Mailman 3 May 2012 - SciPy-User

ANN: SfePy 2012.2
by Robert Cimrman 29 May '12

29 May '12

I am pleased to announce release 2012.2 of SfePy. Description ----------- SfePy (simple finite elements in Python) is a software for solving systems of coupled partial differential equations by the finite element method. The code is based on NumPy and SciPy packages. It is distributed under the new BSD license. Home page: http://sfepy.org Downloads, mailing list, wiki: http://code.google.com/p/sfepy/ Git (source) repository, issue tracker: http://github.com/sfepy Highlights of this release -------------------------- - reimplemented acoustic band gaps code using the homogenization engine - high order quadrature rules - unified dot product and mass terms, lots of other term updates/fixes, - updated the PDE solver application For full release notes see http://docs.sfepy.org/doc/release_notes.html#id1 (rather long and technical). Best regards, Robert Cimrman and Contributors (*) (*) Contributors to this release (alphabetical order): Vladimír Lukeš, Andre Smit

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Re: [SciPy-User] SciPy installation troubles on CentOS 6.2
by Sergio Rojas 28 May '12

28 May '12

> From: Magician > /usr/bin/ld: cannot find -lpython2.7 Magician, This error listed indicates that python libraries are not being found. Try this: linux> locate libpython2.7.so linux> echo $LD_LIBRARY_PATH and verify that in your library path are the lib and include directories corresponding to the python you want to built. I don't recall this but, did you built your own python? Sergio ----- Original Message ----- From: Magician Sent: 05/26/12 10:05 PM To: Ralf Gommers, sergio_r(a)mail.com Subject: Re: [SciPy-User] SciPy installation troubles on CentOS 6.2 Hi Ralf and Sergio, I thought my problems inclined to NumPy, and I posted to NumPy mailing list. But I couldn't get any answers for several days, so I'd like to ask again. I tried to build NumPy again with site.cfg, but I got these errors: > building 'numpy.core._sort' extension > compiling C sources > C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC > > compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/local/python-2.7.3/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c' > gcc: build/src.linux-x86_64-2.7/numpy/core/src/_sortmodule.c > gcc -pthread -shared build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/_sortmodule.o -L. -Lbuild/temp.linux-x86_64-2.7 -lnpymath -lm -lpython2.7 -o build/lib.linux-x86_64-2.7/numpy/core/_sort.so > /usr/bin/ld: cannot find -lpython2.7 > collect2: ld returned 1 exit status > /usr/bin/ld: cannot find -lpython2.7 > collect2: ld returned 1 exit status > error: Command "gcc -pthread -shared build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/_sortmodule.o -L. -Lbuild/temp.linux-x86_64-2.7 -lnpymath -lm -lpython2.7 -o build/lib.linux-x86_64-2.7/numpy/core/_sort.so" failed with exit status 1 Before I built NumPy, I uncommented and modified site.cfg as below: > [DEFAULT] > library_dirs = /usr/local/python-2.7.3/lib:/usr/lib64:/usr/lib64/atlas > include_dirs = /usr/local/python-2.7.3/include:/usr/include:/usr/include/atlas > > [blas_opt] > libraries = f77blas, cblas, atlas > > [lapack_opt] > libraries = lapack, f77blas, cblas, atlas And "setup.py config" dumped these messages: > Running from numpy source directory.F2PY Version 2 > blas_opt_info: > blas_mkl_info: > libraries mkl,vml,guide not found in /usr/local/python-2.7.3/lib > libraries mkl,vml,guide not found in /usr/lib64 > libraries mkl,vml,guide not found in /usr/lib64/atlas > NOT AVAILABLE > > atlas_blas_threads_info: > Setting PTATLAS=ATLAS > libraries ptf77blas,ptcblas,atlas not found in /usr/local/python-2.7.3/lib > Setting PTATLAS=ATLAS > customize GnuFCompiler > Could not locate executable g77 > Could not locate executable f77 > customize IntelFCompiler > Could not locate executable ifort > Could not locate executable ifc > customize LaheyFCompiler > Could not locate executable lf95 > customize PGroupFCompiler > Could not locate executable pgf90 > Could not locate executable pgf77 > customize AbsoftFCompiler > Could not locate executable f90 > customize NAGFCompiler > Found executable /usr/bin/f95 > customize VastFCompiler > customize CompaqFCompiler > Could not locate executable fort > customize IntelItaniumFCompiler > Could not locate executable efort > Could not locate executable efc > customize IntelEM64TFCompiler > customize Gnu95FCompiler > Found executable /usr/bin/gfortran > customize Gnu95FCompiler > customize Gnu95FCompiler using config > compiling '_configtest.c': > > /* This file is generated from numpy/distutils/system_info.py */ > void ATL_buildinfo(void); > int main(void) { > ATL_buildinfo(); > return 0; > } > > C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC > > compile options: '-c' > gcc: _configtest.c > gcc -pthread _configtest.o -L/usr/lib64/atlas -lptf77blas -lptcblas -latlas -o _configtest > ATLAS version 3.8.4 built by mockbuild on Wed Dec 7 18:04:21 GMT 2011: > UNAME : Linux c6b5.bsys.dev.centos.org 2.6.32-44.2.el6.x86_64 #1 SMP Wed Jul 21 12:48:32 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux > INSTFLG : -1 0 -a 1 > ARCHDEFS : -DATL_OS_Linux -DATL_ARCH_PII -DATL_CPUMHZ=2261 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GAS_x8664 > F2CDEFS : -DAdd_ -DF77_INTEGER=int -DStringSunStyle > CACHEEDGE: 8388608 > F77 : gfortran, version GNU Fortran (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) > F77FLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -g -Wa,--noexecstack -fPIC -m64 > SMC : gcc, version gcc (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) > SMCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -g -Wa,--noexecstack -fPIC -m64 > SKC : gcc, version gcc (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) > SKCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -g -Wa,--noexecstack -fPIC -m64 > success! > removing: _configtest.c _configtest.o _configtest > Setting PTATLAS=ATLAS > FOUND: > libraries = ['ptf77blas', 'ptcblas', 'atlas'] > library_dirs = ['/usr/lib64/atlas'] > language = c > define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')] > include_dirs = ['/usr/include'] > > FOUND: > libraries = ['ptf77blas', 'ptcblas', 'atlas'] > library_dirs = ['/usr/lib64/atlas'] > language = c > define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')] > include_dirs = ['/usr/include'] > > lapack_opt_info: > lapack_mkl_info: > mkl_info: > libraries mkl,vml,guide not found in /usr/local/python-2.7.3/lib > libraries mkl,vml,guide not found in /usr/lib64 > libraries mkl,vml,guide not found in /usr/lib64/atlas > NOT AVAILABLE > > NOT AVAILABLE > > atlas_threads_info: > Setting PTATLAS=ATLAS > libraries ptf77blas,ptcblas,atlas not found in /usr/local/python-2.7.3/lib > libraries lapack_atlas not found in /usr/local/python-2.7.3/lib > libraries lapack_atlas not found in /usr/lib64/atlas > numpy.distutils.system_info.atlas_threads_info > Setting PTATLAS=ATLAS > Setting PTATLAS=ATLAS > FOUND: > libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas'] > library_dirs = ['/usr/lib64/atlas'] > language = f77 > define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')] > include_dirs = ['/usr/include'] > > FOUND: > libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas'] > library_dirs = ['/usr/lib64/atlas'] > language = f77 > define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')] > include_dirs = ['/usr/include'] > > running config I couldn't get enough informations about numscons/bento, so I'm still trying to build it with site.cfg and CFLAGS. How could I solve it? Magician On 2012/05/21, at 1:50, Ralf Gommers wrote: > > > On Sun, May 20, 2012 at 4:16 PM, Magician <f_magician(a)mac.com> wrote: > Hi Ralf, > > > Thanks for your advice. > I tried to install BLAS/Lapack/ATLAS as below: > > yum install blas-devel lapack-devel atlas-devel > > Next I installed NumPy as below: > > tar xzvf numpy-1.6.1.tar.gz > > cd numpy-1.6.1 > > export CFLAGS="-L/usr/local/python-2.7.3/lib" > > Note that this overrides CFLAGS instead of appending that flag to the rest. If it doesn't work without that line, you have to either specify all cflags or use numscons/bento. > > Ralf > > > > python setup.py build > > But then I got those errors: > > building 'numpy.linalg.lapack_lite' extension > > compiling C sources > > C compiler: gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -L/usr/local/python-2.7.3/lib -fPIC > > > > creating build/temp.linux-x86_64-2.7/numpy/linalg > > compile options: '-DATLAS_INFO="\"3.8.4\"" -I/usr/include -Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/local/python-2.7.3/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c' > > gcc: numpy/linalg/lapack_litemodule.c > > gcc: numpy/linalg/python_xerbla.c > > /usr/bin/gfortran -Wall -Wall -shared build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o -L/usr/lib64/atlas -L. -Lbuild/temp.linux-x86_64-2.7 -llapack -lptf77blas -lptcblas -latlas -lpython2.7 -lgfortran -o build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so > > /usr/bin/ld: cannot find -lpython2.7 > > collect2: ld returned 1 exit status > > /usr/bin/ld: cannot find -lpython2.7 > > collect2: ld returned 1 exit status > > error: Command "/usr/bin/gfortran -Wall -Wall -shared build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o -L/usr/lib64/atlas -L. -Lbuild/temp.linux-x86_64-2.7 -llapack -lptf77blas -lptcblas -latlas -lpython2.7 -lgfortran -o build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so" failed with exit status 1 > > If I haven't install BLAS/Lapack/ATLAS, NumPy will be > successfully built and installed. > > > Magician > > > On 2012/05/20, at 19:40, scipy-user-request(a)scipy.org wrote: > > > Message: 1 > > Date: Sun, 20 May 2012 10:21:12 +0200 > > From: Ralf Gommers <ralf.gommers(a)googlemail.com> > > Subject: Re: [SciPy-User] SciPy installation troubles on CentOS 6.2 > > To: SciPy Users List <scipy-user(a)scipy.org> > > Message-ID: > > <CABL7CQh+WPwpiMtO0UDKo9G01Gj38kTaWV=bSvq9eCK_qihAfQ(a)mail.gmail.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > On Sat, May 19, 2012 at 5:09 PM, Magician <f_magician(a)mac.com> wrote: > > > >> Hi All, > >> > >> > >> I'm trying to build SciPy from source code, > >> but I have some troubles. > >> > >> My environment is below: > >>> CentOS 6.2 on VMware Fusion 4.1.2 (CentOS was installed as Software > >> Development WS) > >>> Python 2.7.3 (already built from sources, installed at > >> /usr/local/python-2.7.3) > >>> NumPy 1.6.1, SciPy 0.10.1, ATLAS 3.8.4, Lapack 3.4.1 (now trying to > >> build) > >> I and my colleagues (other users) want to use recent Python, > >> so I installed Python from sources, and I can't install SciPy > >> by using yum command. > >> > >> Now I'm facing ATLAS compiling errors. > >> Configuration options are "--prefix=/usr/local/atlas-3.8.4 -Fa alg -fPIC". > >> I tried to build it for several times, and always I got errors as below: > >>> res/dgemvN_6_75 : VARIATION EXCEEDS TOLERENCE, RERUN WITH HIGHER REPS. > >>> > >>> ATL_gemvN_mm.c : 1257.99 > >>> ATL_gemvN_1x1_1.c : 581.74 > >>> ATL_gemvN_1x1_1a.c : 1589.45 > >>> ATL_gemvN_4x2_0.c : 813.13 > >>> ATL_gemvN_4x4_1.c : 755.54 > >>> make[3]: *** [res/dMVRES] Error 255 > >>> make[3]: Leaving directory > >> `/home/magician/Desktop/ATLAS/build/tune/blas/gemv' > >>> make[2]: *** > >> [/home/magician/Desktop/ATLAS/build/tune/blas/gemv/res/dMVRES] Error 2 > >>> make[2]: Leaving directory `/home/magician/Desktop/ATLAS/build/bin' > >>> ERROR 734 DURING MVTUNE!!. CHECK INSTALL_LOG/dMVTUNE.LOG FOR DETAILS. > >>> make[2]: Entering directory `/home/magician/Desktop/ATLAS/build/bin' > >>> cd /home/magician/Desktop/ATLAS/build ; make error_report > >>> make[3]: Entering directory `/home/magician/Desktop/ATLAS/build' > >>> make -f Make.top error_report > >>> make[4]: Entering directory `/home/magician/Desktop/ATLAS/build' > >>> uname -a 2>&1 >> bin/INSTALL_LOG/ERROR.LOG > >>> gcc -v 2>&1 >> bin/INSTALL_LOG/ERROR.LOG > >>> Using built-in specs. > >>> Target: x86_64-redhat-linux > >>> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man > >> --infodir=/usr/share/info --with-bugurl= > >> http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared > >> --enable-threads=posix --enable-checking=release --with-system-zlib > >> --enable-__cxa_atexit --disable-libunwind-exceptions > >> --enable-gnu-unique-object > >> --enable-languages=c,c++,objc,obj-c++,java,fortran,ada > >> --enable-java-awt=gtk --disable-dssi > >> --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre > >> --enable-libgcj-multifile --enable-java-maintainer-mode > >> --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib > >> --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 > >> --build=x86_64-redhat-linux > >>> Thread model: posix > >>> gcc version 4.4.6 20110731 (Red Hat 4.4.6-3) (GCC) > >>> gcc -V 2>&1 >> bin/INSTALL_LOG/ERROR.LOG > >>> gcc: '-V' option must have argument > >>> make[4]: [error_report] Error 1 (ignored) > >>> gcc --version 2>&1 >> bin/INSTALL_LOG/ERROR.LOG > >>> tar cf error_Corei264SSE3.tar Make.inc bin/INSTALL_LOG/* > >>> gzip --best error_Corei264SSE3.tar > >>> mv error_Corei264SSE3.tar.gz error_Corei264SSE3.tgz > >>> make[4]: Leaving directory `/home/magician/Desktop/ATLAS/build' > >>> make[3]: Leaving directory `/home/magician/Desktop/ATLAS/build' > >>> make[2]: Leaving directory `/home/magician/Desktop/ATLAS/build/bin' > >>> Error report error_<ARCH>.tgz has been created in your top-level ATLAS > >>> directory. Be sure to include this file in any help request. > >>> cat: ../../CONFIG/error.txt: No such file or directory > >>> cat: ../../CONFIG/error.txt: No such file or directory > >>> make[1]: *** [build] Error 255 > >>> make[1]: Leaving directory `/home/magician/Desktop/ATLAS/build' > >>> make: *** [build] Error 2 > >> > >> It's very troublesome for me to build ATLAS by myself. > >> My purpose is just using SciPy on my Python. > >> Even if it's optimized not so good for my environment, it's OK. > >> > >> Is there an easy or a sure way to build and install SciPy? > > > > > > Building ATLAS is much harder than building scipy, so you should try to > > find some rpm's for it, like > > http://linuxtoolkit.blogspot.com/2010/09/installing-lapack-blas-and-atlas-o…. > > There's no problem building scipy against ATLAS from a binary install. > > > > Ralf

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SciPy install from source fails on fresh Python 3.2.3, 64-bit Ubuntu
by Wes McKinney 27 May '12

27 May '12

I'm getting failure at the end of 2to3 on scipy 0.10.1, with easy_install and also from git master / 0.10.1 tag. I'll try rolling back to Python 3.2.2 (3.2.3 was released on 4/10) later today and see if that works RefactoringTool: /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/sparse/linalg/dsolve/umfpack/setup.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/ndimage/fourier.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/ndimage/interpolation.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/ndimage/measurements.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/ndimage/filters.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/ndimage/morphology.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/integrate/quadpack.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/integrate/_ode.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/integrate/odepack.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/lib/lapack/__init__.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/lib/blas/__init__.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/cluster/__init__.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/cluster/vq.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/cluster/hierarchy.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/stats/mstats_basic.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/stats/morestats.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/stats/distributions.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/stats/kde.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/stats/stats.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/interpolate/fitpack.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/interpolate/interpolate.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/interpolate/ndgriddata.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/interpolate/interpolate_wrapper.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/interpolate/fitpack2.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/io/__init__.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/io/matlab/mio4.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/io/matlab/mio5.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/io/matlab/miobase.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/io/matlab/mio5_params.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/optimize/zeros.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/optimize/nnls.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/optimize/cobyla.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/optimize/lbfgsb.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/optimize/minpack.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/optimize/slsqp.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/spatial/__init__.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/spatial/distance.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/special/__init__.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/special/basic.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/special/add_newdocs.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/special/orthogonal.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/linalg/decomp.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/linalg/basic.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/linalg/misc.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/linalg/flinalg.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/linalg/lapack.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/signal/__init__.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/signal/bsplines.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/signal/signaltools.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/signal/fir_filter_design.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/fftpack/basic.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/fftpack/pseudo_diffs.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/sparse/linalg/eigen/arpack/arpack.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/sparse/linalg/isolve/iterative.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/sparse/linalg/dsolve/linsolve.py /tmp/easy_install-sv1v29/scipy-0.10.1/build/py3k/scipy/sparse/linalg/dsolve/umfpack/umfpack.py Running from scipy source directory. Traceback (most recent call last): File "/usr/local/bin/easy_install-3.2", line 9, in <module> load_entry_point('distribute==0.6.27', 'console_scripts', 'easy_install-3.2')() File "/usr/local/lib/python3.2/site-packages/distribute-0.6.27-py3.2.egg/setuptools/command/easy_install.py", line 1915, in main with_ei_usage(lambda: File "/usr/local/lib/python3.2/site-packages/distribute-0.6.27-py3.2.egg/setuptools/command/easy_install.py", line 1896, in with_ei_usage return f() File "/usr/local/lib/python3.2/site-packages/distribute-0.6.27-py3.2.egg/setuptools/command/easy_install.py", line 1919, in <lambda> distclass=DistributionWithoutHelpCommands, **kw File "/usr/local/lib/python3.2/distutils/core.py", line 148, in setup dist.run_commands() File "/usr/local/lib/python3.2/distutils/dist.py", line 917, in run_commands self.run_command(cmd) File "/usr/local/lib/python3.2/distutils/dist.py", line 936, in run_command cmd_obj.run() File "/usr/local/lib/python3.2/site-packages/distribute-0.6.27-py3.2.egg/setuptools/command/easy_install.py", line 350, in run self.easy_install(spec, not self.no_deps) File "/usr/local/lib/python3.2/site-packages/distribute-0.6.27-py3.2.egg/setuptools/command/easy_install.py", line 590, in easy_install return self.install_item(spec, dist.location, tmpdir, deps) File "/usr/local/lib/python3.2/site-packages/distribute-0.6.27-py3.2.egg/setuptools/command/easy_install.py", line 620, in install_item dists = self.install_eggs(spec, download, tmpdir) File "/usr/local/lib/python3.2/site-packages/distribute-0.6.27-py3.2.egg/setuptools/command/easy_install.py", line 814, in install_eggs return self.build_and_install(setup_script, setup_base) File "/usr/local/lib/python3.2/site-packages/distribute-0.6.27-py3.2.egg/setuptools/command/easy_install.py", line 1094, in build_and_install self.run_setup(setup_script, setup_base, args) File "/usr/local/lib/python3.2/site-packages/distribute-0.6.27-py3.2.egg/setuptools/command/easy_install.py", line 1080, in run_setup run_setup(setup_script, args) File "/usr/local/lib/python3.2/site-packages/distribute-0.6.27-py3.2.egg/setuptools/sandbox.py", line 31, in run_setup lambda: exec(compile(open( File "/usr/local/lib/python3.2/site-packages/distribute-0.6.27-py3.2.egg/setuptools/sandbox.py", line 79, in run return func() File "/usr/local/lib/python3.2/site-packages/distribute-0.6.27-py3.2.egg/setuptools/sandbox.py", line 34, in <lambda> {'__file__':setup_script, '__name__':'__main__'}) File "setup.py", line 196, in <module> File "setup.py", line 187, in setup_package File "/usr/local/lib/python3.2/site-packages/numpy/distutils/core.py", line 152, in setup config = configuration() File "setup.py", line 138, in configuration File "/usr/local/lib/python3.2/site-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage caller_level = 2) File "/usr/local/lib/python3.2/site-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage caller_level = caller_level + 1) File "/usr/local/lib/python3.2/site-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/setup.py", line 4, in configuration File "/usr/local/lib/python3.2/site-packages/numpy/distutils/misc_util.py", line 743, in __init__ raise ValueError("%r is not a directory" % (package_path,)) ValueError: 'build/py3k/scipy' is not a directory

1 1

Re: [SciPy-User] SciPy installation troubles on CentOS 6.2
by Sergio Rojas 27 May '12

27 May '12

Magician, try this: linux> locate libtatlas.so the directory in which it appears and the corresponding include which contains atlas include headears (to find it try "locate cblas.h". In my system the include directory is at /usr/include/ and inside it there should be an atlas directory) are the ones you need in site.cfg Since I built my own atlas I have: [DEFAULT] library_dirs = /home/srojas/myPROG/LapackLib_gfortran/Atlas64b/lib include_dirs = /home/srojas/myPROG/LapackLib_gfortran/Atlas64b/include [blas_opt] libraries = ptf77blas, ptcblas, atlas [lapack_opt] libraries = lapack, ptf77blas, ptcblas, atlas to compile numpy I use: python setup.py build --fcompiler=gfortran (you need to use the same compiler used to built atlas) If finished sucessfully, then to verify atlas support, before installing, try: ldd ./build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so which should show links to the library. If still you have problems, maybe you need to start doing things from scratch, installing python and atlas in your own path. Sergio ----- Original Message ----- From: Magician Sent: 05/26/12 10:05 PM To: Ralf Gommers, sergio_r(a)mail.com Subject: Re: [SciPy-User] SciPy installation troubles on CentOS 6.2 Hi Ralf and Sergio, I thought my problems inclined to NumPy, and I posted to NumPy mailing list. But I couldn't get any answers for several days, so I'd like to ask again. I tried to build NumPy again with site.cfg, but I got these errors: > building 'numpy.core._sort' extension > compiling C sources > C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC > > compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/local/python-2.7.3/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c' > gcc: build/src.linux-x86_64-2.7/numpy/core/src/_sortmodule.c > gcc -pthread -shared build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/_sortmodule.o -L. -Lbuild/temp.linux-x86_64-2.7 -lnpymath -lm -lpython2.7 -o build/lib.linux-x86_64-2.7/numpy/core/_sort.so > /usr/bin/ld: cannot find -lpython2.7 > collect2: ld returned 1 exit status > /usr/bin/ld: cannot find -lpython2.7 > collect2: ld returned 1 exit status > error: Command "gcc -pthread -shared build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/_sortmodule.o -L. -Lbuild/temp.linux-x86_64-2.7 -lnpymath -lm -lpython2.7 -o build/lib.linux-x86_64-2.7/numpy/core/_sort.so" failed with exit status 1 Before I built NumPy, I uncommented and modified site.cfg as below: > [DEFAULT] > library_dirs = /usr/local/python-2.7.3/lib:/usr/lib64:/usr/lib64/atlas > include_dirs = /usr/local/python-2.7.3/include:/usr/include:/usr/include/atlas > > [blas_opt] > libraries = f77blas, cblas, atlas > > [lapack_opt] > libraries = lapack, f77blas, cblas, atlas And "setup.py config" dumped these messages: > Running from numpy source directory.F2PY Version 2 > blas_opt_info: > blas_mkl_info: > libraries mkl,vml,guide not found in /usr/local/python-2.7.3/lib > libraries mkl,vml,guide not found in /usr/lib64 > libraries mkl,vml,guide not found in /usr/lib64/atlas > NOT AVAILABLE > > atlas_blas_threads_info: > Setting PTATLAS=ATLAS > libraries ptf77blas,ptcblas,atlas not found in /usr/local/python-2.7.3/lib > Setting PTATLAS=ATLAS > customize GnuFCompiler > Could not locate executable g77 > Could not locate executable f77 > customize IntelFCompiler > Could not locate executable ifort > Could not locate executable ifc > customize LaheyFCompiler > Could not locate executable lf95 > customize PGroupFCompiler > Could not locate executable pgf90 > Could not locate executable pgf77 > customize AbsoftFCompiler > Could not locate executable f90 > customize NAGFCompiler > Found executable /usr/bin/f95 > customize VastFCompiler > customize CompaqFCompiler > Could not locate executable fort > customize IntelItaniumFCompiler > Could not locate executable efort > Could not locate executable efc > customize IntelEM64TFCompiler > customize Gnu95FCompiler > Found executable /usr/bin/gfortran > customize Gnu95FCompiler > customize Gnu95FCompiler using config > compiling '_configtest.c': > > /* This file is generated from numpy/distutils/system_info.py */ > void ATL_buildinfo(void); > int main(void) { > ATL_buildinfo(); > return 0; > } > > C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC > > compile options: '-c' > gcc: _configtest.c > gcc -pthread _configtest.o -L/usr/lib64/atlas -lptf77blas -lptcblas -latlas -o _configtest > ATLAS version 3.8.4 built by mockbuild on Wed Dec 7 18:04:21 GMT 2011: > UNAME : Linux c6b5.bsys.dev.centos.org 2.6.32-44.2.el6.x86_64 #1 SMP Wed Jul 21 12:48:32 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux > INSTFLG : -1 0 -a 1 > ARCHDEFS : -DATL_OS_Linux -DATL_ARCH_PII -DATL_CPUMHZ=2261 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GAS_x8664 > F2CDEFS : -DAdd_ -DF77_INTEGER=int -DStringSunStyle > CACHEEDGE: 8388608 > F77 : gfortran, version GNU Fortran (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) > F77FLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -g -Wa,--noexecstack -fPIC -m64 > SMC : gcc, version gcc (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) > SMCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -g -Wa,--noexecstack -fPIC -m64 > SKC : gcc, version gcc (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) > SKCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -g -Wa,--noexecstack -fPIC -m64 > success! > removing: _configtest.c _configtest.o _configtest > Setting PTATLAS=ATLAS > FOUND: > libraries = ['ptf77blas', 'ptcblas', 'atlas'] > library_dirs = ['/usr/lib64/atlas'] > language = c > define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')] > include_dirs = ['/usr/include'] > > FOUND: > libraries = ['ptf77blas', 'ptcblas', 'atlas'] > library_dirs = ['/usr/lib64/atlas'] > language = c > define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')] > include_dirs = ['/usr/include'] > > lapack_opt_info: > lapack_mkl_info: > mkl_info: > libraries mkl,vml,guide not found in /usr/local/python-2.7.3/lib > libraries mkl,vml,guide not found in /usr/lib64 > libraries mkl,vml,guide not found in /usr/lib64/atlas > NOT AVAILABLE > > NOT AVAILABLE > > atlas_threads_info: > Setting PTATLAS=ATLAS > libraries ptf77blas,ptcblas,atlas not found in /usr/local/python-2.7.3/lib > libraries lapack_atlas not found in /usr/local/python-2.7.3/lib > libraries lapack_atlas not found in /usr/lib64/atlas > numpy.distutils.system_info.atlas_threads_info > Setting PTATLAS=ATLAS > Setting PTATLAS=ATLAS > FOUND: > libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas'] > library_dirs = ['/usr/lib64/atlas'] > language = f77 > define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')] > include_dirs = ['/usr/include'] > > FOUND: > libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas'] > library_dirs = ['/usr/lib64/atlas'] > language = f77 > define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')] > include_dirs = ['/usr/include'] > > running config I couldn't get enough informations about numscons/bento, so I'm still trying to build it with site.cfg and CFLAGS. How could I solve it? Magician On 2012/05/21, at 1:50, Ralf Gommers wrote: > > > On Sun, May 20, 2012 at 4:16 PM, Magician <f_magician(a)mac.com> wrote: > Hi Ralf, > > > Thanks for your advice. > I tried to install BLAS/Lapack/ATLAS as below: > > yum install blas-devel lapack-devel atlas-devel > > Next I installed NumPy as below: > > tar xzvf numpy-1.6.1.tar.gz > > cd numpy-1.6.1 > > export CFLAGS="-L/usr/local/python-2.7.3/lib" > > Note that this overrides CFLAGS instead of appending that flag to the rest. If it doesn't work without that line, you have to either specify all cflags or use numscons/bento. > > Ralf > > > > python setup.py build > > But then I got those errors: > > building 'numpy.linalg.lapack_lite' extension > > compiling C sources > > C compiler: gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -L/usr/local/python-2.7.3/lib -fPIC > > > > creating build/temp.linux-x86_64-2.7/numpy/linalg > > compile options: '-DATLAS_INFO="\"3.8.4\"" -I/usr/include -Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/local/python-2.7.3/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c' > > gcc: numpy/linalg/lapack_litemodule.c > > gcc: numpy/linalg/python_xerbla.c > > /usr/bin/gfortran -Wall -Wall -shared build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o -L/usr/lib64/atlas -L. -Lbuild/temp.linux-x86_64-2.7 -llapack -lptf77blas -lptcblas -latlas -lpython2.7 -lgfortran -o build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so > > /usr/bin/ld: cannot find -lpython2.7 > > collect2: ld returned 1 exit status > > /usr/bin/ld: cannot find -lpython2.7 > > collect2: ld returned 1 exit status > > error: Command "/usr/bin/gfortran -Wall -Wall -shared build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o -L/usr/lib64/atlas -L. -Lbuild/temp.linux-x86_64-2.7 -llapack -lptf77blas -lptcblas -latlas -lpython2.7 -lgfortran -o build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so" failed with exit status 1 > > If I haven't install BLAS/Lapack/ATLAS, NumPy will be > successfully built and installed. > > > Magician > > > On 2012/05/20, at 19:40, scipy-user-request(a)scipy.org wrote: > > > Message: 1 > > Date: Sun, 20 May 2012 10:21:12 +0200 > > From: Ralf Gommers <ralf.gommers(a)googlemail.com> > > Subject: Re: [SciPy-User] SciPy installation troubles on CentOS 6.2 > > To: SciPy Users List <scipy-user(a)scipy.org> > > Message-ID: > > <CABL7CQh+WPwpiMtO0UDKo9G01Gj38kTaWV=bSvq9eCK_qihAfQ(a)mail.gmail.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > On Sat, May 19, 2012 at 5:09 PM, Magician <f_magician(a)mac.com> wrote: > > > >> Hi All, > >> > >> > >> I'm trying to build SciPy from source code, > >> but I have some troubles. > >> > >> My environment is below: > >>> CentOS 6.2 on VMware Fusion 4.1.2 (CentOS was installed as Software > >> Development WS) > >>> Python 2.7.3 (already built from sources, installed at > >> /usr/local/python-2.7.3) > >>> NumPy 1.6.1, SciPy 0.10.1, ATLAS 3.8.4, Lapack 3.4.1 (now trying to > >> build) > >> I and my colleagues (other users) want to use recent Python, > >> so I installed Python from sources, and I can't install SciPy > >> by using yum command. > >> > >> Now I'm facing ATLAS compiling errors. > >> Configuration options are "--prefix=/usr/local/atlas-3.8.4 -Fa alg -fPIC". > >> I tried to build it for several times, and always I got errors as below: > >>> res/dgemvN_6_75 : VARIATION EXCEEDS TOLERENCE, RERUN WITH HIGHER REPS. > >>> > >>> ATL_gemvN_mm.c : 1257.99 > >>> ATL_gemvN_1x1_1.c : 581.74 > >>> ATL_gemvN_1x1_1a.c : 1589.45 > >>> ATL_gemvN_4x2_0.c : 813.13 > >>> ATL_gemvN_4x4_1.c : 755.54 > >>> make[3]: *** [res/dMVRES] Error 255 > >>> make[3]: Leaving directory > >> `/home/magician/Desktop/ATLAS/build/tune/blas/gemv' > >>> make[2]: *** > >> [/home/magician/Desktop/ATLAS/build/tune/blas/gemv/res/dMVRES] Error 2 > >>> make[2]: Leaving directory `/home/magician/Desktop/ATLAS/build/bin' > >>> ERROR 734 DURING MVTUNE!!. CHECK INSTALL_LOG/dMVTUNE.LOG FOR DETAILS. > >>> make[2]: Entering directory `/home/magician/Desktop/ATLAS/build/bin' > >>> cd /home/magician/Desktop/ATLAS/build ; make error_report > >>> make[3]: Entering directory `/home/magician/Desktop/ATLAS/build' > >>> make -f Make.top error_report > >>> make[4]: Entering directory `/home/magician/Desktop/ATLAS/build' > >>> uname -a 2>&1 >> bin/INSTALL_LOG/ERROR.LOG > >>> gcc -v 2>&1 >> bin/INSTALL_LOG/ERROR.LOG > >>> Using built-in specs. > >>> Target: x86_64-redhat-linux > >>> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man > >> --infodir=/usr/share/info --with-bugurl= > >> http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared > >> --enable-threads=posix --enable-checking=release --with-system-zlib > >> --enable-__cxa_atexit --disable-libunwind-exceptions > >> --enable-gnu-unique-object > >> --enable-languages=c,c++,objc,obj-c++,java,fortran,ada > >> --enable-java-awt=gtk --disable-dssi > >> --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre > >> --enable-libgcj-multifile --enable-java-maintainer-mode > >> --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib > >> --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 > >> --build=x86_64-redhat-linux > >>> Thread model: posix > >>> gcc version 4.4.6 20110731 (Red Hat 4.4.6-3) (GCC) > >>> gcc -V 2>&1 >> bin/INSTALL_LOG/ERROR.LOG > >>> gcc: '-V' option must have argument > >>> make[4]: [error_report] Error 1 (ignored) > >>> gcc --version 2>&1 >> bin/INSTALL_LOG/ERROR.LOG > >>> tar cf error_Corei264SSE3.tar Make.inc bin/INSTALL_LOG/* > >>> gzip --best error_Corei264SSE3.tar > >>> mv error_Corei264SSE3.tar.gz error_Corei264SSE3.tgz > >>> make[4]: Leaving directory `/home/magician/Desktop/ATLAS/build' > >>> make[3]: Leaving directory `/home/magician/Desktop/ATLAS/build' > >>> make[2]: Leaving directory `/home/magician/Desktop/ATLAS/build/bin' > >>> Error report error_<ARCH>.tgz has been created in your top-level ATLAS > >>> directory. Be sure to include this file in any help request. > >>> cat: ../../CONFIG/error.txt: No such file or directory > >>> cat: ../../CONFIG/error.txt: No such file or directory > >>> make[1]: *** [build] Error 255 > >>> make[1]: Leaving directory `/home/magician/Desktop/ATLAS/build' > >>> make: *** [build] Error 2 > >> > >> It's very troublesome for me to build ATLAS by myself. > >> My purpose is just using SciPy on my Python. > >> Even if it's optimized not so good for my environment, it's OK. > >> > >> Is there an easy or a sure way to build and install SciPy? > > > > > > Building ATLAS is much harder than building scipy, so you should try to > > find some rpm's for it, like > > http://linuxtoolkit.blogspot.com/2010/09/installing-lapack-blas-and-atlas-o…. > > There's no problem building scipy against ATLAS from a binary install. > > > > Ralf

1 0

Re: [SciPy-User] SciPy installation troubles on CentOS 6.2
by Magician 27 May '12

27 May '12

Hi Ralf and Sergio, I thought my problems inclined to NumPy, and I posted to NumPy mailing list. But I couldn't get any answers for several days, so I'd like to ask again. I tried to build NumPy again with site.cfg, but I got these errors: > building 'numpy.core._sort' extension > compiling C sources > C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC > > compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/local/python-2.7.3/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c' > gcc: build/src.linux-x86_64-2.7/numpy/core/src/_sortmodule.c > gcc -pthread -shared build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/_sortmodule.o -L. -Lbuild/temp.linux-x86_64-2.7 -lnpymath -lm -lpython2.7 -o build/lib.linux-x86_64-2.7/numpy/core/_sort.so > /usr/bin/ld: cannot find -lpython2.7 > collect2: ld returned 1 exit status > /usr/bin/ld: cannot find -lpython2.7 > collect2: ld returned 1 exit status > error: Command "gcc -pthread -shared build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/_sortmodule.o -L. -Lbuild/temp.linux-x86_64-2.7 -lnpymath -lm -lpython2.7 -o build/lib.linux-x86_64-2.7/numpy/core/_sort.so" failed with exit status 1 Before I built NumPy, I uncommented and modified site.cfg as below: > [DEFAULT] > library_dirs = /usr/local/python-2.7.3/lib:/usr/lib64:/usr/lib64/atlas > include_dirs = /usr/local/python-2.7.3/include:/usr/include:/usr/include/atlas > > [blas_opt] > libraries = f77blas, cblas, atlas > > [lapack_opt] > libraries = lapack, f77blas, cblas, atlas And "setup.py config" dumped these messages: > Running from numpy source directory.F2PY Version 2 > blas_opt_info: > blas_mkl_info: > libraries mkl,vml,guide not found in /usr/local/python-2.7.3/lib > libraries mkl,vml,guide not found in /usr/lib64 > libraries mkl,vml,guide not found in /usr/lib64/atlas > NOT AVAILABLE > > atlas_blas_threads_info: > Setting PTATLAS=ATLAS > libraries ptf77blas,ptcblas,atlas not found in /usr/local/python-2.7.3/lib > Setting PTATLAS=ATLAS > customize GnuFCompiler > Could not locate executable g77 > Could not locate executable f77 > customize IntelFCompiler > Could not locate executable ifort > Could not locate executable ifc > customize LaheyFCompiler > Could not locate executable lf95 > customize PGroupFCompiler > Could not locate executable pgf90 > Could not locate executable pgf77 > customize AbsoftFCompiler > Could not locate executable f90 > customize NAGFCompiler > Found executable /usr/bin/f95 > customize VastFCompiler > customize CompaqFCompiler > Could not locate executable fort > customize IntelItaniumFCompiler > Could not locate executable efort > Could not locate executable efc > customize IntelEM64TFCompiler > customize Gnu95FCompiler > Found executable /usr/bin/gfortran > customize Gnu95FCompiler > customize Gnu95FCompiler using config > compiling '_configtest.c': > > /* This file is generated from numpy/distutils/system_info.py */ > void ATL_buildinfo(void); > int main(void) { > ATL_buildinfo(); > return 0; > } > > C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC > > compile options: '-c' > gcc: _configtest.c > gcc -pthread _configtest.o -L/usr/lib64/atlas -lptf77blas -lptcblas -latlas -o _configtest > ATLAS version 3.8.4 built by mockbuild on Wed Dec 7 18:04:21 GMT 2011: > UNAME : Linux c6b5.bsys.dev.centos.org 2.6.32-44.2.el6.x86_64 #1 SMP Wed Jul 21 12:48:32 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux > INSTFLG : -1 0 -a 1 > ARCHDEFS : -DATL_OS_Linux -DATL_ARCH_PII -DATL_CPUMHZ=2261 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GAS_x8664 > F2CDEFS : -DAdd_ -DF77_INTEGER=int -DStringSunStyle > CACHEEDGE: 8388608 > F77 : gfortran, version GNU Fortran (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) > F77FLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -g -Wa,--noexecstack -fPIC -m64 > SMC : gcc, version gcc (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) > SMCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -g -Wa,--noexecstack -fPIC -m64 > SKC : gcc, version gcc (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3) > SKCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -g -Wa,--noexecstack -fPIC -m64 > success! > removing: _configtest.c _configtest.o _configtest > Setting PTATLAS=ATLAS > FOUND: > libraries = ['ptf77blas', 'ptcblas', 'atlas'] > library_dirs = ['/usr/lib64/atlas'] > language = c > define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')] > include_dirs = ['/usr/include'] > > FOUND: > libraries = ['ptf77blas', 'ptcblas', 'atlas'] > library_dirs = ['/usr/lib64/atlas'] > language = c > define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')] > include_dirs = ['/usr/include'] > > lapack_opt_info: > lapack_mkl_info: > mkl_info: > libraries mkl,vml,guide not found in /usr/local/python-2.7.3/lib > libraries mkl,vml,guide not found in /usr/lib64 > libraries mkl,vml,guide not found in /usr/lib64/atlas > NOT AVAILABLE > > NOT AVAILABLE > > atlas_threads_info: > Setting PTATLAS=ATLAS > libraries ptf77blas,ptcblas,atlas not found in /usr/local/python-2.7.3/lib > libraries lapack_atlas not found in /usr/local/python-2.7.3/lib > libraries lapack_atlas not found in /usr/lib64/atlas > numpy.distutils.system_info.atlas_threads_info > Setting PTATLAS=ATLAS > Setting PTATLAS=ATLAS > FOUND: > libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas'] > library_dirs = ['/usr/lib64/atlas'] > language = f77 > define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')] > include_dirs = ['/usr/include'] > > FOUND: > libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas'] > library_dirs = ['/usr/lib64/atlas'] > language = f77 > define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')] > include_dirs = ['/usr/include'] > > running config I couldn't get enough informations about numscons/bento, so I'm still trying to build it with site.cfg and CFLAGS. How could I solve it? Magician On 2012/05/21, at 1:50, Ralf Gommers wrote: > > > On Sun, May 20, 2012 at 4:16 PM, Magician <f_magician(a)mac.com> wrote: > Hi Ralf, > > > Thanks for your advice. > I tried to install BLAS/Lapack/ATLAS as below: > > yum install blas-devel lapack-devel atlas-devel > > Next I installed NumPy as below: > > tar xzvf numpy-1.6.1.tar.gz > > cd numpy-1.6.1 > > export CFLAGS="-L/usr/local/python-2.7.3/lib" > > Note that this overrides CFLAGS instead of appending that flag to the rest. If it doesn't work without that line, you have to either specify all cflags or use numscons/bento. > > Ralf > > > > python setup.py build > > But then I got those errors: > > building 'numpy.linalg.lapack_lite' extension > > compiling C sources > > C compiler: gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -L/usr/local/python-2.7.3/lib -fPIC > > > > creating build/temp.linux-x86_64-2.7/numpy/linalg > > compile options: '-DATLAS_INFO="\"3.8.4\"" -I/usr/include -Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/local/python-2.7.3/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c' > > gcc: numpy/linalg/lapack_litemodule.c > > gcc: numpy/linalg/python_xerbla.c > > /usr/bin/gfortran -Wall -Wall -shared build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o -L/usr/lib64/atlas -L. -Lbuild/temp.linux-x86_64-2.7 -llapack -lptf77blas -lptcblas -latlas -lpython2.7 -lgfortran -o build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so > > /usr/bin/ld: cannot find -lpython2.7 > > collect2: ld returned 1 exit status > > /usr/bin/ld: cannot find -lpython2.7 > > collect2: ld returned 1 exit status > > error: Command "/usr/bin/gfortran -Wall -Wall -shared build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o -L/usr/lib64/atlas -L. -Lbuild/temp.linux-x86_64-2.7 -llapack -lptf77blas -lptcblas -latlas -lpython2.7 -lgfortran -o build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so" failed with exit status 1 > > If I haven't install BLAS/Lapack/ATLAS, NumPy will be > successfully built and installed. > > > Magician > > > On 2012/05/20, at 19:40, scipy-user-request(a)scipy.org wrote: > > > Message: 1 > > Date: Sun, 20 May 2012 10:21:12 +0200 > > From: Ralf Gommers <ralf.gommers(a)googlemail.com> > > Subject: Re: [SciPy-User] SciPy installation troubles on CentOS 6.2 > > To: SciPy Users List <scipy-user(a)scipy.org> > > Message-ID: > > <CABL7CQh+WPwpiMtO0UDKo9G01Gj38kTaWV=bSvq9eCK_qihAfQ(a)mail.gmail.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > On Sat, May 19, 2012 at 5:09 PM, Magician <f_magician(a)mac.com> wrote: > > > >> Hi All, > >> > >> > >> I'm trying to build SciPy from source code, > >> but I have some troubles. > >> > >> My environment is below: > >>> CentOS 6.2 on VMware Fusion 4.1.2 (CentOS was installed as Software > >> Development WS) > >>> Python 2.7.3 (already built from sources, installed at > >> /usr/local/python-2.7.3) > >>> NumPy 1.6.1, SciPy 0.10.1, ATLAS 3.8.4, Lapack 3.4.1 (now trying to > >> build) > >> I and my colleagues (other users) want to use recent Python, > >> so I installed Python from sources, and I can't install SciPy > >> by using yum command. > >> > >> Now I'm facing ATLAS compiling errors. > >> Configuration options are "--prefix=/usr/local/atlas-3.8.4 -Fa alg -fPIC". > >> I tried to build it for several times, and always I got errors as below: > >>> res/dgemvN_6_75 : VARIATION EXCEEDS TOLERENCE, RERUN WITH HIGHER REPS. > >>> > >>> ATL_gemvN_mm.c : 1257.99 > >>> ATL_gemvN_1x1_1.c : 581.74 > >>> ATL_gemvN_1x1_1a.c : 1589.45 > >>> ATL_gemvN_4x2_0.c : 813.13 > >>> ATL_gemvN_4x4_1.c : 755.54 > >>> make[3]: *** [res/dMVRES] Error 255 > >>> make[3]: Leaving directory > >> `/home/magician/Desktop/ATLAS/build/tune/blas/gemv' > >>> make[2]: *** > >> [/home/magician/Desktop/ATLAS/build/tune/blas/gemv/res/dMVRES] Error 2 > >>> make[2]: Leaving directory `/home/magician/Desktop/ATLAS/build/bin' > >>> ERROR 734 DURING MVTUNE!!. CHECK INSTALL_LOG/dMVTUNE.LOG FOR DETAILS. > >>> make[2]: Entering directory `/home/magician/Desktop/ATLAS/build/bin' > >>> cd /home/magician/Desktop/ATLAS/build ; make error_report > >>> make[3]: Entering directory `/home/magician/Desktop/ATLAS/build' > >>> make -f Make.top error_report > >>> make[4]: Entering directory `/home/magician/Desktop/ATLAS/build' > >>> uname -a 2>&1 >> bin/INSTALL_LOG/ERROR.LOG > >>> gcc -v 2>&1 >> bin/INSTALL_LOG/ERROR.LOG > >>> Using built-in specs. > >>> Target: x86_64-redhat-linux > >>> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man > >> --infodir=/usr/share/info --with-bugurl= > >> http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared > >> --enable-threads=posix --enable-checking=release --with-system-zlib > >> --enable-__cxa_atexit --disable-libunwind-exceptions > >> --enable-gnu-unique-object > >> --enable-languages=c,c++,objc,obj-c++,java,fortran,ada > >> --enable-java-awt=gtk --disable-dssi > >> --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre > >> --enable-libgcj-multifile --enable-java-maintainer-mode > >> --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib > >> --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 > >> --build=x86_64-redhat-linux > >>> Thread model: posix > >>> gcc version 4.4.6 20110731 (Red Hat 4.4.6-3) (GCC) > >>> gcc -V 2>&1 >> bin/INSTALL_LOG/ERROR.LOG > >>> gcc: '-V' option must have argument > >>> make[4]: [error_report] Error 1 (ignored) > >>> gcc --version 2>&1 >> bin/INSTALL_LOG/ERROR.LOG > >>> tar cf error_Corei264SSE3.tar Make.inc bin/INSTALL_LOG/* > >>> gzip --best error_Corei264SSE3.tar > >>> mv error_Corei264SSE3.tar.gz error_Corei264SSE3.tgz > >>> make[4]: Leaving directory `/home/magician/Desktop/ATLAS/build' > >>> make[3]: Leaving directory `/home/magician/Desktop/ATLAS/build' > >>> make[2]: Leaving directory `/home/magician/Desktop/ATLAS/build/bin' > >>> Error report error_<ARCH>.tgz has been created in your top-level ATLAS > >>> directory. Be sure to include this file in any help request. > >>> cat: ../../CONFIG/error.txt: No such file or directory > >>> cat: ../../CONFIG/error.txt: No such file or directory > >>> make[1]: *** [build] Error 255 > >>> make[1]: Leaving directory `/home/magician/Desktop/ATLAS/build' > >>> make: *** [build] Error 2 > >> > >> It's very troublesome for me to build ATLAS by myself. > >> My purpose is just using SciPy on my Python. > >> Even if it's optimized not so good for my environment, it's OK. > >> > >> Is there an easy or a sure way to build and install SciPy? > > > > > > Building ATLAS is much harder than building scipy, so you should try to > > find some rpm's for it, like > > http://linuxtoolkit.blogspot.com/2010/09/installing-lapack-blas-and-atlas-o…. > > There's no problem building scipy against ATLAS from a binary install. > > > > Ralf

2 2

ANN: Spyder v2.1.10
by Pierre Raybaut 26 May '12

26 May '12

Hi all, On the behalf of Spyder's development team (http://code.google.com/p/spyderlib/people/list), I'm pleased to announce that Spyder v2.1.10 has been released and is available for Windows XP/Vista/7, GNU/Linux and MacOS X: http://code.google.com/p/spyderlib/ This is a pure maintenance release -- a lot of bugs were fixed since v2.1.9: http://code.google.com/p/spyderlib/wiki/ChangeLog Spyder is a free, open-source (MIT license) interactive development environment for the Python language with advanced editing, interactive testing, debugging and introspection features. Originally designed to provide MATLAB-like features (integrated help, interactive console, variable explorer with GUI-based editors for dictionaries, NumPy arrays, ...), it is strongly oriented towards scientific computing and software development. Thanks to the `spyderlib` library, Spyder also provides powerful ready-to-use widgets: embedded Python console (example: http://packages.python.org/guiqwt/_images/sift3.png), NumPy array editor (example: http://packages.python.org/guiqwt/_images/sift2.png), dictionary editor, source code editor, etc. Description of key features with tasty screenshots can be found at: http://code.google.com/p/spyderlib/wiki/Features On Windows platforms, Spyder is also available as a stand-alone executable (don't forget to disable UAC on Vista/7). This all-in-one portable version is still experimental (for example, it does not embed sphinx -- meaning no rich text mode for the object inspector) but it should provide a working version of Spyder for Windows platforms without having to install anything else (except Python 2.x itself, of course). Don't forget to follow Spyder updates/news: * on the project website: http://code.google.com/p/spyderlib/ * and on our official blog: http://spyder-ide.blogspot.com/ Last, but not least, we welcome any contribution that helps making Spyder an efficient scientific development/computing environment. Join us to help creating your favourite environment! (http://code.google.com/p/spyderlib/wiki/NoteForContributors) Enjoy! -Pierre

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griddata not working after update to Python 2.7
by Umut Yildiz 24 May '12

24 May '12

Dear All, I used to use griddata in order to make my contourmaps. However, after I updated my Python from 2.6 to 2.7 griddata is not working anymore. I tried some workarounds but no success. The countourmap that I produced before is here. http://dl.dropbox.com/u/17983476/matplotlib/contour_dT_workingbefore.png After the Python 2.7 update, it turns to the following. http://dl.dropbox.com/u/17983476/matplotlib/contour_dT_broken.png Here is the datafile. http://dl.dropbox.com/u/17983476/matplotlib/contour_dT.dat And the associated python script (which is also below). http://dl.dropbox.com/u/17983476/matplotlib/contour_dT.py The code that I was using before is here. I had to comment out #import griddata line because this is the only way that it continues. Is this a bug in griddata, or if there are new workarounds, I would be glad to know a new method to produce my contourplots again. Thanks a lot ---------------------------- #! /usr/bin python import os import sys import math from math import * from numpy import * #import griddata from pylab import * from matplotlib.ticker import FormatStrFormatter params = {'axes.labelsize': 20, 'text.fontsize': 15, 'legend.fontsize': 14, 'xtick.labelsize': 20, 'ytick.labelsize': 20, 'text.usetex': True } rcParams.update(params) par1 = [] par2 = [] chis = [] rfile = file('contour_dT.dat','r') line = rfile.readline() data = line.split() while len(data) >1: par1.append(float(data[0])) par2.append(float(data[1])) chis.append(float(data[2])) line = rfile.readline() data = line.split() par1 = array(par1) par2 = array(par2) chis = array(chis) xi = linspace(3.2,7.8,50) yi = linspace(15,300,50) zi = griddata(par2,par1,chis,xi,yi) levels = [0.4,0.5,0.6,0.7,0.8,0.9,1.0,1.2,1.5,2,3,4,6,10,12,15,20,25,30,40,50] CS = contourf(xi,yi,zi,levels,cmap=cm.jet) CS2 = contour(CS, levels=CS.levels[::2], colors = 'r', hold='on') cbar = colorbar(CS) cbar.add_lines(CS2) savefig("contour_dT.png") show()

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Re: [SciPy-User] subclassing ndarray : i want slice to return > ndarray, not subclass
by M Daoust 24 May '12

24 May '12

> > Subclassing ndarray is a very tricky business -- I did it once and > > regretted having done it for years, because there's so much you can't do > > etc.. You're almost certainly better off with embedding an array as an > > attribute, and then forward properties etc. to it. > > Yes, it's almost always the wrong thing... I've sub-classes numpy.ndarray in some of my personal code, so I'm just hoping to understand why this is the wrong choice before I dig the hole any deeper. So it's only wrong because it's hard to do right, and you can't do certain things? (which things?) If you want a object to act mostly like a numpy.ndarray, making a sub-class *should* be the right answer. Because isn't forwarding lookups to a wrapped class just a re-implementation of the sub-classing mechanism? Isn't it also tricky to get that "wrapping subclassing" right? If you're going to sub-class something, it would be nice to use the built in sub-class machinery, for clarity... etc...

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Some numpy funcs for PyPy
by Dmitrey 24 May '12

24 May '12

hi all, maybe you're aware of numpypy - numpy port for pypy (pypy.org) - Python language implementation with dynamic compilation. Unfortunately, numpypy developmnent is very slow due to strict quality standards and some other issues, so for my purposes I have provided some missing numpypy funcs, in particular * atleast_1d, atleast_2d, hstack, vstack, cumsum, isscalar, asscalar, asfarray, flatnonzero, tile, zeros_like, ones_like, empty_like, where, searchsorted * with "axis" parameter: nan(arg)min, nan(arg)max, all, any and have got some OpenOpt / FuncDesigner functionality working faster than in CPython. File with this functions you can get here Also you may be interested in some info at http://openopt.org/PyPy Regards, Dmitrey.

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Linear algebra problem
by federico vaggi 23 May '12

23 May '12

Hi, I have a standard system, of type: AX = B Where: X is a nxm matrix. B is a mxn matrix. A is a nxn matrix. I have B and X, and I am trying to calculate A - however, B, is null matrix. Using the default numpy solvers ( http://docs.scipy.org/doc/numpy/reference/generated/numpy.linalg.lstsq.html…) I obtain the trivial correct solution of A being a null matrix. What's the most robust way to search for the solution which minimizes the residuals, while still not returning a null matrix of A? X, is usually rank deficient, so I know I won't have an exact solution. Thanks for all the help, Federico

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