BioExcel’s webinar series continue with a presentation by Michael Gecht



Molecular dynamics software is optimized to yield the highest performance on available resources. The details of why computations perform better or worse depends on various parameters. As an example, common biomolecular simulations stop to scale linearly when too much computational power is provided. Optimization of available parameters is a tedious task and is perfectly suited for automation procedures.
MDBenchmark is a tool that provides a straightforward way to perform scaling studies of molecular dynamics simulations across a different number of nodes, as well as different parameters. Given an input file, e.g., a TPR file for GROMACS, MDBenchmark handles submission of jobs to any given queuing system, retrieval of performance data and creation of a plot for an easy estimation of the most efficient usage of computational resources.
In this webinar, we will present how to use MDBenchmark, starting with the installation process, going over benchmark generation, submission and analysis. Furthermore, we will provide explanations on how to set up MDBenchmark and customize submission scripts, to perform scaling simulations on any high performance cluster. We will also discuss the future vision for the project and how anyone can get involved in the development.


Michael Gecht

Michael Gecht received his B.S. and M.S. in Biochemistry from the Goethe University Frankfurt. He completed his master thesis in 2017, where he worked on a joint project
between Prof. Robert Ernst and Prof. Gerhard Hummer, answering biological questions in a combined theoretical and experimental approach. He is currently a Ph.D. candidate
in the Theoretical Biophysics department of Prof. Gerhard Hummer at the Max Planck Institute of Biophysics (Frankfurt, Germany). His main focus is the interaction between
proteins and lipids within biological membranes. Michael is also interested in workflow automation, data visualization and the modern web.


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Title: MDBenchmark: a tedious task – made straightforward

Date: 23rd November, 2018
Time: 14:00 GMT / 15:00 CET

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Webinar ID: 737-002-555


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