Transcript OSC Powerpoint Template

Ohio Bioinformatics Consortium Research
Infrastructure
Ashok Krishnamurthy
Michael Raymer
Zhong Hui Duan
Steven Gordon
Lonnie Welch
Ohio Supercomputer Center
Wright State University
University of Akron
Ohio Supercomputer Center
Ohio University
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What is the role of the Research Infrastructure
Group?
• Premise: A vibrant research program is essential to drive
world-class education
• Goals:
– Facilitate interactions
– Identify academic and industry researchers in Ohio
– Create a website to highlight all known research expertise within
the State
– Identify research opportunities for students to be supported by
undergraduate and graduate scholarships.
– Assist in seeking external funding for education e.g., NSF
Research Experience for Undergraduate (REU) and Integrative
Graduate Education and Research Traineeship (IGERT)
– Support inter-institutional summer research opportunities and
collaborative projects such as intra- and inter-collegial
competitions.
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Ohio Bioinformatics Consortium members
Institution
No. of
faculty
Bowling Green State /University of Toledo
10
Case Western Reserve University (CWRU)
6
Central State University (CSU)
4
Miami University (MU)
10
Ohio State University (OSU)
3
Ohio University (OU)
10
University of Akron (UA)
4
Univ. of Cincinnati (UC)
8
Wittenberg University (WU)
4
Wright State University (WSU)
6
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Ohio Bioinformatics Consortium research
expertise
Genome annotation, Comparative genomics, Pathway reconstruction,
RNA 3D structure, Genetic variation analysis, Network and systems
biology, Statistical and functional genomics, Metabolomics, Biomedical
ontologies and image analysis, DNA sequencing, Ribotyping,
Microarray expression analysis, Genome annotation and databases,
Signal recognition and modeling, Computational biology, Molecular
Evolution, Proteomics and Metabolomics, Structural genomics, Gene
and medical ontologies, Computational genomics, Regulatory
genomics, Proteomics and Disease research, Functional and
regulatory genomics, Proteomics, Disease research, Plant genomics,
Medical information/ cancer biology, Proteomics, Comparative
genomics, Computational biology, Medical informatics/ molecular
cardiology, Evolutionary genetics, Medical informatics, Proteomics,
Computational biology, Marine biology, Environmental science, Health
information/ image processing, Metabolomics, Biomarker
identification/feature selection, Protein structure, Molecular evolution,
Forensic DNA
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Stable computational infrastructure
to support the research and innovation process
PRODUCTION COMPUTING
Intel P4 Cluster
•2.46 TF
•512 processors
•1 TBytes memory
Itanium2 Cluster
•2.7 TF
•596 processors
3x16 Alt
•1 TBytes memory
Gateway to
User Science
Infiniband or Myrinet Interconnect
IBM 1350
• Opteron dual-core w/IBM Cell
• 4,000+ cores
• 8 TBytes memory
• 22+ teraflops
• Blend of 4 core and 8 core nodes
– Large processor count
– Large memory SMP jobs
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Mass Storage
470 TBytes disk
80 TBytes tape
NFS, PVFS, iSCSI
Providing agile computational infrastructure
to support the research and innovation process
RESEARCH COMPUTING
Gateway to
User Science
Mass Storage
470 TBytes disk
80 TBytes tape
NFS, PVFS, iSCSI
BALE Cluster
•AMD Athlon 64
•110 processors
•220 GBytes memory
•nVIDIA GeForce
6150 GPU
MATLAB/GRI Cluster
•AMD Opteron
•164 processors
•328 GBytes memory
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Visualization Cluster
•AMD Opteron
•72 processors
•144 GBytes memory
•nVIDIA Quadro 5600
graphics card(330 GF)
Cell Blades
•4 cell blade array
•Accessible from
IBM e1350
OSC supports a variety of software applications
for scientific research
Top 5 Software Applications by CPU Hours
Software
Area of Interest
CPU Hrs.
Gaussian
03
Electronic Structures, Chemistry, Chem.
Engineering, Biochem., Physics
942,103
VASP
Ab-initio Quantum-mechanical Mol. Dynamics,
Physics, Materials Science
768,019
Amber
Molecular Dynamics, Chemistry, Biochem.
515,661
Gromacs
Mol. Dynamics, Chemistry, Biochem.
265,507
LMF
Molecular Dynamics
195,302
Top 5 Software Applications by Projects
Software
Area of Interest
Projects
Gaussian
03
Electronic Structures, Chemistry, Chem.
Engineering, Biochem., Physics
73
MATLAB
Higher Level Language
33
Amber
Molecular Dynamics, Chem., Biochem.
15
ADF
Molecular Dynamics, DFT
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FLUENT
Fluid Dynamics, Engineering, Aerospace
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Center staff maintain more
than 30 software
applications, and we provide
access to more than 70
different software packages
OSC CI Mission
• OSC Cyberinfrastructure (CI) Mission
– Participating in national CI initiatives (e.g., TeraGrid)
– Hosting CI applications (e.g., GridChem)
– Developing CI Applications
• CI Software Development (CSD) Group created in July 2007
• Vision: Connect people to supercomputing applications, large data
sets, research instruments, and virtual communities
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OSC Cyberinfrastructure Applications
• Web portal applications
– Web-based access to cycles, data, software, expertise
– Basis for OSC collaborations (E-Weld, GRIDP)
– Enable research teams to create and plug in their own
portal
• Instrumentation and Analytics Services
– Web-based access to instruments, data sets and image
processing
– MATLAB as analytics engine for rapid prototyping
– Basis for OSC collaborations (CAMM, MU NMR)
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Example 1: GRI Discovery Platform (GRIDP)
• Collaboration between OSC,
the University of Cincinnati's
Genome Research Institute
(GRI) and the Ralph Regula
School of Computational
Science (RRSCS)
• Designed to reduce the
technical hurdles associated
with modern computational
drug discovery with an intuitive
web-based user interface to
the software
• High performance computing
(HPC) computational biology
programs are made available
as web services
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OSC Instrumentation and Analytics Services
• Remote instrumentation uses OSC’s state-wide resources
– Networking, Storage, HPC, Analytics (web service)
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Remote Instrumentation and Analytics with
Miami University
• Remote Instrumentation Projects
– NMR Spectrometer, Chemistry and Biochemistry
Dept.
• Development of software for remote observation &
operation and for storage, retrieval and analysis of NMR
data. (under development, funded by OBR)
– Unipulsed EPR Spectrometer, Chemistry and
Biochemistry Dept.
Brucker
850 Mhz
NMR in
Dr.
Kennedy’s
Miami
Univ. lab
• Development of software for remote operations and/or
observation
– High Resolution TEM, Electron Microscopy Facility
(EMF), Geography Dept.
• Development of software for remote operations and/or
observation
• Biomarker discovery engine
– Development of a web-portal for data hosting and
analytics in support of biomarker-based diagnostic
testing research (Frantz Biomarkers and MU, ODOD
BRCP Proposal, pending)
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Joel TEM
in the EM
Facility at
Miami
Univ.
MATLAB® Distributed Computing Toolbox
Architecture
Image source: http://www.mathworks.com
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