e-BioGridE-Science infrastructure for life science researchE-BioGrid workshop, November 10, 2011Introduction
Big Grid infrastructureHigh-performance computing and storage resources,Grid – Life Science GridHigh Performance CloudHadoop (soon)Non-Big Grid but available via NWO/NCF:Huygens, LISA, GPU
How to apply for access?All applications go into the NWO/NCFIRIS system.Basically: specify what you need, whyAnd give an estimate how much you need.All applications go to Big Grid whenBig Grid infrastructure is involved. Please contact us for assistance.For Huygens and Lisa, NWO/NCF will We are working to simplifyconsider all applications this procedure.
What does SARA do?SARA doesn’t own the systems.SARA doesn’t decide on user access.SARA doesn’t host websites, small scale services, wiki’s etc.SARA maintains HPC systems, provides assistance and consultancy.SARA works in scientific projects like eBioGrid to assist in the useof HPC hardware and e-science environments.SARA works on parallelization projects (funded by NWO):parallelize your software for use on HPC hardware.
The Life Science Grid WHAT IT IS •Several clusters at academic medical centers and universities. •Open to all life scientists based in the Netherlands. •Clusters can be used separately or together by using Grid middleware. •Currently more than 3700 job slots for concurrent processing. •Distributive storage capabilities and automatic replication of data. •Maintained and supported by SARA.
The Life Science Grid sitesLUMC – LeidenWUR – WageningenUU – UtrechtNKI – AmsterdamAMC – AmsterdamRadboud Universiteit – NijmegenErasmusMC – RotterdamTechnische Universiteit - DelftRijksuniversiteit GroningenKeygene - WageningenEach of these clusters have either 16 or 32 cores and 18 Tb of storage space.
Grid nodesCurrently 6 small clusters :16 job slots each, soon to be upgraded5 clusters: 32 job slots each32 job slot each- 20TB storageAll clusters run CentOS 5– 64 bitsGina cluster SARA 2800 job slotsPhilips 1470Nikhef 2160Groningen 164
High Performance Cloud19 nodes of 32 cores each (608 cores)Each node has 256 GB RAM400 TB storage.Nodes are connected by four 10 Gb interfaces to a non-blocking switch.So maximum 40 GB access to storage (per node).
High Performance CloudWhen to use cloud?Start up your own Virtual Machines. Be your own boss. Users have their own Virtual Cluster, running their OS and software of choice.Expand when you need to. You must be able to organize system administration yourself.
Huygens National SupercomputerHuygens is an IBM pSeries 575 system.The number of IBM Power6 cores is 3456.The total peak performance is 65 Tflop/s.The total memory is 15.75 TB.The inter-node InfiniBand interconnect is 160 Gbit/s.The net disk space is 700 TB.The system runs Linux (SLES11 SP1)
Huygens: when to useOften used for large scale simulationsParallel systems with interdependencies and a need for high speed interconnects.Software typically uses MPI or openMP.Parallel jobs communicate heavily with each other.Existing sofware is often ported in NWO fundedparallelization projects.
LISA: DescriptionTotal number of cores 4480Total amount of memory12 TBTotal peak performance20 TFlop/secDisk space 48 TBOperating systemDebian Linux AMD64 OSAffiliates of UvA and VU can use this system directly.LISA is a popular PBS cluster.