[SciPy-User] SciPy installation troubles on CentOS 6.2
Magician
f_magician at mac.com
Sat May 26 22:05:27 EDT 2012
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 at 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 at scipy.org wrote:
>
> > Message: 1
> > Date: Sun, 20 May 2012 10:21:12 +0200
> > From: Ralf Gommers <ralf.gommers at googlemail.com>
> > Subject: Re: [SciPy-User] SciPy installation troubles on CentOS 6.2
> > To: SciPy Users List <scipy-user at scipy.org>
> > Message-ID:
> > <CABL7CQh+WPwpiMtO0UDKo9G01Gj38kTaWV=bSvq9eCK_qihAfQ at mail.gmail.com>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > On Sat, May 19, 2012 at 5:09 PM, Magician <f_magician at 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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