[SciPy-User] SciPy installation troubles on CentOS 6.2

Sun May 27 13:21:11 EDT 2012

> 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 at 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 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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