Re: [SciPy-User] SciPy installation troubles on CentOS 6.2
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.... There's no problem building scipy against ATLAS from a binary install.
Ralf
On Sun, May 20, 2012 at 4:16 PM, Magician <f_magician@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@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... .
There's no problem building scipy against ATLAS from a binary install.
Ralf
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Ralf Gommers