Yes, it worked! But I had to remove all instances of "<i>-fexcess-precision=fast</i>" again.<br><br>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 laptop.<br>
<br>Many thanks for your help!<br><br><br>Reading file test.tpr, VERSION 4.6-dev-20120820-1ac8743 (single precision)<br>Using 8 OpenMP threads per tMPI thread<br><br>WARNING! Binary not matching hardware - you are likely losing performance.<br>
Acceleration most likely to fit this hardware: AVX_256<br>Acceleration selected at Gromacs compile time: SSE2<br><br><br>1 GPU detected:<br> #0: NVIDIA GeForce GT 650M, compute cap.: 3.0, ECC: no, stat: compatible<br><br>
1 GPU auto-selected to be used for this run: #0<br><br>Using CUDA 8x8x8 non-bonded kernels<br><br>* WARNING * WARNING * WARNING * WARNING * WARNING * WARNING *<br>We have just committed the new CPU detection code in this branch,<br>
and will commit new SSE/AVX kernels in a few days. However, this<br>means that currently only the NxN kernels are accelerated!<br>In the mean time, you might want to avoid production runs in 4.6.<br><br><br>Back Off! I just backed up test_out.xtc to ./#test_out.xtc.5#<br>
<br>Back Off! I just backed up test_out.edr to ./#test_out.edr.5#<br>starting mdrun 'Protein in water'<br>1000 steps, 2.0 ps.<br><br>Writing final coordinates.<br><br>Back Off! I just backed up test_out.gro to ./#test_out.gro.4#<br>
<br><br>NOTE: The GPU has >20% more load than the CPU. This imbalance causes<br> performance loss, consider using a shorter cut-off.<br><br> Core t (s) Wall t (s) (%)<br> Time: 60.740 15.692 387.1<br>
(ns/day) (hour/ns)<br>Performance: 11.023 2.177<br><br><br><br><br><div class="gmail_quote">On 25 August 2012 00:30, Christoph Junghans <span dir="ltr"><<a href="mailto:junghans@votca.org" target="_blank">junghans@votca.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">2012/8/24 Thomas Evangelidis <<a href="mailto:tevang3@gmail.com" target="_blank">tevang3@gmail.com</a>>:<br>
<div>> Yes there is a fftw3.pc file. I completely removed any fftw3 module from<br>
> Fedora repositories, I set -DPKG_CONFIG_PATH to my home installation, but<br>
> still got an error:<br>
><br>
> $cmake ../gromacs -DGMX_ACCELERATION=SSE2<br>
> -DPKG_CONFIG_PATH=/home/thomas/Programs/fftw-3.3.2/single_precision_installation_dir/lib/pkgconfig<br>
</div>Sorry, I was not very precise. I meant the environment variable PKG_CONFIG_PATH<br>
<br>
export PKG_CONFIG_PATH=/home/thomas/Programs/fftw-3.3.2/single_precision_installation_dir/lib/pkgconfig<br>
(bash)<br>
setenv PKG_CONFIG_PATH<br>
/home/thomas/Programs/fftw-3.3.2/single_precision_installation_dir/lib/pkgconfig<br>
(tcsh)<br><br>
</blockquote></div>