[gmx-developers] GROMACS 4.6 error in file src/gromacs/analysisdata/analysisdata.cpp:45:0

Roland Schulz roland at utk.edu
Sat Aug 25 01:13:08 CEST 2012

On Fri, Aug 24, 2012 at 6:31 PM, Thomas Evangelidis <tevang3 at gmail.com> wrote:
> Yes, it worked! But I had to remove all instances of
> "-fexcess-precision=fast" again.
> I've tested the new GROMACS-GPU on a 36K atom system (protein-water). It
> seems that everything works well apart from that warning about AVX_256. I
> guess I must compile FFTW3 with --enable-avx, is that all?
No the warning is for Gromacs not FFTW. So you would need to compile
Gromacs with GMX_ACCELERATION=AVX_256 to get full performance and
remove the warning. To be able to do that you need to have a gcc which
supports avx. You could either compile gcc by yourself, use icc, or
find out why Fedora's doesn't accept "-mavx". E.g. by looking up how
Fedora compiles gcc.

>  How can I find
> out if my GPU is utilized during the calculations?
The output says the GPU has been detected and the relative load of
CPU/GPU. So it is being used.

> NOTE: The GPU has >20% more load than the CPU. This imbalance causes
>       performance loss, consider using a shorter cut-off.
You could get extra performance by changing the cut-off.

>                Core t (s)   Wall t (s)        (%)
>        Time:       60.740       15.692      387.1
>                  (ns/day)    (hour/ns)
> Performance:       11.023        2.177

You could get better performance by using v-sites and 4fs time-step.
Also you could get better performance by using Cuda5 because it allows
optimization for Kepler.


> On 25 August 2012 00:30, Christoph Junghans <junghans at votca.org> wrote:
>> 2012/8/24 Thomas Evangelidis <tevang3 at gmail.com>:
>> > Yes there is a fftw3.pc file. I completely removed any fftw3 module from
>> > Fedora repositories, I set -DPKG_CONFIG_PATH to my home installation,
>> > but
>> > still got an error:
>> >
>> > $cmake ../gromacs -DGMX_ACCELERATION=SSE2
>> >
>> > -DPKG_CONFIG_PATH=/home/thomas/Programs/fftw-3.3.2/single_precision_installation_dir/lib/pkgconfig
>> Sorry, I was not very precise. I meant the environment variable
>> export
>> PKG_CONFIG_PATH=/home/thomas/Programs/fftw-3.3.2/single_precision_installation_dir/lib/pkgconfig
>> (bash)
>> /home/thomas/Programs/fftw-3.3.2/single_precision_installation_dir/lib/pkgconfig
>> (tcsh)

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

More information about the gromacs.org_gmx-developers mailing list