Attention

The ShARC HPC cluster was decommissioned on the 30th of November 2023 at 17:00. It is no longer possible for users to access that cluster.

Dakota

Dakota is a general-purpose software toolkit for performing systems analysis and design on high performance computers. Dakota provides algorithms for design optimization, uncertainty quantification, parameter estimation, design of experiments, and sensitivity analysis, as well as a range of parallel computing and simulation interfacing services.

General Usage

Dakota 6.14.0 can be activated using the module file

module load apps/dakota/6.14.0/gcc-8.2-cmake-3.17.1

Hint

  • It is recommended that users submit each Dakota subtask to the scheduler: simulator_script.sh should submit numerous SGE jobs.

  • Bash Heredoc scripting may be useful or required as part of submitting Dakota subtasks to the scheduler engine with simulator_script.sh to adjust resource requests or sub-script variables.

Interactive Usage

Dakota can be used on the command line with a IDE style GUI editor also available. To do so start a X11 GUI forwarding supported SSH session then start an interactive session with the qrshx command (which supports graphical applications).

The Dakota module can be loaded and used as below:

# Load Dakota Module
module load apps/dakota/6.14.0/gcc-8.2-cmake-3.17.1
# Show Dakota version
dakota --v
# Copy example
cp /usr/local/packages/apps/dakota/6.14.0/gcc-8.2-cmake-3.17.1/share/dakota/examples/users/rosen_multidim.in ./
# Run example
dakota -i rosen_multidim.in -o rosen_multidim.out
# Or optionally start  and use the Dakota GUI
DakotaUI

Batch Usage

Caution

  • Use of the #$ -V SGE option will instruct SGE to import your current terminal environment variables to be imported - CAUTION - this may not be desirable as it could cause conflicts between modules.

#!/bin/bash
#$ -cwd
#$ -V
#$ -M a.person@sheffield.ac.uk
#$ -m abe
#$ -l h_rt=00:10:00
#$ -l rmem=2G
#$ -pe smp 1
#$ -N DakotaExample

# Load Dakota Module
module load apps/dakota/6.14.0/gcc-8.2-cmake-3.17.1
# Copy example
cp /usr/local/packages/apps/dakota/6.14.0/gcc-8.2-cmake-3.17.1/share/dakota/examples/users/rosen_multidim.in ./
# Run example
dakota -i rosen_multidim.in -o rosen_multidim.out

Installation notes

Version 6.14.0

Dakota 6.14.0 was compiled from source using the install_dakota.sh script.

The module file is automatically generated by the script but has been edited to provide the required environment as detailed here: https://dakota.sandia.gov/content/set-environment-linux-mac-os-x

The Dakota GUI binaries (Linux - 6.14 GUI Only tar.gz) have been added to the module manually by adding a gui subdirectory to the root installation folder with subsequent download and untar of the GUI binaries provided at https://dakota.sandia.gov/download.html. An insertion of the appropriate PATH prepend for this gui subdirectory has also been added to the module file.

Testing

Both the Dakota CLI and Dakota GUI appear to function correctly under a qrshx / batch sessions, running the rosen_multidim.in example successfully both in the CLI and GUI but no extensive further testing has been undertaken.