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Examples

Here we have a few examples how to use HPCAdvisor. For each example, we have different mechanisms to setup the application. As the application setup is based on bash script, users can install in different ways, using for instance source code, binary download, easybuild, EESSI, spack, etc..

Examples of applications to be tested using hpcadvisor:

Matrix Multiplication

As a "Hello World" example, we are gonna use matrix multiplication application, which receives two parameters: size of the squared matrix (dimension) and number of times such multiplication should happen (e.g. only once, 10 times, 100 times, and so on).

The files for this example are in the examples folder which has three files:

  • mpi_matrix_mult.c: source code of the application.
  • appsetup_matrix.sh: shell script that downloads the source file, compiles it, and generates the application run script that will be used for each execution scenario.
  • plotfilter_matrixmult.json: filter to consider only data for this application when generating the plots and the recommendation (pareto-front data).
  • ui_defaults.yaml: user input to create the environment, setup application, and define scenarios to be explored.
ui_defaults.yaml
subscription: mysubscription
skus: [Standard_HC44rs, Standard_HB120rs_v2, Standard_HB120rs_v3]
rgprefix: nettoaha
appsetupurl: https://raw.githubusercontent.com/Azure/hpcadvisor/main/examples/matrixmult/appsetup_matrix.sh
nnodes: [2, 3, 4]
appname: matrixmult
tags:
  appname: matrixmult
  version: v1
region: southcentralus
createjumpbox: true
ppr: 100
appinputs:
  appinteractions: 3
  appmatrixsize: [4000, 7000]

WRF

The Weather Research and Forecasting (WRF) Model is a well known system for meteorologists and researchers to simulate and predict weather patterns at various spatial and temporal scales. WRF can simulate atmospheric processes, including dynamics, thermodynamics, and microphysical processes. The model can be configured for different domains, resolutions, and parameterizations, and it is widely used for benchmarking HPC systems.

The example for this app (files here) is based on installation using EESSI.

GROMACS

The GROMACS (GROningen MAchine for Chemical Simulations) project originally began in 1991 at Department of Biophysical Chemistry, University of Groningen, Netherlands. GROMACS is widely used in computational chemistry, biochemistry, and related fields for simulating the behavior of molecules at the atomic level.

The example for this app (files here) is based on installation using EESSI.

OpenFOAM

OpenFOAM (Open Field Operation and Manipulation) is a free, open-source computational fluid dynamics (CFD) software package developed by the OpenFOAM Foundation. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics. OpenFOAM uses the finite volume method to discretize and solve the governing equations of fluid flow and other related physical phenomena. OpenFOAM is used in several industries including automotive, aerospace, energy, environmental engineering, chemical processing, and academic research. OpenFOAM is professionally released every six months to include customer sponsored developments and contributions from the community. It is written in C++ is modular, which allows customizations.

The example for this app (files here) is based on installation using EESSI.

NAMD

Nanoscale Molecular Dynamics (NAMD) is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems, including proteins, nucleic acids, and membranes, at the atomic level over time.It is particularly valuable for understanding processes such as protein folding, biomolecular recognition, and drug binding, among others. NAMD is developed and maintained by the Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign.

The example for this app (files here) is based on installation using the binary from NAMD official website.

LAMMPS

Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a molecular dynamics simulator designed to model particles in a variety of scientific and engineering applications. Developed by Sandia National Laboratories, it is highly scalable, so one can run it on single processors or in parallel using message-passing techniques. LAMMPS uses spatial-decomposition techniques to partition the simulation domain into small 3D sub-domains, one of which is assigned to each processor.

The example for this app (files here) is based on installation using EESSI.