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I. Introduction to HPC
II. Life science research and development
III. Coping with cloud concerns
Conclusion
3/23
Outline
High performance computing
• Is the use of parallel processing for running
advanced application programs efficiently,
reliably and quickly.
• The term applies especially to systems that
function above a teraflop or 1012 floating-point
operations per second.
High performance computing
Designed to address computationally intensive
problems such as :
• Weather prediction
• Oil exploration
• Problems in biochemistry
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The problem
• HPC has not been a good candidate for
cloud computing due to a number of
factors such as :
• its requirement for tight integration
between server nodes via low-latency
interconnects
• high-speed networking
6/23
The problem
• quickly erodes application scalability and
efficiency in an HPC context which often
involves sending messages back and forth
many times per second
Host virtualization
a process that is likely to increase the
possibility of latency 7/23
The solution
• reduce the virtualization management
through enabling native performance
capabilities from :
the virtual machines (VMs)
New virtualization (KVM)
the network
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Life science research and
development
The genome :
• Is the entire hereditary information of
an organism
• It consists of DNA
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• DNA sequencing which involves determining
the order of the nucleotide bases : adenine,
guanine, cytosine, and thymine in DNA
Determination of genome
This is a complex and
time-consuming
process
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Area applications
• Creating individual genetic “maps” that can be
used to provide medicines tailored according
to each person’s genome.
• There is great potential for this process to be
advanced through the unlimited processing
power and storage of cloud computing.
Next-generation DNA sequencing
machines
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13/23
Providers
Amazon Web Services (AWS),
its cloud service infrastructure (EC2),
its main IaaS platform.
Google Compute Engine (IaaS)
SaaS solution (sequence alignment,data mining)
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Real scientific example
In a case study designed to use statistical analysis to
discover cancer (eQTLs3) :
• Integration of two high-dimensional genomic data
types (gene expression and genotype)
• The authors used Amazon’s EC2 to provision one
hundred virtual server instances
• They provide the computational power required for
the experiment’s 13 billion distinct statistical
computations
• Demonstrate the viability and economy of using
cloud computing for such HPC tasks. 15/23
Coping with cloud concerns
• Moreover, the cloud reduces power
consumption.
• A great proportion of the costs of
running an IT infrastructure relates to
electricity use which is essential for
running and cooling which is also
needed to reduce the heating
generated by the hardware.
Coping with cloud concerns
For organizations
involved in scientific and
medical research , most of
the aforementioned
concerns may not be as
important to them as they
might be to those who
provide products and
services to consumers.
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Coping with cloud concerns
The researchers were finally able to
use an open source IaaS platform .
another way .
The benefits of virtualization were
clear to us.
We can configure the virtual machine
image exactly to our needs and have
a fully validated experimental
software stack ready for use .
The image can then be overlaid on top
of remote resources using
infrastructure. 18/23
Coping with cloud concerns
• Not with standing these advantages,
there are currently three major
concerns that inhibit many
organizations from using cloud
computing; notably: security,
interoperability and outages.
• Early and recent surveys indicate that
security and availability are rated
highly by organizations
contemplating the adoption of cloud
computing. 19/23
Coping with cloud concerns
• An another part Many cloud providers
offer their services through proprietary
APIs that means users of one cloud
provider may not be able to switch easily to
another provider if they decided they
wanted to due to poor service by the
original provider.
• The cloud may have a long way to go
before becoming autility such as that of
water or electricity whose suppliers can
be changed without too much disruption
to the users.
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Conclusion
• Untel recently, many companies have not perceived the use of
cloud computing for HPC as a viable option due to the
performance overhead (virtualization), security reasons and
availability.
• However, some scientific organizations find that cloud
computing’s disadvantages are more likely to be outweighed by
their current advantages.
• The potential of using cloud computing in advancing development
in life science research offers many exciting possibilities for
professionals and organizations working in this field and could be
a key in accelerating the quest of finding cures to humanity’s
major illnesses.
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