[SciPy-User] SciPy installation troubles on CentOS 6.2

Sergio Rojas sergio_r@mail....
Sun May 20 15:34:44 CDT 2012


Magician, since I did not see any mention of it, I think you are missing to include in your build up a "site.cfg" file (see for instance http://www.scipy.org/Installing_SciPy/Linux Step 4: Build numpy(1.5.0) ). In that file you need to specify where your libraries are. That file needs to be used in building both Numpy and Scipy. Sergio ---------------------------------------------------------------------- Message: 1 Date: Sun, 20 May 2012 23:16:48 +0900 From: Magician <f_magician@mac.com> Subject: Re: [SciPy-User] SciPy installation troubles on CentOS 6.2 To: ralf.gommers@googlemail.com Cc: scipy-user@scipy.org Message-ID: <C3368B14-EED1-4E87-A7E9-80F76990A0E2@mac.com> Content-Type: text/plain; CHARSET=US-ASCII 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" > 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@scipy.org wrote: > Message: 1 > Date: Sun, 20 May 2012 10:21:12 +0200 > From: Ralf Gommers <ralf.gommers@googlemail.com> > Subject: Re: [SciPy-User] SciPy installation troubles on CentOS 6.2 > To: SciPy Users List <scipy-user@scipy.org> > Message-ID: > <CABL7CQh+WPwpiMtO0UDKo9G01Gj38kTaWV=bSvq9eCK_qihAfQ@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > On Sat, May 19, 2012 at 5:09 PM, Magician <f_magician@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-on.html. > There's no problem building scipy against ATLAS from a binary install. > > Ralf -
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