Mailman 3 January 2011 - SciPy-User

[ANN] FEMTEC: Trac on open source scientific software
by Gael Varoquaux 30 Jan '11

30 Jan '11

Hi list, This is just a note that an extra track at FEMTEC, a conference for computational methods in engineering and science, is open for open source scientific software. The organisers have a taste for Python, so if you want to submit a paper on numerical methods with Python, this is an excellent venue. Abstract submission is open till end of February. To submit you need to create an account and edit you profile. Gael ________________________________________________________________________________ The 3rd International Conference on Finite Element Methods in Engineering and Science (FEMTEC 2011, http://hpfem.org/events/femtec-2011/) will have a track on Open-source projects and Python in scientific computing. FEMTEC 2011 is co-organized by the University of Nevada (Reno), Desert Reseach Institute (Reno), Idaho National Laboratory (Idaho Falls, Idaho), and U.S. Army Engineer Research and Development Center (Vicksburg, Mississippi). The objective of the meeting is to strengthen the interaction between researchers who develop new computational methods, and scientists and engineers from various fields who employ numerical methods in their research. Specific focus areas of FEMTEC 2011 include, but are not limited to, the following: * Computational methods in hydrology, atmospheric modeling, and other earth sciences. * Computational methods in nuclear, mechanical, civil, electrical, and other engineering fields. * Mesh generation and scientific visualization. * Open-source projects and Python in scientific computing. Part of the conference will be a software afternoon featuring open source projects of participants. Proceedings Proceedings of FEMTEC 2011 will appear as a special issue of Journal of Computational and Applied Mathematics (2008 SCI impact factor 1.292), and additional high-impact international journals as needed.

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Scipy.Optimize on GPUs?
by Patrick Holvey 28 Jan '11

28 Jan '11

Good morning everyone. I'm currently calling scipy.optimize.fmin_cg() to minimize the energy of a crystal system by changing the xyz coordinates of atoms in the system. I'm working on deriving the fprime function, but currently, the gradient is being estimated by fmin_cg. I have access to some Nvidia Tesla's but not much experience running Python on GPUs. I was wondering if there was an already GPU-enabled optimization algorithm somewhere in scipy or some other package. Does anyone know of one? Many thanks, Patrick -- Patrick Holvey Graduate Student Dept. of Materials Science and Engineering Johns Hopkins University pholvey1(a)jhu.edu Cell: (865)-659-9908

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weave throws no match for operator in seemingly good code
by David Michael Pennington 28 Jan '11

28 Jan '11

I'm trying to accelerate scoreatpercentile() from scipy.stats.stats with weave, but when I put it all together, it won't compile properly... perhaps this is a C-coding error on my part, but it looks right to me. Any assistance tracking down the reason for the errors would be appreciated. Thanks in advance... === weave code === def cpctl(a, per): values=np.sort(a,axis=0) shp = values.shape[0] nanval = np.nan retval = np.float64(0) expr = """ #include <math.h> double idx = per/100.0*(shp-1); long int idx_l = (long int)idx; if (fmod(idx,1.0) == 0.0) { retval = values[idx_l]; } else if (shp == 0) { retval = nanval; } else { retval = (values[idx_l]+(values[(idx_l+1)]))*fmod(idx,1.0); } """ wv.inline(expr, ['retval','a','per','values','nanval','shp'], \ type_converters=converters.blitz, \ compiler = 'gcc') return retval psyco.unbind(cpctl) === === execution errors === [mpenning@Bucksnort data]$ python reverse.py /home/mpenning/.python25_compiled/sc_948b3eed0cf550344f0bcefdd75e62940.cpp: In function ?PyObject* compiled_func(PyObject*, PyObject*)?: /home/mpenning/.python25_compiled/sc_948b3eed0cf550344f0bcefdd75e62940.cpp:740: error: no match for ?operator=? in ?retval = values.blitz::Array<T, N>::operator[] [with T_indexContainer = long int, P_numtype = double, int N_rank = 1](((const long int&)((const long int*)(& idx_l))))? /usr/lib/python2.5/site-packages/scipy/weave/scxx/object.h:179: note: candidates are: py::object& py::object::operator=(const py::object&) /home/mpenning/.python25_compiled/sc_948b3eed0cf550344f0bcefdd75e62940.cpp:748: error: no match for ?operator+? in ?values.blitz::Array<T, N>::operator[] [with T_indexContainer = long int, P_numtype = double, int N_rank = 1](((const long int&)((const long int*)(& idx_l)))) + values.blitz::Array<T, N>::operator[] [with T_indexContainer = long int, P_numtype = double, int N_rank = 1](((const long int&)((const long int*)(&(idx_l + 1l)))))? /home/mpenning/.python25_compiled/sc_948b3eed0cf550344f0bcefdd75e62940.cpp: In function ?PyObject* compiled_func(PyObject*, PyObject*)?: /home/mpenning/.python25_compiled/sc_948b3eed0cf550344f0bcefdd75e62940.cpp:740: error: no match for ?operator=? in ?retval = values.blitz::Array<T, N>::operator[] [with T_indexContainer = long int, P_numtype = double, int N_rank = 1](((const long int&)((const long int*)(& idx_l))))? /usr/lib/python2.5/site-packages/scipy/weave/scxx/object.h:179: note: candidates are: py::object& py::object::operator=(const py::object&) /home/mpenning/.python25_compiled/sc_948b3eed0cf550344f0bcefdd75e62940.cpp:748: error: no match for ?operator+? in ?values.blitz::Array<T, N>::operator[] [with T_indexContainer = long int, P_numtype = double, int N_rank = 1](((const long int&)((const long int*)(& idx_l)))) + values.blitz::Array<T, N>::operator[] [with T_indexContainer = long int, P_numtype = double, int N_rank = 1](((const long int&)((const long int*)(&(idx_l + 1l)))))? Traceback (most recent call last): File "reverse.py", line 1177, in <module> long_stats = stat_cache(sig,current) File "reverse.py", line 64, in __init__ self.create_stat('t_l_std_diff_vel600_7200_enter',fn,sig,current,300) File "reverse.py", line 113, in create_stat self.stats[fnkey] = func(sig,current) File "reverse.py", line 63, in <lambda> fn = lambda sig,current: pct(sig['fut_std_diff_600_median_600_vel600'][sig['fut_std_diff_600_median_600_vel600']>0],1,15,current,7200) File "reverse.py", line 934, in pct return cpctl(array.truncate(before=current-dt.timedelta(seconds=backdelta),after=current).valid().values,value) File "reverse.py", line 899, in cpctl compiler = 'gcc') File "/usr/lib/python2.5/site-packages/scipy/weave/inline_tools.py", line 355, in inline **kw) File "/usr/lib/python2.5/site-packages/scipy/weave/inline_tools.py", line 482, in compile_function verbose=verbose, **kw) File "/usr/lib/python2.5/site-packages/scipy/weave/ext_tools.py", line 367, in compile verbose = verbose, **kw) File "/usr/lib/python2.5/site-packages/scipy/weave/build_tools.py", line 273, in build_extension setup(name = module_name, ext_modules = [ext],verbose=verb) File "/usr/lib/python2.5/site-packages/numpy/distutils/core.py", line 186, in setup return old_setup(**new_attr) File "/usr/lib/python2.5/distutils/core.py", line 168, in setup raise SystemExit, "error: " + str(msg) scipy.weave.build_tools.CompileError: error: Command "g++ -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -fPIC -I/usr/lib/python2.5/site-packages/scipy/weave -I/usr/lib/python2.5/site-packages/scipy/weave/scxx -I/usr/lib/python2.5/site-packages/scipy/weave/blitz -I/usr/lib/python2.5/site-packages/numpy/core/include -I/usr/include/python2.5 -c /home/mpenning/.python25_compiled/sc_948b3eed0cf550344f0bcefdd75e62940.cpp -o /tmp/mpenning/python25_intermediate/compiler_0308e7b8c023f1021702bfe033c392a4/home/mpenning/.python25_compiled/sc_948b3eed0cf550344f0bcefdd75e62940.o" failed with exit status 1 [mpenning@Bucksnort data]$ ===

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Extremely slow scipy.sparse lil_diags - any walkaround?
by Dmitrey 28 Jan '11

28 Jan '11

The following script takes 26 sec on my computer and consumes several hundreds MB RAM. from numpy import ones from time import time import scipy.sparse as SP N = 10**6 a =ones(N) t = time() SP.lil_diags([a], [0], (N,N)) print('time elapsed: ' + str(time()-t)) Can I somehow in other way create a scipy.sparse format matrix from the single diagonal? Thank you in advance, D.

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Redundancy in SciPy
by Nicolò Perino 28 Jan '11

28 Jan '11

Hi, do you know how SciPy (or numpy) is redundant? For example if there are many way to initialize the same object or to compute some operations in different way (using different method calls). Thanks. Nicolò Perino ______ PhD Student @ USI - Faculty of Informatics http://www.people.usi.ch/perinon/

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Re: [SciPy-User] matplotlib installation
by Joon Ro 27 Jan '11

27 Jan '11

Hi, Why don't you just goto yast -> software management and install them? openSUSE's powerful package manager would do those things for you.It will take care of all the dependency problems. Just add the science repository (you can do this in the software management as well) and search for matplotlib, and install python-matplotlib and python-matplotlib-tk or python-matplotlib-wx. In addition, I believe the science and education repo and have pretty much all the scientific python packages you might need. -Joon On Wed, 26 Jan 2011 22:52:20 -0600, <scipy-user-request(a)scipy.org> wrote: > ------------------------------ > > Message: 3 > Date: Fri, 21 Jan 2011 14:41:11 +0000 > From: "Wang, Xiao" <Xiao.Wang(a)liverpool.ac.uk> > Subject: [SciPy-User] matplotlib installation > To: "'scipy-user(a)scipy.org'" <scipy-user(a)scipy.org> > Message-ID: > <FA6EDB7A8437F241A8B826FAF9953FE52434E9B2B5(a)STAFFMBX2.livad.liv.ac.uk> > Content-Type: text/plain; charset="iso-8859-1" > > Hello, > > I am trying to install matplotlib in my openSuSE 11.3 system, but > encountered a problem. I look your documentation from the link of > http://scipy.org/Installing_SciPy/Linux#head-3dbbf9abe395e974d3ec911ae56863…. > I followed the section of openSUSE to access > http://download.opensuse.org/repositories/science/openSUSE_11.3/src/ and > downloaded python-matplotlib-1.0.0-19.2.i586.rpm. when I ran rpm, I got > warning. > > The message is displayed at below: > > # rpm -U python-matplotlib-1.0.0-19.2.i586.rpm > # warning: python-matplotlib-1.0.0-19.2.i586.rpm: Header V3 DSA/SHA1 > Signature, key ID 943d8bb8: NOKEY > # error: Failed dependencies: > Python-configobj is needed by python-matplotlib-1.0.0-19.2.i586 > Python-dateutil is needed by python-matplotlib-1.0.0-19.2.i586 > Python-tk is needed by python-matplotlib-1.0.0-19.2.i586 > > So I downloaded python-tz-2006p-1.2.i586.rpm from the above link and > installed. But where can I find out rpm of python-configobj and > python-dateutil? > > > Thanks in advance, > > Xiao > > > >

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Re: [SciPy-User] SciPy-User Digest, Vol 89, Issue 52
by Fang Xu 27 Jan '11

27 Jan '11

Hi， Thank you. I checked there is no openoffice or libreoffice. and no problem with libpython2.6.so.1.0. Best On Thu, Jan 27, 2011 at 7:00 PM, <scipy-user-request(a)scipy.org> wrote: > Send SciPy-User mailing list submissions to > scipy-user(a)scipy.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://mail.scipy.org/mailman/listinfo/scipy-user > or, via email, send a message with subject or body 'help' to > scipy-user-request(a)scipy.org > > You can reach the person managing the list at > scipy-user-owner(a)scipy.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of SciPy-User digest..." > > > Today's Topics: > > 1. Re: error of compiling scipy on x86_64 linux cluster > (Bruce Southey) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 27 Jan 2011 10:02:38 -0600 > From: Bruce Southey <bsouthey(a)gmail.com> > Subject: Re: [SciPy-User] error of compiling scipy on x86_64 linux > cluster > To: scipy-user(a)scipy.org > Message-ID: <4D41971E.7000309(a)gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > On 01/27/2011 09:27 AM, Fang Xu wrote: > > Hi all, > > > > I managed to compile numpy, but there're some errors of compiling > > scipy. > > > > computer information: Linux node008 2.6.18.2-34-default #1 SMP Mon > > Nov 27 11:46:27 UTC 2006 x86_64 x86_64 x86_64 GNU/Linux > > > > OS: openSUSE 10.2 (X86-64) > > > > kernel: 2.6.18.2-34-default > > > > python-2.6 > > > > error message: > > > > Traceback (most recent call last): > > File "setup.py", line 160, in <module> > > setup_package() > > File "setup.py", line 127, in setup_package > > from numpy.distutils.core import setup > > File > > > "/projects/AlyssaMaster2008/ext/lib64/python2.6/site-packages/numpy/__init__.py", > > line 136, in <module> > > import add_newdocs > > File > > > "/projects/AlyssaMaster2008/ext/lib64/python2.6/site-packages/numpy/add_newdocs.py", > > line 9, in <module> > > from numpy.lib import add_newdoc > > File > > > "/projects/AlyssaMaster2008/ext/lib64/python2.6/site-packages/numpy/lib/__init__.py", > > line 4, in <module> > > from type_check import * > > File > > > "/projects/AlyssaMaster2008/ext/lib64/python2.6/site-packages/numpy/lib/type_check.py", > > line 8, in <module> > > import numpy.core.numeric as _nx > > File > > > "/projects/AlyssaMaster2008/ext/lib64/python2.6/site-packages/numpy/core/__init__.py", > > line 5, in <module> > > import multiarray > > /*ImportError: libpython2.6.so.1.0: cannot open shared object file: No > > such file or directory*/ > > > > I have been digging the web for a while, but didn't come with > > solution. Could you help me ? Thank you. > > > > Best > > Fang > > > > > > _______________________________________________ > > SciPy-User mailing list > > SciPy-User(a)scipy.org > > http://mail.scipy.org/mailman/listinfo/scipy-user > Out of curiosity, do you have openoffice or libreoffice installed? > I do not recall the exact problem or solution but it related to > incorrect usage of shared libraries. > > If you do search for libpython such as some of the examples on my system: > $ locate libpython | grep so > /opt/libreoffice/basis3.3/program/libpython2.6.so > /opt/libreoffice/basis3.3/program/libpython2.6.so.1.0 > /usr/lib64/libpython2.7.so > /usr/lib64/libpython2.7.so.1.0 > /usr/lib64/libpython3.1.so > /usr/lib64/libpython3.1.so.1.0 > > The 2.7 and 3.1 versions are from the distro (F14) and 2.6 version from > the one I build myself. The other is from libreoffice and it probably > the one that is being found instead of the correct python library for > your system. > > Obviously removing or probably updating libreoffice (3.3 final was > released 2 days ago) would solve it. > > Bruce > >

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error of compiling scipy on x86_64 linux cluster
by Fang Xu 27 Jan '11

27 Jan '11

Hi all, I managed to compile numpy, but there're some errors of compiling scipy. computer information: Linux node008 2.6.18.2-34-default #1 SMP Mon Nov 27 11:46:27 UTC 2006 x86_64 x86_64 x86_64 GNU/Linux OS: openSUSE 10.2 (X86-64) kernel: 2.6.18.2-34-default python-2.6 error message: Traceback (most recent call last): File "setup.py", line 160, in <module> setup_package() File "setup.py", line 127, in setup_package from numpy.distutils.core import setup File "/projects/AlyssaMaster2008/ext/lib64/python2.6/site-packages/numpy/__init__.py", line 136, in <module> import add_newdocs File "/projects/AlyssaMaster2008/ext/lib64/python2.6/site-packages/numpy/add_newdocs.py", line 9, in <module> from numpy.lib import add_newdoc File "/projects/AlyssaMaster2008/ext/lib64/python2.6/site-packages/numpy/lib/__init__.py", line 4, in <module> from type_check import * File "/projects/AlyssaMaster2008/ext/lib64/python2.6/site-packages/numpy/lib/type_check.py", line 8, in <module> import numpy.core.numeric as _nx File "/projects/AlyssaMaster2008/ext/lib64/python2.6/site-packages/numpy/core/__init__.py", line 5, in <module> import multiarray *ImportError: libpython2.6.so.1.0: cannot open shared object file: No such file or directory* I have been digging the web for a while, but didn't come with solution. Could you help me ? Thank you. Best Fang

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future of maxentropy module (was: sparse rmatvec and maxentropy)
by Ralf Gommers 27 Jan '11

27 Jan '11

(excuse the cross-post, but this may be of interest to scipy-user and the scikits.learn crowd) On Sat, Jan 22, 2011 at 10:44 PM, <josef.pktd(a)gmail.com> wrote: > On Sat, Jan 22, 2011 at 8:50 AM, Ralf Gommers > <ralf.gommers(a)googlemail.com> wrote: > > On Thu, Jan 20, 2011 at 10:13 PM, Skipper Seabold <jsseabold(a)gmail.com> > > wrote: > >> > >> I picked up the montecarlo code when I was playing around with these. > >> > >> > http://bazaar.launchpad.net/~jsseabold/statsmodels/statsmodels-skipper-maxe…<http://bazaar.launchpad.net/%7Ejsseabold/statsmodels/statsmodels-skipper-ma…> > >> > >> I'm curious if the maxentropy stuff as it is in scipy wouldn't find > >> more use and maintenance in scikits.learn. The implementation is > >> somewhat use specific (natural language processing), though this is > >> not by any means set in stone. > >> > > Probably, but wouldn't it need a lot of work before it could be moved? It > > has a grand total of one test, mostly non-working examples, and is > obviously > > hardly used at all (see r6919 and r6920 for more examples of broken > code). > > > > Perhaps it's worth asking the scikits.learn guys, and otherwise consider > > deprecating it if they're not interested? > > I haven't seen or heard anyone using it besides Skipper. There are > also still some features that where designed for pysparse and never > fully updated to scipy.sparse. > http://projects.scipy.org/scipy/ticket/856 > > I also thought deprecating and removing maxentropy will be the best > idea, if nobody volunteers to give it a workout. > So I guess we just have to ask this out loud: is anyone using the scipy.maxentropy module or interested in doing so? If you are, would you be interested in putting some work into it, like making the examples work and adding some tests? The current status is that 3 out of 4 examples are broken, the module has only a single test, and from broken code that went unnoticed for a long time it is clear that there are very few users. If no one steps up, I propose to deprecate the module for the 0.10 release. If there are any users out there that missed this email and step up then, we can always un-deprecate again. To the scikits.learn developers: would this code fit better and see more use in scikits.learn than in scipy? Would you be interested to pick it up? Ralf

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matplotlib installation
by Wang, Xiao 26 Jan '11

26 Jan '11

Hello, I am trying to install matplotlib in my openSuSE 11.3 system, but encountered a problem. I look your documentation from the link of http://scipy.org/Installing_SciPy/Linux#head-3dbbf9abe395e974d3ec911ae56863…. I followed the section of openSUSE to access http://download.opensuse.org/repositories/science/openSUSE_11.3/src/ and downloaded python-matplotlib-1.0.0-19.2.i586.rpm. when I ran rpm, I got warning. The message is displayed at below: # rpm -U python-matplotlib-1.0.0-19.2.i586.rpm # warning: python-matplotlib-1.0.0-19.2.i586.rpm: Header V3 DSA/SHA1 Signature, key ID 943d8bb8: NOKEY # error: Failed dependencies: Python-configobj is needed by python-matplotlib-1.0.0-19.2.i586 Python-dateutil is needed by python-matplotlib-1.0.0-19.2.i586 Python-tk is needed by python-matplotlib-1.0.0-19.2.i586 So I downloaded python-tz-2006p-1.2.i586.rpm from the above link and installed. But where can I find out rpm of python-configobj and python-dateutil? Thanks in advance, Xiao

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