Application Experts

If you're not an expert in high performance computing (HPC) but you want to do research in your area using HPC systems and software at PDC.... no worries: PDC's Application Experts can assist you.

We have Application Experts available at PDC (and also through other computing centres in Sweden) who can help with high performance computing related to specific research areas. These experts have a background in research in a particular scientific area, along with extensive experience using HPC programs and applications in that area. If you would like assistance from an Application Expert, please contact our experts by sending an email to support@pdc.kth.se . If the expertise of the current PDC Application Experts does not cover your research area, we will help you to find an Application Expert based at another Swedish National Infrastructure for Computing (SNIC) centre who can assist you.

What Application Experts can assist with

In general application experts can help researchers with

  • problems running programs in specific research areas,
  • optimizing code,
  • advanced software issues,
  • installing more complicated software,
  • applications for time allocations on HPC systems, and
  • more advanced questions about system software or storage.

Areas of expertise at PDC

PDC's current application experts have backgrounds in the following areas.

Bioinformatics & Molecular Biology

Henric Zazzi
Molecular Biology
(Ph.D., Karolinska Institute)

Current work

Can help PDC users with

  • genetics, molecular biology, bioinformatics
  • development for biological analysis tools

Previous research and work

  • bioinformatics research at AstraZeneca
  • sequencing within the human genome project
  • proteomics tool for data extraction/integration: github.com/percolator/pout2mzid

 

Computational Fluid Dynamics

Jing Gong
Scientific Computing
(Ph.D., Uppsala University)

Current work

  • computational fluid dynamics 
  • PRACE project
  • Scania research collaboration project

Can help PDC users with

  • computational fluid dynamics
  • general scientific computing problems
  • parallelization and optimization of code development

Previous research and work

  • industrial FEM code development
  • computational fluid dynamics in conjunction with the Department of Mechanics, Scania, and the Department of Aeronautical and Vehicle Engineering, KTH
  • various EU research projects (such as ExaFLOW)

 

Molecular Dynamics

Thor Wikfeldt
Computational Chemistry & Chemical Physics
(Ph.D., Stockholm University)
 

Current work

  • instructor at CodeRefinery: coderefinery.org
  • PDC/SNIC training coordinator
  • development of HPC training material
  • application support for molecular dynamics and electronic structure software packages
  • technical infrastructure at PDC

Can help PDC users with

  • molecular dynamics and electronic structure codes
  • modern HPC usage patterns (Jupyter Notebooks, HPC workflow management tools)

Previous research and work

  • molecular-level simulations of liquid, solid and surface systems using electronic structure, molecular dynamics, Monte Carlo, enhanced sampling and path-integral methods
  • ab initio calculations of x-ray and neutron scattering spectra
  • development of a hybrid force field based on polarisable electrostatics and many-body machine learning potentials

Multiscale Modelling

Xin Li
Theoretical Chemistry & Biology
(Ph.D., KTH Royal Institute of Technology)

Current work

  • hybrid simulation approaches for optoelectronic responses of biomolecules
  • large-scale parallelization of quantum chemistry calculations
  • benchmark and optimization of scientific computing codes
  • support and training for PDC users

Can help PDC users with

  • general scientific computing problems
  • troubleshooting scientific software
  • parallelization of scientific computing codes

Previous research and work

  • multiscale modelling of optoelectronic and magnetic properties of organic functional materials
  • optimization of force field parameters for organic molecules and metal nanoparticles
  • ab initio exciton model for efficient and scalable simulations of multichromophoric systems

Code Optimization

Tor Kjellsson Lindblom
Theoretical & Computational Physics
(Ph.D., Stockholm University)
 

Current work

  • support and training for PDC users
  • postdoctoral researcher at Oslo Metropolitan University: conducting research on relativistic light-matter interactions, including effects beyond the so-called electric dipole approximation, between ultrastrong near-infrared laser pulses and atomic systems

Can help PDC users with

  • general debugging and code optimization, especially in FORTRAN but also Python and C++

  • parallelization with OpenMP, MPI and hybridization strategies

Previous research and work

  • development of computational code to solve the time dependent Dirac (and Schrödinger) equation for atomic systems interacting with ultrastrong laser pulses, specifically treating effects beyond the electric dipole interaction

  • implementation of analytical methods for light-matter interaction based on asymptotic behaviour of wavefunctions

Machine Learning & Performance Analysis

Xavier Aguilar
Computer Science
(Ph.D. candidate 2019, KTH Royal Institute of Technology)
 

Current work

  • support for PDC users

  • performance analysis and benchmarking of parallel codes and infrastructures

  • machine learning methods applied to performance data

Can help PDC users with

  • deep learning/machine learning

  • performance analysis of parallel code

  • code parallelization and optimization

Previous research and work

  • design and implementation of scalable methods for performance monitoring and analysis
  • development of parallel runtime systems

  • analysis and optimization of parallel code