[gmx-users] Installing 4.6 beta1

[Roland Schulz]

Hi,

a small addition to Mark's answer. If you want/need to use an older gcc
version 4.4.6 and 4.5.3 have the necessary fix too. Also you can disable
AVX with cmake -DGMX_CPU_ACCELERATION=SSE4.1 . But you will get somewhat
lower performance (AFAIK only 10% with group kernels but more with verlet
kernels).
If you want to track the status of the this Gromacs bug you can find it
here: http://redmine.gromacs.org/issues/1058

Roland


On Mon, Dec 3, 2012 at 4:43 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> Looks like a compiler bug to me, and google agrees
> http://gcc.gnu.org/bugzilla/show_bug.cgi?id=47318.
>
> Even if there were not this bug, we would strongly encourage you to get the
> better performance available from more recent versions of gcc. I was about
> to suggest 4.6 or newer, but the above URL suggests 4.6.0 has the same bug
> :-O. So go higher than that, or Intel's compiler.
>
> We will probably try detecting this at configure time in a future beta.
> Clearly our test matrix doesn't cover this case, but as Szilard has
> mentioned in another thread, the multiplicative explosion of possibilities
> for us to try to anticipate to make users' lives easier during installation
> makes our lives pretty tough :-)
>
> Mark
>
> On Mon, Dec 3, 2012 at 8:05 PM, sebastian <
> sebastian.waltz at physik.uni-freiburg.de> wrote:
>
> > Hey Dear,
> >
> > when I try to install the GROMACS-4.6-beta1 version I get an error which
> I
> > can not pin down when do make.
> >
> > My system:
> >
> > CPU: i7
> > GPU: NVIDIA GTX670
> > gcc: Debian 4.4.5-8
> > CUDA: 4.2
> > fft3w: 3.3.2 including sse2
> > Debian Linux 64-bit
> >
> > First I do:
> >
> > cmake ../ -DCMAKE_INSTALL_PREFIX=/usr/**local/gromacs_4.6
> >
> > which works fine. When I do:
> >
> > make -j6
> >
> > I get a bunch of errors which look more or less the same:
> >
> > gromacs-4.6-beta1/src/gmxlib/**nonbonded/nb_kernel_avx_256_**
> > single/kernelutil_x86_avx_256_**single.h:600: error: incompatible type
> > for argument 2 of ‘_mm_maskload_ps’
> > /usr/lib/gcc/x86_64-linux-gnu/**4.4.5/include/avxintrin.h:919: note:
> > expected ‘__m128’ but argument is of type ‘__m128i’
> >
> > or like:
> >
> > gromacs-4.6-beta1/src/gmxlib/**nonbonded/nb_kernel_avx_256_**
> > single/kernelutil_x86_avx_256_**single.h:607: error: incompatible type
> > for argument 2 of ‘_mm_maskstore_ps’
> > /usr/lib/gcc/x86_64-linux-gnu/**4.4.5/include/avxintrin.h:926: note:
> > expected ‘__m128’ but argument is of type ‘__m128i’
> >
> > and it breaks with this output:
> >
> > make[2]: *** [src/gmxlib/CMakeFiles/gmx.**dir/nonbonded/nb_kernel_avx_**
> > 256_single/nb_kernel_ElecCoul_**VdwCSTab_GeomW4W4_avx_256_**single.c.o]
> > Error 1
> > make[1]: *** [src/gmxlib/CMakeFiles/gmx.**dir/all] Error 2
> > make: *** [all] Error 2
> >
> > I don't know what goes wrong and maybe I just miss a flag.
> >
> > Dears,
> >
> > Sebastian
> >
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > * Please search the archive at http://www.gromacs.org/**
> > Support/Mailing_Lists/Search<
> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> > * Please don't post (un)subscribe requests to the list. Use the www
> > interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> http://www.gromacs.org/Support/Mailing_Lists>
> >
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
>


-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309