There are ATLAS libraries installed on the system that are incompatible with the scipy install. I have built my own ATLAS/LAPACK libraries but how do I block setup.py from looking in /usr/lib and /usr/local/lib? I have tried setting $BLAS and $LAPACK, but that doesn't help. I still get Import Errors with the wrong library listed. Any help is appreciated. Eric
Hi Eric, On Monday 02 May 2005 2:11 pm, Eric Zollars wrote:
There are ATLAS libraries installed on the system that are incompatible with the scipy install. I have built my own ATLAS/LAPACK libraries but how do I block setup.py from looking in /usr/lib and /usr/local/lib? I have tried setting $BLAS and $LAPACK, but that doesn't help. I still get Import Errors with the wrong library listed.
Try editing scipy_core/scipy_distutils/sample_site.cfg and save it as site.cfg. Also, if you are not installing from CVS, you need to edit six lines in system_info.py, in that same directory, starting at line #285 try: f = __file__ except NameError,msg: f = sys.argv[0] cf = os.path.join(os.path.split(os.path.abspath(f))[0], 'site.cfg') hope this helps, Darren -- Darren S. Dale Bard Hall Department of Materials Science and Engineering Cornell University Ithaca, NY. 14850 dd55@cornell.edu
On Mon, 2005-05-02 at 11:26, Darren Dale wrote:
Hi Eric,
On Monday 02 May 2005 2:11 pm, Eric Zollars wrote:
There are ATLAS libraries installed on the system that are incompatible with the scipy install. I have built my own ATLAS/LAPACK libraries but how do I block setup.py from looking in /usr/lib and /usr/local/lib? I have tried setting $BLAS and $LAPACK, but that doesn't help. I still get Import Errors with the wrong library listed.
Try editing scipy_core/scipy_distutils/sample_site.cfg and save it as site.cfg. Also, if you are not installing from CVS, you need to edit six lines in system_info.py, in that same directory, starting at line #285
try: f = __file__ except NameError,msg: f = sys.argv[0] cf = os.path.join(os.path.split(os.path.abspath(f))[0], 'site.cfg')
hope this helps, Darren
Thanks, that blocked setup.py from getting the wrong libs but nothing I do seems to get scipy installed. I had to modify site.cfg: [DEFAULT] library_dirs = /ul/zollars/lib include_dirs = /ul/zollars/include because setup continued to find the bad libs when the default system lib directories were listed. Will this be a problem? [atlas] library_dirs = /ul/zollars/opt/ATLAS/lib/Linux_g77_32 atlas_libs = lapack_g77_32, f77blas_g77_32, cblas_g77_32,atlas_g77_32 I am getting this with setup.py install: gcc -pthread -shared build/temp.linux-ppc64-2.4/build/src/atlas_version_-0x74e85a32.o -L/ul/zollars/opt/ATLAS/lib/Linux_g77_32 -latlas_g77_32 -o build/temp.linux-ppc64-2.4/atlas_version.so FOUND: libraries = ['lapack_g77_32', 'f77blas_g77_32', 'cblas_g77_32', 'atlas_g77_32'] library_dirs = ['/ul/zollars/opt/ATLAS/lib/Linux_g77_32'] language = c define_macros = [('ATLAS_INFO', '"\\"3.4.2\\""')] lapack_opt_info: atlas_threads_info: scipy_distutils.system_info.atlas_threads_info scipy_core/scipy_distutils/system_info.py:598: UserWarning: ********************************************************************* Could not find lapack library within the ATLAS installation. ********************************************************************* I built the full lapack library according to the instructions with ATLAS. What else can I check? I have also tried setting the $BLAS and $LAPACK variables which do lead to a successful scipy install, but then fails the t=scipy.test(level=1). In this case the errors indicate problems with the scipy.linalg module, further suggesting problems with LAPACK. But I don't know what else to check. Any suggestions? Eric
On Monday 02 May 2005 8:42 pm, you wrote:
Thanks, that blocked setup.py from getting the wrong libs but nothing I do seems to get scipy installed.
I had to modify site.cfg: [DEFAULT] library_dirs = /ul/zollars/lib include_dirs = /ul/zollars/include because setup continued to find the bad libs when the default system lib directories were listed. Will this be a problem?
[atlas] library_dirs = /ul/zollars/opt/ATLAS/lib/Linux_g77_32 atlas_libs = lapack_g77_32, f77blas_g77_32, cblas_g77_32,atlas_g77_32 I am getting this with setup.py install:
gcc -pthread -shared build/temp.linux-ppc64-2.4/build/src/atlas_version_-0x74e85a32.o -L/ul/zollars/opt/ATLAS/lib/Linux_g77_32 -latlas_g77_32 -o build/temp.linux-ppc64-2.4/atlas_version.so FOUND: libraries = ['lapack_g77_32', 'f77blas_g77_32', 'cblas_g77_32', 'atlas_g77_32'] library_dirs = ['/ul/zollars/opt/ATLAS/lib/Linux_g77_32'] language = c define_macros = [('ATLAS_INFO', '"\\"3.4.2\\""')]
lapack_opt_info: atlas_threads_info: scipy_distutils.system_info.atlas_threads_info scipy_core/scipy_distutils/system_info.py:598: UserWarning: ********************************************************************* Could not find lapack library within the ATLAS installation. *********************************************************************
I built the full lapack library according to the instructions with ATLAS. What else can I check?
I have also tried setting the $BLAS and $LAPACK variables which do lead to a successful scipy install, but then fails the t=scipy.test(level=1). In this case the errors indicate problems with the scipy.linalg module, further suggesting problems with LAPACK. But I don't know what else to check.
It looks like there is a problem with some of your libraries. Are you sure you built the full libraries, and successfully? Just for kicks, how big are they? I havent tried building Scipy against 3.4.2, can you upgrade? $ ls -lh /usr/lib/lapack/atlas/ total 9.6M -rw-r--r-- 1 root root 5.5M Apr 11 15:31 liblapack.a -rwxr-xr-x 1 root root 855 Apr 11 15:31 liblapack.la lrwxrwxrwx 1 root root 18 Apr 11 15:31 liblapack.so -> liblapack.so.0.0.0 lrwxrwxrwx 1 root root 18 Apr 11 15:31 liblapack.so.0 -> liblapack.so.0.0.0 -rwxr-xr-x 1 root root 4.1M Apr 11 15:31 liblapack.so.0.0.0 $ ls -lh /usr/lib/blas/atlas/ total 944K -rw-r--r-- 1 root root 356K Apr 11 15:17 libblas.a -rwxr-xr-x 1 root root 824 Apr 11 15:17 libblas.la lrwxrwxrwx 1 root root 16 Apr 11 15:17 libblas.so -> libblas.so.0.0.0 lrwxrwxrwx 1 root root 16 Apr 11 15:17 libblas.so.0 -> libblas.so.0.0.0 -rwxr-xr-x 1 root root 139K Apr 11 15:17 libblas.so.0.0.0 -rw-r--r-- 1 root root 299K Apr 11 15:17 libcblas.a -rwxr-xr-x 1 root root 825 Apr 11 15:17 libcblas.la lrwxrwxrwx 1 root root 17 Apr 11 15:17 libcblas.so -> libcblas.so.0.0.0 lrwxrwxrwx 1 root root 17 Apr 11 15:17 libcblas.so.0 -> libcblas.so.0.0.0 -rwxr-xr-x 1 root root 138K Apr 11 15:17 libcblas.so.0.0.0 -- Darren S. Dale Bard Hall Department of Materials Science and Engineering Cornell University Ithaca, NY. 14850 dd55@cornell.edu
It looks like there is a problem with some of your libraries. Are you sure you built the full libraries, and successfully? Just for kicks, how big are they? I havent tried building Scipy against 3.4.2, can you upgrade?
$ ls -lh /usr/lib/lapack/atlas/ total 9.6M -rw-r--r-- 1 root root 5.5M Apr 11 15:31 liblapack.a -rwxr-xr-x 1 root root 855 Apr 11 15:31 liblapack.la lrwxrwxrwx 1 root root 18 Apr 11 15:31 liblapack.so -> liblapack.so.0.0.0 lrwxrwxrwx 1 root root 18 Apr 11 15:31 liblapack.so.0 -> liblapack.so.0.0.0 -rwxr-xr-x 1 root root 4.1M Apr 11 15:31 liblapack.so.0.0.0
$ ls -lh /usr/lib/blas/atlas/ total 944K -rw-r--r-- 1 root root 356K Apr 11 15:17 libblas.a -rwxr-xr-x 1 root root 824 Apr 11 15:17 libblas.la lrwxrwxrwx 1 root root 16 Apr 11 15:17 libblas.so -> libblas.so.0.0.0 lrwxrwxrwx 1 root root 16 Apr 11 15:17 libblas.so.0 -> libblas.so.0.0.0 -rwxr-xr-x 1 root root 139K Apr 11 15:17 libblas.so.0.0.0 -rw-r--r-- 1 root root 299K Apr 11 15:17 libcblas.a -rwxr-xr-x 1 root root 825 Apr 11 15:17 libcblas.la lrwxrwxrwx 1 root root 17 Apr 11 15:17 libcblas.so -> libcblas.so.0.0.0 lrwxrwxrwx 1 root root 17 Apr 11 15:17 libcblas.so.0 -> libcblas.so.0.0.0 -rwxr-xr-x 1 root root 138K Apr 11 15:17 libcblas.so.0.0.0
Thank you for your continued help Darren. ls -lh -rw-r--r-- 1 zollars mayo 8.0M May 2 15:41 libatlas_g77_32.a -rw-r--r-- 1 zollars mayo 282K May 2 15:41 libcblas_g77_32.a -rw-r--r-- 1 zollars mayo 334K May 2 15:41 libf77blas_g77_32.a -rw-r--r-- 1 zollars mayo 6.6M May 2 15:41 liblapack_g77_32.a -rw-r--r-- 1 zollars mayo 319K May 2 15:41 libtstatlas_g77_32.a As you can see the lapack library has been supplemented with the full lapack set of routines. I agree I think the problem is here. I need to confirm that I am doing everything correct with g77/gcc interoperability. In my ATLAS Makefile I have: F2CDEFS = -DAdd__ -DStringSunStyle The only libraries linked in are: LIBS = -lm (i.e. no g2c,f2c,etc.) The LAPACK makefile does not have any of these options. My suspicion is that -DAdd__ may have something to do with the problem. In the meantime I have built scipy with BLAS_SRC and LAPACK_SRC. Also, I am sticking with ATLAS 3.4.2 for now because 3.6 requires gcc-3.3 and I haven't been motivated to attempt a local build of gcc. Thanks again. Eric
On Tuesday 03 May 2005 2:43 pm, Eric Zollars wrote:
It looks like there is a problem with some of your libraries. Are you sure you built the full libraries, and successfully? Just for kicks, how big are they? I havent tried building Scipy against 3.4.2, can you upgrade?
$ ls -lh /usr/lib/lapack/atlas/ total 9.6M -rw-r--r-- 1 root root 5.5M Apr 11 15:31 liblapack.a -rwxr-xr-x 1 root root 855 Apr 11 15:31 liblapack.la lrwxrwxrwx 1 root root 18 Apr 11 15:31 liblapack.so -> liblapack.so.0.0.0 lrwxrwxrwx 1 root root 18 Apr 11 15:31 liblapack.so.0 -> liblapack.so.0.0.0 -rwxr-xr-x 1 root root 4.1M Apr 11 15:31 liblapack.so.0.0.0
$ ls -lh /usr/lib/blas/atlas/ total 944K -rw-r--r-- 1 root root 356K Apr 11 15:17 libblas.a -rwxr-xr-x 1 root root 824 Apr 11 15:17 libblas.la lrwxrwxrwx 1 root root 16 Apr 11 15:17 libblas.so -> libblas.so.0.0.0 lrwxrwxrwx 1 root root 16 Apr 11 15:17 libblas.so.0 -> libblas.so.0.0.0 -rwxr-xr-x 1 root root 139K Apr 11 15:17 libblas.so.0.0.0 -rw-r--r-- 1 root root 299K Apr 11 15:17 libcblas.a -rwxr-xr-x 1 root root 825 Apr 11 15:17 libcblas.la lrwxrwxrwx 1 root root 17 Apr 11 15:17 libcblas.so -> libcblas.so.0.0.0 lrwxrwxrwx 1 root root 17 Apr 11 15:17 libcblas.so.0 -> libcblas.so.0.0.0 -rwxr-xr-x 1 root root 138K Apr 11 15:17 libcblas.so.0.0.0
Thank you for your continued help Darren. ls -lh -rw-r--r-- 1 zollars mayo 8.0M May 2 15:41 libatlas_g77_32.a -rw-r--r-- 1 zollars mayo 282K May 2 15:41 libcblas_g77_32.a -rw-r--r-- 1 zollars mayo 334K May 2 15:41 libf77blas_g77_32.a -rw-r--r-- 1 zollars mayo 6.6M May 2 15:41 liblapack_g77_32.a -rw-r--r-- 1 zollars mayo 319K May 2 15:41 libtstatlas_g77_32.a
As you can see the lapack library has been supplemented with the full lapack set of routines. I agree I think the problem is here. I need to confirm that I am doing everything correct with g77/gcc interoperability.
In my ATLAS Makefile I have: F2CDEFS = -DAdd__ -DStringSunStyle The only libraries linked in are: LIBS = -lm (i.e. no g2c,f2c,etc.)
The LAPACK makefile does not have any of these options. My suspicion is that -DAdd__ may have something to do with the problem.
In the meantime I have built scipy with BLAS_SRC and LAPACK_SRC. Also, I am sticking with ATLAS 3.4.2 for now because 3.6 requires gcc-3.3 and I haven't been motivated to attempt a local build of gcc.
I sorry I can't help you with the ATLAS compile issues. I use Gentoo, and for better or worse have never edited a makefile. Why do I feel ashamed of this? -- Darren S. Dale Bard Hall Department of Materials Science and Engineering Cornell University Ithaca, NY. 14850 dd55@cornell.edu
participants (2)
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Darren Dale -
Eric Zollars