1. Grid computing Assaf Gottlieb Tel-Aviv University
Grid computing Assaf Gottlieb Tel-Aviv University
EGEE is a project funded by the European Union under contract IST

2. Outline What is a grid & e-Research The EGEE grid and BioMed VO
Joining the grid
EGEE tutorial

3. The Grid Metaphor Mobile Access G R I Supercomputer, PC-Cluster D M LW A
Visualising
Workstation
Mobile Access
Supercomputer, PC-Cluster
Data-storage, Sensors, Experiments
Internet, networks
EGEE tutorial

4. What is Grid computing? (2/2)
The term “Grid” has become popular!
Sometimes in Industry : “Grids” = clusters
Motivations: better use of resources; scope for commercial services
Also used to refer to the harvesting of donated, unused compute cycles
Climateprediction.net)
These are e-Infrastructure but are not “grids” from the e-Research viewpoint!
EGEE tutorial

5. Typical grid
Grid middleware runs on each shared resource to provide
Data services
Computation services
Single sign-on
Virtual Organisation: People in different organisations seeking to cooperate and share resources across their organisational boundaries
Virtual organisations negotiate with sites to agree access to resources
INTERNET
EGEE tutorial

6. Outline What is a grid & e-Research The EGEE grid and BioMed VO
Joining the grid
EGEE tutorial

7. EGEE is …
EU-funded project that has established the largest multi-VO production grid in the world
Project leader : CERN
245 sites
45 countries
>60 VOs
35K CPUs
147PB Storage
Avg 30K jobs/day
Data transfers >1.5 GB/s
Applet at
EGEE tutorial

8. Main components Access service How users logon to a Grid
Resource Broker (RB): Service that matches the user’s requirements with the available resources on a Grid
Information System: Characteristics and status of resources
Computing Element (CE): A batch queue on a site’s computers where
the user’s job is executed
Storage Element (SE): provides (large-scale) storage for files
EGEE tutorial

9. Grid Applications
Medical/Healthcare (imaging, diagnosis and treatment )
Bioinformatics (study of the human genome and proteome to understand genetic diseases)
Nanotechnology (design of new materials from the molecular scale)
Engineering (design optimization, simulation, failure analysis and remote Instrument access and control)
Natural Resources and the Environment (weather forecasting, earth observation, modeling and prediction of complex systems)
EGEE tutorial

10. The BioMed VO at a glance (1/2)
140 Computing Elements (~20,000 CPUs)
131 Storage Elements (~5 PB disks)
in 12 countries
EGEE tutorial

11. Data Challenge example: WISDOM-Wide In Silico Docking On Malaria
~300 million people worldwide are affected
1-1.5 million people die every year
Widely spread
Caused by protozoan parasites of the genus Plasmodium
Malaria
EGEE tutorial

12. There is a real need for new drugs to fight malaria
Drug resistance has emerged for all classes of antimalarials except artemisinins.
Resistance to chloroquine, the cheapest and the most used drug, is spreading in almost all the endemic countries.
There is even the threat of resistance to artemisinin too, as it is already observed in murine Plasmodium yoelii
The available drugs focus on a limited number of biological targets => cross-resistance to antimalarials
There is a consensus that substantial scientific effort is needed to identify new targets for antimalarials
EGEE tutorial

13. Identification of new malarial targets
With the advent of the plasmodium genome, many targets came into light
The potential antimalarial drug targets are broadly classified into three categories, and each category has many individual targets.
Targets involved in human hemoglobin degradation (proteases)
Targets involved in parasite metabolism (Folate, phospholipid… )
Targets engaged in parasite membrane transport and signalling (choline carrier etc).
WISDOM focused on hemoglobin metabolism and especially on Plasmepsin II and Plasmepsin IV
EGEE tutorial

14. Docking Dataflow placing the ligand Scoring ligand data base junk hit
Structure
optimization
Ranking
Scoring
crystal structure
Protein surface
Water
molecule
Ligand
EGEE tutorial

15. Filtering process 50 compounds to be tested in experimental lab
500, 000 chemical compounds
Sorting based on scoring in different parameter sets;
Consensus scoring
1000 compounds selected
Based on key interactions
Catalaytic and
flap residues
500 compounds
Key interactions, binding modes, descriptors, knowledge of active site
MD=Molecular Dynamics
100 compounds MD
50 compounds to be tested in experimental lab
EGEE tutorial

16. High Throughput Virtual Docking
Millions of chemical
compounds available
in laboratories
High Throughput Screening
1-10$/compound, nearly impossible
Molecular docking (FlexX, AutoDock)
~80 CPU years, 1 TB data
Chemical compounds (ZINC):
Chembridge – 500,000
Drug like – 500,000
Data challenge on EGEE
~6 weeks on ~1700 computers
Targets (PDB):
Plasmepsin II (1lee,1lf2,1lf3)
Plasmepsin IV (1ls5)
Hits screening
using assays
performed on
living cells
Leads
Clinical testing
Drug
EGEE tutorial

17. Number of Docked Ligands (millions) vs. Time (days)1 2 3 4 5 6
1: Intensive submission of FlexX jobs with Chembridge ligands base
2: Resubmission
3: Intensive submission of FlexX jobs with drug like ligands base
4: Resubmission
5: Intensive submission of Autodock jobs with Chembridge ligands base
6: Resubmission
EGEE tutorial

18. Number of Running and Waiting Jobs vs. Time3 5 1 2 4 6
EGEE tutorial

19. WISDOM statistics (1/2) Docking conditions Computing statistics
Metrics
Value (Total)
Value (FlexX)
Value (Autodock)
Number of targets 11 8 10
Number of parameters 6 4 2
Number of docked ligands
999810
499918
Computing statistics
Metrics
Value (Total)
Value (FlexX)
Value (Autodock)
Effective duration
37 days
22 days
15 days
Effective CPU time
67.15 years
24.77 years
42.38 years
Number of Computing Elements 58 56 57
Total number of jobs
72751
41520
31231
Max running jobs at the same time
1758
1643
EGEE tutorial

20. WISDOM statistics (2/2)
Data statistics
Metrics
Value (Total)
Value (FlexX)
Value (Autodock)
Cumulated number of docked ligands (millions)
41.27
31.41
9.87
Total saved data (GB)
946.82
506.05
440.77
Total transferred data (GB)
Similar data challenge for H5N1 Neuraminidase (avian flu) is in progress
EGEE tutorial

21. WISDOM- Total Amount of CPU Provided by EGEE Federation
South Eastern Europe,
10%
South Western Europe,
12%
Italy, 16%
France, 18%
UK, 29%
Northern Europe, 7%
Central Europe, 4%
Asia Pacific, 2%
Germany Switzerland, 1%
Russia, 1%
EGEE tutorial

22. Outline What is a grid & e-Research The EGEE grid and BioMed VO
Joining the grid
EGEE tutorial

23. Basic security concepts
Authentication
Verify the identity of the peer
Authorization
Map an entity to some set of privileges
Confidentiality
Encrypt the message so that only the recipient can understand it
Integrity
Ensure that the message has not be altered in the transmission
Non-repudiation
Impossibility of denying the authenticity of a digital signature
Accounting
What did you do, when did you do it and where did you do it from?
EGEE tutorial

24. Public Key Infrastructure
Provides authentication, integrity, confidentiality, non-repudiation
Asymmetric encryption
Digital signatures
A hash derived from the message and encrypted with the signer’s private key
Signature checked decrypting with the signer’s public key
Allows key exchange in an insecure medium using a trust model
Keys trusted only if signed by a trusted third party (Certification Authority)
A CA certifies that a key belongs to a given principal
Certificate
Public key + information about the principal + CA signature
X.509 format most used
PKI used by SSL, PGP, GSI, WS security, S/MIME, etc.
Encrypted text
Private Key
Public Key
Clear text message
EGEE tutorial

25. X.509: content of the Certificate
An X.509 Certificate contains:
owner’s public key;
identity of the owner;
info on the CA;
time of validity;
digital signature of the CA
Public key
Subject:C=CH, O=CERN, OU=GRID, CN=Name Surname 8968
Issuer: C=CH, O=CERN, OU=GRID, CN=CERN CA
Expiration date: Dec 26 08:08: GMT
CA Digital signature
EGEE tutorial

26. User Responsibilities
Keep your private key secure.
Do not loan your certificate to anyone.
Report to your local/regional contact if your certificate has been compromised.
Do not launch a delegation service for longer than your current task needs.
If your certificate or delegated service is used by someone other than you, it cannot be proven that it was not you.
IT IS YOUR PASSPORT AND CREDIT CARD
EGEE tutorial

27. Globus Grid Security Infrastructure (GSI)
de facto standard for Grid middleware
Based on PKI
Implements some important features
Single sign-on: no need to give one’s password every time
Delegation: a service can act on behalf of a person
Mutual authentication: both sides must authenticate to the other
Introduces proxy certificates
Short-lived certificates including their private key and signed with the user’s certificate
EGEE tutorial

28. Virtual Organizations and authorization
Users MUST belong to a Virtual Organization
Sets of users belonging to a collaboration
Each VO user has the same access privileges to Grid resources
List of supported VOs:
VOs maintain a list of their members
Sites decide which VOs to accept
A list of supported VOs can be found here:
EGEE tutorial

29. Summary EGEE hold the largest production grid in the world to-date.
Academic users can join a VO without cost.
In order to use the grid a user must have
A valid certificate, given by the CA
Join a VO.
Each action on the grid requires a valid Proxy, generated from your certificate.
EGEE tutorial