Back to Table of contents

Primeur weekly 2013-08-12

Special

Hybrid architectures and stream computing are becoming the norm in life sciences ...

Focus

UberCloud successful in bringing HPC Cloud to SMEs - and interview with Wolfgang Gentzsch ...

The Cloud

New IBM Flex Systems allow clients to build larger Clouds in smaller data centres ...

Orion Health chooses HP to support managed health services ...

Oracle Enterprise Manager 12c delivers comprehensive management for Oracle Database 12c ...

Capitalonline taps IBM to offer enhanced Cloud services ...

IBM to help Geraldton become smarter, more sustainable city with new Cloud data centre ...

Adaptive Computing unveils Moab Cloud Optimizer Integration for HP Cloud Service Automation 3.2 ...

EuroFlash

Putting Big Data into Perspective ...

Magnetic switching simplified ...

Quantum communication controlled by resonance in 'artificial atoms' ...

Skoda Auto selects SGI ICE X and SGI UV 2000 HPC systems to accelerate automotive innovation ...

ClusterVision strengthens commercial teams in the UK and Germany ...

Wroclaw University Library turns to IBM Big Data solution to preserve European heritage, open digital archives to the world ...

USFlash

Fujitsu receives order for new supercomputer system from Canon ...

IBM Research creates new foundation to program SyNAPSE chips ...

Google, IBM, Mellanox, NVIDIA, and Tyan announce development group for data centres ...

HP helps New Zealand Government Council boost employee productivity ...

Cray names John Josephakis Vice President of Worldwide Sales ...

CSIRO takes charge of Australia's information overload ...

Supercomputer-enabled metagenomic research explores ecosystems in oceans and microbes in the human esophagus ...

Speed limit set for ultrafast electrical switch ...

SGI reports fourth quarter and fiscal year 2013 financial results ...

NVIDIA reports financial results for second quarter fiscal 2014 ...

How superbug spreads among regional hospitals: a domino effect ...

Hybrid architectures and stream computing are becoming the norm in life sciences


19 Jun 2013 Leipzig - In the session titled "Better Understanding Brains, Genomes and Life Using HPC Systems" at ISC'13 in Leipzig Rossen Apostolov from the KTH Royal Institute of Technology in Stockholm, Sweden and the EC-funded ScalaLife project, talked about efficient and scalable bio-molecular simulations on HPC systems. Rossen Apostolov confirmed that a large fraction of the European Commission's research funding is directed to life sciences. He also claimed that life science researchers are heavily interested in Ensemble computing.

The art of simulation in the life sciences involves a large spectrum, starting from the atom over the small molecule to the macromolecule and further beyond to the cell, tissue, and organ, explained Rossen Apostolov. The time scales of molecular simulations are increasing accordingly.

The ScalaLife project is a joint EU-FP7 funded project between HPC centres and institutes in Germany, Sweden, Spain and the United Kingdom. The consortium is dealing with hierarchical parallellization, as the speaker explained.

To this end hybrid architectures and stream computing are becoming the norm in order to scale the code. This includes hybrid-MPI/OpenMP, hybrid-GPU/CPU, and accelerators with FPGA.

The researchers are scaling the problem with Ensemble computing, Rossen Apostolov told the audience. He mentioned GROMACS, a project which started in 1995 in Groningen, the Netherlands but most of the core developers are now in Sweden. The GROMACS team developed a highly tuned code for molecular dynamics.

Hybrid-MPI/OpenMP is being used in GROMACS, the speaker showed. Using the Ewald summation,

separate electrostatics are moving into long and short range parts. The short range decays fast while the

long range is solved in receprocal space, just as for crystals. This corresponds to the sum over the infinite periodic copies, Rossen Apostolov explained.

PME requires all-2-all communications, but PP does not, the speaker continued. Typically 1/4th of the CPUs do all-to-all PME, the rest are particle-particle interactions.

Hybrid-CPU/GPU architecture consists of MPI between domains, involving hybrid parallelization and GPUs. There is a good basic scaling, the speaker explained. FPGAs with GROMACS are a successful formula with regard to performance, time to market, prototyping cost, reliability of execution, and long-term maintenance.

Rossen Apostolov showed some rough initial results: 300 M/s using 4 core CPU with hyperthreading; 960 M/s using 4 core CPU with hyperthreading using SSE; and 3125 M/s using a C2075 GPU.

The DALTON project started in 1982. In this project, the master/worker scheme is turned into a multiple master/team of worker scheme, Rossen Apostolov explained.

For scaling the problem, Ensemble computing is on the rise. For example, fault tolerant with checkpointing and heartbeat monitoring is applied in the Copernicus project.

With regard to the performance, the most important metric is the real time to result. This is tunable since more cores per simulation give the results sooner, as the speaker showed.

The DISCRETE package has been developed at BSC/IRB in Barcelona. It implements the Discrete MD method in which particles move until conclusion.

Rossen Apostolov concluded by describing the future needs in simulation. The researchers need smart job dispatchers and auto-tuning mechanisms. There is a variety of software and hardware nowadays, so dispatchers and auto-tuners are very much in demand.

Leslie Versweyveld

Back to Table of contents

Primeur weekly 2013-08-12

Special

Hybrid architectures and stream computing are becoming the norm in life sciences ...

Focus

UberCloud successful in bringing HPC Cloud to SMEs - and interview with Wolfgang Gentzsch ...

The Cloud

New IBM Flex Systems allow clients to build larger Clouds in smaller data centres ...

Orion Health chooses HP to support managed health services ...

Oracle Enterprise Manager 12c delivers comprehensive management for Oracle Database 12c ...

Capitalonline taps IBM to offer enhanced Cloud services ...

IBM to help Geraldton become smarter, more sustainable city with new Cloud data centre ...

Adaptive Computing unveils Moab Cloud Optimizer Integration for HP Cloud Service Automation 3.2 ...

EuroFlash

Putting Big Data into Perspective ...

Magnetic switching simplified ...

Quantum communication controlled by resonance in 'artificial atoms' ...

Skoda Auto selects SGI ICE X and SGI UV 2000 HPC systems to accelerate automotive innovation ...

ClusterVision strengthens commercial teams in the UK and Germany ...

Wroclaw University Library turns to IBM Big Data solution to preserve European heritage, open digital archives to the world ...

USFlash

Fujitsu receives order for new supercomputer system from Canon ...

IBM Research creates new foundation to program SyNAPSE chips ...

Google, IBM, Mellanox, NVIDIA, and Tyan announce development group for data centres ...

HP helps New Zealand Government Council boost employee productivity ...

Cray names John Josephakis Vice President of Worldwide Sales ...

CSIRO takes charge of Australia's information overload ...

Supercomputer-enabled metagenomic research explores ecosystems in oceans and microbes in the human esophagus ...

Speed limit set for ultrafast electrical switch ...

SGI reports fourth quarter and fiscal year 2013 financial results ...

NVIDIA reports financial results for second quarter fiscal 2014 ...

How superbug spreads among regional hospitals: a domino effect ...