[gmx-developers] Question about Gromacs BLAS / LAPACK.

[Roland Schulz]

Hi,


On Sat, Nov 10, 2012 at 11:59 AM, Lee-Ping Wang <leeping at stanford.edu>wrote:
>
>  On my local machine, I migrated my fluctuating charge code from Gromacs
> 4.0.7 to 4.5.5.  It took a bit of time, but I think the implementation is
> now a lot cleaner.  At some point, I would like to create a branch on the
> Gromacs repository, but first I need to solve a few issues with BLAS and
> LAPACK.  Basically, when I was originally writing the code I used the Intel
> headers and libraries, but now I want to convert this to something more
> compatible.
>

If you want to submit this code at some time you will have to submit it
against the master branch which is going to be 5.0. 5.0 is suppose to be
partially migrated to C++. And I personally think that this should include
a C++ vector/matrix interface. I started this discussion here:
http://redmine.gromacs.org/issues/1017.  So the interface might be changed
when this is decided. Feel free to comment on the issue.

> **
>
> **
>
> cblas_dgemm(101,111,111,N,N,N,1,VT,N,A1,N,0,Ai,N);****
>
> dgelss(&N,&N,&nrhs,A1,&N,x,&N,S,&rcond,&rank,work,&lwork,&info);
>
Is your code not accurately enough in single precision? Or could you
benefit as the rest of Gromacs from using single precision (with the user
having the choice to compile with GMX_DOUBLE)?

> However, when Gromacs calls its own BLAS and LAPACK functions it looks
> quite different:****
>
> ** **
>
> #ifdef GMX_DOUBLE****
>
>
> F77_FUNC(dsyevr,DSYEVR)(jobz,"I","L",&n,a,&n,&vl,&vu,&index_lower,&index_upper,
> ****
>
>                             &abstol,&m,eigenvalues,eigenvectors,&n,****
>
>                             isuppz,&w0,&lwork,&iw0,&liwork,&info);****
>
> #else****
>
>
> F77_FUNC(ssyevr,SSYEVR)(jobz,"I","L",&n,a,&n,&vl,&vu,&index_lower,&index_upper,
> ****
>
>                             &abstol,&m,eigenvalues,eigenvectors,&n,****
>
>                             isuppz,&w0,&lwork,&iw0,&liwork,&info);****
>
> #endif
>
I would write a macro (untested!)
#ifdef GMX_DOUblE
#define GMX_BLAS(A,B)  F77_FUNC(d ## A, D ## B)
#else
#define GMX_BLAS(A,B)  F77_FUNC(s ## A, S ## B)
#endif

So that you can call it as

GMX_BLAS(syevr,SYEVR)(jobz,"I","L",&n,a,&n,&vl,&vu,&index_lower,&index_upper,
****

                            &abstol,&m,eigenvalues,eigenvectors,&n,****

                            isuppz,&w0,&lwork,&iw0,&liwork,&info);
without having to worry about the #ifdef GMX_DOUBLE at the callsite. Of
course if you always want to use double you don't need to worry about it.

>  **2)      **How should I write my code so that a user can compile and
> link using Intel headers / libraries if they want to?  I imagine it’s
> related to the --use-external-blas and --use-external-lapack command line
> options to the configure script, but I don’t know how to use this.
>
That should automatically work.


  Roland


-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20121110/31bf0ad5/attachment.html>