David,

You should instead specificaly link the GOTO library to numpy, by customizing the site.cfg,

That was one of the many things I tried came to the list. Peter Ashford

Eloi,

please below a script that will build numpy using a relevant site.cfg for your configuration (you need to update GOTODIR and LAPACKDIR and PYTHONDIR):

#copy site.cfg cp ./site.cfg PYTHONDIR/lib/python2.6/site-packages/numpy/distutils/.

I believe this needs a $ prior to PYTHONDIR. I tried this, and the benchmark still came in at 8.5S. Any ideas? How long should the following benchmark take on a Core-i7 930, with Atlas or Goto? time python -c "import numpy as N; a=N.random.randn(1000, 1000); N.dot(a, a)" Thank you. Peter Ashford

Peter, As mentionned, you need to replace the values of GOTODIR, LAPACKDIR and PYTHONDIR in this script with the ones matching your environment. Eloi On Wednesday 18 August 2010 00:39:48 ashford@whisperpc.com wrote:

Eloi,

...

please below a script that will build numpy using a relevant site.cfg for your configuration (you need to update GOTODIR and LAPACKDIR and PYTHONDIR):

#copy site.cfg cp ./site.cfg PYTHONDIR/lib/python2.6/site-packages/numpy/distutils/.

I believe this needs a $ prior to PYTHONDIR.

I tried this, and the benchmark still came in at 8.5S.

Any ideas? How long should the following benchmark take on a Core-i7 930, with Atlas or Goto?

time python -c "import numpy as N; a=N.random.randn(1000, 1000); N.dot(a, a)"

Thank you.

Peter Ashford

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-- Eloi Gaudry Free Field Technologies Company Website: http://www.fft.be Company Phone: +32 10 487 959

I'm no expert, but I just pulled off the scipy+numpy+GotoBLAS2 installation.

From what I gather, the Makefile for libgoto2 downloads and compiles the generic lapack from netlib. It also wraps lapack into libgoto2.so/.a. I believe the idea is as long as the BLAS implementation is fast(TM), the lapack performance will be good.

To wit*, what I did was to tell numpy where libgoto2 was: env BLAS=/path/to/libgoto2.so python setup.py install Scipy also wants the path to lapack, which is wrapped inside libgoto2: env BLAS=/path/to/libgoto2.so LAPACK=/path/to/libgoto2.so python setup.py install Afterwards, I added the path to LD_LIBRARY_PATH. This was on a linux cluster, if that matters. At any rate, I can testify that it was not a big job to get numpy and scipy working with goto blas. Good luck, Paul. *) I have notes on this on a different computer, but not available right now. On Tue, Mar 22, 2011 at 10:13 AM, Giuseppe Aprea wrote:

Hi all,

I wonder if Peter finally got Gotoblas working with numpy. I am trying with gotoblas 1.13 installed in the same way:

$ ls -R .: include lib

./include: goto

./include/goto: blaswrap.h cblas.h clapack.h f2c.h

./lib: libgoto2.a libgoto2_nehalemp-r1.13.a libgoto2_nehalemp-r1.13.so libgoto2.so

and numpy 1.5.1 with this site.cfg

[DEFAULT] library_dirs = /usr/local/gcc/4.5.2/gcc/lib64:/usr/local/gcc/4.5.2/gcc/lib:/usr/local/gcc/4.5.2/gcc/lib32:/usr/local/gcc/4.5.2/gotoblas2/1.13/lib:/usr/local/gcc/4.5.2/suiteSparse/3.6.0/lib:/usr/local/gcc/4.5.2/fftw/3.2.2/lib include_dirs = /usr/local/gcc/4.5.2/gcc/include:/usr/local/gcc/4.5.2/gotoblas2/1.13/include/goto:/usr/local/gcc/4.5.2/suiteSparse/3.6.0/include:/usr/local/gcc/4.5.2/fftw/3.2.2/include search_static_first = 1 [blas_opt] libraries = goto2 language = fortran [lapack_opt] libraries = goto2 language = fortran [amd] amd_libs = amd [umfpack] umfpack_libs = umfpack [fftw] libraries = fftw3

(I also tried without "_opt" and "language = fortran"); I used goto2 for lapack because I read lapack should be included in libgoto (anyway things do not change using "lapack"). I am quite sure the system is not using my goto-lapack stuff since every time I buid i get:

building extension "numpy.numarray._capi" sources building extension "numpy.fft.fftpack_lite" sources building extension "numpy.linalg.lapack_lite" sources creating build/src.linux-x86_64-2.7/numpy/linalg *### Warning: Using unoptimized lapack ###* * adding 'numpy/linalg/lapack_litemodule.c' to sources.* adding 'numpy/linalg/python_xerbla.c' to sources. adding 'numpy/linalg/zlapack_lite.c' to sources. adding 'numpy/linalg/dlapack_lite.c' to sources. adding 'numpy/linalg/blas_lite.c' to sources. adding 'numpy/linalg/dlamch.c' to sources. adding 'numpy/linalg/f2c_lite.c' to sources. building extension "numpy.random.mtrand" sources creating build/src.linux-x86_64-2.7/numpy/random C compiler: /usr/local/gcc/4.5.2//gcc/bin/gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -O1 -pthread -fPIC -march=native -mtune=native -I/usr/local/gcc/4.5.2//gcc/include -I/usr/local/gcc/4.5.2//suiteSparse/3.6.0/include -I/usr/local/gcc/4.5.2//fftw/3.2.2/include -fPIC

during numpy installation (which ends successfully). Moreover I cannot see any -lgoto2 as I would have expected. Incidentally, I cannot see -lamd, -lumfpack, -lfftw3 (or any reference to amd, umfpack, fftw3) neither, although there seems to be something to handle them in system_info.py. The failure is so complete that I must have done some big mistake but I can't correct my site.cfg even after searching the internet. This seems to be one of the major discussion about this topic so I am asking here for some help, please. Is the problem related with site.cfg or with gotoblas2 installation? Is it true that gotoblas2 hosts a full lapack inside?

thank you very much!

giuseppe

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Dear Paul Anton, thanks a lot for your suggestion. I was also successful with [blas] libraries = blas library_dirs = $PREFIX/gotoblas2/lib [lapack] libraries = lapack library_dirs = $PREFIX/gotoblas2/lib but I had compile clapack as a shared library and place a symbolic link ln -s $PREFIX/gotoblas2/lib/libgoto2.so $PREFIX/gotoblas2/lib/libblas.so I think your solution works better (the only difference is that I had to define LAPACK variable before installing numpy to avoid that warning about an optimized lapack lib missing), but what about source dirs? do you also set BLAS_SRC and LAPACK_SRC? how? cheers On Tue, Mar 22, 2011 at 11:18 PM, Paul Anton Letnes < paul.anton.letnes@gmail.com> wrote:

I'm no expert, but I just pulled off the scipy+numpy+GotoBLAS2 installation. From what I gather, the Makefile for libgoto2 downloads and compiles the generic lapack from netlib. It also wraps lapack into libgoto2.so/.a. I believe the idea is as long as the BLAS implementation is fast(TM), the lapack performance will be good.

To wit*, what I did was to tell numpy where libgoto2 was: env BLAS=/path/to/libgoto2.so python setup.py install Scipy also wants the path to lapack, which is wrapped inside libgoto2: env BLAS=/path/to/libgoto2.so LAPACK=/path/to/libgoto2.so python setup.py install Afterwards, I added the path to LD_LIBRARY_PATH. This was on a linux cluster, if that matters. At any rate, I can testify that it was not a big job to get numpy and scipy working with goto blas.

Good luck, Paul.

*) I have notes on this on a different computer, but not available right now.

On Tue, Mar 22, 2011 at 10:13 AM, Giuseppe Aprea

...

wrote:

...

Hi all,

I wonder if Peter finally got Gotoblas working with numpy. I am trying with gotoblas 1.13 installed in the same way:

$ ls -R .: include lib

./include: goto

./include/goto: blaswrap.h cblas.h clapack.h f2c.h

./lib: libgoto2.a libgoto2_nehalemp-r1.13.a libgoto2_nehalemp-r1.13.so libgoto2.so

and numpy 1.5.1 with this site.cfg

[DEFAULT] library_dirs = /usr/local/gcc/4.5.2/gcc/lib64:/usr/local/gcc/4.5.2/gcc/lib:/usr/local/gcc/4.5.2/gcc/lib32:/usr/local/gcc/4.5.2/gotoblas2/1.13/lib:/usr/local/gcc/4.5.2/suiteSparse/3.6.0/lib:/usr/local/gcc/4.5.2/fftw/3.2.2/lib include_dirs = /usr/local/gcc/4.5.2/gcc/include:/usr/local/gcc/4.5.2/gotoblas2/1.13/include/goto:/usr/local/gcc/4.5.2/suiteSparse/3.6.0/include:/usr/local/gcc/4.5.2/fftw/3.2.2/include search_static_first = 1 [blas_opt] libraries = goto2 language = fortran [lapack_opt] libraries = goto2 language = fortran [amd] amd_libs = amd [umfpack] umfpack_libs = umfpack [fftw] libraries = fftw3

(I also tried without "_opt" and "language = fortran"); I used goto2 for lapack because I read lapack should be included in libgoto (anyway things do not change using "lapack"). I am quite sure the system is not using my goto-lapack stuff since every time I buid i get:

building extension "numpy.numarray._capi" sources building extension "numpy.fft.fftpack_lite" sources building extension "numpy.linalg.lapack_lite" sources creating build/src.linux-x86_64-2.7/numpy/linalg *### Warning: Using unoptimized lapack ###* * adding 'numpy/linalg/lapack_litemodule.c' to sources.* adding 'numpy/linalg/python_xerbla.c' to sources. adding 'numpy/linalg/zlapack_lite.c' to sources. adding 'numpy/linalg/dlapack_lite.c' to sources. adding 'numpy/linalg/blas_lite.c' to sources. adding 'numpy/linalg/dlamch.c' to sources. adding 'numpy/linalg/f2c_lite.c' to sources. building extension "numpy.random.mtrand" sources creating build/src.linux-x86_64-2.7/numpy/random C compiler: /usr/local/gcc/4.5.2//gcc/bin/gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -O1 -pthread -fPIC -march=native -mtune=native -I/usr/local/gcc/4.5.2//gcc/include -I/usr/local/gcc/4.5.2//suiteSparse/3.6.0/include -I/usr/local/gcc/4.5.2//fftw/3.2.2/include -fPIC

during numpy installation (which ends successfully). Moreover I cannot see any -lgoto2 as I would have expected. Incidentally, I cannot see -lamd, -lumfpack, -lfftw3 (or any reference to amd, umfpack, fftw3) neither, although there seems to be something to handle them in system_info.py. The failure is so complete that I must have done some big mistake but I can't correct my site.cfg even after searching the internet. This seems to be one of the major discussion about this topic so I am asking here for some help, please. Is the problem related with site.cfg or with gotoblas2 installation? Is it true that gotoblas2 hosts a full lapack inside?

thank you very much!

giuseppe

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