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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