Third Freiburg HPC-Newsletter (Jun. 2014)
Dear ladies and gentlemen, dear colleagues!
Due to an application for the bwForCluster ENM, some time has passed since the last newsletter. Now we have compiled an overview of developments and activities at our Freiburg location.
We hope you enjoy reading our newsletter and are of course available for questions anytime!
Your HPC team at Freiburg’s IT-Services
Michael Janczyk, Dirk von Suchodoletz, and Janne Schulz
If you do not wish to receive our newsletter in the future, please contact us via e-mail or use the following form: http://www.bwhpc-c5.uni-freiburg.de/hpc-newsletter/abmeldung
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Overview:
bwForCluster
Application
Both applications (Tübingen and bwForCluster ENM from Freiburg) are on their way to the DFG via the Ministry for Science and Culture Stuttgart. Tübingen’s application comprises 3 Million Euros and Freiburg’s application comprises 3,7 Million Euros, due to contributions from scientists in neuroscience and elementary particle physics. The adventure of applying is not yet entirely over since we still need to supply vitae of our research group leaders.
For including the Cluster, which will comprise more than 10 data cupboards and which will need up to 200kW in energy, the reconstruction in the IT Services building are being coordinated together with the university building authorities. For this a new computer room IIb will be reserved in the basement. This will entail extensive works on air-conditioning and energy supply, all of which will take place in the second half of 2014.
HPC-competence center ENM in Freiburg (bwHPC-C5 ENM)
Freiburg’s HPC team will be strengthened by our colleague Bernd Wiebelt as of 1 July, who has diverse experience in HPC in Freiburg as well as in Jülich. He will specifically support the user side through courses and support for programming and software-library improvement. He will moreover be the coordinator for the respective “Tiger-Teams” on specific questions. More information on bwHPC-C5 and Tiger-Teams can be found under http://www.bwhpc-c5.de.
Tryout of Xeon-PHI
For support and development of HPC-computing diverse directions are evaluated. For this purpose Freiburg’s HPC group has been running a test machine of Fa. Fujitsu with an Intel accelerator (Intel Xeon Phi Modell 5110P (8GB, 1.053 GHz, 60 core, 240 threads)), see: http://ark.intel.com/de/products/71992/Intel-Xeon-Phi-Coprocessor-5110P-8GB-1_053-GHz-60-core.
Different to General-Purpose-GPUs, Intel accelerators do not need elaborate code adaptation. A simple adaptation of the parameter “number_of_threads” can, for example, already effect the calculation of a problem. First tests have shown small advantages in the calculation of a Xeon-PHI-card in comparison to Xeon-CPUs with 20 cores (simulation grid for Lattice-Boltzmann).
For individual tests and experiments a bwGRiD-Cluster-Account is necessary in order to connect with the machine via SSH:
ssh -l fr_<RZ-UID> phiphi.bfg.uni-freiburg.de
There are several ways of using the accelerator. As with GPUs, the code can be executed on the host, only sourcing some parts to the PHI card. The PHI itself is a small Linux system, which means that one can log on to it in order to execute the code directly on the card. For the best results the Intel Parallel Studio XE 2013 (Compiler, etc…) has been installed.
Please e-mail admin@bfg.uni-freiburg.de with questions.
bwUniCluster
bwUniCluster started in Karlsruhe
As announced already in our last newsletter, the bwUniCluster in Karlsruhe is starting. Already some users from Freiburg are running jobs on this cluster. The bwUniCluster is Baden-Württemberg’s General Purpose Tier 3 High Performance Computing (HPC) Cluster, financed by MWK and the following shareholders:
- Albert Ludwig Universität Freiburg
- Eberhard Karls Universität Tübingen
- Karlsruhe Institute of Technology (KIT)
- Ruprecht-Karls-Universität Heidelberg
- Ulm Universität
- Universität Hohenheim
- Universität Konstanz
- Universität Mannheim
- Universität Stuttgart
It is located at KIT Karlsruhe. The University of Freiburg has a 10% share in this Cluster. The machine is in high demand, resulting in an already filled queue. Freiburg’s part with at the moment less than half (most of the time 2 to 5 percent) is far below the limit currently. Freiburg’s users are therefore given priority through a fair-share mechanism until 10 percent have been reached.
Workshops for bwUniCluster
The bwUniCluster offers the possibility of migrating old HPC resources, which are being dismantled in computer room I of the IT Services Building, step by step. This is being supported through the introductory course “How To Use the bwUni Cluster” on 9 July 2014 in the IT Services Building. To participate in this course, you should have activated the login to the cluster. Detailed steps can be found here http://www.bwhpc-c5.de/wiki/index.php/BwUniCluster_User_Access.
For further information on the bwUniCluster and the installed software, see: http://www.bwhpc-c5.de/wiki/index.php/Main_Page.
HPC at the Freiburg location
Publication
We are delighted to be able to announce the availability of the collection "Hochleistungsrechnen in Baden-Württemberg – Ausgewählte Aktivitäten im bwGRiD". It was published by KIT Scientific Publishing (DOI http://dx.doi.org/10.5445/KSP/1000039516).
Establishing a Freiburg site group
At the moment we are working on constructing a joint HPC administration and support group for the following areas: bwForCluster ENM and bwHPC-C5 at Freiburg. This is intended to consolidate resources and to prepare the change to operating systems and environments, all of which is to advance a fast start of the new cluster. At the same time it is meant to support researchers in realizing their HPC projects on the level of programming and job-optimization.
Computer room consolidation
With regard to the consolidation of computer room I, work has progressed. Numerous old systems have been removed, and we would like to thank all involved parties. After consulting with the operations group, we ask that all old systems be removed or migrated until the end of July/August (Individual operators have already been contacted).
Computer room IIb (basement, IT Services, currently computer lab -104, which will be integrated into the existing computer room IIa, is being planned together with the building authorities. For future use of IT Services administrated computer rooms (after all measures have been implemented, there will be three since in KGII there will be capacity for geographical redundancy), a computer room user guide will be provided. It will be finalized and circulated over the next weeks.
Survey on research management
The research data management provides the basis for easy usage and sustainable storage of all kinds of scientific data. The pertaining questions and issues are complex due to the diversity of multiple research communities and existing approaches. The IT Services at Freiburg University has been involved in the topic for some time through a research group working on research data management/functional long term archiving. They are pursuing two goals: research for potential country-wide services for the functional access to old data sets and original environments as well as research for services and solutions for the research community in Freiburg.
For this, interview guidelines have been developed together with our colleagues. Currently we are identifying central players at the University for address data: SFBs, EU projects, excellence clusters, users of HPC resources. These will be contacted over the next week in order to ask them to enter into conversation with us. Especially the area of data intensive research and HPC are our bigger challenges. The following themes are to be discussed: data sources, kinds of data, scope, IPR, processes of data processing, data storage, goals, publication and data sharing. The following e-mail address has been reserved for coordination and questions: forschungsdaten@rz.uni-freiburg.de.
Dates
Workshop bwUniCluster
This workshop is about "How to use the bwUniCluster". It is held in the computer lab, Room -100. There are only 15 places available. If you want to attend, just send a mail to admin@bfg.uni-freiburg.de.
Only the first 15 applicants will be given a place in the lab.
WHEN: 09.07.2014, 9:30 - 11:30
WHERE: Computer Center, room -100 (basement).
Restructuring of computer room 1
At the end July/August: Migration/removal of old systems (older than 5 years (computer-nodes) or 6 years (infrastructure)).
GridKA School "Big Data, Cloud Computing and Modern Programming"
The International GridKa School is one of the leading summer schools for advanced computing techniques in Europe. The school provides a forum for scientists and technology leaders, experts and novices to facilitate knowledge sharing and information exchange.
More information is available at
http://gridka-school.scc.kit.edu/2014/
WHEN: 01. - 05.09.2014
WHERE: Karlsruhe, Steinbuch Centre for Computing, KIT
