiref90) File "/home/nwagner/svn/numpy/numpy/distutils/fcompiler/__init__.py", line 723, in _find_existing_fcompiler c.customize(dist) File "/home/nwagner/svn/numpy/numpy/distutils/fcompiler/__init__.py", line 475, in customize get_flags('opt', oflags) File "/home/nwagner/svn/numpy/numpy/distutils/fcompiler/__init__.py", line 466, in get_flags flags.extend(getattr(self.flag_vars, tag)) File "/home/nwagner/svn/numpy/numpy/distutils/environment.py", line 37, in __getattr__ return self._get_var(name, conf_desc) File "/home/nwagner/svn/numpy/numpy/distutils/environment.py", line 51, in _get_var var = self._hook_handler(name, hook) File "/home/nwagner/svn/numpy/numpy/distutils/fcompiler/__init__.py", line 668, in _environment_hook return hook() File "/home/nwagner/svn/numpy/numpy/distutils/fcompiler/gnu.py", line 166, in get_flags_opt if self.get_version()<='3.3.3': File "/home/nwagner/svn/numpy/numpy/distutils/fcompiler/__init__.py", line 408, in get_version return CCompiler.get_version(force=force, ok_status=ok_status) TypeError: unbound method CCompiler_get_version() must be called with CCompiler instance as first argument (got nothing instead)

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Print number of significant digits ?
by Stef Mientki June 15, 2007

June 15, 2007

hello, is there a simple way (some flag or something like that), in which you can limit the number of significant digits, when using the plain print statement ? so that you get an output like this: >>> print pi 3.14 thanks, Stef Mientki Kamer van Koophandel - handelsregister 41055629 / Netherlands Chamber of Commerce - trade register 41055629

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Re: [SciPy-user] another (little) installation problem
by Volker Lorrmann June 14, 2007

June 14, 2007

Volker Lorrmann <lorrmann(a)physik.uni-wuerzburg.de> [2007-06-13 06:56]: > > > i'm trying to get scipy build. I've installed python-numpy and atlas > > with lapack support without any problems. > > "python setup.py build" fails with > > > building extension "scipy.fftpack._fftpack" sources > > target build/src.linux-i686-2.5/_fftpackmodule.c does not exist: > > Assuming _fftpackmodule.c was generated with "build_src --inplace" > > command. > > error: '_fftpackmodule.c' missing > > > Is there an easy workaround? Do you need some more informations? I've > > added the whole output. > > Hello Volker, > > These errors look very similar to the errors I got using numpy-1.0.3. On > the SciPy-dev list, Pearu pointed out that my errors were due to a bug > in the 1.0.3 tarball, and suggested building numpy from the svn > version. I did, and it fixed that problem. > > What OS and version are you building on? > > For anyone wondering about how to get the svn versions, the commands > below will download all the files into directories (they will be > automatically created) numpy and scipy below the current directory. > > svn co http://svn.scipy.org/svn/numpy/trunk numpy > svn co http://svn.scipy.org/svn/scipy/trunk scipy > > -rex Hi rex, thanks for your advice. Building numpy and scipy from svn fixed my problem. > What OS and version are you building on? I´m using Arch Linux... volker

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