[Numpy-discussion] numpy failures for rc1
I was hoping to tag the 1.2.0rc1 soon, but I noticed that a couple of failures on the buildbots: http://buildbot.scipy.org/builders/Windows_XP_x86_64_MSVC/builds/701/steps/shell_2/logs/stdio http://buildbot.scipy.org/builders/FreeBSD_64/builds/621/steps/shell_2/logs/stdio Are there any other issues that need to be resolved before tagging the rc? Thanks, -- Jarrod Millman Computational Infrastructure for Research Labs 10 Giannini Hall, UC Berkeley phone: 510.643.4014 http://cirl.berkeley.edu/ ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy failures for rc1
Jarrod Millman wrote: I was hoping to tag the 1.2.0rc1 soon, but I noticed that a couple of failures on the buildbots: http://buildbot.scipy.org/builders/Windows_XP_x86_64_MSVC/builds/701/steps/shell_2/logs/stdio http://buildbot.scipy.org/builders/FreeBSD_64/builds/621/steps/shell_2/logs/stdio The FreeBSD one is a bogus test (again, my fault), which should be trivial to fix. For the Win64 problem, I don't understand how it would appear only on windows; maybe a build bot configuration problem ? cheers, David ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Problem building NumPy with information from ~/.numpy-site.cfg
David Cournapeau [EMAIL PROTECTED] writes: On Mon, 2008-09-01 at 11:26 +0200, Berthold Höllmann wrote: I am trying to build numpy 1.1.1 with ATLAS support. the f77blas library I am trying to use is named f77blas_gfortran to distinguish it From builds for other compilers. First from the documentation it is unclear whether the default section is named DEFAULT or ALL (I tried both). So I set Hi Berthold, To help you, we need more information: the build log would be useful. Please re-run the python setup.py build from scratch (deleting the build directory): python setup.py build build.log I tried to send the logfile to the list, but the mail still awaits moderation. Kind regards Berthold Höllmann -- Germanischer Lloyd AG CAE Development Vorsetzen 35 20459 Hamburg Phone: +49(0)40 36149-7374 Fax: +49(0)40 36149-7320 e-mail: [EMAIL PROTECTED] Internet: http://www.gl-group.com pgpvL6xkCDzcW.pgp Description: PGP signature disclaimer.txt Description: Binary data ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy failures for rc1
David Cournapeau wrote: The FreeBSD one is a bogus test (again, my fault), which should be trivial to fix. Fixed in r5741 cheers, David ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy failures for rc1
I think there is a thread on that matter on the list, and it seems to be fixed now ;) Cheers, Matthieu 2008/9/2, David Cournapeau [EMAIL PROTECTED]: Jarrod Millman wrote: I was hoping to tag the 1.2.0rc1 soon, but I noticed that a couple of failures on the buildbots: http://buildbot.scipy.org/builders/Windows_XP_x86_64_MSVC/builds/701/steps/shell_2/logs/stdio http://buildbot.scipy.org/builders/FreeBSD_64/builds/621/steps/shell_2/logs/stdio The FreeBSD one is a bogus test (again, my fault), which should be trivial to fix. For the Win64 problem, I don't understand how it would appear only on windows; maybe a build bot configuration problem ? cheers, David ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion -- French PhD student Website : http://matthieu-brucher.developpez.com/ Blogs : http://matt.eifelle.com and http://blog.developpez.com/?blog=92 LinkedIn : http://www.linkedin.com/in/matthieubrucher ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy failures for rc1
Jarrod Millman wrote: I was hoping to tag the 1.2.0rc1 soon, but I noticed that a couple of failures on the buildbots: http://buildbot.scipy.org/builders/Windows_XP_x86_64_MSVC/builds/701/steps/shell_2/logs/stdio http://buildbot.scipy.org/builders/FreeBSD_64/builds/621/steps/shell_2/logs/stdio Both are green now (as well as all other ones). cheers, David ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Problem building NumPy with information from ~/.numpy-site.cfg
On Tue, Sep 2, 2008 at 12:56 AM, Berthold Höllmann [EMAIL PROTECTED] wrote: David Cournapeau [EMAIL PROTECTED] writes: On Mon, 2008-09-01 at 11:26 +0200, Berthold Höllmann wrote: I am trying to build numpy 1.1.1 with ATLAS support. the f77blas library I am trying to use is named f77blas_gfortran to distinguish it From builds for other compilers. First from the documentation it is unclear whether the default section is named DEFAULT or ALL (I tried both). So I set Hi Berthold, To help you, we need more information: the build log would be useful. Please re-run the python setup.py build from scratch (deleting the build directory): python setup.py build build.log I tried to send the logfile to the list, but the mail still awaits moderation. Yeah, the list has a rather small size limit. Zip it up and send it to David directly. Chuck ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
[Numpy-discussion] NumPy 1.2.0rc1 to be tagged in 5 hours
Hello, I am planning to tag 1.2.0rc1 in 5 hours. The tests are passing on the buildbots and I don't know of anything else that needs to be fixed before making the final 1.2.0 release, which will come out after the release candidate has been more widely tested. If you know of any release blockers, please let me know ASAP. Thanks, -- Jarrod Millman Computational Infrastructure for Research Labs 10 Giannini Hall, UC Berkeley phone: 510.643.4014 http://cirl.berkeley.edu/ ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
[Numpy-discussion] numpy 1.1.1 fails because of missing md5
Joseph, Ok all failed because numpy couldn't build... It's looking for md5 on my machine i type: whereis md5 md5: /usr/include/md5.h /usr/share/man/man1/md5.1ssl.gz /usr/share/man/man3/md5.3ssl.gz I'm ccing the numpy discussion list on this. The numpy we're trying to build is 1.1.1 I'm attaching the numpy log. Is it fixed in 1.2 ? Joseph in the mean time you might want to try to install md5 on your system. C. Joseph Hargitai wrote: here are the logs - OS: 2.6.9-55.ELsmp #1 SMP Fri Apr 20 16:36:54 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux Rocks 4.3 with Redhat installation cluster. rm -rf logs/numpy.LOG; cd build; cp ../exsrc/src/numpy* .; gunzip numpy*gz; tar xf numpy-1.1.1.tar; rm numpy-1.1.1.tar; cd numpy*; LDFLAGS=-L/state/partition1/cdat/Externals/lib -L/usr/X11R6/lib64 -L/usr/local/lib -Wl,-R/state/partition1/cdat/Externals/lib -L/state/partition1/cdat/Externals/HDF5/lib -L/state/partition1/cdat/Externals/NetCDF/lib; export LDFLAGS ; CPPFLAGS=-I/state/partition1/cdat/Externals/include -I/state/partition1/cdat/Externals/HDF5/include -I/state/partition1/cdat/Externals/HDF5/include -I/state/partition1/cdat/Externals/NetCDF/include ; export CPPFLAGS ; CC=gcc ; export CC ; FC=g77 ; export FC ; FCFLAGS=-g -O2 ; export FCFLAGS ;FCLIBS= -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6 -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/../../../../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/../../.. -L/lib/../lib64 -L/usr/lib/../lib64 -lfrtbegin -lg2c -lm ; export FCLIBS ; F77=g77 ; export F77;FFLAGS=-g -O2 ; export FFLAGS;FLIBS= -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6 -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/../../../../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/../../.. -L/lib/../lib64 -L/usr/lib/../lib64 -lfrtbegin -lg2c -lm ; export FLIBS ;CPP=gcc -E; export CPP;CXX=g++; export CXX ; EXTERNALS=/state/partition1/cdat/Externals; export EXTERNALS ; PKG_CONFIG_PATH=/state/partition1/cdat/Externals/lib/pkgconfig: ; export PKG_CONFIG_PATH ;PATH=/state/partition1/cdat/Externals/bin:/state/partition1/cdat/bin:/usr/kerberos/bin:/usr/java/jdk1.5.0_10/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:/opt/ganglia/bin:/opt/ganglia/sbin:/usr/local/matlab/R2007a/bin:/usr/sbin:/opt/openmpi/bin/:/opt/maui/bin:/opt/torque/bin:/opt/torque/sbin:/opt/rocks/bin:/opt/rocks/sbin:/usr/local/toolworks/totalview.8.4.1-5/bin:/usr/local/toolworks/totalview.8.4.1-5/man:/home/hargitai/bin:/opt/torque/bin:/opt/intel/fce/10.0.023/bin:/opt/intel/cce/10.0.023/bin:/usr/mpi/intel/openmpi-1.2.2-1/bin:/usr/local/toolworks/totalview.8.4.1-5/bin ; export PATH; cp /state/partition1/cdat5/site.cfg . ; unset LDFLAGS;; /state/partition1/cdat/bin/python setup.py build --force install --prefix=/state/partition1/cdat; Running from numpy source directory. F2PY Version 2_5585 blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in /state/partition1/cdat/Externals/lib NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /state/partition1/cdat/Externals/lib NOT AVAILABLE atlas_blas_info: libraries f77blas,cblas,atlas not found in /state/partition1/cdat/Externals/lib NOT AVAILABLE /state/partition1/cdat5/build/numpy-1.1.1/numpy/distutils/system_info.py:1340: 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 /state/partition1/cdat/Externals/lib NOT AVAILABLE /state/partition1/cdat5/build/numpy-1.1.1/numpy/distutils/system_info.py:1349: 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 /state/partition1/cdat5/build/numpy-1.1.1/numpy/distutils/system_info.py:1352: 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__) NOT AVAILABLE lapack_opt_info: lapack_mkl_info: mkl_info: libraries mkl,vml,guide not found in /state/partition1/cdat/Externals/lib NOT AVAILABLE NOT AVAILABLE atlas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /state/partition1/cdat/Externals/lib libraries lapack_atlas not found in /state/partition1/cdat/Externals/lib numpy.distutils.system_info.atlas_threads_info NOT AVAILABLE atlas_info: libraries f77blas,cblas,atlas not found in /state/partition1/cdat/Externals/lib libraries
Re: [Numpy-discussion] numpy 1.1.1 fails because of missing md5
On Tue, Sep 2, 2008 at 16:40, Charles Doutriaux [EMAIL PROTECTED] wrote: Joseph, Ok all failed because numpy couldn't build... It's looking for md5 That's part of the standard library. Please check your Python installation. -- Robert Kern I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth. -- Umberto Eco ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
[Numpy-discussion] distance matrix and (weighted) p-norm
Hi,
I'm trying to compute the distance matrix (weighted p-norm [*])
between two sets of vectors (data1 and data2). Example:
import numpy as N
p = 3.0
data1 = N.random.randn(100,20)
data2 = N.random.randn(80,20)
weight = N.random.rand(20)
distance_matrix = N.zeros((data1.shape[0],data2.shape[0]))
for d in range(data1.shape[1]):
distance_matrix +=
(N.abs(N.subtract.outer(data1[:,d],data2[:,d]))*weight[d])**p
pass
distance_matrix = distance_matrix**(1.0/p)
Is there a way to speed up the for loop? When the dimension
of the vectors becomes big (e.g. 1000) the for loop
becomes really annoying.
Thanks,
Emanuele
[*] : ||x - x'||_w = (\sum_{i=1...N} (w_i*|x_i - x'_i|)**p)**(1/p)
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Re: [Numpy-discussion] distance matrix and (weighted) p-norm
Emanuele Olivetti wrote: Hi, I'm trying to compute the distance matrix (weighted p-norm [*]) between two sets of vectors (data1 and data2). Example: You may want to look at scipy.cluster.distance, which has a bunch of distance matrix implementation. I believe most of them have optional compiled version, for fast execution. cheers, David ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
