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@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
On Sun, May 27, 2012 at 4:05 AM, Magician <f_magician@mac.com> wrote:
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.
You specified the additional library dir you need in site.cfg. You therefore don't need to use CFLAGS anymore. This is probably still what's going wrong, because the build error says it can't find Python itself anymore. So make sure that CFLAGS is not defined and try again. Ralf
Hi Ralf, Maybe I'm misunderstanding how to handle site.cfg, so I'm trying easy tests about CFLAGS and site.cfg. These tests are done on independent snapshots (already installed Python 2.7.3) of VMware. My libpython2.7.so and libpython2.7.so.1.0 are on /usr/local/python-2.7.3/lib. Lapack and ATLAS are not installed yet. With CFLAGS:
export CFLAGS="-L/usr/local/python-2.7.3/lib" python setup.py config
Running from numpy source directory.non-existing path in 'numpy/distutils': 'site.cfg' 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/local/lib64 libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib64 libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE
atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /usr/local/python-2.7.3/lib libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64 libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib libraries ptf77blas,ptcblas,atlas not found in /usr/lib64/atlas libraries ptf77blas,ptcblas,atlas not found in /usr/lib64/sse2 libraries ptf77blas,ptcblas,atlas not found in /usr/lib64 libraries ptf77blas,ptcblas,atlas not found in /usr/lib NOT AVAILABLE
atlas_blas_info: libraries f77blas,cblas,atlas not found in /usr/local/python-2.7.3/lib libraries f77blas,cblas,atlas not found in /usr/local/lib64 libraries f77blas,cblas,atlas not found in /usr/local/lib libraries f77blas,cblas,atlas not found in /usr/lib64/atlas libraries f77blas,cblas,atlas not found in /usr/lib64/sse2 libraries f77blas,cblas,atlas not found in /usr/lib64 libraries f77blas,cblas,atlas not found in /usr/lib NOT AVAILABLE
/home/magician/Desktop/numpy-1.6.1/numpy/distutils/system_info.py:1414: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) blas_info: libraries blas not found in /usr/local/python-2.7.3/lib libraries blas not found in /usr/local/lib64 libraries blas not found in /usr/local/lib libraries blas not found in /usr/lib64 libraries blas not found in /usr/lib NOT AVAILABLE
/home/magician/Desktop/numpy-1.6.1/numpy/distutils/system_info.py:1423: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. warnings.warn(BlasNotFoundError.__doc__) blas_src_info: NOT AVAILABLE
/home/magician/Desktop/numpy-1.6.1/numpy/distutils/system_info.py:1426: UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. warnings.warn(BlasSrcNotFoundError.__doc__) NOT AVAILABLE
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/local/lib64 libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib64 libraries mkl,vml,guide not found in /usr/lib 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 ptf77blas,ptcblas,atlas not found in /usr/local/lib64 libraries lapack_atlas not found in /usr/local/lib64 libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib libraries ptf77blas,ptcblas,atlas not found in /usr/lib64/atlas libraries lapack_atlas not found in /usr/lib64/atlas libraries ptf77blas,ptcblas,atlas not found in /usr/lib64/sse2 libraries lapack_atlas not found in /usr/lib64/sse2 libraries ptf77blas,ptcblas,atlas not found in /usr/lib64 libraries lapack_atlas not found in /usr/lib64 libraries ptf77blas,ptcblas,atlas not found in /usr/lib libraries lapack_atlas not found in /usr/lib numpy.distutils.system_info.atlas_threads_info NOT AVAILABLE
atlas_info: libraries f77blas,cblas,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 f77blas,cblas,atlas not found in /usr/local/lib64 libraries lapack_atlas not found in /usr/local/lib64 libraries f77blas,cblas,atlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib libraries f77blas,cblas,atlas not found in /usr/lib64/atlas libraries lapack_atlas not found in /usr/lib64/atlas libraries f77blas,cblas,atlas not found in /usr/lib64/sse2 libraries lapack_atlas not found in /usr/lib64/sse2 libraries f77blas,cblas,atlas not found in /usr/lib64 libraries lapack_atlas not found in /usr/lib64 libraries f77blas,cblas,atlas not found in /usr/lib libraries lapack_atlas not found in /usr/lib numpy.distutils.system_info.atlas_info NOT AVAILABLE
/home/magician/Desktop/numpy-1.6.1/numpy/distutils/system_info.py:1330: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) lapack_info: libraries lapack not found in /usr/local/python-2.7.3/lib libraries lapack not found in /usr/local/lib64 libraries lapack not found in /usr/local/lib libraries lapack not found in /usr/lib64 libraries lapack not found in /usr/lib NOT AVAILABLE
/home/magician/Desktop/numpy-1.6.1/numpy/distutils/system_info.py:1341: UserWarning: Lapack (http://www.netlib.org/lapack/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [lapack]) or by setting the LAPACK environment variable. warnings.warn(LapackNotFoundError.__doc__) lapack_src_info: NOT AVAILABLE
/home/magician/Desktop/numpy-1.6.1/numpy/distutils/system_info.py:1344: UserWarning: Lapack (http://www.netlib.org/lapack/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [lapack_src]) or by setting the LAPACK_SRC environment variable. warnings.warn(LapackSrcNotFoundError.__doc__) NOT AVAILABLE
running config Then I executed "python setup.py build", NumPy was built successfully.
Next with site.cfg:
[DEFAULT] library_dirs = /usr/local/python-2.7.3/lib include_dirs = /usr/local/python-2.7.3/include
cp site.cfg.example site.cfg vi site.cfg python setup.py config
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 NOT AVAILABLE
atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /usr/local/python-2.7.3/lib NOT AVAILABLE
atlas_blas_info: libraries f77blas,cblas,atlas not found in /usr/local/python-2.7.3/lib NOT AVAILABLE
/home/magician/Desktop/numpy-1.6.1/numpy/distutils/system_info.py:1414: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) blas_info: libraries blas not found in /usr/local/python-2.7.3/lib NOT AVAILABLE
/home/magician/Desktop/numpy-1.6.1/numpy/distutils/system_info.py:1423: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. warnings.warn(BlasNotFoundError.__doc__) blas_src_info: NOT AVAILABLE
/home/magician/Desktop/numpy-1.6.1/numpy/distutils/system_info.py:1426: UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. warnings.warn(BlasSrcNotFoundError.__doc__) NOT AVAILABLE
lapack_opt_info: lapack_mkl_info: mkl_info: libraries mkl,vml,guide not found in /usr/local/python-2.7.3/lib 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 numpy.distutils.system_info.atlas_threads_info NOT AVAILABLE
atlas_info: libraries f77blas,cblas,atlas not found in /usr/local/python-2.7.3/lib libraries lapack_atlas not found in /usr/local/python-2.7.3/lib numpy.distutils.system_info.atlas_info NOT AVAILABLE
/home/magician/Desktop/numpy-1.6.1/numpy/distutils/system_info.py:1330: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) lapack_info: libraries lapack not found in /usr/local/python-2.7.3/lib NOT AVAILABLE
/home/magician/Desktop/numpy-1.6.1/numpy/distutils/system_info.py:1341: UserWarning: Lapack (http://www.netlib.org/lapack/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [lapack]) or by setting the LAPACK environment variable. warnings.warn(LapackNotFoundError.__doc__) lapack_src_info: NOT AVAILABLE
/home/magician/Desktop/numpy-1.6.1/numpy/distutils/system_info.py:1344: UserWarning: Lapack (http://www.netlib.org/lapack/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [lapack_src]) or by setting the LAPACK_SRC environment variable. warnings.warn(LapackSrcNotFoundError.__doc__) NOT AVAILABLE
running config Then I executed "python setup.py build", I got errors about -lpython which I posted before.
If I edit site.cfg as below, config messages become same as CFLAGS, but same -lpython errors are dumped:
vi site.cfg
[DEFAULT] library_dirs = /usr/local/python-2.7.3/lib:/usr/local/lib64:/usr/local/lib:/usr/lib64:/usr/lib include_dirs = /usr/local/python-2.7.3/include
Magician On 2012/05/27, at 17:16, Ralf Gommers wrote:
On Sun, May 27, 2012 at 4:05 AM, Magician <f_magician@mac.com> wrote:
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.
You specified the additional library dir you need in site.cfg. You therefore don't need to use CFLAGS anymore. This is probably still what's going wrong, because the build error says it can't find Python itself anymore. So make sure that CFLAGS is not defined and try again.
Ralf
participants (2)
-
Magician -
Ralf Gommers