5th bwHPC Symposium

Sep 24, 2018, 8:20 AM → Sep 25, 2018, 1:00 PM Europe/Berlin

Großer Hörsaal der Physik (University of Freiburg)

The 5th bwHPC symposium will be held on September 24/25 in Freiburg. Its focus is on scientific projects carried out with the help of high performance computing resources supplied within the framework of the bwHPC initiative of the state of Baden-Württemberg. The symposium is free of charge and open to researchers from all scientific fields. Participation from outside Baden-Württemberg is explicitly encouraged.

The bwHPC symposium focuses on the presentation of scientific computing projects as well as on the progress and the success stories of the bwHPC initiative. The event offers a unique opportunity to engage in an active dialog between scientists using high performance compute resources, operators of bwHPC sites, and the bwHPC-S5 support centers.

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Monday, September 24

9:30 AM → 10:30 AM Registration

10:30 AM → 12:30 PM Welcome and Session 1: Welcome, Keynote and selected talks from researchers (bwHPC)

10:30 AM Grußwort der Universität Freiburg

Speaker: Gunther Neuhaus (Universität Freiburg)

10:45 AM Grußwort des Ministeriums für Wissenschaft, Forschung und Kunst Baden-Württemberg

Speaker: Peter Castellaz (Ministerium für Wissenschaft, Forschung und Kunst Baden-Württemberg)

11:00 AM Computational Neuroscience and Neurotechnology

Speaker: Stefan Rotter (Bernstein Center Freiburg, University of Freiburg)

11:30 AM Molecular Dynamics Simulations for Solid Mechanics

Speaker: Lars Pastewka (University of Freiburg)

11:50 AM Recent Results from the ATLAS Experiment

Speaker: Felix Bührer (Universität Freiburg)

12:10 PM Make Halogen Bonds Strong Again - From Theoretical Studies to Experimental Strategies for Drug Discovery

Speaker: Frank Böckler (Universität Tübingen)

12:30 PM → 1:30 PM Lunch / Poster Session 1

1:30 PM → 2:50 PM Session 2: Selected talks from researchers (bwHPC)

1:30 PM Immunology going wild: genetic variation and immunocompetence in ducks

Wild animals are vectors and reservoirs of emerging infectious diseases with major implications on human health. Still little is known about the interactions of these pathogens and their main hosts in their natural environment. In my PhD project I studied several aspects of the immune and its interactions between the mallard duck and its pathogens. The methods ranged from gene expression profiling by RNA sequencing of experimentally immune-challenged mallards to large-scale re-sequencing of >100 immune genes in 96 wild duck samples of mallards and related duck species. To analyse these large data sets of genomic and transcriptomic nature I utilised the HPC systems of the HPCC5 in several ways. By combining population-scale genomic information and experimentally induced transcriptomic responses to pathogens with further approaches to measure physiological parameters of mallards I arrived at a comprehensive view on the interaction of diseases and their hosts in the wild.

Speaker: Ms Elinor Jax (Konstanz University)

1:50 PM Chicken caeca microbiome is altered by feed supplementation of phosphorous and calcium

This study investigates the disturbance of the chicken microbiome under the influence of minerals phosphorus (P) and calcium (Ca). Microbial taxonomy was elucidated targeting the taxonomic marker 16S rRNA gene, and functionality was acquired through metagenome sequencing. Both tasks comprise bioinformatic processing, which demands computational calculations, and they were done in the bwHPC infrastructure. A significant difference in the microbiota was observed in all diets. Lachnospiraceae was the most abundant family, in the treatment supplemented with P (33% digesta, and 37% mucosa). In the Ca supplemented diet, the presence of Peptococcaceae (11%, and 8%, respectively) was increased when compared with the other treatments. At the functional level, for both digesta and mucosa, the metabolite information registered higher abundance of genes (50%) in P and Ca diets, while in control was only 40%. Thus, changes in supplementations result in important modifications on the microbiome.

Speaker: Mr Daniel Borda-Molina (University of Hohenheim)

2:10 PM Proteins under pressure: crash-testing cellular junctions in supercomputers

Speaker: Csaba Daday (Heidelberg Institute for Theoretical Studies)

2:30 PM Dynamics of large-scale spiking neural networks

The focus of our work lies in exploring and analyzing the function of large-scale spiking neural networks that are inspired by the cerebral cortex of the mammalian brain. The Leaky Integrate-and-Fire model serves as a starting point to investigate, e.g., biologically inspired learning methods, auditory information processing, or phase transitions in large networks. While there is plenty of biological evidence for the existence of large-scale structures in neuronal networks, experimental access is limited. In addition to our neuromorphic hardware system, we rely on large-scale software simulations, e.g. using the NEST simulator, to examine aforementioned phenomena.
This talk gives an overview over research topics that take advantage of the bwHPC ecosystem.

Speaker: Eric Müller (Kirchhoff-Institute for Physics, Heidelberg University)

2:50 PM → 3:20 PM Coffee Break / Poster Session 2

Posters from Poster Session 1

3:20 PM → 4:20 PM Session 3: Selected talks from researchers (bwHPC)

3:20 PM Testing Einstein's theory of gravity with simulations of tidal disruption events

Speaker: Gela Haemmerling (University of Tuebingen)

3:40 PM Collisions in the early Solar System

Speaker: Christoph Schäfer (University of Tübingen)

4:00 PM NF-Core: Community-based best-practice pipeline development in Nextflow

Speaker: Alexander Peltzer (Quantitative Biology Center (QBiC) Tübingen)

4:20 PM → 4:40 PM Coffee Break

Posters from Poster Session 1

4:40 PM → 6:00 PM Session 4: Selected talks from researchers (bwHPC)

Selected talks from researchers (bwHPC)

4:40 PM Simulating tactoids of chiral rod-like particles

Speaker: Anja Kuhnhold (University of Freiburg)

5:00 PM Numerical Challenges in Financial Models

Speaker: Christoph Gerhart (University of Freiburg)

5:20 PM Numerical simulation of drop impact and rebound phenomena on smooth and micro-structured hydrophobic substrates

Speaker: Martin Wörner (Karlsruher Institut für Technologie (KIT))

7:00 PM → 10:00 PM Evening Lecture: Evening Lecture & Conference Dinner (Fingerfood Buffet)

7:00 PM Evening Lecture: Welcome (Peterhofkeller)

7:20 PM Sorry, I have digitized my scholarship: Small and big data in humanities computing

Speaker: Gerhard Lauer (University of Basel)

7:50 PM Conference Dinner: Fingerfood and Drinks

Tuesday, September 25

9:00 AM → 10:20 AM Sesison 5: Kickoff bwHPC-S5 and Selected Talks from other Projects

9:00 AM Umsetzungskonzept HPC, DIC und LS2DM

Speaker: Thomas Walter (Universität Tübingen)

9:10 AM Kickoff bwHPC-S5

Speaker: Robert Barthel (KIT - Steinbuch Centre for Computing)

9:20 AM Pre- und Postprocessing in der bwCloud

Speaker: Janne Schulz (Rechenzentrum Universität Mannheim)

9:40 AM HPC tools for GSS : Advances and Challenges

Speaker: Sergiy Gogolenko (High Performance Computing Center Stuttgart (HLRS))

10:00 AM Hessisches Kompetenzzentrum für Hochleistungsrechnen - Erfahrungsbericht

Speaker: Dörte Sternel (Hessisches Kompetenzzentrum für Hochleistungsrechnen (HKHLR))

10:20 AM → 10:40 AM Coffee Break

10:40 AM → 12:00 PM Session 6: Provision of Scientific Software

10:40 AM OpenHPC Talk

Speaker: Adrian Reber (Red Hat)

11:00 AM Unified Container Environments for Scientific Cluster Scenarios

Providing dependencies for computational workflows in shared environments, like HPC clusters, requires consideration from users to define the software stack for a workflow to execute. The Environment Modules system is the tool of choice on BinAC for this purpose. In this work, we present a use case which requires an application stack not available via Environment Modules on BinAC. We propose the usage of a containerized software stack for this particular problem using the Singularity and Docker container platforms. We present a solution for the reproducible provisioning of identical software stacks across HPC and non-HPC environments. The approach uses a Docker image as the basis for a Singularity container. This allows to define arbitrary software stacks and to execute workflows across different environments, from local workstations to HPC clusters, providing identical versions of software and hence leading to the same computational output.

Speaker: Mark Leznik (Institute of Information Resource Management, Ulm University, Germany)

11:20 AM Ein hierarchisches Modulsystem - Konzeption und Implementierung

Speaker: Holger Obermaier (Karlsruher Institut für Technologie (KIT))

11:40 AM Dynamic Resource Extension for Data Intensive Computing with Specialized Software Environments on HPC systems

Speaker: Matthias Schnepf (KIT SCC)

12:00 PM → 1:00 PM Registration for ZKI AK Supercomputing

Registration for ZKI AK Supercomputing