Introduction at Workshop e-BioGrid november 2011

1. e-BioGrid
E-Science infrastructure for life
science research
E-BioGrid workshop, November 10, 2011
Introduction

2. Big Grid infrastructure
High-performance computing and storage resources,
Grid – Life Science Grid
High Performance Cloud
Hadoop (soon)
Non-Big Grid but available via NWO/NCF:
Huygens, LISA, GPU

4. How to apply for access?
All applications go into the NWO/NCF
IRIS system.
Basically: specify what you need, why
And give an estimate how much you need.
All applications go to Big Grid when
Big Grid infrastructure is involved. Please contact us for assistance.
For Huygens and Lisa, NWO/NCF will We are working to simplify
consider all applications
this procedure.

5. 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 use
of HPC hardware and e-science environments.
SARA works on parallelization projects (funded by NWO):
parallelize your software for use on HPC hardware.

6. 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.

7. The Life Science Grid sites
LUMC – Leiden
WUR – Wageningen
UU – Utrecht
NKI – Amsterdam
AMC – Amsterdam
Radboud Universiteit – Nijmegen
ErasmusMC – Rotterdam
Technische Universiteit - Delft
Rijksuniversiteit Groningen
Keygene - Wageningen
Each of these clusters have either 16 or 32 cores and 18 Tb of storage space.

8. Grid nodes
Currently 6 small clusters :16 job slots each, soon to be
upgraded
5 clusters: 32 job slots each
32 job slot each- 20TB storage
All clusters run CentOS 5– 64 bits
Gina cluster SARA 2800 job slots
Philips 1470
Nikhef 2160
Groningen 164

9. High Performance Cloud
19 nodes of 32 cores each (608 cores)
Each node has 256 GB RAM
400 TB storage.
Nodes are connected by four 10 Gb
interfaces to a non-blocking switch.
So maximum 40 GB access to storage
(per node).

10. High Performance Cloud
When 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.

11. Huygens National Supercomputer
Huygens 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)

12. Huygens: when to use
Often used for large scale simulations
Parallel 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 funded
parallelization projects.

13. LISA: Description
Total number of cores 4480
Total amount of memory12 TB
Total peak performance20 TFlop/sec
Disk space 48 TB
Operating systemDebian Linux AMD64 OS
Affiliates of UvA and VU can use this system
directly.
LISA is a popular PBS cluster.

15. Hadoop (soon to come)

16. Hadoop (soon to come)

17. Finally
Which infrastructure to choose for your problem?
Ask eBioGrid.
How to get access?
NWO/NCF Iris system
Ask eBioGrid/SARA for help.
How to get assistance?
Ask eBioGrid for support.