HITS – computational sciences on the way into the cloud? Frauke Gräter HITS Heidelberg

Heidelberg Institute for Theoretical Studies

HITS

Heidelberg Institute for Theoretical Studies

Klaus Tschira Stiftung: Supports informatics, natural sciences, mathematics

Klaus Tschira 1972 - Co-founded the German software giant SAP AG 1995 – Bought Villa Bosch, founded Klaus Tschira Stiftung

Setup: ●  110 scientists in 12 research groups ●  non-profit ●  from physics to biology to computer science ●  strong ties in Heidelberg and world-wide Agenda: multidisciplinary computational sciences ●  Molecular modeling and simulation ●  Computational biology ●  Bioinformatics & databases ●  Computational linguistics ●  Theoretical astrophysics ●  Computational Statistics, big data

Heidelberg Institute for Theoretical Studies

big data big scales big challenges

Compute Infrastructure @ HITS

•  110 scientists in 12 research groups •  Small HPC cluster for testing:

–  5732 cores –  5 nodes with nVidia Kepler GPUs,

2 nodes with Intel Xeon Phi –  28TB RAM, one node with 4TB RAM –  QDR Infiniband –  1.8PB storage

à  No scale out possibility due to rack space

à  Main HPC workloads done in (inter)national supercomputing centers

Molecular Biomechanics group, Frauke Gräter

Forces in biology!

blood spider web muscle focal adhesion

Proteins in the crash test

macro (meter) scale

molecular (nano) scale

Mechanics of large structures

The  challenge:  

The  challenge:  

.  .  .  .  .  

Gromacs (or NAMD): scale up to ~500 atoms / processor

typical demand:

50-1,000 CPUs (& GPUs) TBs data

HITS in the cloud? MD simulations

cores freq performance normalized

HITS 24 cores, 48 HT 1.8Ghz 47ns/day 47ns/day AWS c4.8xlarge 36vCPU 2.9GHz 60ns/day 49ns/day

41,000 atoms, Gromacs 5.0 AVX2 optimized binaries

HITS in the cloud? MD simulations

SMALL: shared HITS internal cluster: ~3,000 cores LARGE: supercomputing infrastructure (Stuttgart, Munich, PRACE): ~2-20 Mio CPU hours / project

SMALL-SIZED but MANY! Gromacs on AWS: flexible c4 instances: #CPUs = #hyperthreaded cores

com

puta

tiona

l cos

t

Current AWS developments @ HITS

•  Covering peak requests on development cluster with EC2 instances

•  Archiving of results on Glacier

•  Current developments: –  Transparent scheduling of independent jobs on hybrid

computing environment using spot market instances –  Budget/Quota-management within research teams –  Collaborative working platform for large datasets with

international partners, e.g. Square-Kilometre-Array (SKA) –  Genome assembly with huge temporal storage requirements

(PB-scale) –  Molecular Dynamics simulations, mid-sized instances

13

More information: www.h-its.org Twitter: @HITStudies Facebook: /HITStudies Youtube: /TheHITSters