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

Thomas Evangelidis tevang3 at gmail.com
Sat Aug 25 00:31:49 CEST 2012

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? How can I find
out if my GPU is utilized during the calculations? There's an tool named
nvidia-smi but it does not seem to support my GPU as it is set up on my

Many thanks for your help!

Reading file test.tpr, VERSION 4.6-dev-20120820-1ac8743 (single precision)
Using 8 OpenMP threads per tMPI thread

WARNING! Binary not matching hardware - you are likely losing performance.
Acceleration most likely to fit this hardware: AVX_256
Acceleration selected at Gromacs compile time: SSE2

1 GPU detected:
  #0: NVIDIA GeForce GT 650M, compute cap.: 3.0, ECC:  no, stat: compatible

1 GPU auto-selected to be used for this run: #0

Using CUDA 8x8x8 non-bonded kernels

We have just committed the new CPU detection code in this branch,
and will commit new SSE/AVX kernels in a few days. However, this
means that currently only the NxN kernels are accelerated!
In the mean time, you might want to avoid production runs in 4.6.

Back Off! I just backed up test_out.xtc to ./#test_out.xtc.5#

Back Off! I just backed up test_out.edr to ./#test_out.edr.5#
starting mdrun 'Protein in water'
1000 steps,      2.0 ps.

Writing final coordinates.

Back Off! I just backed up test_out.gro to ./#test_out.gro.4#

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

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

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)
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