2021 HPC School

2021 HPC School Application Form Registration open till July 1st

Scientific and High Performance Computing School 2021

Final Program

30 August 2021 – 3 September 2021

Venue: The course will be held in the BIB room in the DICAM - Mesiano


Monday's schedule will be

9:00 - 10:30 Lecture

10:30 - 11:00 Break

11:00 - 12:30 Lecture

12:30 - 13:30 Lunch break

13:30 - 15:00 Lecture

15:00 - 15:30 Break

15:30 - 17:00 Lecture

The schedule for Tuesday through Friday will be

9:00 - 11:00 Lecture

11:00 - 11:30 Break

11:30 - 13:00 Lecture

13:00 - 14:00 Lunch break

14:00 - 16:00 Lecture

16:00 - 16:30 Break

16:30 - 18:00 Lecture

Mon, 30 August 2021: Introduction to bash scripting and scientific Python programming (Marianne Corvellec)

  • Bash scripting introduction

    • filesystem

    • pipes and filters

    • loops

    • shell scripts

  • Git basics

    • repository (git init)

    • changes (git status, git diff)

    • versions (git add, git commit)

    • (git checkout)

  • Scientific programming in Python

    • assignment

    • data types

    • libraries

    • dataframes

  • Makefiles

    • reproducible research workflows

    • rules (targets, dependencies, and actions)

    • automatic variables and pattern rules

    • help (self-documentation)

Tue, 31 August 2021: Introduction to the HPC cluster. Best practices on HPC (Laura del Rı́o)

  • Introduction to the HPC cluster

    • Hardware description:

      • Head nodes and storage nodes

      • Compute nodes: CPU and GPU nodes

      • Node communication: Infiniband and Omni-Path

    • Queueing system: public and private queues

    • Software: modules and compilers

  • Cluster usage

    • Access and login

    • Transferring files

    • Job Processing

      • Interactive job submission

      • Bash job submission

      • Job arrays

      • Managing jobs

  • Best Practices for HPC

Wed, 1 September 2021: Parallel computing with MPI. Applications to numerical methods for PDE (Michael Dumbser and Laura del Rı́o)

  • Introduction to Message Passing Interface (MPI)

    • Parallel computing overview

    • MPI fundamental concepts

    • Blocking and non-blocking communication

    • Collective communication

  • Parallelization of explicit and implicit finite volume methods

    • Description of parallel algorithms for computing and assembling stiffness matrices and solution of systems of linear equations by using iterative methods, such as the conjugate gradient method

    • Partitioning of the computational domain, e.g. using Metis

    • Performing computations on each processor to update its own data set

    • Communicating data between processors by using message passage interface

  • Applications to Fluid and Solid Mechanics

Thu, 2 September 2021: Basic topics on Molecular Dynamics (Raffaello Potestio, Luca Tubiana, Emanuele Locatelli and Binayak Mukherjee)

  • Introduction to molecular dynamics simulations

    • Equations of motion

    • Canonical and microcanonical ensemble

    • Langevin and Brownian dynamics

    • Pair potentials and the LJ fluid

    • Some trick of the trade

  • Introduction to Lammps (with hands-on exercises)

    • What is LAMMPS

    • How to setup and analyse a simulation of liquid Argon

    • Introduction to VMD for visualization

  • Simulating Macromolecules with LAMMPS

    • Basic properties of polymers

    • Defining and simulating polymers

    • Hands-on numerical experiments

Fri, 3 September 2021: Advanced topics on Molecular Dynamics (Luca Tubiana, Emanuele Locatelli and Lorenzo Rovigatti)

  • Simulating supramolecular (topological) systems

    • Introduction to catenanes

    • Building complex architectures with Python and Jinja2

    • Simulating and analysing systems having multiple molecules

  • Managing simulations

    • Managing multiple simulations in parallel.

    • Checking for the correctness of results: caveat, tips & tricks.

  • Modifying LAMMPS to simulate active systems

    • Active systems in nature.

    • Introducing new potentials in LAMMPS.

    • Simulating active polymers with LAMMPS.

    • Analysing the results.

2021 HPC School Application Form Registration is open till July 1st


The strategic project "Modelling & Simulation" organizes the third school of high-performance computing (HPC).

The school is structured to be followed entirely, but also in single days, based on the level of competence and initial knowledge, as well as specific interests.

The first day, accessible also to those with limited computer and computation skills, is dedicated to some basic tools, such as Python for scientific programming, Git for version control, Bash and Make for the automation of scientific workflows. In addition to being functional to the rest of the school, this day offers a good first contact with the HPC.

The second day will cover the use of the university's HPC cluster. The fundamental objective is to provide participants with the necessary knowledge for the preparation and submission of jobs, making the most of the potential of the cluster. Particular attention will be paid to the practical rules that help improve performance, which is why a broad participation of both students and grant holders, and University staff is encouraged.

The third day will focus on parallel computing with MPI. The fundamental concepts of parallel programming will be introduced, with particular reference to the solution of partial differential equations (PDE). In particular, examples of parallelization of methods to implicit and explicit finite volumes will be proposed, with applications to the mechanics of fluids and solids.

The last two days are dedicated to Molecular Dynamics (MD) and simulations with Lammps, starting with basic elements and simple simulations, and continuing with in-depth studies both on research topics, such as active and topological polymeric systems, and on the automated management of multiple parallel simulations to explore parameter spaces.

The preliminary program only summarizes the titles and topics of the different days. In the second circular, to be distributed at the beginning of June, information on the registration and the final program will be available, with more details on the planned activities.

The school, which includes both lectures and practical "hands-on" sessions, will be held in Mesiano, in the presence, with 30 participants. Other participants will be allowed to follow in streaming. In the first two days, given the themes of widespread interest, a dozen participants may be admitted over the set limit.

Organizing committee: Marianne Corvellec, Laura Del Rio, Michael Dumbser, Luca Tubiana, Raffaello Potestio, Binayak Mukherjee, Sergio Setti & Paolo Scardi

Project website: http://mas.unitn.it/

Università di Trento
Via Calepina, 14 - I -38122 Trento
P.IVA-C.F. 00340520220
Reception Rettorato +39 0461 281111
ateneo@pec.unitn.it - ateneo@unitn.it

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