<div>Dear Paul Anton, </div><div><br></div><div>thanks a lot for your suggestion. I was also successful with</div><div><br></div><div>[blas]</div><div>libraries = blas</div><div>library_dirs = $PREFIX/gotoblas2/lib</div><div>
[lapack]</div><div>libraries = lapack</div><div>library_dirs = $PREFIX/gotoblas2/lib</div><div><br></div><div>but I had compile clapack as a shared library and place a symbolic link</div><div>ln -s $PREFIX/gotoblas2/lib/libgoto2.so $PREFIX/gotoblas2/lib/libblas.so</div>
<div><br></div><div>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?</div>
<div><br></div><div>cheers</div><div><br></div><div><br></div><br><div class="gmail_quote">On Tue, Mar 22, 2011 at 11:18 PM, Paul Anton Letnes <span dir="ltr"><<a href="mailto:paul.anton.letnes@gmail.com">paul.anton.letnes@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">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 <a href="http://libgoto2.so/.a" target="_blank">libgoto2.so/.a</a>. I believe the idea is as long as the BLAS implementation is fast(TM), the lapack performance will be good.<br>
<br>To wit*, what I did was to tell numpy where libgoto2 was:<br>env BLAS=/path/to/libgoto2.so python setup.py install<br>Scipy also wants the path to lapack, which is wrapped inside libgoto2:<br>env BLAS=/path/to/libgoto2.so LAPACK=/path/to/libgoto2.so python setup.py install<br>
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.<br><br>Good luck,<br>Paul.<br>
<br>*) I have notes on this on a different computer, but not available right now.<br><br><br><div class="gmail_quote"><div><div></div><div class="h5">On Tue, Mar 22, 2011 at 10:13 AM, Giuseppe Aprea <span dir="ltr"><<a href="mailto:giuseppe.aprea@gmail.com" target="_blank">giuseppe.aprea@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="border-left:1px solid rgb(204, 204, 204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex"><div><div></div><div class="h5">Hi all,<div><br></div><div>I wonder if Peter finally got Gotoblas working with numpy. I am trying with gotoblas 1.13 installed in the same way:</div>
<div><br></div><div><div>$ ls -R</div><div>.:</div><div>include lib</div>
<div><br></div><div>./include:</div><div>goto</div><div><br></div><div>./include/goto:</div><div>blaswrap.h cblas.h clapack.h f2c.h</div><div><br></div><div>./lib:</div><div>libgoto2.a libgoto2_nehalemp-r1.13.a <a href="http://libgoto2_nehalemp-r1.13.so" target="_blank">libgoto2_nehalemp-r1.13.so</a> libgoto2.so</div>
</div><div><br></div><div>and numpy 1.5.1 with this site.cfg</div><div><br></div><div><div>[DEFAULT]</div><div>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</div>
<div>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</div><div>search_static_first = 1</div>
<div>[blas_opt]</div><div>libraries = goto2</div><div>language = fortran</div><div>[lapack_opt]</div><div>libraries = goto2</div><div>language = fortran</div><div>[amd]</div><div>amd_libs = amd</div><div>[umfpack]</div><div>
umfpack_libs = umfpack</div><div>[fftw]</div><div>libraries = fftw3</div><div><br></div>(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:</div>
<div><br></div><div>building extension "numpy.numarray._capi" sources</div><div>building extension "numpy.fft.fftpack_lite" sources</div><div>building extension "numpy.linalg.lapack_lite" sources</div>
<div>creating build/src.linux-x86_64-2.7/numpy/linalg</div><div><b>### Warning: Using unoptimized lapack ###</b></div><div><b> adding 'numpy/linalg/lapack_litemodule.c' to sources.</b></div><div> adding 'numpy/linalg/python_xerbla.c' to sources.</div>
<div> adding 'numpy/linalg/zlapack_lite.c' to sources.</div><div> adding 'numpy/linalg/dlapack_lite.c' to sources.</div><div> adding 'numpy/linalg/blas_lite.c' to sources.</div><div> adding 'numpy/linalg/dlamch.c' to sources.</div>
<div> adding 'numpy/linalg/f2c_lite.c' to sources.</div><div>building extension "numpy.random.mtrand" sources</div><div>creating build/src.linux-x86_64-2.7/numpy/random</div><div>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</div>
<div><br></div><div>during numpy installation (which ends successfully). Moreover I cannot see any -lgoto2 as I would have expected. </div><div>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.</div>
<div>Is the problem related with site.cfg or with gotoblas2 installation? Is it true that gotoblas2 hosts a full lapack inside?</div><div><br></div><div>thank you very much!</div><div><br></div><font color="#888888"><div>
giuseppe</div>
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