General question on scipy
Hi, I am relative new to python, but I would like to use python for post-processing of data etc. I am using a LINUX machine with python installed on it, but to use if for scientific analysis and creating pictures etc. I need to install: matplotlib, numpy, scipy. It was quite difficult to install matplotlib and compile it against numpy (or something like that), but now I really would like to have a package that can handle matrix calculations (e.g. matrix multiplication, singular value decomosition) and similar. The package then I need to install is: scipy. So I tried to install scipy, but, as I expected, it does not work (multiple libraries are not found). The whole error message is attached to the end of the email. My question: Why do I need to install additional packages? Isn't it possible to code them up in scipy and use pure python for this? Or is it for computational reasons (to put computative intense calculations in C or whatever)? Or do most of the functions not yet exist in scipy (because its version 0.XX)? What is the reason for not having an entire-pure-python extension to python.numpy? My second question: How to install scipy? What packages are missing? I am sure I have numpy installed correctly, but I failes installing LAPACK, which error-message is here: g77 aladhd.o alaerh.o alaesm.o alahd.o alareq.o alasum.o alasvm.o chkxer.o icopy.o ilaenv.o xlaenv.o xerbla.o slaord.o schkaa.o schkeq.o schkgb.o schkge.o schkgt.o schklq.o schkpb.o schkpo.o schkpp.o schkpt.o schkq3.o schkql.o schkqp.o schkqr.o schkrq.o schksp.o schksy.o schktb.o schktp.o schktr.o schktz.o sdrvgb.o sdrvge.o sdrvgt.o sdrvls.o sdrvpb.o sdrvpo.o sdrvpp.o sdrvpt.o sdrvsp.o sdrvsy.o serrge.o serrgt.o serrlq.o serrls.o serrpo.o serrql.o serrqp.o serrqr.o serrrq.o serrsy.o serrtr.o serrtz.o serrvx.o sgbt01.o sgbt02.o sgbt05.o sgelqs.o sgeqls.o sgeqrs.o sgerqs.o sget01.o sget02.o sget03.o sget04.o sget06.o sget07.o sgtt01.o sgtt02.o sgtt05.o slaptm.o slarhs.o slatb4.o slattb.o slattp.o slattr.o slavsp.o slavsy.o slqt01.o slqt02.o slqt03.o spbt01.o spbt02.o spbt05.o spot01.o spot02.o spot03.o spot05.o sppt01.o sppt02.o sppt03.o sppt05.o sptt01.o sptt02.o sptt05.o sqlt01.o sqlt02.o sqlt03.o sqpt01.o sqrt01.o sqrt02.o sqrt03.o sqrt11.o sqrt12.o sqrt13.o sqrt14.o sqrt15.o sqrt16.o sqrt17.o srqt01.o srqt02.o srqt03.o srzt01.o srzt02.o sspt01.o ssyt01.o stbt02.o stbt03.o stbt05.o stbt06.o stpt01.o stpt02.o stpt03.o stpt05.o stpt06.o strt01.o strt02.o strt03.o strt05.o strt06.o stzt01.o stzt02.o \ ../../tmglib_LINUX.a ../../lapack_LINUX.a ../../blas_LINUX.a -o ../xlintsts g77: ../../blas_LINUX.a: No such file or directory
(because there is no blas_LINUX.a file, only lapack_LINUX.a and blas_LINUX.a...)
Thanks Alex ===== ERROR message === kl_info: libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE fftw3_info: libraries fftw3 not found in /usr/local/lib libraries fftw3 not found in /usr/lib fftw3 not found NOT AVAILABLE fftw2_info: libraries rfftw,fftw not found in /usr/local/lib libraries rfftw,fftw not found in /usr/lib fftw2 not found NOT AVAILABLE dfftw_info: libraries drfftw,dfftw not found in /usr/local/lib libraries drfftw,dfftw not found in /usr/lib dfftw not found NOT AVAILABLE djbfft_info: NOT AVAILABLE blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries lapack,blas not found in /usr/local/lib libraries lapack,blas not found in /usr/lib/sse2 libraries lapack,blas not found in /usr/lib NOT AVAILABLE atlas_blas_info: libraries lapack,blas not found in /usr/local/lib libraries lapack,blas not found in /usr/lib/sse2 libraries lapack,blas not found in /usr/lib NOT AVAILABLE /usr/lib/python2.4/site-packages/numpy/distutils/system_info.py:1301: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) blas_info: libraries blas not found in /usr/local/lib libraries blas not found in /usr/lib NOT AVAILABLE /usr/lib/python2.4/site-packages/numpy/distutils/system_info.py:1310: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. warnings.warn(BlasNotFoundError.__doc__) blas_src_info: NOT AVAILABLE /usr/lib/python2.4/site-packages/numpy/distutils/system_info.py:1313: UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. warnings.warn(BlasSrcNotFoundError.__doc__) Traceback (most recent call last): File "setup.py", line 55, in ? setup_package() File "setup.py", line 47, in setup_package configuration=configuration ) File "/usr/lib/python2.4/site-packages/numpy/distutils/core.py", line 144, in setup config = configuration() File "setup.py", line 19, in configuration config.add_subpackage('Lib') File "/usr/lib/python2.4/site-packages/numpy/distutils/misc_util.py", line 765, in add_subpackage caller_level = 2) File "/usr/lib/python2.4/site-packages/numpy/distutils/misc_util.py", line 748, in get_subpackage caller_level = caller_level + 1) File "/usr/lib/python2.4/site-packages/numpy/distutils/misc_util.py", line 695, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "./Lib/setup.py", line 7, in configuration config.add_subpackage('integrate') File "/usr/lib/python2.4/site-packages/numpy/distutils/misc_util.py", line 765, in add_subpackage caller_level = 2) File "/usr/lib/python2.4/site-packages/numpy/distutils/misc_util.py", line 748, in get_subpackage caller_level = caller_level + 1) File "/usr/lib/python2.4/site-packages/numpy/distutils/misc_util.py", line 695, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "Lib/integrate/setup.py", line 11, in configuration blas_opt = get_info('blas_opt',notfound_action=2) File "/usr/lib/python2.4/site-packages/numpy/distutils/system_info.py", line 256, in get_info return cl().get_info(notfound_action) File "/usr/lib/python2.4/site-packages/numpy/distutils/system_info.py", line 403, in get_info raise self.notfounderror,self.notfounderror.__doc__ numpy.distutils.system_info.NotFoundError: Some third-party program or library is not found.
Alexander Dietz wrote:
Hi,
I am relative new to python, but I would like to use python for post-processing of data etc. I am using a LINUX machine with python installed on it, but to use if for scientific analysis and creating pictures etc. I need to install: matplotlib, numpy, scipy. It was quite difficult to install matplotlib and compile it against numpy (or something like that), but now I really would like to have a package that can handle matrix calculations ( e.g. matrix multiplication, singular value decomosition) and similar. The package then I need to install is: scipy.
What distribution are you using? For ubuntu e.g. all third-party libraries are available and building numpy/scipy is as simple as cooking tea.
So I tried to install scipy, but, as I expected, it does not work (multiple libraries are not found). The whole error message is attached to the end of the email. My question: Why do I need to install additional packages? Isn't it possible to code them up in scipy and use pure python for this? Or is it for computational reasons (to put computative intense calculations in C or whatever)? Or do most of the functions not yet exist in scipy (because its version 0.XX)? What is the reason for not having an entire-pure-python extension to python.numpy?
Speed. Andd the fact that most of the algorithms have been coded in fortran many years ago and are known to be stable and good, I think. I would like to point you to http://www.scipy.org/Installing_SciPy but unfortunately that link is dead currently. Can somebody please fix it. Once on SuSE I build lapack/atlas based on those instructions and everything went fine.
My second question: How to install scipy? What packages are missing? I am sure I have numpy installed correctly, but I failes installing LAPACK, which error-message is here:
For numpy no third party libs are needed as there is a 'light' version of blas included. For scipy you need either blas/lapack or atlas and the fftw libs if you want to use the fft package. So maybe wait until the webpage mentioned above is back and try again. Christian
Christian K wrote:
Alexander Dietz wrote:
My second question: How to install scipy? What packages are missing? I am sure I have numpy installed correctly, but I failes installing LAPACK, which error-message is here:
For numpy no third party libs are needed as there is a 'light' version of blas included. For scipy you need either blas/lapack or atlas and the fftw libs if you want to use the fft package. fftw is not required: if you have it, it will be used, but you can install scipy without it.
Alexander, the most needed information from you to help is your distribution and architecture (eg x86, x86_64, other, etc...). David
Hi, here is what I am using exactly: FC5 and Linux 2.6.20-1.2316.fc5smp. Hope this helps. Can I install scipy (and all the dependend libraries) using 'yum' or something similar? 'yum' itself does not work... Cheers Alex On 6/29/07, David Cournapeau <david@ar.media.kyoto-u.ac.jp> wrote:
Alexander Dietz wrote:
My second question: How to install scipy? What packages are missing? I am sure I have numpy installed correctly, but I failes installing LAPACK, which error-message is here:
For numpy no third party libs are needed as there is a 'light' version of blas included. For scipy you need either blas/lapack or atlas and the fftw
Christian K wrote: libs if
you want to use the fft package. fftw is not required: if you have it, it will be used, but you can install scipy without it.
Alexander, the most needed information from you to help is your distribution and architecture (eg x86, x86_64, other, etc...).
David _______________________________________________ SciPy-user mailing list SciPy-user@scipy.org http://projects.scipy.org/mailman/listinfo/scipy-user
Alexander Dietz wrote:
Hi,
here is what I am using exactly: FC5 and Linux 2.6.20-1.2316.fc5smp. Hope this helps. Can I install scipy (and all the dependend libraries) using 'yum' or something similar? 'yum' itself does not work... What do you mean by yum does not work ? I have packaged numpy and scipy for FC 5 over there:
http://software.opensuse.org/download/home:/ashigabou/Fedora_Extras_5/ (more details instructions are on the scipy webpage, which unfortunately is down right now) David
2007/6/29, Alexander Dietz <Alexander.Dietz@astro.cf.ac.uk>:
Hi,
here is what I am using exactly: FC5 and Linux 2.6.20-1.2316.fc5smp. Hope this helps. Can I install scipy (and all the dependend libraries) using 'yum' or something similar? 'yum' itself does not work...
Cheers Alex
yum install numpy yum install scipy But FC5's scipy is old IIRC, can you update to FC 6 at least ? Matthieu
Hi, here is my try: # yum install scipy Loading "installonlyn" plugin Setting up Install Process .... ..... No Match for argument: scipy Nothing to do So there is no scipy found or so. Cheers Alex On 6/29/07, Matthieu Brucher <matthieu.brucher@gmail.com> wrote:
2007/6/29, Alexander Dietz <Alexander.Dietz@astro.cf.ac.uk>:
Hi,
here is what I am using exactly: FC5 and Linux 2.6.20-1.2316.fc5smp. Hope this helps. Can I install scipy (and all the dependend libraries) using 'yum' or something similar? 'yum' itself does not work...
Cheers Alex
yum install numpy yum install scipy
But FC5's scipy is old IIRC, can you update to FC 6 at least ?
Matthieu
_______________________________________________ SciPy-user mailing list SciPy-user@scipy.org http://projects.scipy.org/mailman/listinfo/scipy-user
try python-scipy (or even more better, yum search scipy to find the real name of the package) Matthieu 2007/6/29, Alexander Dietz <Alexander.Dietz@astro.cf.ac.uk>:
Hi,
here is my try:
# yum install scipy Loading "installonlyn" plugin Setting up Install Process .... ..... No Match for argument: scipy Nothing to do
So there is no scipy found or so.
Cheers Alex
On 6/29/07, Matthieu Brucher <matthieu.brucher@gmail.com> wrote:
2007/6/29, Alexander Dietz < Alexander.Dietz@astro.cf.ac.uk>:
Hi,
here is what I am using exactly: FC5 and Linux 2.6.20-1.2316.fc5smp. Hope this helps. Can I install scipy (and all the dependend libraries) using 'yum' or something similar? 'yum' itself does not work...
Cheers Alex
yum install numpy yum install scipy
But FC5's scipy is old IIRC, can you update to FC 6 at least ?
Matthieu
_______________________________________________ SciPy-user mailing list SciPy-user@scipy.org http://projects.scipy.org/mailman/listinfo/scipy-user
_______________________________________________ SciPy-user mailing list SciPy-user@scipy.org http://projects.scipy.org/mailman/listinfo/scipy-user
Hi, I got it to work, finally, thanks to the back-online installing page. What I did was: yum install lapack-devel blas-devel cd scipy-0.5.2 python setup.py install >& install.log This finally worked. Thanks a lot for helping me installing scipy!!! Alex On 6/29/07, Matthieu Brucher <matthieu.brucher@gmail.com> wrote:
try python-scipy (or even more better, yum search scipy to find the real name of the package)
Matthieu
2007/6/29, Alexander Dietz < Alexander.Dietz@astro.cf.ac.uk>:
Hi,
here is my try:
# yum install scipy Loading "installonlyn" plugin Setting up Install Process .... ..... No Match for argument: scipy Nothing to do
So there is no scipy found or so.
Cheers Alex
On 6/29/07, Matthieu Brucher < matthieu.brucher@gmail.com> wrote:
2007/6/29, Alexander Dietz < Alexander.Dietz@astro.cf.ac.uk>:
Hi,
here is what I am using exactly: FC5 and Linux 2.6.20-1.2316.fc5smp. Hope this helps. Can I install scipy (and all the dependend libraries) using 'yum' or something similar? 'yum' itself does not work...
Cheers Alex
yum install numpy yum install scipy
But FC5's scipy is old IIRC, can you update to FC 6 at least ?
Matthieu
_______________________________________________ SciPy-user mailing list SciPy-user@scipy.org http://projects.scipy.org/mailman/listinfo/scipy-user
_______________________________________________ SciPy-user mailing list SciPy-user@scipy.org http://projects.scipy.org/mailman/listinfo/scipy-user
_______________________________________________ SciPy-user mailing list SciPy-user@scipy.org http://projects.scipy.org/mailman/listinfo/scipy-user
Hi, I tried to install scipy the same way on my laptop, but this time it did not work. I got an error this time: error: Command "/usr/bin/g77 -g -Wall -fno-second-underscore -fPIC -O2 -funroll-loops -march=i686 -mmmx -msse2 -msse -fomit-frame-pointer -malign-double -c -c Lib/fftpack/dfftpack/zfftb1.f -o build/temp.linux- i686-2.4/Lib/fftpack/dfftpack/zfftb1.o" failed with exit status 1 Any ideas? Cheers Alex On 6/29/07, Alexander Dietz <Alexander.Dietz@astro.cf.ac.uk> wrote:
Hi,
I got it to work, finally, thanks to the back-online installing page. What I did was:
yum install lapack-devel blas-devel cd scipy-0.5.2 python setup.py install >& install.log
This finally worked. Thanks a lot for helping me installing scipy!!!
Alex
On 6/29/07, Matthieu Brucher <matthieu.brucher@gmail.com > wrote:
try python-scipy (or even more better, yum search scipy to find the real name of the package)
Matthieu
2007/6/29, Alexander Dietz < Alexander.Dietz@astro.cf.ac.uk>:
Hi,
here is my try:
# yum install scipy Loading "installonlyn" plugin Setting up Install Process .... ..... No Match for argument: scipy Nothing to do
So there is no scipy found or so.
Cheers Alex
On 6/29/07, Matthieu Brucher < matthieu.brucher@gmail.com> wrote:
2007/6/29, Alexander Dietz < Alexander.Dietz@astro.cf.ac.uk>:
Hi,
here is what I am using exactly: FC5 and Linux 2.6.20-1.2316.fc5smp. Hope this helps. Can I install scipy (and all the dependend libraries) using 'yum' or something similar? 'yum' itself does not work...
Cheers Alex
yum install numpy yum install scipy
But FC5's scipy is old IIRC, can you update to FC 6 at least ?
Matthieu
_______________________________________________ SciPy-user mailing list SciPy-user@scipy.org http://projects.scipy.org/mailman/listinfo/scipy-user
_______________________________________________ SciPy-user mailing list SciPy-user@scipy.org http://projects.scipy.org/mailman/listinfo/scipy-user
_______________________________________________ SciPy-user mailing list SciPy-user@scipy.org http://projects.scipy.org/mailman/listinfo/scipy-user
On Tue, Jul 31, 2007 at 09:35:11PM +0100, Alexander Dietz wrote:
I got an error this time:
error: Command "/usr/bin/g77 -g -Wall -fno-second-underscore -fPIC -O2 -funroll-loops -march=i686 -mmmx -msse2 -msse -fomit-frame-pointer -malign-double -c -c Lib/fftpack/dfftpack/zfftb1.f -o build/temp.linux- i686-2.4/Lib/fftpack/dfftpack/zfftb1.o" failed with exit status 1
What happens if you type '/usr/bin/g77' on a command line? James
Hi, On 7/31/07, zunzun@zunzun.com <zunzun@zunzun.com> wrote:
On Tue, Jul 31, 2007 at 09:35:11PM +0100, Alexander Dietz wrote:
I got an error this time:
error: Command "/usr/bin/g77 -g -Wall -fno-second-underscore -fPIC -O2 -funroll-loops -march=i686 -mmmx -msse2 -msse -fomit-frame-pointer -malign-double -c -c Lib/fftpack/dfftpack/zfftb1.f -o build/temp.linux- i686-2.4/Lib/fftpack/dfftpack/zfftb1.o" failed with exit status 1
What happens if you type '/usr/bin/g77' on a command line?
I get the following output: f77: no input files (so this seems to work...) There were other suggestions on how to install scipy and numpy through rpm's, but when I tried it it screwed up all my installtion (e.g. some pieces of code did not work anymore). I removered everything, re-installed numpy 1.0.1 and matplotlib 0.90.1 successfully, and now trying to install scipy 0.5.2, but it fails with the above error. Below I attach for completeness the whole screen-dump when trying to install scipy. Thanks Alex
Alexander Dietz wrote:
Hi,
On 7/31/07, *zunzun@zunzun.com <mailto:zunzun@zunzun.com>* <zunzun@zunzun.com <mailto:zunzun@zunzun.com>> wrote:
On Tue, Jul 31, 2007 at 09:35:11PM +0100, Alexander Dietz wrote: > I got an error this time: > > error: Command "/usr/bin/g77 -g -Wall -fno-second-underscore -fPIC -O2 > -funroll-loops -march=i686 -mmmx -msse2 -msse -fomit-frame-pointer > -malign-double -c -c Lib/fftpack/dfftpack/zfftb1.f -o build/temp.linux- > i686-2.4/Lib/fftpack/dfftpack/zfftb1.o" failed with exit status 1
What happens if you type '/usr/bin/g77' on a command line?
I get the following output:
f77: no input files
(so this seems to work...)
There were other suggestions on how to install scipy and numpy through rpm's, but when I tried it it screwed up all my installtion ( e.g. some pieces of code did not work anymore). What was screwed up when you tried to install rpms ? What did not work anymore ?
David
participants (5)
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Alexander Dietz -
Christian K -
David Cournapeau -
Matthieu Brucher -
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