HPC Newsletter 03/15
Dear colleagues,
Welcome to the 3rd newsletter in 2015. The biggest news is that the DFG has granted our application for the bwForCluster ENM. We can thus proceed with the acquisition procedure as planned, starting the procurement in the second half of April. This also means that any pending feedback from you regarding the procurement procedure (e.g. benchmarks, storage requirements) is required as soon as possible.
With best regards,
Your HPC Team, Rechenzentrum, Universität Freiburg
Table of Contents
bwForCluster ENM application granted
Final preparations for acquisition procedure
HPC course in Freiburg (report)
BFG: GPU nodes performance improvements
bwForCluster EMN consultation in Tübingen
Upcoming Events
08.04.2015 "Hands-On Workshop - Einführung Linux & HPC" in Mannheim (given in German language)
bwForCluster ENM application granted
On Friday, March 27th, the Rechenzentrum finally received the official letter from the DFG stating that our bwForCluster ENM application has been granted. We also received the comments of the reviewers from the DFG review session last year on November 6th. We are happy to say that the reviewers' comments were generally favourable and that the application has been granted without any budget cuts.
Final preparations for acquisition procedure
We plan to formally start the acquisition procedure with a “preliminary qualification competition” in the second half of April. If there is any pending feedback from your side, e.g. benchmarks or answers to our storage requirements poll, please get back to us as soon as possible.
With the feedback that we already received via personal discussions, by domain specific consultation meetings and during our HPC workshops, we have a fairly complete picture on how the cluster should look like. In other words, we are about to finalize the bwForCluster ENM specification for the procurement procedure.
HPC course in Freiburg (report)
On March 25th, the HPC Competence Center in Freiburg invited scientists from Baden-Württemberg to the course “Introduction to HPC Computing in Baden-Württemberg“. The intention of this course was to introduce the participants to the bwHPC concept and to let them take their first steps on the bwUniCluster and NEMO. We also gave an outlook on the forthcoming bwForCluster ENM.
There was a total of 24 participants coming from the universities of Heidelberg, Karlsruhe and Freiburg. The attendants covered all of our three scientific communities: Elementary Particle Physics, Neuroscience and Microsystems Engineering.
BFG: GPU nodes performance improvements
The 16 GPU nodes in the Black Forest Grid fitted with K10 Nvidia Tesla cards had their BIOS updated to the latest version. Unfortunately, with this specific model of compute node, BIOS updates are a time consuming process, involving the removal of the case from the rack and removal of further onboard components to access a BIOS update jumper.
We are therefore more than happy to report that the effort has paid off. The communication between CPU and GPU over the PCI bus has improved in speed and gained in reliability. Before the BIOS update, the running time of a hybrid CPU/GPU Gromacs test program would largely fluctuate and sometimes become absurdly slow. With the BIOS update applied, we see a constant running time and fewer CPU waiting times. Overall, we experience a 10% increase in performance. Many thanks to Sebastian Buchenberg from Prof Gerhard Stock's group for these measurements. Thanks for your patience during the downtime of the GPU nodes.
NEMO: Matlab R2015a available
We have upgraded Matlab to the newest R2015a release from Mathworks. If you just do the usual “module load math/matlab”, you will automatically use this version. The cluster specific license has been renewed and moved to a new license server. The old version (R2013a) is still available, but we recommend that you verify that your code runs with the latest version.
NEMO: Update to Moab 8.1
The Moab scheduling suite has been upgraded to version 8.1. In an HPC cluster environment, the scheduler manages when, where and how user jobs get executed. It also keeps track of the “fairshare” metric, which makes sure that computing resources are distributed among the users and working groups in a fair fashion, according to the sharing policies.
Moab 8.1 is the first official version which has support for features that we need for proper governance of jobs running in virtual machines. The development and inclusion of these features is partly the result of various meetings we had with Adaptive Computing during the past months. We will be testing the new features on NEMO.
bwForCluster EMN consultation in Tübingen
On March 5th, after attending the OpenStack/Clustervision workshop organized by the HPC competence center in Tübingen, we met with scientists from our communities in Tübingen. We discussed the ongoing preparations for the procurement procedure and the specific needs of the Tübingen communities (Neuroscience and Elementary Particle Physics) with respect to the software and the hardware configuration. We verified that our current plan for the cluster configuration for the most part matches with what they expect. Additionally, feedback received during the meeting will serve as additional input to the bwForCluster ENM procurement specification document.
HPC Team, Rechenzentrum, Universität Freiburg
http://www.hpc.uni-freiburg.de
bwHPC-C5 Project
http://www.bwhpc-c5.de
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