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Huygens CMLE, QMLE and GMLE deconvolution on GPU

Increase your computing performance by using the power of the graphics processing unit (GPU). GPU accelerated Huygens deconvolution is now available in the Huygens software.

Since the 15.10 release GPU accelerated Huygens deconvolution is available for Windows and GNU/Linux (Ubuntu / Debian / Red Hat / Fedora / CentOS) and for deconvolutionwith all types of MLE algorithms.

As Apple does not sell new systems with NVidia CUDA cards and has stated that they will not do so, unfortunately, SVI cannot offer the GPU Options for Apple Mac systems. In cases of older Apple Mac systems including an NVidia CUDA card the required level of support and services cannot be guaranteed so it cannot be offered in those cases either.

The GPU acceleration option is available for small CUDA-enabled Nvidia graphics cards for GNU/Linux and Windows. For an overview of suitable GPU cards, please visit this page.
Note that for most mid- and high-end range GPU cards, an additional Medium or Large GPU option is required in your Huygens license.

If you have an Nvidia graphics card that is larger than 2Gb of video RAM and max 512 CUDA cores/shading units and requires a test-license, please contact license at svi.nl.

Activating the GPU Option in your Huygens


Usage of the GPU option in a computer must be activated within the Huygens software.

Go to Edit -> Preferences
Go to tab 'General options'.
Mark the box of 'GPU acceleration'.
Press OK.

If 'GPU acceleration' box is marked GPU acceleration will be used whenever possible.
If 'GPU acceleration' box is not marked GPU acceleration will not at all be used.

You can encounter the following situations:

Computer has no GPU card. 'GPU acceleration' is greyed out.
Computer has a GPU card but the Huygens license does not include the GPU option. 'GPU acceleration' is greyed out.
Computer has a GPU card and the Huygens license does include the GPU option. 'GPU acceleration' is black and can be marked.

Installation instructions


Installation instructions for Windows:
  1. Install the NVIDIA drivers for the graphics card.
  2. Download the latest CUDA Network installer for Windows.
  3. Install CUDA using the Network installer.
  4. Install the Huygens GPU version for Windows.
  5. Request a testlicense by sending an email to license at svi.nl
  6. Install the testlicense and restart Huygens.
  7. GPU acceleration is active. You can de-activate it in the Huygens preferences window. If this is not the case because the option is greyed-out, please check the GPU Checklist.

Installation instructions for Debian / Ubuntu:
  1. Download the latest CUDA Network Installer for Debian / Ubuntu.
  2. Install CUDA repository:
    sudo dpkg -i cuda-repo-ubuntuXXX_X.X-XX_amd64.deb
  3. Refresh package list:
    sudo apt-get update
  4. Install the CUDA FFT package:
    sudo apt-get install cuda
  5. Install the Huygens GPU version for Linux:
    sudo dpkg -i huygens_16.10.0-p2_amd64.deb
  6. Request a testlicense by sending an email to license at svi.nl
  7. Install the testlicense and restart Huygens.
  8. GPU acceleration is active. You can de-activate it in the Huygens preferences window. If this is not the casebecause the option is greyed-out, please check the GPU Checklist.




Performing a Benchmark


To perform a benchmark on Huygens software to compare between CPU and GPU performance please download the following script and image:
benchGPU.tcl
mcrp.h5

Save all the files in the same directory. Then in the Tcl Shell (Huygens Professional or Huygens Scripting) or at the Huygens Core prompt, change directory (cd) to the directory where you placed bench.tcl and the image. For example if the files are saved on the desktop of a user named "John", type in the Tcl-shell or prompt:
cd /home/john/Desktop

Then type:
source benchGPU.tcl

Depending on the speed of your computer this may take several minutes, when the test run is finished, you will see a report like the one below:
-------------------------------------------------------
--- Huygens GPU benchmark results on mcrp image
--- Benchmark v1.0, Huygens Compute Engine 15.05.0p1b
-------------------------------------------------------
CMLE CPU: 116.20
CMLE GPU: 34.37
Speedup: 3.38



Benchmark results


To add your own benchmark results to the list below, please send the report to support at svi.nl. To see the results of a number of cards graphically go to the General GPU page





Contact Information

Scientific Volume Imaging B.V.

Laapersveld 63
1213 VB Hilversum
The Netherlands


Phone: +31 (0)35 64216 26
Fax: +31 (0)35 683 7971
E-mail: info at svi.nl

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