[gmx-users] Re: [gmx-developers] Gromacs 4.6.1 ATLAS/CUDA detection problems...

Berk Hess gmx3 at hotmail.com
Thu Mar 7 10:41:17 CET 2013


Hi,

Note that the linear algebra in Gromacs is limited to eigenvalue solving in two analysis tools,
the MD engine does not use any (large) linear algebra.
So linear algebra library performance is irrelevant, except for the cases where users
would want to repeated uses one of the two tools with large systems.
Even then, our built-in code is not bad.

Cheers,

Berk

----------------------------------------
> Date: Thu, 7 Mar 2013 11:27:27 +0200
> From: eyurtese at abo.fi
> To: junghans at votca.org
> CC: gmx-users at gromacs.org
> Subject: [gmx-users] Re: [gmx-developers] Gromacs 4.6.1 ATLAS/CUDA detection problems...
>
> On Wed, 6 Mar 2013, Christoph Junghans wrote:
>
> > I had a another look at the issue and I guess cmake's blas detention
> > is a bit flaky, when it comes to static libraries.
> > You are using liblapack.a, which has no link information, with
> > liblapack.so it should have worked.
> > Anyhow, thanks for reporting the issue.
>
> There is no liblapack.so with ATLAS? Anyway, I tried to explain the issues
> more clearly below. I am not going to insist but it would be nice to be
> able to use the ATLAS library I guess... :)
>
> The following library files are available with ATLAS and your cmake
> config checks use "f77blas;atlas"
>
> libatlas.a
> libcblas.a
> libf77blas.a
> liblapack.a
> libptcblas.a
> libptf77blas.a
> libsatlas.so
> libtatlas.so
>
> At: http://ac-archive.sourceforge.net/ac-archive/acx_blas.html
> It says that you will have to use the same "FORTRAN" compiler to link
> ATLAS. However your checker is using gcc to check linking.
>
> So the first bug is because the checker is trying to link f77blas
> with gcc. This requires -lgfortran. You can see many related information
> if you do a web search for "undefined reference to `_gfortran_st_write'").
> Otherwise you should use gfortran for the tests.
>
> Therefore it is impossible for gromacs to use ATLAS library.
>
>
> The second problem is because "f77blas;atlas" should include "cblas" for
> linking. Again, at the example which is present at:
> http://ac-archive.sourceforge.net/ac-archive/acx_blas.html
> BLAS_LIBS="-lcblas -lf77blas -latlas" is used.
>
> Therefore it is again impossible to find ATLAS library even when it
> exists.
>
>
>
> The third problem is ambiguity in the manual at:
> http://www.gromacs.org/Documentation/Installation_Instructions#4.1._Configuring_with_CMake
> It says: "A key thing to consider here is the setting of
> CMAKE_INSTALL_PREFIX." However it is not clear what 'setting' means in
> here. (Being unfamiliar with cmake, I defaulted to setting it in the
> environment which was wrong)
>
> Later I found out CMAKE_INSTALL_PREFIX can only be used as a cmake
> variable (not set in environment). But DESTDIR should be set for setting
> installation prefix instead ?
> See:
> http://www.cmake.org/cmake/help/v2.8.8/cmake.html#variable%3aCMAKE_INSTALL_PREFIX
> http://www.cmake.org/Wiki/CMake_FAQ#Does_CMake.27s_.22make_install.22_support_DESTDIR.3F
>
>
>
> I hope the problems in ATLAS detection and documentation would be fixed.
> Thanks for your interest in these small issues.
>
>
> Thanks,
> Evren
> --
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