From F.L.Burton at udcf.gla.ac.uk Sat Jun 1 08:36:21 2002 From: F.L.Burton at udcf.gla.ac.uk (Francis Burton) Date: Sat, 01 Jun 2002 13:36:21 +0100 Subject: [SciPy-user] Equivalent of the X Public Access Mechanism Message-ID: <3.0.32.20020601133619.006b99c4@lenzie.cent.gla.ac.uk> At 10:51 14/05/02 -0400, Eric wrote: >You might also look into other methods that are currently available in Python. >You can expose Python functions to separate processes (even over the web) >through xml-rpc, SOAP, http, custom socket servers, etc. These are all >cross-platforms and often trivial to implement if you just need to expose a >single function. I discovered Systems Biology Workbench (SBW) that seems to do pretty much what I want. It has C, C++, Delphi and Java APIs - as well as Python, of course! http://www.cds.caltech.edu/erato/sbw/docs/index.html Francis From marimont at nxpdata.com Sun Jun 2 21:31:52 2002 From: marimont at nxpdata.com (David Marimont) Date: Sun, 02 Jun 2002 18:31:52 -0700 Subject: [SciPy-user] installation problem w/ scipy 0.2: flbas.so has undefined symbol srotmg_ Message-ID: <3CFAC708.60707@nxpdata.com> I just downloaded the CVS version of scipy (0.2.0_alpha_101.3442) and built and installed it without any apparent problems (after many false starts). When I try to import it, here's what happens: Python 2.2 (#1, Dec 24 2001, 15:43:58) [GCC 2.96 20000731 (Red Hat Linux 7.1 2.96-98)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import scipy exceptions.ImportError: /usr/local/lib/python2.2/site-packages/scipy/linalg/fblas.so: undefined symbol: srotmg_ >>> Does anyone know what's going wrong here? I've spent a little time poking through the archives to see what might be causing this problem, but nothing obvious popped up. I apologize if I missed the relevant message... David Marimont From pearu at cens.ioc.ee Mon Jun 3 02:57:17 2002 From: pearu at cens.ioc.ee (Pearu Peterson) Date: Mon, 3 Jun 2002 09:57:17 +0300 (EEST) Subject: [SciPy-user] installation problem w/ scipy 0.2: flbas.so has undefined symbol srotmg_ In-Reply-To: <3CFAC708.60707@nxpdata.com> Message-ID: On Sun, 2 Jun 2002, David Marimont wrote: > I just downloaded the CVS version of scipy (0.2.0_alpha_101.3442) and Reminder to scipy maintainers: this CVS version 0.2.0_alpha_101.3442 has been constant for two months already... > built and installed it without any apparent problems (after many false > starts). When I try to import it, here's what happens: > > Python 2.2 (#1, Dec 24 2001, 15:43:58) > [GCC 2.96 20000731 (Red Hat Linux 7.1 2.96-98)] on linux2 > Type "help", "copyright", "credits" or "license" for more information. > >>> import scipy > exceptions.ImportError: /usr/local/lib/python2.2/site-packages/scipy/linalg/fblas.so: undefined > symbol: srotmg_ > >>> > > Does anyone know what's going wrong here? I've spent a little time poking > through the archives to see what might be causing this problem, but nothing > obvious popped up. I apologize if I missed the relevant message... See the thread starting at http://www.scipy.org/site_content/mailman?fn=scipy-user/2002-May/000434.html Your problem is releated to incomplete BLAS library that some systems provide. I would suggest using ATLAS that would give upto 10 speed up compared to plain BLAS/LAPACK. HTH, Pearu From gvermeul at grenoble.cnrs.fr Mon Jun 3 02:59:40 2002 From: gvermeul at grenoble.cnrs.fr (Gerard Vermeulen) Date: Mon, 3 Jun 2002 08:59:40 +0200 Subject: [SciPy-user] installation problem w/ scipy 0.2: flbas.so has undefined symbol srotmg_ In-Reply-To: <3CFAC708.60707@nxpdata.com> References: <3CFAC708.60707@nxpdata.com> Message-ID: <200206030659.g536xkM09134@grenoble.cnrs.fr> On Monday 03 June 2002 03:31, David Marimont wrote: > I just downloaded the CVS version of scipy (0.2.0_alpha_101.3442) and > built and installed it without any apparent problems (after many false > starts). When I try to import it, here's what happens: > > Python 2.2 (#1, Dec 24 2001, 15:43:58) > [GCC 2.96 20000731 (Red Hat Linux 7.1 2.96-98)] on linux2 > Type "help", "copyright", "credits" or "license" for more information. > > >>> import scipy > > exceptions.ImportError: > /usr/local/lib/python2.2/site-packages/scipy/linalg/fblas.so: undefined > symbol: srotmg_ > > > Does anyone know what's going wrong here? I've spent a little time poking > through the archives to see what might be causing this problem, but nothing > obvious popped up. I apologize if I missed the relevant message... > Yes, srotmg_ is missing in the BLAS libraries that are included in LAPACK. You have to download http://netlib2.cs.utk.edu/blas/blas.tgz and rebuild BLAS to fix it. Regards - Gerard. From marimont at nxpdata.com Mon Jun 3 10:59:12 2002 From: marimont at nxpdata.com (David Marimont) Date: Mon, 03 Jun 2002 07:59:12 -0700 Subject: [SciPy-user] installation problem w/ scipy 0.2: flbas.so has undefined symbol srotmg_ References: Message-ID: <3CFB8440.9060906@nxpdata.com> Hmm... I did install ATLAS, and SciPy claimed it had found the libraries when I built it. But I may have installed ATLAS incorrectly -- I built it in /usr/local/src, and the installation step didn't put the ATLAS libraries in any of the usual places, so I just moved them manually to /usr/local/lib. (As you may have already guessed, I'm not a pro at this sort of thing.) Was there more I needed to do to complete the installation? Usually configure, build, install ends up putting the libraries someplace reasonable, so I was at something of a loss when the ATLAS install left them in /usr/local/src/. David Pearu Peterson wrote: > > > See the thread starting at > > http://www.scipy.org/site_content/mailman?fn=scipy-user/2002-May/000434.html > > Your problem is releated to incomplete BLAS library that some systems > provide. I would suggest using ATLAS that would give upto 10 speed up > compared to plain BLAS/LAPACK. > > HTH, > Pearu > > _______________________________________________ > SciPy-user mailing list > SciPy-user at scipy.net > http://www.scipy.net/mailman/listinfo/scipy-user > From pearu at cens.ioc.ee Mon Jun 3 11:15:07 2002 From: pearu at cens.ioc.ee (Pearu Peterson) Date: Mon, 3 Jun 2002 18:15:07 +0300 (EEST) Subject: [SciPy-user] installation problem w/ scipy 0.2: flbas.so has undefined symbol srotmg_ In-Reply-To: <3CFB8440.9060906@nxpdata.com> Message-ID: On Mon, 3 Jun 2002, David Marimont wrote: > Hmm... I did install ATLAS, and SciPy claimed it had found the libraries > when I built it. But I may have installed ATLAS incorrectly -- I built > it in /usr/local/src, and the installation step didn't put the ATLAS > libraries in any of the usual places, so I just moved them manually to > /usr/local/lib. (As you may have already guessed, I'm not a pro at > this sort of thing.) Was there more I needed to do to complete the > installation? Usually configure, build, install ends up putting the > libraries someplace reasonable, so I was at something of a loss when > the ATLAS install left them in /usr/local/src/. What is the output of python scipy_distutils/system_info.py ? Note that you can use ATLAS environment variable to indicate the location of atlas libraries. It is assumed that the corresponding directory will contain the following libraries: lapack f77blas cblas atlas where the lapack library *must* be also complete. See http://math-atlas.sourceforge.net/errata.html#completelp Pearu From marimont at nxpdata.com Mon Jun 3 11:30:37 2002 From: marimont at nxpdata.com (David Marimont) Date: Mon, 03 Jun 2002 08:30:37 -0700 Subject: [SciPy-user] installation problem w/ scipy 0.2: flbas.so has undefined symbol srotmg_ References: Message-ID: <3CFB8B9D.3080005@nxpdata.com> Here's what system_info.py tells me: atlas_info: FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/local/lib'] blas_info: FOUND: libraries = ['blas'] library_dirs = ['/usr/lib'] fftw_info: FOUND: libraries = ['fftw', 'rfftw', 'fftw_threads', 'rfftw_threads', 'sfftw', 'srfftw', 'sfftw_threads', 'srfftw_threads'] library_dirs = ['/usr/local/lib'] define_macros = [('SCIPY_FFTW_H', 1), ('SCIPY_SFFTW_H', 1)] include_dirs = ['/usr/local/include'] lapack_info: FOUND: libraries = ['lapack'] library_dirs = ['/usr/local/lib'] x11_info: FOUND: libraries = ['X11'] library_dirs = ['/usr/X11R6/lib'] include_dirs = ['/usr/X11R6/include'] > Note that you can use ATLAS environment variable to indicate the location > of atlas libraries. It is assumed that the corresponding directory will > contain the following libraries: > > lapack f77blas cblas atlas > > where the lapack library *must* be also complete. See > > http://math-atlas.sourceforge.net/errata.html#completelp > Can you tell from the lapack info above whether my lapack library is complete? If not, I'll go ahead and do what the "completelp" URL says to do. This is all pretty complicated! Thanks a lot for your help. David From pearu at cens.ioc.ee Mon Jun 3 11:46:43 2002 From: pearu at cens.ioc.ee (Pearu Peterson) Date: Mon, 3 Jun 2002 18:46:43 +0300 (EEST) Subject: [SciPy-user] installation problem w/ scipy 0.2: flbas.so has undefined symbol srotmg_ In-Reply-To: <3CFB8B9D.3080005@nxpdata.com> Message-ID: On Mon, 3 Jun 2002, David Marimont wrote: > Here's what system_info.py tells me: > > > atlas_info: > FOUND: > libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] > library_dirs = ['/usr/local/lib'] This looks OK and SciPy should use it. > > Note that you can use ATLAS environment variable to indicate the location > > of atlas libraries. It is assumed that the corresponding directory will > > contain the following libraries: > > > > lapack f77blas cblas atlas > > > > where the lapack library *must* be also complete. See > > > > http://math-atlas.sourceforge.net/errata.html#completelp > > > > Can you tell from the lapack info above whether my lapack library is > complete? Not directly. `ls -l /usr/local/lib/libatlas.a' would be more informative (the size of libatlas.a should be about 5.8MB) but since you are asking, I conclude that your lapack library is not complete. A good place to copy the atlas libraries would be /usr/local/lib/atlas where SciPy also looks for. > If not, I'll go ahead and do what the "completelp" URL says to do. Go ahead. > This is all pretty complicated! Thanks a lot for your help. Yes, but hopefully you'll need to do that only once ;-) Pearu From pearu at cens.ioc.ee Mon Jun 3 11:51:09 2002 From: pearu at cens.ioc.ee (Pearu Peterson) Date: Mon, 3 Jun 2002 18:51:09 +0300 (EEST) Subject: [SciPy-user] installation problem w/ scipy 0.2: flbas.so has undefined symbol srotmg_ In-Reply-To: Message-ID: On Mon, 3 Jun 2002, Pearu Peterson wrote: > Not directly. `ls -l /usr/local/lib/libatlas.a' would be more informative > (the size of libatlas.a should be about 5.8MB) but since you are asking, > I conclude that your lapack library is not complete. I meant ls -l /usr/local/lib/liblapack.a and the size should be about 6MB. Pearu From marimont at nxpdata.com Mon Jun 3 11:58:10 2002 From: marimont at nxpdata.com (David Marimont) Date: Mon, 03 Jun 2002 08:58:10 -0700 Subject: [SciPy-user] installation problem w/ scipy 0.2: flbas.so has undefined symbol srotmg_ References: Message-ID: <3CFB9212.6000002@nxpdata.com> > On Mon, 3 Jun 2002, Pearu Peterson wrote: > > >> Not directly. `ls -l /usr/local/lib/libatlas.a' would be more informative >> (the size of libatlas.a should be about 5.8MB) but since you are asking, >> I conclude that your lapack library is not complete. > > > I meant > > ls -l /usr/local/lib/liblapack.a > > and the size should be about 6MB. > Well, my liblapack.a is only 315KB -- apparently not very complete! My libatlas.a is 5.5MB, which I find more encouraging. So... I'm off to install the more complete lapack. Thanks again. David From marimont at nxpdata.com Mon Jun 3 14:44:32 2002 From: marimont at nxpdata.com (David Marimont) Date: Mon, 03 Jun 2002 11:44:32 -0700 Subject: [SciPy-user] installation problem w/ scipy 0.2: flbas.so has undefined symbol srotmg_ References: Message-ID: <3CFBB910.4000204@nxpdata.com> I built and installed the complete lapack library (AFAIK), rebuilt atlas and scipy, and I'm still getting errors. Here's what happens where I try to import scipy: [marimont at serenity scipy_distutils]$ python Python 2.2 (#1, Dec 24 2001, 15:43:58) [GCC 2.96 20000731 (Red Hat Linux 7.1 2.96-98)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import scipy exceptions.ImportError: /usr/local/lib/python2.2/site-packages/scipy/linalg/flapack.so: undefined symbol: sgesdd_ exceptions.ImportError: /usr/local/lib/python2.2/site-packages/scipy/linalg/_flinalg.so: undefined symbol: dlaswp_ Traceback (most recent call last): File "", line 1, in ? File "/usr/local/lib/python2.2/site-packages/scipy/__init__.py", line 42, in ? import special, io, linalg, stats, fftpack File "/usr/local/lib/python2.2/site-packages/scipy/special/__init__.py", line 325, in ? import orthogonal File "/usr/local/lib/python2.2/site-packages/scipy/special/orthogonal.py", line 59, in ? from scipy.linalg import eig File "/usr/local/lib/python2.2/site-packages/scipy/linalg/__init__.py", line 40, in ? from basic import * File "/usr/local/lib/python2.2/site-packages/scipy/linalg/basic.py", line 17, in ? import calc_lwork ImportError: /usr/local/lib/python2.2/site-packages/scipy/linalg/calc_lwork.so: undefined symbol: ieeeck_ >>> I noticed in the install file with the scipy distribution that I should include all sorts of version info when I ask for help -- it's below. The only strange thing I noticed is that when I build scipy, it only listed the atlas libraries as found, not the blas or lapack ones, but when I ask for system_info, the blas and lapack ones are listed. Does that mean that scipy isn't using the atlas versions? David [root at serenity root]# python -c 'import os,sys;print os.name,sys.platform' posix linux2 [root at serenity root]# uname -a Linux serenity 2.4.13 #1 SMP Fri Dec 21 20:53:17 PST 2001 i686 unknown [root at serenity root]# gcc -v Reading specs from /usr/lib/gcc-lib/i386-redhat-linux/2.96/specs gcc version 2.96 20000731 (Red Hat Linux 7.1 2.96-98) [root at serenity root]# g77 --version GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.1 2.96-98) Copyright (C) 1997 Free Software Foundation, Inc. For more version information on components of the GNU Fortran compilation system, especially useful when reporting bugs, type the command `g77 --verbose'. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING or type the command `info -f g77 Copying'. [root at serenity root]# python -c 'import sys;print sys.version' 2.2 (#1, Dec 24 2001, 15:43:58) [GCC 2.96 20000731 (Red Hat Linux 7.1 2.96-98)] [root at serenity root]# python -c 'import Numeric;print Numeric.__version__' 21.0 [root at serenity root]# f2py -v 2.13.175-1250 [root at serenity root]# python scipy_distutils/system_info.py python: can't open file 'scipy_distutils/system_info.py' [root at serenity root]# cd /usr/local/lib/python2.2/site-packages/ [root at serenity site-packages]# python scipy_distutils/system_info.py atlas_info: FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/local/lib'] blas_info: FOUND: libraries = ['blas'] library_dirs = ['/usr/lib'] fftw_info: FOUND: libraries = ['fftw', 'rfftw', 'fftw_threads', 'rfftw_threads', 'sfftw', 'srfftw', 'sfftw_threads', 'srfftw_threads'] library_dirs = ['/usr/local/lib'] define_macros = [('SCIPY_FFTW_H', 1), ('SCIPY_SFFTW_H', 1)] include_dirs = ['/usr/local/include'] lapack_info: FOUND: libraries = ['lapack'] library_dirs = ['/usr/local/lib'] x11_info: FOUND: libraries = ['X11'] library_dirs = ['/usr/X11R6/lib'] include_dirs = ['/usr/X11R6/include'] [root at serenity site-packages]# python scipy_distutils/command/build_flib.py command: f77 -V -c /tmp/__dummy.f -o /tmp/__dummy.o 256 f77: invalid version number format command: f77 -version 256 f77: unrecognized option `-version' /usr/lib/gcc-lib/i386-redhat-linux/2.96/libg2c.a(main.o): In function `main': main.o(.text+0x2a): undefined reference to `MAIN__' collect2: ld returned 1 exit status command: f90 -V 32512 sh: f90: command not found command: ifc -FI -V -c /tmp/__dummy.f -o /tmp/__dummy.o 32512 sh: ifc: command not found command: efc -FI -V -c /tmp/__dummy.f -o /tmp/__dummy.o 32512 sh: efc: command not found command: f95 -V 32512 sh: f95: command not found command: fort -V 32512 sh: fort: command not found command: DF /what 32512 sh: DF: command not found command: g77 --version 0 GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.1 2.96-98) Copyright (C) 1997 Free Software Foundation, Inc. For more version information on components of the GNU Fortran compilation system, especially useful when reporting bugs, type the command `g77 --verbose'. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING or type the command `info -f g77 Copying'. command: vf90 -v 32512 sh: vf90: command not found command: f90 +version 32512 sh: f90: command not found command: g77 --version 0 GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.1 2.96-98) Copyright (C) 1997 Free Software Foundation, Inc. For more version information on components of the GNU Fortran compilation system, especially useful when reporting bugs, type the command `g77 --verbose'. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING or type the command `info -f g77 Copying'. command: F -V 32512 sh: F: command not found command: g77 --version 0 GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.1 2.96-98) Copyright (C) 1997 Free Software Foundation, Inc. For more version information on components of the GNU Fortran compilation system, especially useful when reporting bugs, type the command `g77 --verbose'. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING or type the command `info -f g77 Copying'. Gnu 0.5.26 From pearu at cens.ioc.ee Mon Jun 3 15:09:20 2002 From: pearu at cens.ioc.ee (Pearu Peterson) Date: Mon, 3 Jun 2002 22:09:20 +0300 (EEST) Subject: [SciPy-user] installation problem w/ scipy 0.2: flbas.so has undefined symbol srotmg_ In-Reply-To: <3CFBB910.4000204@nxpdata.com> Message-ID: On Mon, 3 Jun 2002, David Marimont wrote: > I built and installed the complete lapack library (AFAIK), rebuilt > atlas and scipy, and I'm still getting errors. Here's what happens > where I try to import scipy: > > [marimont at serenity scipy_distutils]$ python > Python 2.2 (#1, Dec 24 2001, 15:43:58) > [GCC 2.96 20000731 (Red Hat Linux 7.1 2.96-98)] on linux2 > Type "help", "copyright", "credits" or "license" for more information. > >>> import scipy > exceptions.ImportError: /usr/local/lib/python2.2/site-packages/scipy/linalg/flapack.so: undefined > symbol: sgesdd_ How did you rebuilt scipy? It is possible that this flapack.so is from the previous built. I suggest `rm -rf build' and `python setup.py'. You can also check if a library contains a specific symbol using nm command. E.g. nm /usr/local/lib/liblapack.a | grep sgesdd should show something like sgesdd.o: 00000000 T sgesdd_ > I noticed in the install file with the scipy distribution that I > should include all sorts of version info when I ask for help -- it's > below. Thanks. > The only strange thing I noticed is that when I build scipy, > it only listed the atlas libraries as found, not the blas or lapack > ones, but when I ask for system_info, the blas and lapack ones are > listed. Does that mean that scipy isn't using the atlas versions? This is OK. When excecuting `python system_info.py', it will display all resources. But when building scipy, it finds atlas and therefore it does not need to check for blas or lapack libraries. If scipy build would not find atlas, then it would also look for blas/atlas libraries. > [root at serenity site-packages]# python scipy_distutils/system_info.py > atlas_info: > FOUND: > libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] > library_dirs = ['/usr/local/lib'] To make sure, when you rebuild atlas, did you installed it to /usr/local/lib or /usr/local/lib/atlas? If none of the hints above are helpful, could you explain exactly how did you built/installed lapack,atlas, and scipy. Outputs of command executions can be useful. Pearu From wjiang at blake.3dem.bioch.bcm.tmc.edu Mon Jun 3 17:00:54 2002 From: wjiang at blake.3dem.bioch.bcm.tmc.edu (Wen Jiang) Date: Mon, 03 Jun 2002 16:00:54 -0500 Subject: [SciPy-user] problem with scipy.cow Message-ID: <3CFBD906.4060903@blake.bcm.tmc.edu> hi, I am having problem to make scipy.cow work. Basically I could only be able to run cow.info() and others would fail. cow.start got stuck and I found it was trapped at is_running() call in cow.start(). I am using the 0.20 linux versions. Could anyone give me any suggestion how to solve this problem? Wen From gvermeul at grenoble.cnrs.fr Mon Jun 3 17:44:03 2002 From: gvermeul at grenoble.cnrs.fr (gvermeul at grenoble.cnrs.fr) Date: Mon, 3 Jun 2002 21:44:03 GMT Subject: [SciPy-user] installation problem w/ scipy 0.2: flbas.so has Message-ID: <200206032144.g53Li3M20987@grenoble.cnrs.fr> David, The LAPACK that comes with ATLAS is incomplete, you should merge it with you Fortran LAPACK into a combined "Fortran/Atlas" LAPACK, after building the ATLAS libs. There are instructions how to do this in the Doc directory (README.lib?) or see http://math-atlas.sourceforge.net/errata.html#completelp -- Start quote -- Building a complete LAPACK library ATLAS does not provide a full LAPACK library. However, there is a simple way to get ATLAS to provide its faster LAPACK routines to a full LAPACK library. ATLAS's internal routines are distinct from LAPACK's, so it is safe to compile ATLAS's LAPACK routines directly into a netlib-style LAPACK library. First, download and install the standard LAPACK library from the LAPACK homepage. Then, in your ATLAS/lib/ARCH directory (where you should have a liblapack.a), issue the following commands: mkdir tmp cd tmp ar x ../liblapack.a cp ../liblapack.a ar r ../liblapack.a *.o cd .. rm -rf tmp Just linking in ATLAS's liblapack.a first will not get you the best LAPACK performance, mainly because LAPACK's untuned ILAENV will be used instead of ATLAS's tuned one. So, if you use any LAPACK routine that is not provided by ATLAS, it is essential that you create this hybrid LAPACK/ATLAS library in order to get the best performance. -- End quote -- Gerard > I built and installed the complete lapack library (AFAIK), rebuilt atlas and scipy, and I'm > still getting errors. Here's what happens where I try to import scipy: > > [marimont at serenity scipy_distutils]$ python > Python 2.2 (#1, Dec 24 2001, 15:43:58) > [GCC 2.96 20000731 (Red Hat Linux 7.1 2.96-98)] on linux2 > Type "help", "copyright", "credits" or "license" for more information. > >>> import scipy > exceptions.ImportError: /usr/local/lib/python2.2/site-packages/scipy/linalg/flapack.so: undefined > symbol: sgesdd_ > exceptions.ImportError: /usr/local/lib/python2.2/site-packages/scipy/linalg/_flinalg.so: undefined > symbol: dlaswp_ > Traceback (most recent call last): > File "", line 1, in ? > File "/usr/local/lib/python2.2/site-packages/scipy/__init__.py", line 42, in ? > import special, io, linalg, stats, fftpack > File "/usr/local/lib/python2.2/site-packages/scipy/special/__init__.py", line 325, in ? > import orthogonal > File "/usr/local/lib/python2.2/site-packages/scipy/special/orthogonal.py", line 59, in ? > from scipy.linalg import eig > File "/usr/local/lib/python2.2/site-packages/scipy/linalg/__init__.py", line 40, in ? > from basic import * > File "/usr/local/lib/python2.2/site-packages/scipy/linalg/basic.py", line 17, in ? > import calc_lwork > ImportError: /usr/local/lib/python2.2/site-packages/scipy/linalg/calc_lwork.so: undefined symbol: > ieeeck_ > >>> > > I noticed in the install file with the scipy distribution that I should include all sorts > of version info when I ask for help -- it's below. The only strange thing I noticed is that > when I build scipy, it only listed the atlas libraries as found, not the blas or lapack ones, > but when I ask for system_info, the blas and lapack ones are listed. Does that mean that scipy > isn't using the atlas versions? > > David > > [root at serenity root]# python -c 'import os,sys;print os.name,sys.platform' > posix linux2 > [root at serenity root]# uname -a > Linux serenity 2.4.13 #1 SMP Fri Dec 21 20:53:17 PST 2001 i686 unknown > [root at serenity root]# gcc -v > Reading specs from /usr/lib/gcc-lib/i386-redhat-linux/2.96/specs > gcc version 2.96 20000731 (Red Hat Linux 7.1 2.96-98) > [root at serenity root]# g77 --version > GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.1 2.96-98) > Copyright (C) 1997 Free Software Foundation, Inc. > For more version information on components of the GNU Fortran > compilation system, especially useful when reporting bugs, > type the command `g77 --verbose'. > > GNU Fortran comes with NO WARRANTY, to the extent permitted by law. > You may redistribute copies of GNU Fortran > under the terms of the GNU General Public License. > For more information about these matters, see the file named COPYING > or type the command `info -f g77 Copying'. > [root at serenity root]# python -c 'import sys;print sys.version' > 2.2 (#1, Dec 24 2001, 15:43:58) > [GCC 2.96 20000731 (Red Hat Linux 7.1 2.96-98)] > [root at serenity root]# python -c 'import Numeric;print Numeric.__version__' > 21.0 > [root at serenity root]# f2py -v > 2.13.175-1250 > [root at serenity root]# python scipy_distutils/system_info.py > python: can't open file 'scipy_distutils/system_info.py' > [root at serenity root]# cd /usr/local/lib/python2.2/site-packages/ > [root at serenity site-packages]# python scipy_distutils/system_info.py > atlas_info: > FOUND: > libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] > library_dirs = ['/usr/local/lib'] > > blas_info: > FOUND: > libraries = ['blas'] > library_dirs = ['/usr/lib'] > > fftw_info: > FOUND: > libraries = ['fftw', 'rfftw', 'fftw_threads', 'rfftw_threads', 'sfftw', 'srfftw', > 'sfftw_threads', 'srfftw_threads'] > library_dirs = ['/usr/local/lib'] > define_macros = [('SCIPY_FFTW_H', 1), ('SCIPY_SFFTW_H', 1)] > include_dirs = ['/usr/local/include'] > > lapack_info: > FOUND: > libraries = ['lapack'] > library_dirs = ['/usr/local/lib'] > > x11_info: > FOUND: > libraries = ['X11'] > library_dirs = ['/usr/X11R6/lib'] > include_dirs = ['/usr/X11R6/include'] > > [root at serenity site-packages]# python scipy_distutils/command/build_flib.py > command: f77 -V -c /tmp/__dummy.f -o /tmp/__dummy.o > 256 f77: invalid version number format > command: f77 -version > 256 f77: unrecognized option `-version' > /usr/lib/gcc-lib/i386-redhat-linux/2.96/libg2c.a(main.o): In function `main': > main.o(.text+0x2a): undefined reference to `MAIN__' > collect2: ld returned 1 exit status > command: f90 -V > 32512 sh: f90: command not found > command: ifc -FI -V -c /tmp/__dummy.f -o /tmp/__dummy.o > 32512 sh: ifc: command not found > command: efc -FI -V -c /tmp/__dummy.f -o /tmp/__dummy.o > 32512 sh: efc: command not found > command: f95 -V > 32512 sh: f95: command not found > command: fort -V > 32512 sh: fort: command not found > command: DF /what > 32512 sh: DF: command not found > command: g77 --version > 0 GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.1 2.96-98) > Copyright (C) 1997 Free Software Foundation, Inc. > For more version information on components of the GNU Fortran > compilation system, especially useful when reporting bugs, > type the command `g77 --verbose'. > > GNU Fortran comes with NO WARRANTY, to the extent permitted by law. > You may redistribute copies of GNU Fortran > under the terms of the GNU General Public License. > For more information about these matters, see the file named COPYING > or type the command `info -f g77 Copying'. > command: vf90 -v > 32512 sh: vf90: command not found > command: f90 +version > 32512 sh: f90: command not found > command: g77 --version > 0 GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.1 2.96-98) > Copyright (C) 1997 Free Software Foundation, Inc. > For more version information on components of the GNU Fortran > compilation system, especially useful when reporting bugs, > type the command `g77 --verbose'. > > GNU Fortran comes with NO WARRANTY, to the extent permitted by law. > You may redistribute copies of GNU Fortran > under the terms of the GNU General Public License. > For more information about these matters, see the file named COPYING > or type the command `info -f g77 Copying'. > command: F -V > 32512 sh: F: command not found > command: g77 --version > 0 GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.1 2.96-98) > Copyright (C) 1997 Free Software Foundation, Inc. > For more version information on components of the GNU Fortran > compilation system, especially useful when reporting bugs, > type the command `g77 --verbose'. > > GNU Fortran comes with NO WARRANTY, to the extent permitted by law. > You may redistribute copies of GNU Fortran > under the terms of the GNU General Public License. > For more information about these matters, see the file named COPYING > or type the command `info -f g77 Copying'. > Gnu 0.5.26 > > _______________________________________________ > SciPy-user mailing list > SciPy-user at scipy.net > http://www.scipy.net/mailman/listinfo/scipy-user > --------------------------------------------- This message was sent using Endymion MailMan. http://www.endymion.com/products/mailman/ From marimont at nxpdata.com Tue Jun 4 00:31:15 2002 From: marimont at nxpdata.com (David Marimont) Date: Mon, 03 Jun 2002 21:31:15 -0700 Subject: [SciPy-user] installation problem w/ scipy 0.2: flbas.so has undefined symbol srotmg_ References: Message-ID: <3CFC4293.7080205@nxpdata.com> I finally installed it without error -- see below. Pearu Peterson wrote: > > How did you rebuilt scipy? It is possible that this flapack.so is from the > previous built. I suggest `rm -rf build' and `python setup.py'. Well, that sounds smarter than what I did, which was to rm the entire scipy directory and untar it again. I wanted to be sure that *everything* was gone. > If none of the hints above are helpful, could you explain exactly how did > you built/installed lapack,atlas, and scipy. Outputs of command executions > can be useful. A good suggestion -- when I went back over everything, I realized that I may have misinterpreted the instructions for building the complete atlas lapack library. As stupid as it sounds, I didn't realize that I was supposed to do the ar x stuff in the tmp directory *after* building atlas. I would have gotten the error the first time I tried doing it before building atlas if I hadn't already built atlas once already. This is the kind of mistake it's easy to make if (1) you have no idea what you're doing, and (2) are blindly following instructions! Anyway, once I did things in the right order, importing scipy didn't trigger any errors. Now I'm eager to see what I can do with it! After all this, I'm ready to write "Installing SciPy for Dummies." I know at least one person who would have found this useful. This list is great -- thanks to everyone who helped. David From eric at enthought.com Tue Jun 4 02:57:41 2002 From: eric at enthought.com (eric) Date: Tue, 4 Jun 2002 02:57:41 -0400 Subject: [SciPy-user] problem with scipy.cow References: <3CFBD906.4060903@blake.bcm.tmc.edu> Message-ID: <049701c20b95$1ef52490$6b01a8c0@ericlaptop> Hey Wen, SciPy has been through quite a bit of change since I last tested cow, and unfortunately it doesn't have unit tests. I'd like to look into it, but probably will not have time this week. Here are a few hints I can remember: The start up process sometimes runs into troubles because of issues with ssh. I remember debugging this by starting up individual servers on remote machines by hand instead of using start. Also, I'd try a simple test where you run a couple of servers on the local machine and see if start() works in this case. Use the actual IP number of the machine instead of 127.0.0.1, as the loop-back address was also problematic. hope that provides some clues. eric ----- Original Message ----- From: "Wen Jiang" To: Sent: Monday, June 03, 2002 5:00 PM Subject: [SciPy-user] problem with scipy.cow > hi, > I am having problem to make scipy.cow work. Basically I could only be > able to run cow.info() and others would fail. cow.start got stuck and I > found it was trapped at is_running() call in cow.start(). I am using the > 0.20 linux versions. > Could anyone give me any suggestion how to solve this problem? > > Wen > > _______________________________________________ > SciPy-user mailing list > SciPy-user at scipy.net > http://www.scipy.net/mailman/listinfo/scipy-user > From poornima_jain at hotmail.com Tue Jun 4 04:57:46 2002 From: poornima_jain at hotmail.com (poornima jain) Date: Tue, 04 Jun 2002 08:57:46 +0000 Subject: [SciPy-user] code Message-ID: Hi I Have stuck up with a project based on clustering using K-Means algorithm Please help me find the relevent C code for theK-Means algorithm Regards _________________________________________________________________ MSN Photos is the easiest way to share and print your photos: http://photos.msn.com/support/worldwide.aspx From doug at idsia.ch Tue Jun 4 09:37:20 2002 From: doug at idsia.ch (Douglas Eck) Date: Tue, 04 Jun 2002 15:37:20 +0200 Subject: [SciPy-user] plt.plot titles problem Message-ID: <3CFCC290.40703@idsia.ch> Hi Folks, Any idea how I might set the title of a plt.plot() from a python script? The menu works fine in the plot window but the plt.title('str') fails. I'm using debian with the scipy source from SciPy-0.2.0_alpha_101.3442_src.tar.gz >>> plt.plot(rand(1,10)) >>> plt.xlabel('hello') >>> plt.ylabel('hello') >>> plt.title('hello') Traceback (most recent call last): File "", line 1, in ? File "/usr/lib/python2.1/site-packages/scipy/plt/interface.py", line 136, in title _active.title.text = name TypeError: read-only attribute: text Regards, Doug Eck -- Dr. Douglas Eck, http://www.idsia.ch/~doug Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA) Neural Networks, Rhythm Perception and Production, Dynamical Systems From eric at enthought.com Tue Jun 4 11:29:38 2002 From: eric at enthought.com (eric) Date: Tue, 4 Jun 2002 11:29:38 -0400 Subject: [SciPy-user] code References: Message-ID: <002101c20bdc$a4b65a80$54d3fea9@ericlaptop> Only the vector quantization code is in C (well C++). Look in scipy/cluster/src/vq.h The k-means algorithm is all implemented in Python int the scipy/cluster/vq module. eric ----- Original Message ----- From: "poornima jain" To: Sent: Tuesday, June 04, 2002 4:57 AM Subject: [SciPy-user] code > Hi > > I Have stuck up with a project based on clustering using K-Means algorithm > Please help me find the relevent C code for theK-Means algorithm > > Regards > > > > > _________________________________________________________________ > MSN Photos is the easiest way to share and print your photos: > http://photos.msn.com/support/worldwide.aspx > > _______________________________________________ > SciPy-user mailing list > SciPy-user at scipy.net > http://www.scipy.net/mailman/listinfo/scipy-user > > From doug at idsia.ch Thu Jun 6 07:24:55 2002 From: doug at idsia.ch (Douglas Eck) Date: Thu, 06 Jun 2002 13:24:55 +0200 Subject: [SciPy-user] plot.plt speed Message-ID: <3CFF4687.7030305@idsia.ch> I need to plot 10 time series on the same plot window. But it's quite slow: plot.plt(rand(10,200)) takes 18 seconds. plot.plt(rand(1,2000)) takes less than one second There are some tricks for speeding up the first case in gnuplot by reshaping the array to be 1,2000 and adding a second array for the x values. [[1:200][1:200]....[1:200]]. But this has other problems. Any ideas? My timeseries are more on the order of (25,2500).... not pretty. Cheers, Doug -- Dr. Douglas Eck, http://www.idsia.ch/~doug Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA) Neural Networks, Rhythm Perception and Production, Dynamical Systems From Remco.Strijbos at jdsu.com Thu Jun 6 05:20:33 2002 From: Remco.Strijbos at jdsu.com (Remco.Strijbos at jdsu.com) Date: Thu, 6 Jun 2002 11:20:33 +0200 Subject: [SciPy-user] problems with scipy.io.readarray Message-ID: I try to read a file into an array in with from scipy import io x=io.read_array('test.dat') but get the following traceback Traceback (most recent call last): File "", line 1, in ? File "C:\Python22\Lib\site-packages\scipy\io\array_import.py", line 319, in read_array colsize, collist = getcolumns(ascii_object, columns, sep) File "C:\Python22\Lib\site-packages\scipy\io\array_import.py", line 247, in getcolumns val = process_line(firstline, separator, collist, [Numeric.Float]*N, 0) File "C:\Python22\Lib\site-packages\scipy\io\array_import.py", line 227, in process_line vals[k] = extract_columns(arlist, collist[k], atype[k], missing) File "C:\Python22\Lib\site-packages\scipy\io\array_import.py", line 205, in extract_columns return numpyio.convert_objectarray(toconvlist, atype, missing) SystemError: D: \trentm\main\Apps\ActivePython-2_2\src\Core\Objects\methodobject.c:33: bad argument to internal function I used: SciPy-0_2_0_alpha_102_3553_win32-py2_2.exe on Win NT Any idea what is going wrong? Best regards, Remco Strijbos This email contains information that may be confidential and privileged. Unless you are the addressee (or authorized to receive for the addressee), you may not use, copy or disclose this message to anybody or the information contained herein. If you have received this email in error, please notify the sender and delete this message. Thank you. From oliphant at ee.byu.edu Thu Jun 6 14:02:39 2002 From: oliphant at ee.byu.edu (Travis Oliphant) Date: Thu, 6 Jun 2002 12:02:39 -0600 (MDT) Subject: [SciPy-user] problems with scipy.io.readarray In-Reply-To: Message-ID: > > from scipy import io > x=io.read_array('test.dat') > > but get the following traceback > > Traceback (most recent call last): > File "", line 1, in ? > File "C:\Python22\Lib\site-packages\scipy\io\array_import.py", line 319, > in read_array > colsize, collist = getcolumns(ascii_object, columns, sep) > File "C:\Python22\Lib\site-packages\scipy\io\array_import.py", line 247, > in getcolumns > val = process_line(firstline, separator, collist, [Numeric.Float]*N, 0) > File "C:\Python22\Lib\site-packages\scipy\io\array_import.py", line 227, > in process_line > vals[k] = extract_columns(arlist, collist[k], atype[k], missing) > File "C:\Python22\Lib\site-packages\scipy\io\array_import.py", line 205, > in extract_columns > return numpyio.convert_objectarray(toconvlist, atype, missing) > SystemError: D: > \trentm\main\Apps\ActivePython-2_2\src\Core\Objects\methodobject.c:33: bad > argument to internal function > I don't know what's going on. Could you send me the test.dat file? This function reads text files. Is test.dat a text file? If you could isolate the part of the file that gives the error in test.dat that would be helpful. It could be a problem with opening text files versus binary files on Windows systems. Good luck, -Travis From Remco.Strijbos at jdsu.com Fri Jun 7 02:45:07 2002 From: Remco.Strijbos at jdsu.com (Remco.Strijbos at jdsu.com) Date: Fri, 7 Jun 2002 08:45:07 +0200 Subject: [SciPy-user] problems with scipy.io.read_array Message-ID: The same error occurs on both Linux (mandrake 8,2 with binary rpm of scipy ) and Windows. There is nothing special with the text file, the same error occurs when you write and read back an array as in the code below: import Numeric import scipy.io x=Numeric.identity(3,Numeric.Float) scipy.io.write_array('test2.dat',x) y=scipy.io.read_array('test2.dat') Remco. This email contains information that may be confidential and privileged. Unless you are the addressee (or authorized to receive for the addressee), you may not use, copy or disclose this message to anybody or the information contained herein. If you have received this email in error, please notify the sender and delete this message. Thank you. From doug at idsia.ch Fri Jun 7 06:28:02 2002 From: doug at idsia.ch (Douglas Eck) Date: Fri, 07 Jun 2002 12:28:02 +0200 Subject: [SciPy-user] plot.plt speed References: <3CFF4687.7030305@idsia.ch> Message-ID: <3D008AB2.2020200@idsia.ch> I found a solution to this problem, albeit not a perfect one. Simply build a long plot string and then use eval() That is: x=rand(20,20000) pltstr="plt.plot("; for i in range(shape(x)[0]) : pltstr = "%sy,x[%i,:]+%i,'b-'" % (pltstr,i,i) if i I need to plot 10 time series on the same plot window. But it's quite slow: > > plot.plt(rand(10,200)) > takes 18 seconds. > > plot.plt(rand(1,2000)) > takes less than one second > > There are some tricks for speeding up the first case in gnuplot by > reshaping > the array to be 1,2000 and adding a second array for the x values. > [[1:200][1:200]....[1:200]]. But this has other problems. > > Any ideas? My timeseries are more on the order of (25,2500).... not > pretty. > > Cheers, > Doug -- Dr. Douglas Eck, http://www.idsia.ch/~doug Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA) Neural Networks, Rhythm Perception and Production, Dynamical Systems From bernard604 at netscape.net Sat Jun 8 12:35:24 2002 From: bernard604 at netscape.net (damian) Date: Sat, 08 Jun 2002 11:35:24 -0500 Subject: [SciPy-user] ATLAS and LAPACK libraries Message-ID: <3D02324C.7060804@netscape.net> Hello, I am trying to build scipy from source, and I have installed LAPACK and ATLAS but I am a bit confussed on how to link them. More to the point, the directions state to do the following ... mkdir tmp cd tmp ar x ../liblapack.a cp ../liblapack.a ar r ../liblapack.a *.o cd .. rm -rf tmp .................................... I don't understand the line " cp ../liblapack.a " . What exactly do I copy? To me it looks like you extract the library then archive it again. My guess is that you are trying to add extra object files ito the liblapack.a archive, but I am not quite sure how the above commnads acomplish that. dbernard From kern at caltech.edu Sat Jun 8 18:50:30 2002 From: kern at caltech.edu (Robert Kern) Date: Sat, 8 Jun 2002 15:50:30 -0700 Subject: [SciPy-user] ATLAS and LAPACK libraries In-Reply-To: <3D02324C.7060804@netscape.net> References: <3D02324C.7060804@netscape.net> Message-ID: <20020608225030.GA26811@taliesen.caltech.edu> On Sat, Jun 08, 2002 at 11:35:24AM -0500, damian wrote: > Hello, > I am trying to build scipy from source, and I have installed LAPACK and > ATLAS but I am > a bit confussed on how to link them. More to the point, the directions > state to do the following ... > > mkdir tmp > cd tmp > ar x ../liblapack.a Unpacks ATLAS's liblapack.a into separate object files in tmp. > cp ../liblapack.a Replace with the location of your netlib LAPACK library: /usr/local/lib/liblapack.a or something like that. Search your system. Probably any liblapack.a is suitable. Overwrites the ATLAS liblapack.a with the netlib one. > ar r ../liblapack.a *.o Archives all of the object files in tmp into ../liblapack.a, overwriting the unoptimized routines. > cd .. > rm -rf tmp Hope that helps. -- Robert Kern Ruddock House President kern at caltech.edu "In the fields of hell where the grass grows high Are the graves of dreams allowed to die." -- Richard Harter From damian at localhost.localdomain Sun Jun 9 23:49:23 2002 From: damian at localhost.localdomain (damian) Date: Sun, 9 Jun 2002 22:49:23 -0500 Subject: [SciPy-user] failure of scipy.test(level=5) Message-ID: <200206092249.23362.damian@localhost.localdomain> Hello, The result I get from the test are : .................................................................................................................... ====================================================================== ERROR: check_exceptions (test_inline_tools.test_inline) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.2/site-packages/scipy/weave/tests/test_inline_tools.py", line 25, in check_exceptions result = inline_tools.inline(code,['a']) File "/usr/local/lib/python2.2/site-packages/scipy/weave/inline_tools.py", line 327, in inline auto_downcast = auto_downcast, File "/usr/local/lib/python2.2/site-packages/scipy/weave/inline_tools.py", line 426, in compile_function verbose=verbose, **kw) File "/usr/local/lib/python2.2/site-packages/scipy/weave/ext_tools.py", line 321, in compile verbose = verbose, **kw) File "/usr/local/lib/python2.2/site-packages/scipy/weave/build_tools.py", line 203, in build_extension setup(name = module_name, ext_modules = [ext],verbose=verb) File "/usr/local/lib/python2.2/distutils/core.py", line 157, in setup raise SystemExit, "error: " + str(msg) CompileError: error: command 'gcc' failed with exit status 1 ---------------------------------------------------------------------- Ran 601 tests in 244.250s FAILED (errors=1) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Platform information: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> posix linux2 uname -a: Linux localhost.localdomain 2.4.18-3smp #1 SMP Thu Apr 18 07:27:31 EDT 2002 i686 OS: redhat 7.3 gcc -v: Reading specs from /usr/lib/gcc-lib/i386-redhat-linux/2.96/specs gcc version 2.96 20000731 (Red Hat Linux 7.3 2.96-110) g77 --version GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.3 2.96-110) python22 -c 'import sys;print sys.version' 2.2.1 (#1, Jun 2 2002, 08:38:08) [GCC 2.96 20000731 (Red Hat Linux 7.3 2.96-110)] python22 -c 'import Numeric;print Numeric.__version__' 21.0 f2py: F2PY-2.13.175-1250 atlas: atlas3.4.0. the atlas libraries are located in /usr/local/lib/atals the lpack libraries are located in /usr/local/lib system_info.py: atlas_info: FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/local/lib', '/usr/local/lib/atlas'] fftw_info: FOUND: libraries = ['dfftw', 'drfftw', 'dfftw_threads', 'drfftw_threads'] library_dirs = ['/usr/local/lib'] define_macros = [('SCIPY_DFFTW_H', 1)] include_dirs = ['/usr/local/include'] x11_info: FOUND: libraries = ['X11'] library_dirs = ['/usr/X11R6/lib'] include_dirs = ['/usr/X11R6/include'] ....................................................................................................... python22 build_flib.py command: f77 -V -c /tmp/__dummy.f -o /tmp/__dummy.o 256 f77: invalid version number format command: f77 -version 256 f77: unrecognized option `-version' /usr/bin/ld: cannot open output file a.out: Permission denied collect2: ld returned 1 exit status command: f90 -V 32512 sh: f90: command not found command: ifc -FI -V -c /tmp/__dummy.f -o /tmp/__dummy.o 32512 sh: ifc: command not found command: efc -FI -V -c /tmp/__dummy.f -o /tmp/__dummy.o 32512 sh: efc: command not found command: f95 -V 32512 sh: f95: command not found command: fort -V 32512 sh: fort: command not found command: DF /what 32512 sh: DF: command not found command: g77 --version 0 GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.3 2.96-110) Copyright (C) 1997 Free Software Foundation, Inc. For more version information on components of the GNU Fortran compilation system, especially useful when reporting bugs, type the command `g77 --verbose'. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING or type the command `info -f g77 Copying'. command: vf90 -v 32512 sh: vf90: command not found command: f90 +version 32512 sh: f90: command not found command: g77 --version 0 GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.3 2.96-110) Copyright (C) 1997 Free Software Foundation, Inc. For more version information on components of the GNU Fortran compilation system, especially useful when reporting bugs, type the command `g77 --verbose'. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING or type the command `info -f g77 Copying'. command: F -V 32512 sh: F: command not found command: g77 --version 0 GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.3 2.96-110) Copyright (C) 1997 Free Software Foundation, Inc. For more version information on components of the GNU Fortran compilation system, especially useful when reporting bugs, type the command `g77 --verbose'. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING or type the command `info -f g77 Copying'. Gnu 0.5.26 Thanks, D. Bernard From eric at enthought.com Mon Jun 10 03:15:50 2002 From: eric at enthought.com (eric jones) Date: Mon, 10 Jun 2002 02:15:50 -0500 Subject: [SciPy-user] failure of scipy.test(level=5) In-Reply-To: <200206092249.23362.damian@localhost.localdomain> Message-ID: <000501c2104e$a6860650$6b01a8c0@ericlaptop> Hey Damian, I expect this is a recently fixed bug in the weave tests. The fixed version is in CVS. The nightly Linux tests/building of packages seems to be hanging occasionally, so the source code on the download page may be a little behind the actual CVS. The old test in test_inline_tools.py around line 25 was something like: throw throw_error(PyExc_ValueError, "the variable 'a' should not be less than 2"); the new test code should be: throw_error(PyExc_ValueError, "the variable 'a' should not be less than 2"); If your code is like the second and you're still getting this error, let me know. Thanks, eric > -----Original Message----- > From: scipy-user-admin at scipy.net [mailto:scipy-user-admin at scipy.net] On > Behalf Of damian > Sent: Sunday, June 09, 2002 10:49 PM > To: scipy-user at scipy.net > Subject: [SciPy-user] failure of scipy.test(level=5) > > Hello, > > The result I get from the test are : > ........................................................................ .. > .......................................... > ====================================================================== > ERROR: check_exceptions (test_inline_tools.test_inline) > ---------------------------------------------------------------------- > Traceback (most recent call last): > File > "/usr/local/lib/python2.2/site- > packages/scipy/weave/tests/test_inline_tools.py", > line 25, in check_exceptions > result = inline_tools.inline(code,['a']) > File "/usr/local/lib/python2.2/site- > packages/scipy/weave/inline_tools.py", > line 327, in inline > auto_downcast = auto_downcast, > File "/usr/local/lib/python2.2/site- > packages/scipy/weave/inline_tools.py", > line 426, in compile_function > verbose=verbose, **kw) > File "/usr/local/lib/python2.2/site-packages/scipy/weave/ext_tools.py", > line > 321, in compile > verbose = verbose, **kw) > File "/usr/local/lib/python2.2/site- > packages/scipy/weave/build_tools.py", > line 203, in build_extension > setup(name = module_name, ext_modules = [ext],verbose=verb) > File "/usr/local/lib/python2.2/distutils/core.py", line 157, in setup > raise SystemExit, "error: " + str(msg) > CompileError: error: command 'gcc' failed with exit status 1 > > ---------------------------------------------------------------------- > Ran 601 tests in 244.250s > > FAILED (errors=1) > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Platform information: > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> > >>>>>>>>>>>>>>>>>>>>>>>>> > > posix linux2 > uname -a: > Linux localhost.localdomain 2.4.18-3smp #1 SMP Thu Apr 18 07:27:31 > EDT 2002 > i686 > > OS: redhat 7.3 > > gcc -v: > Reading specs from /usr/lib/gcc-lib/i386-redhat-linux/2.96/specs > gcc version 2.96 20000731 (Red Hat Linux 7.3 2.96-110) > > g77 --version > GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.3 2.96-110) > > python22 -c 'import sys;print sys.version' > 2.2.1 (#1, Jun 2 2002, 08:38:08) > [GCC 2.96 20000731 (Red Hat Linux 7.3 2.96-110)] > > python22 -c 'import Numeric;print Numeric.__version__' > 21.0 > > f2py: > F2PY-2.13.175-1250 > > atlas: > atlas3.4.0. > the atlas libraries are located in /usr/local/lib/atals > the lpack libraries are located in /usr/local/lib > > system_info.py: > atlas_info: > FOUND: > libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] > library_dirs = ['/usr/local/lib', '/usr/local/lib/atlas'] > > fftw_info: > FOUND: > libraries = ['dfftw', 'drfftw', 'dfftw_threads', 'drfftw_threads'] > library_dirs = ['/usr/local/lib'] > define_macros = [('SCIPY_DFFTW_H', 1)] > include_dirs = ['/usr/local/include'] > > x11_info: > FOUND: > libraries = ['X11'] > library_dirs = ['/usr/X11R6/lib'] > include_dirs = ['/usr/X11R6/include'] > ........................................................................ .. > ............................. > python22 build_flib.py > command: f77 -V -c /tmp/__dummy.f -o /tmp/__dummy.o > 256 f77: invalid version number format > command: f77 -version > 256 f77: unrecognized option `-version' > /usr/bin/ld: cannot open output file a.out: Permission denied > collect2: ld returned 1 exit status > command: f90 -V > 32512 sh: f90: command not found > command: ifc -FI -V -c /tmp/__dummy.f -o /tmp/__dummy.o > 32512 sh: ifc: command not found > command: efc -FI -V -c /tmp/__dummy.f -o /tmp/__dummy.o > 32512 sh: efc: command not found > command: f95 -V > 32512 sh: f95: command not found > command: fort -V > 32512 sh: fort: command not found > command: DF /what > 32512 sh: DF: command not found > command: g77 --version > 0 GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.3 2.96-110) > Copyright (C) 1997 Free Software Foundation, Inc. > For more version information on components of the GNU Fortran > compilation system, especially useful when reporting bugs, > type the command `g77 --verbose'. > > GNU Fortran comes with NO WARRANTY, to the extent permitted by law. > You may redistribute copies of GNU Fortran > under the terms of the GNU General Public License. > For more information about these matters, see the file named COPYING > or type the command `info -f g77 Copying'. > command: vf90 -v > 32512 sh: vf90: command not found > command: f90 +version > 32512 sh: f90: command not found > command: g77 --version > 0 GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.3 2.96-110) > Copyright (C) 1997 Free Software Foundation, Inc. > For more version information on components of the GNU Fortran > compilation system, especially useful when reporting bugs, > type the command `g77 --verbose'. > > GNU Fortran comes with NO WARRANTY, to the extent permitted by law. > You may redistribute copies of GNU Fortran > under the terms of the GNU General Public License. > For more information about these matters, see the file named COPYING > or type the command `info -f g77 Copying'. > command: F -V > 32512 sh: F: command not found > command: g77 --version > 0 GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.3 2.96-110) > Copyright (C) 1997 Free Software Foundation, Inc. > For more version information on components of the GNU Fortran > compilation system, especially useful when reporting bugs, > type the command `g77 --verbose'. > > GNU Fortran comes with NO WARRANTY, to the extent permitted by law. > You may redistribute copies of GNU Fortran > under the terms of the GNU General Public License. > For more information about these matters, see the file named COPYING > or type the command `info -f g77 Copying'. > Gnu 0.5.26 > > > > > Thanks, > D. Bernard > > > > > > > > > > _______________________________________________ > SciPy-user mailing list > SciPy-user at scipy.net > http://www.scipy.net/mailman/listinfo/scipy-user From travis at enthought.com Mon Jun 17 19:38:52 2002 From: travis at enthought.com (Travis N. Vaught) Date: Mon, 17 Jun 2002 18:38:52 -0500 Subject: [SciPy-user] [ANN] SciPy '02 - Python for Scientific Computing Workshop Message-ID: ---------------------------------------- Python for Scientific Computing Workshop ---------------------------------------- CalTech, Pasadena, CA Septemer 5-6, 2002 http://www.scipy.org/site_content/scipy02 This workshop provides a unique opportunity to learn and affect what is happening in the realm of scientific computing with Python. Attendees will have the opportunity to review the available tools and how they apply to specific problems. By providing a forum for developers to share their Python expertise with the wider industrial, academic, and research communities, this workshop will foster collaboration and facilitate the sharing of software components, techniques and a vision for high level language use in scientific computing. The two-day workshop will be a mix of invited talks and training sessions in the morning. The afternoons will be breakout sessions with the intent of getting standardization of tools and interfaces. The cost of the workshop is $50.00 and includes 2 breakfasts and 2 lunches on Sept. 5th and 6th, one dinner on Sept. 5th, and snacks during breaks. There is a limit of 50 attendees. Should we exceed the limit of 50 registrants, the 50 persons selected to attend will be invited individually by the organizers. Discussion about the conference may be directed to the SciPy-user mailing list: mailto:scipy-user at scipy.org http://www.scipy.org/MailList ------------- Co-Hosted By: ------------- The National Biomedical Computation Resource (NBCR, SDSC, San Diego, CA) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ http://nbcr.sdsc.edu The mission of the National Biomedical Computation Resource at the San Diego Supercomputer Center is to conduct, catalyze, and enable biomedical research by harnessing advanced computational technology. The Center for Advanced Computing Research (CACR, CalTech, Pasadena, CA) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ http://nbcr.sdsc.edu CACR is dedicated to the pursuit of excellence in the field of high-performance computing, communication, and data engineering. Major activities include carrying out large-scale scientific and engineering applications on parallel supercomputers and coordinating collaborative research projects on high-speed network technologies, distributed computing and database methodologies, and related topics. Our goal is to help further the state of the art in scientific computing. Enthought, Inc. (Austin, TX) ^^^^^^^^^^^^^^^ http://enthought.com Enthought, Inc. provides business and scientific computing solutions through software development, consulting and training. From travis at enthought.com Mon Jun 24 18:56:06 2002 From: travis at enthought.com (Travis N. Vaught) Date: Mon, 24 Jun 2002 17:56:06 -0500 Subject: [SciPy-user] [ANN] SciPy '02 - Python for Scientific Computing Workshop Message-ID: Apologies if you are receiving this a second time. (mailing list problems should be fixed now) ---------------------------------------- Python for Scientific Computing Workshop ---------------------------------------- CalTech, Pasadena, CA Septemer 5-6, 2002 http://www.scipy.org/site_content/scipy02 This workshop provides a unique opportunity to learn and affect what is happening in the realm of scientific computing with Python. Attendees will have the opportunity to review the available tools and how they apply to specific problems. By providing a forum for developers to share their Python expertise with the wider industrial, academic, and research communities, this workshop will foster collaboration and facilitate the sharing of software components, techniques and a vision for high level language use in scientific computing. The two-day workshop will be a mix of invited talks and training sessions in the morning. The afternoons will be breakout sessions with the intent of getting standardization of tools and interfaces. The cost of the workshop is $50.00 and includes 2 breakfasts and 2 lunches on Sept. 5th and 6th, one dinner on Sept. 5th, and snacks during breaks. There is a limit of 50 attendees. Should we exceed the limit of 50 registrants, the 50 persons selected to attend will be invited individually by the organizers. Discussion about the conference may be directed to the SciPy-user mailing list: mailto:scipy-user at scipy.org http://www.scipy.org/MailList ------------- Co-Hosted By: ------------- The National Biomedical Computation Resource (NBCR, SDSC, San Diego, CA) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ http://nbcr.sdsc.edu The mission of the National Biomedical Computation Resource at the San Diego Supercomputer Center is to conduct, catalyze, and enable biomedical research by harnessing advanced computational technology. The Center for Advanced Computing Research (CACR, CalTech, Pasadena, CA) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ http://nbcr.sdsc.edu CACR is dedicated to the pursuit of excellence in the field of high-performance computing, communication, and data engineering. Major activities include carrying out large-scale scientific and engineering applications on parallel supercomputers and coordinating collaborative research projects on high-speed network technologies, distributed computing and database methodologies, and related topics. Our goal is to help further the state of the art in scientific computing. Enthought, Inc. (Austin, TX) ^^^^^^^^^^^^^^^ http://enthought.com Enthought, Inc. provides business and scientific computing solutions through software development, consulting and training. Enthought also fosters the development of SciPy, an open source library of scientific tools for Python. From ptak at pha.jhu.edu Thu Jun 27 15:33:18 2002 From: ptak at pha.jhu.edu (Andrew Ptak) Date: Thu, 27 Jun 2002 15:33:18 -0400 (EDT) Subject: [SciPy-user] scipy workshop Message-ID: Hello, I submitted a registration form for the scipy workshop (about a week ago, I think) but I haven't gotten any email since then. Has the 50 person limit been reached? Thanks, Andy Ptak From travis at enthought.com Thu Jun 27 16:10:19 2002 From: travis at enthought.com (Travis N. Vaught) Date: Thu, 27 Jun 2002 15:10:19 -0500 Subject: [SciPy-user] scipy workshop In-Reply-To: Message-ID: Andy, As of 2:50pm CST we are up to 19 registrants for the workshop (so tell all your friends and colleagues to register). Ability to pay the registration fee online is still about a week away. We'll email all the registrants at that time. To enable people to firm up travel plans, we've decided to confirm spots for the first 40 registrants who sign up. If we have more than 10 additional registrants, the remaining attendees will be subjectively chosen (since we're limited to 50). I'll post this policy to the web this afternoon. I'll forward a copy of the mail you should have gotten confirming your registration to you privately. Thanks, Travis > -----Original Message----- > From: scipy-user-admin at scipy.net [mailto:scipy-user-admin at scipy.net]On > Behalf Of Andrew Ptak > Sent: Thursday, June 27, 2002 2:33 PM > To: scipy-user at scipy.net > Subject: [SciPy-user] scipy workshop > > > Hello, > I submitted a registration form for the scipy workshop (about a week ago, > I think) but I haven't gotten any email since then. Has the 50 person > limit been reached? > > Thanks, > Andy Ptak > > > _______________________________________________ > SciPy-user mailing list > SciPy-user at scipy.net > http://www.scipy.net/mailman/listinfo/scipy-user > > From chrish at cynovad.com Fri Jun 28 15:16:09 2002 From: chrish at cynovad.com (Christian Hudon) Date: Fri, 28 Jun 2002 15:16:09 -0400 Subject: [SciPy-user] Re: problems with scipy.io.readarray References: Message-ID: <3D1CB5F9.7000903@cynovad.com> Travis Oliphant wrote: >>SystemError: D: >>\trentm\main\Apps\ActivePython-2_2\src\Core\Objects\methodobject.c:33: bad >>argument to internal function >> > > I don't know what's going on. Could you send me the test.dat file? This > function reads text files. Is test.dat a text file? > > If you could isolate the part of the file that gives the error in test.dat > that would be helpful. It could be a problem with opening text files > versus binary files on Windows systems. > I'm getting exact same problem. Running ActivePython 2.2.1 build 222 on Windows 2000. Both SciPy 0.2.0 103.3564 and 103.3567 (the latest) exhibit this problem. I can't even load a baby array like: 1 2 3 4 Tried both with CRLF (Windows) and LF (Unix) line terminators. They both cause crashes with the same backtrace. Christian From confirm-s2-HCTsdVqzD8g1mTjjwQSMdV_sutI-scipy-user=scipy.net at yahoogroups.com Sun Jun 30 10:12:31 2002 From: confirm-s2-HCTsdVqzD8g1mTjjwQSMdV_sutI-scipy-user=scipy.net at yahoogroups.com (Yahoo!Groups) Date: 30 Jun 2002 14:12:31 -0000 Subject: [SciPy-user] Please confirm your request to join FlyLadyMentors Message-ID: <1025446351.80.23591.m6@yahoogroups.com> Hello scipy-user at scipy.net, We have received your request to join the FlyLadyMentors group hosted by Yahoo! Groups, a free, easy-to-use community service. This request will expire in 21 days. TO BECOME A MEMBER OF THE GROUP: 1) Go to the Yahoo! 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