[SciPy-user] BLAS, LAPACK, ATLAS libraries.

fie.pye@atl... fie.pye@atl...
Wed Jul 11 14:18:00 CDT 2007


>---------------------------------------------------------
>Od: David Cournapeau
>Přijato: 3.7.2007 4:16:32
>Předmět: Re: [SciPy-user] BLAS, LAPACK, ATLAS libraries.
>
>fie.pye@atlas.cz wrote:
>
>> Hello.
>
>>
>
>> I would like to install NumPy and SciPy modules. I compiled and install BLAS, LAPACK and ATLAS libraries. After installation and importing NumPy I obtained message:
>
>>
>
>>>>> import numpy
>
>> Traceback (most recent call last):
>
>> File "", line 1, in 
>
>> File "/usr/local/python/python2.5.1/lib/python2.5/site-packages/numpy/__init__.py", line 43, in 
>
>> import linalg
>
>> File "/usr/local/python/python2.5.1/lib/python2.5/site-packages/numpy/linalg/__init__.py", line 4, in 
>
>> from linalg import *
>
>> File "/usr/local/python/python2.5.1/lib/python2.5/site-packages/numpy/linalg/linalg.py", line 25, in 
>
>> from numpy.linalg import lapack_lite
>
>> ImportError: liblapack.so: cannot open shared object file: No such file or directory
>
>> It seams to me that BLAS and LAPACK installation is OK.
>
>Well, it may not be :) If you do (once you exported LD_LIBRARY_PATH):
>
>
>
>ldd 
>
>/usr/local/python/python2.5.1/lib/python2.5/site-packages/numpy/linalg/lapack_lite.so
>
>
>
>What do you get ? The most useful information, actually, is to give us 
>
>the log of python setup.py config &> log when building numpy and scipy.
>
>>
>
>> # LAPACK installation Make.inc
>
>> PLAT = _LINUX
>
>> FORTRAN = gfortran
>
>> OPTS = -funroll-all-loops -O3 -fpic
>
>> DRVOPTS = $(OPTS)
>
>> NOOPT =
>
>Here you forgot NOOPT = -fpic. Then, how did you compile atlas ? You 
>
>should try first without atlas at all, I think: compile blas, lapack, 
>
>and check that python setup.py config picks up the libraries.
>
>
>
>As a note, there are source rpms available for blas/lapack/atlas/scipy: 
>
>the binary rpms do not support CENTOS, but I think building the rpm on 
>
>CENTOS should not be too difficult. Everything is taken care of in the 
>
>rpms: options, compatible fortran ABI, full pic version of liblapack to 
>
>build complete LAPACK based on ATLAS, etc...
>
>
>
>http://software.opensuse.org/download/home:/ashigabou/ (pick up source 
>
>rpm for FC 6 or 7, this should be the more similar to centos).
>
>
>
>If this does not work, I would like to hear about it,
>
>
>
>David
>
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>
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>
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>
>
>
Hi David.

Thank you for your response. Based on your notes I recompiled BLAS and LAPACK libraries and build and installed python2.5.1 and numpy again. Unfortunately the error appears again

>>> import numpy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/python/python2.5.1/lib/python2.5/site-packages/numpy/__init__.py", line 43, in <module>
    import linalg
  File "/usr/local/python/python2.5.1/lib/python2.5/site-packages/numpy/linalg/__init__.py", line 4, in <module>
    from linalg import *
  File "/usr/local/python/python2.5.1/lib/python2.5/site-packages/numpy/linalg/linalg.py", line 25, in <module>
    from numpy.linalg import lapack_lite
ImportError: /usr/local/python/python2.5.1/lib/python2.5/site-packages/numpy/linalg/lapack_lite.so: undefined symbol: _gfortran_concat_string

Installation information:

# ldd /usr/local/python/python2.5.1/lib/python2.5/site-packages/numpy/linalg/lapack_lite.so
	libg2c.so.0 => /usr/lib64/libg2c.so.0 (0x00002aaaaae52000)
	libm.so.6 => /lib64/libm.so.6 (0x00002aaaab073000)
	libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002aaaab2f6000)
	libc.so.6 => /lib64/libc.so.6 (0x00002aaaab504000)
	/lib64/ld-linux-x86-64.so.2 (0x0000555555554000)

# /usr/local/lib64/blas
-rw-r--r-- 1 root root 612242 Jul 10 23:25 libblas.a
-rwxr-xr-x 1 root root 358087 Jul 10 23:25 libblas.so
lrwxrwxrwx 1 root root      9 Jul 10 23:27 libfblas.a -> libblas.a

# /usr/local/lib64/lapack
lrwxrwxrwx 1 root root       11 Jul 10 23:36 libflapack.a -> liblapack.a
-rw-r--r-- 1 root root 10938922 Jul 10 23:34 liblapack.a
-rwxr-xr-x 1 root root  6948895 Jul 10 23:38 liblapack.so

for python2.5.1 configuration see attached file: python_config.log.gz
for numpy building and installation see attached files: numpy_build.log.gz, numpy_install.log.gz

fie pye


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