How to use GOTOBLAS (instead of ATLAS)?

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From what I understand, the question is "how do I completely replace BLAS with GOTOBLAS"? The first place to start would be to take a look at $SAGE_ROOT/devel/sage/module_list.py. This is sort of a master file describing how Sage's various Cython code links with the various libraries included with Sage. For example, dense general matrices use BLAS to handle multiplication whereas integer matrices uses Flint. (Or something like that.)

Near the top of the file module_list.py is a section called "BLAS setup". You can add a line like

...
elif os.path.exists('%s/lib/libgotoblas.so'%os.environ['SAGE_LOCAL']):
    BLAS='gotoblas'
    BLAS2='atlas'
elif ...

replacing "gotoblas" with whatever the library is actually named. (I took an educated guess. :) ) There's a note at the top of this section about possibly having to modify sage/misc/cython.py as well. It looks like you'd have to add something similar there in the function cblas() such that it returns the name of the library.

Finally, you should probably rebuild Sage with the -a flag a la

$ sage -ba

Anyway, the end result should be that all of Sage's Cython-based objects (like matrices) will use GOTOBLAS for the appropriate computations instead of BLAS. I haven't tried this myself but it looks like this is the way to go. I'm just curious if there's a less "invasive" way to do it. (Like your suggestion of symblinking to libcblas.so or whatever the standard "BLAS" library is called.)

A major problem that I already mentioned on sage-devel is that ATLAS produces 2 libraries: libf77blas for fortran and libcblas for C. GOTOBlas is only producing libf77blas. lapack is perfectly happy with libf77blas as it is a fortran library. However most of the packages in sage and sage itself require libcblas.

So to use GOTOBlas instead of atlas you need to produce an extra layer that will translate fortran to C, or recode a substantial portion of sage to use libf77blas. Whichever way you want to go, that's a big amount of work.

You can use C libraries from Sage via Cython. Cython is a Python-like language that makes it easy to write Python programs that manipulate pure C data types allowing for faster computations and the like. In you're unfamiliar with Cython you should take a look at these tutorials for more information.

I'm not familiar with ATLAS or GOTOBLAS but I can provide an example of how to link to some BLAS routines. Suppose I wanted to add two vectors using BLAS, which is included with Sage. To do $y \leftarrow \alpha x + y$ where $x$ and $y$ are double vectors and $\alpha$ is a double scalar, I start by extern-ing the appropriate function, cblas_daxpy() into my Cython code. (i.e. #import-ing) In the Sage notebook, I begin a cell with the following:

%cython

cdef extern from "gsl/gsl_cblas.h":
    void cblas_daxpy    (int N, double alpha, double *x, int incX, double *y, int incY)

Then, to perform this addition I add the following (to the same cell)

cdef double x[3]
cdef double y[3]
cdef double alpha = -1

x[0] = 1.0; x[1] = 1.0; x[2] = 1.0
y[0] = 1.0; y[1] = 2.0; y[2] = 3.0

print "x =",x[0],x[1],x[2]
print "y =",y[0],y[1],y[2]
print "a =",alpha

cblas_daxpy(3,alpha,x,1,y,1)

print "alpha x + y =",y[0],y[1],y[2]

The output is

x = 1.0 1.0 1.0
y = 1.0 2.0 3.0
a = -1.0
alpha x + y = 0.0 1.0 2.0

You might need to compile GOTOBLAS in the Sage shell (type "sage -sh") in the terminal but it might also work if you have a system-wide install.

I hope this is a decent enough introduction to using C libraries in Sage. You can fine more information at the Cython website and documentation at http://www.cython.org

I think this is a great question, although it should probably include a reference to the sage-devel thread.

Of course (as you know) there isn't really much information there, except some concerns that it is no longer actively maintained, and therefore might not be a worthwhile pursuit for Sage. Also there seems to be some concern that there would be trouble communicating between the C code in Sage and the Fortran code in GotoBLAS. Maybe someone proposed a resolution for that, but I can't tell :(

In any case, thanks for asking; maybe someone who knows better will notice the question here . . .

UPDATE:

Oh, maybe I do have an idea: The answer to this question is probably the same as the answer to "How do I use a compiled C library in Python?". For that, the answer must begin with Cython. In particular, here is the Cython documentation page for Using C libraries. Strangely, however, the examples on that page don't seem to ever explain what to do if you already have the .a or .so files. Maybe you can figure that out, or already know -- I think distutils has something to do with this. Anyway, there is a related question on Stack Overflow which does seem to address this . . . maybe between these two there's enough to get you going?

p.s. I really don't understand C, libraries, Cython, or distutils, I've just read about them a lot . . . my apologies if this is all totally obvious and unhelpful, or wrong.