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Cloud Computing at PDC
Gert Svensson
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Local private cloud test bed – for researchers
First test bed:
12x32 cores
1 TB per node, 20 TB as NFS
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Galaxy cloud test bed – for bioinformatics
Also on Amazon
via SNIC Clou
administration
Galaxy is an open, web-based platform for data intensive
biomedical research. Whether on the free public server or your
own instance, you can perform, reproduce, and share complete
analyses. See http://galaxy.psu.edu
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Cloud Computing
@ Swedish National
Infrastructure of Computing
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Phase 1: Neon project (2010) - SE, NO, FIN, DK, IS
Phase 2: Public cloud usage for users in all Swedish HPC centras (2011-2012)
Phase 1, CrossNordic project
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Phase 2: Public cloud usage for users in all
Swedish HPC centras (2011-2012)
SNIC Cloud project facilitate Swedish and Norwegian researchers to use
Public cloud in their research - without knowing much technical cloud
details. In the first phase we are focusing on Amazon Web Services and later
expand on adding other Public cloud offerings as-well-as Private cloud.
Each SNIC center has:
A budget of 250 ksek for helping their users into
SNIC Cloud.
A budget of 83 ksek for running on SNIC Cloud (
= Amazon costs, mangaged by PDC)
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SNIC Cloud – Architecture (goal)
Together with
UNINETT SIGMA
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(Norway)
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SNIC Cloud - Current
3 Levels for now
Level 3 - AWS User (isolation)
Level 2 - AWS User (no
isolation)
Level 1 - AWS Instance ( ssh,
isolation)
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Stay updated!
www.pdc.kth.se/resources/computers/swecloud
www.pdc.kth.se/resources/computers/pdc-cloud
SNIC Cloud & SNIC Cloud @ PDC
Åke Edlund
http://www.pdc.kth.se/members/edlund
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Cloud and eScience
Examples from
Venus-C
http://www.venus-c.eu/
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User Communities
Civil Engineering
• Empowering individual researchers with the
ability to run computing intensive tasks
Building Information
Management
Static and dynamic structural simulations
Energy Consumption simulation
Virtual Prototyping
Rendering and visualization
Soil and foundations analysis
• Integration of multiple services
on single platforms - SaaS
• Cloud-enabled management of data
• Target users: SMEs and Research
Centres
• Potential community in the order
of thousands of users
Structural
Analysis
Environment interaction
Simulation
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User Communities
Civil Engineering
• Empowering individual
researchers with the
Cloud serving computing
ability to run computing
intensive
tasks
intensive services
on a
Building Information
Management
global BIM
platform with
Static and dynamic
structural
simulations
several thousands of users
Energy Consumption simulation
Virtual Prototyping
Rendering and visualization
Soil and
foundations
analysis
Based
on ParaFEM, with
more than
world-wide
• Integration500
of citations
multiple
services
on single platforms - SaaS
Based on the code
energy+, officiallyof data
• Cloud-enabled
management
recommended by the North-American
• Target
users: SMEs and Research
DOE Support from their developers
Centres
• Potential community in the order
Integrated in a commercial GUI with a user
of thousands
of users
community
of more than 1000
downloads
seamlessly switching from local to cloud
resources
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Structural
Analysis
Environment interaction
Simulation
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User Communities
Molecular, Cellular and Genetic
Biology 1/2
• Providing bioinformaticians with tools and
worflows for daily intensive research
Gapped Mapping through BLAST or BWA
Simulation of the dynamics of complex
biological systems
Phylogenetic Inference
Assembly and SNP identification
• Web-portals and CLI front-ends to cloud
• Generation of Reference databases
• Target users: Bioinformaticians
• Community in the order of thousands
of users
Bioinformatics
Phylogenic
Analysis
Loci
Mapping
System Biology
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User Communities
Molecular, Cellular and Genetic
Biology 1/2
• Providing bioinformaticians with tools and
Cloud-enabled BLAST with
worflows for the
daily
research
sameintensive
interface as the
Gapped Mappingsequential
through
BLAST or BWA
one
Simulation of the dynamics of complex
biological systems
Analysis ofInference
the evolutionary
Phylogenetic
divergences
of specific
genes among
Assembly
and
SNP identification
Bioinformatics
Assembly of sequences andPhylogenic
• Web-portals and CLI front-endslocation
to cloud
Analysis
of SNPs
species
• Generation of Reference databases
• Target users: Bioinformaticians
Integrated environment of
services
for simulating
• Community inprocessing
the order
of thousands
dynamics of in-silico Biological
of users
Loci
Mapping
System Biology
systems
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User Communities
Molecular, Cellular and Genetic
Biology 2/2
• Providing biologists with tools and
databases for research on molecular basis
of diseases
Micro-Arrays
Quality
Prediction of targets for micro RNA
Analysis of Micro-Array data
• Web-portals and CLI front-ends to cloud
• Integration and population of reference
databases
• Target users: Biologists
• Community in the order of thousands of
users
MicroRNA
Micro-Arrays data
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User Communities
Molecular, Cellular and Genetic
Biology 2/2
• Providing biologists with tools and
databases for research on molecular basis
Statistical analysis of microof diseases
Prediction of targets for micro RNA
Analysis of Micro-Array data
Micro-Arrays
Quality
array data
• Web-portals and CLI front-ends to cloud
Micro-arrays analysis and
• Integration and population
of reference
integration with annotation
databases
databases
• Target users: Biologists
• Community in the order of thousands of
users
MicroRNA
Micro-Arrays data
Prediction of the activation of
proteins, leading to discoveries in
cancer therapies
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User Communities
Chemistry
• Empowering drug design with the ability to
run computing intensive in-silico experiments
Biological activity response
Immune system response
Biological damage of pollutants
Quantitative structure-activity relationship
pipeline
• Integration of well-known tools such as QSAR
pipeline or AutoDock
• Large-scale computing and complex
workflows
• Target users: SMEs and Research Centres
• Existing community in the order of
thousands of users
QSAR Optimisation
Cloud Against
Disease
Molecular Docking
Workflows
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User Communities
Chemistry
• Empowering drug design with the ability to
run computing intensive in-silico experiments
Biological activity response
To identify new inhibitors
through the use of QSAR
Immune system response
Biological damage of pollutants
Quantitative structure-activity relationship
pipeline
Biological
activity
response
of new
• Integration of well-known
tools
such
as QSAR
leads
pipeline or AutoDock
• Large-scale computing and complex
workflows
• Target users: SMEs and Research Centres
• Existing community in the order of
thousands of users
QSAR Optimisation
Cloud Against
Disease
Molecular Docking
Workflows
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User Communities
Medicine
• Providing cloud storage and computing for
personalized medicine
Radiotherap
y
Planning
Simulating Radiotherapy doses in e-IMRT
Analysing vital signs from Intensive Care Units
Analysis of Diffusion Tensor Imaging in
Intensive Care
Functional
Units
Imaging
• Integration of environments such as Matlab
• Working with anonymised data in complex
workflows
• Target users: Hospitals and Research Centres
• Wide existing community in the order of
thousands of users
Functional
Brain Imaging
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User Communities
Medicine
• Providing cloud storage and computing for
personalized medicine
Accurately planning
Radiotherap
y
Planning
Simulating Radiotherapy
radiotherapydoses
doses in e-IMRT
Analysing vital signs from Intensive Care Units
Analysis of Diffusion Tensor Imaging in
Intensive Care
Functional
Units
Imaging
Creating and Analysing a database of
signs from real patients
• Integration ofvital
environments
such as Matlab
• Working with anonymised data in complex
Functional
workflows
Brain Imaging
• Target users: Hospitals
Research
Functionaland
Imaging
analysis for Centres
psychiatric
• Wide existing community
in diseases
the order of
thousands of users
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User Communities
Biology & Biodiversity
• Providing cloud computing resources for the
simulation of
biomechanics and biodiversity
Gait simulation in bipedal species
Occurrence maps of marine species
• Integration of external data sources and data
infrastructures
• Integrated framework for biodiversity
research
• Target users: Biodiversity researchers, Food
organizations and image rendering
• Wide existing community
Gait Simulation
Aquamaps
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User Communities
Biology & Biodiversity
• Providing cloud computing resources for the
simulation
of
Realistic simulation
of
biomechanics and
biodiversity
bipedal
walking animations
differentspecies
creatures
Gait simulation in of
bipedal
including dinosaurs
Occurrence maps of marine species
• Integration of external data sources and data
infrastructures
• Integrated framework for biodiversity
research
• Target users: Biodiversity researchers, Food
organizations and image rendering
• Wide existing community
Gait Simulation
Aquamaps
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User Communities
Maths and Mech Engineering
• Cloud services for naval and mechanical
engineering and cloudenabled software
numeric libraries
Analysing vessel’s traits in oceans
Optimising the configuration of bevel gears
Vessel Taritas
Bevel Gears
Numeric libraries for GAP (Groups, Algorithms
and Programming)
• Components for enhanced computations
• Intensive computing on the cloud
• Target users: Engineers, authorities, academy
• Final services and general-purpose sw
libraries targeting a wide community in
Academia
GAP
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User Communities
Maths and Mech Engineering
• Cloud services for naval and mechanical
engineering and cloudDetecting suspicious
enabled software
behavior of vessels in
numeric libraries Oceans
Vessel Taritas
Analysing vessel’s traits in oceans
Bevel Gears
Optimising the configuration of bevel gears
Numeric librariesPorting
for GAP
(Groups,
Algorithms
of KegelSpan
simulation
software on the cloudand
Programming)
• Components for enhanced computations
• Intensive computing on the cloud
Parallel computing of group theory
• Target users: Engineers, authorities,
computation
academy
• Final services and general-purpose sw
libraries targeting a wide community in
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Academia
GAP
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User Communities
Information and Comm. Tech.
• Cloud services for e-Learning and analysing
public social data
Twitter
Analysis of twitter data
Cloud-enabled e-Learning
Trends
• Combination of structured data and
intensive
computing
• Target users: General Public, sociologists,
eLearning
Academia
• Final services and for political and social
trends
and improved learning
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User Communities
Information and Comm. Tech.
• Cloud services for e-Learning and analysing
public social data
Twitter
Analysis of twitter data
Cloud-enabled
e-Learning
Data mining
to discover social trends
Trends
in twitter data and
• Combination of structured
intensive
computing
• Target users: General Public, sociologists,
eLearning
Academia
Using the cloud for the
of e-learning
material
• Final services andcustomization
for political
and social
trends
and improved learning
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User Communities
Earth Sciences, Civil Protection &
Physics
• Cloud-enables services for reacting against
crisis and
astronomical databases
Estimating Fire Risk and Fire propagation
Simulating the propagation of earth quakes
Computing different configurations of galaxies
• Real-time services for the reaction against
fires and earthquakes
• Key data for studying the origin of the
universe
• Target users: Civil servants, Physics
• Services for public interest and input datafor
key research (such as Dark Matter)
Fire Risk &
Simulation
Earthquakes
Simulation of
Galaxies
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User Communities
Earth Sciences, Civil Protection &
Physics
• Cloud-enables services for reacting against
Dynamically allocating
more and
crisis
resources in high-risk hours
astronomical databases
Fire Risk &
Simulation
for quicker reaction
Estimating Fire Risk and Fire propagation
Simulating the propagation of earth quakes
Computing different
Predictionconfigurations
of induced damage,ofin galaxies
a
very short time after the occurrence of
• Real-time services
for the reaction against
a large
fires and earthquakes
earthquake
• Key data for studying the origin of the
Creatinguniverse
a database of different
potential configuration
• Target users: Civil servants,
Physics of galaxies
after Big Bang , leading to better
• Services for public interest
and input
knowledge
of Dark datafor
Matter
key research (such as Dark Matter)
distribution
Earthquakes
Simulation of
Galaxies
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