Nordic High Performance Computing & Applications Workshop
13-15 June 2018, University of Iceland, Reykjavík
Registration deadline extended to 11. June 2018.
After the successful 2017 workshop, the University of Iceland is offering a free cross-national training workshop on high-performance computing and applications at the University of Iceland in Reykjavík, Iceland, 13-15 June 2018 (noon-to-noon).
The University of Iceland (HÍ) has resident expertise in software engineering, distributed computing, and closely collaborates with the Jülich Supercomputing Centre (JSC) in High-Performance Computing (HPC) research and teaching. The university's Division of Information Technology (UTS) has expertise in cross-national Nordic scientific computing through having hosted the Nordic High Performance Computing (NHPC) cluster Garðar and now on the national level with the Icelandic HPC cluster (IHPC) Garpur. Iceland, in particular the University of Iceland, furthermore has a strong user community, e.g. in computational physics and chemistry, systems biology, and glaciology.
The workshop is organized in cooperation with the Jülich Supercomputing Centre (JSC), associated with the NordForsk e-science NCoE eSTICC (e-Science Tools for Investigating Climate Change), the European Horizon 2020 Pre-Exascale computing project DEEP-EST and the European Horizon 2020 project SIMDAS (Centre of Excellence in Simulation and Data Science), and funded via NordForsk's Nordic e-Infrastructure Collaboration (NeIC) Pooling Competencies focus area.
Note that there is another course on research software development (which is not specific to HPC), namely the CodeRefinery workshop in Reykjavik 21-23 August 2018. While both are funded by NeIC, the topics and trainers are different.
Topics and Trainers
The three-day training workshop will be run by distinguished experts with over a decade of experience in their fields, and cover the following topics, both via lecture and partly hands-on experience (so bring your own laptop to connect via SSH to the provided HPC clusters):
High Performance Computing (Morris Riedel, HÍ/JSC)
The availability of High-Performance Computing (HPC), powered by large-scale supercomputers and scalable cloud computing resources, has changed the way how science and engineering is done today. Innovative HPC technologies enable us to create "bridges" between the traditional scientific pillars "experiment" and "theory" by performing simulations of the real world or technology. Covered topics are parallel programming using MPI and OpenMP as well as more recent approaches using GPGPUs. General elements and challenges of parallel programming like concurrency, domain decomposition, load imbalancing, stencil methods, ghost/halo regions, and related topics will be covered using examples in the programming language C.
The Icelandic HPC Cluster (Máni
Maríus Viðarsson, HÍ UTS)
Short presentation on the High Performance
Computing facilities and services available at
the University of Iceland aimed at new users:
how to log in, how to submit jobs, how to use
the module system used to set up the
appropriate tool environment. Finally, we
will have a short walk to the premises of
UTS to see the HPC hardware and
infrastructure (such as cooling) face to
A physicist's guide to parallelization at the IHPC (Viðar Guðmundsson, HÍ)
Several easy steps to parallelize programs in physics
will be pointed out through the use of OpenMP, Intel-MKL,
and CUBLAS in an effective way maintaining high
code readability. This approach for static or time-dependent
many-body problems in quantum theory and statistical
mechanics points out the convenience of a heavy use of
linear functional spaces and transformations between them.
Cloud Computing (Helmut Neukirchen, HÍ)
Helmut's talk will
cover of how to use Infrastructure-as-a-Service cloud computing, i.e.
using virtual machines in the cloud. This can be a viable solution, if
you need a special machine (e.g. with lots of RAM) that you do not
have available otherwise.
HPC Software Engineering (Matthias Book, HÍ)
The Interaction Room (IR) is a collaboration technique that uses large interactive displays to facilitate the elicitation, joint understanding and prioritization of requirements in teams composed of stakeholders from different backgrounds, such as software engineers and scientific domain experts. By encouraging pragmatic modeling, the IR helps to deal with the complexity of scientific computing applications and map them to HPC solution techniques.
Data Analysis from a Data Center Perspective (Rahul Ramachandran, NASA)
Rahul Ramachadran drives the activities of a NASA data center that stores and makes available large quantities of measurement data such as from satelites. Being in the community of remote sensing in particular and Earth sciences in general, he will talk about the challenges of performing big data analytics from a data center perspective.
Data-intensive Research on Precipitation (Kuo Kwo-Sen, NASA)
Kuo Kwo-Sen works at NASA and is in the research of precipitation that involved studies with large quantities of different datasets. One of the key elements in performing the analysis are big data analytics techniques that involve the use of array databases.
SMITH - Smart Medical Information Technology for Healthcare (Oliver Maaßen, University Hospital RWTH Aachen)
The SMITH project aims at making better use of the wealth of patient data in order to validate the relevance of novel diagnostic and therapeutic methods in systematic trials, ultimately hoping to directly improve care. University Hospital RWTH Aachen, RWTH Aachen University, Bayer AG and the Jülich Supercomputing Centre are collaborating in the clinical use case Algorithmic Surveillance of ICU patients (ASIC). In order to predict individual disease progression of those ICU patients, ASIC will utilize pattern recognition technologies as well as established mechanistic systems medicine models, complemented by machine learning and high-performance computing, both integrated in a hybrid virtual patient (VP) model.
Research and support activities of the Simulation Laboratory Climate Science at JSC (Lars Hoffmann, JSC)
This talk will highlight research and support activities of the SimLab Climate Science that supports the Earth system modelling (ESM) community.
This includes the development and applications of our own open source tools, i.e., the Lagrangian transport model MPTRAC and the radiative transfer model JURASSIC, and support for ultra-high resolution and coupled chemistry-climate simulations with the general circulation model ICON. These activities are typically linked to data analytics projects, making use of big satellite and model data sets. The talk will also cover data support activities for the ESM community, such as our new `meteocloud' data archive.
Location: University of Iceland, Building Lögberg, room L-103 (see below)
Photo impressions from the workshop
13 June 2018
(Chair: Helmut Neukirchen)
|13:00-13:20 Welcome address (slides / video 0:00-22:49) (Helmut Neukirchen)
13:20-14:30 Introduction to using Cloud Computing (slides / video 22:49-end) (Helmut Neukirchen)
14:30-15:00 Coffee break
15:00-16:00 Introduction to the IHPC Cluster (slides / video) (Máni Maríus Viðarsson)
16:00-17:00 Tour of the IHPC Facilities (Máni Maríus Viðarsson)
14 June 2018
(Chair: Matthias Book)
09:00-10:00 Birds Eye View on Analytics from Operational NASA Data Centers Perspective (slides / video) (Rahul Ramachandran)
10:00-11:00 Quest for Value in Big Earth Data (slides / video) (Kuo Kwo-Sen)
11:00-11:30 Coffee break
11:30-12:30 A Physicist's Guide to parallelization at the IHPC (slides / video) (Viðar Guðmundsson)
12:30-14:00 Lunch and after-lunch coffee
14:00-15:30 HPC & GPUs for Machine Learning & Deep Learning (slides / video) (Morris Riedel)
15:30-16:00 Coffee break
16:00-17:00 Introduction to OpenMP & Clustering Applications (had to be skipped due to time reasons: we try to make later slides and a video recording of a similar talk available) (Morris Riedel)
15 June 2018
(Chair: Morris Riedel)
09:00-9:45 SMITH - Smart Medical Information Technology for Healthcare (slides) (Oliver Maaßen); Markov Chains Monte Carlo in SMITH (slides) (Morris Riedel) (video)
09:45-10:30 Research and support activities of the
Simulation Laboratory Climate Science at JSC (slides / video) (Lars Hoffmann)
10:30-11:00 Coffee break
11:00-12:00 HPC Systems Engineering in the Interaction Room (slides / video) (Matthias Book)
12:00-12:15 Closing remarks (slides / video) (Helmut Neukirchen or Matthias Book)
Location and Travel Information
The workshop will take place in room L-103 of the Lögberg building (Saemundargata 8) on the campus of the University of Iceland in Reykjavík.
The University of Iceland campus is in walking distance of Reykjavík's city centre, which offers a wide variety of accommodation options (the closest being the Radisson Blu Saga Hotel, right next to the workshop venue -- contact workshop organizers to get 15 percent special workshop reduction on the rates shown in their booking system; but in general, guesthouses are much cheaper).
Iceland can be reached from many European and American cities within a few hours through its international airport at Keflavík (KEF). The Flybus service provides frequent transfers (no schedule for arrivals, the schedule is rather: each arrival has a matching bus trip) to Reykjavík city center. The Flybus terminal in Reykjavík (BSÍ) is in walking distance to the university campus.
If you would like to extend your stay, there is plenty to see and do around Reykjavík. Have a great time!
To participate in the workshop, please register until 11 June 2018.
Participation in the workshop is free of charge and includes lunch (on Thursday and Friday) and coffee breaks through funding from Nordforsk NeIC. Participants are responsible for their own travel and accommodation.
We are looking forward to welcoming you at the University of Iceland!