Program Director/Principal Investigator (Last, First, Middle):
Facilities
The Center for Computational Science (CCS) holds offices on all three campuses at the University of
Miami: Miller School of Medicine, The Rosenstiel School of Marine and Atmospheric Science, and its main
operations on the Coral Gables campus at the Gables One Tower and the Ungar Building . Each location is
equipped with a dual processing workstations and essential software applications. CCS has three dedicated
conference rooms and communication technology to interact with advisors (phone, web-, and video
conferencing), plus a Visualization Lab with 2D and 3D displays (located at the Ungar Building).
CCS systems are collocated at the Verizon Terremark NAP of the Americas (NOTA or NAP). The NAP
Datacenter in Miami currently features a 750,000 square foot, purpose-built datacenter, Tier IV facility with N+2
14 Megawatt power and cooling infrastructure. The equipment floors start at 32 feet above sea level, and the
roof slope designed to aid in drainage of floodwater in excess of 100-year storm intensity assisted by: 18
rooftop drains, architecture designed to withstand a Category 5 hurricane with approximately 19 million pounds
of concrete roof ballast, and 7-inch-thick steel reinforced concrete exterior panels. Plus, the building is outside
FEMA 500-year designated flood zone. The NAP uses a dry pipe fire-suppression system to minimize the risk
of damage from leaks.
The NAP has a centrally located Command Center manned by 7×24 security and security sensors. In order to
connect the University of Miami with the NOTA Datacenter, UM has invested in a Dense Wavelength Division
Multiplexing (DWDM) optical ring for all of its campuses. The CCS Advanced Computing resources occupy a
discrete, secure wavelength on the ring, which provides a distinct 10 Gigabit HPC network to all UM campuses
and facilities.
Given University of Miami’s past experience including several hurricanes and other natural disasters, we
anticipate no service interruptions due to facilities issues. The NAP was designed and constructed for resilient
operations. UM has gone through several hurricanes, power outages, and other severe weather crises without
any loss of power or connectivity to the NAP. The NAP maintains its own generators with a flywheel power
crossover system. This insures that power is not interrupted when the switch is made to auxiliary power. The
NAP maintains a two-week fuel supply (at 100% utilization), and is on the primary list for fuel replacement due
to its importance as a data-serving facility.
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In addition to hosting the University of Miami’s computing infrastructure, the NAP of the Americas is home to
the US SouthCOM, Amazon, EBay, and several telecommunications companies’ assets. The NAP at Miami
hosts 97% of the network traffic between the US and Central/South America. The NAP is also the local access
point for Florida LambdaRail (FLR), which is gated to Internet 2 (I2) to provide full support to the I2 Innovation
Platform. The NAP also provides TLD information to the DNS infrastructure and is the local peering point for all
networks in the area.
The University of Miami has made the NAP its primary Data Center occupying a very significant footprint on
the third floor. Currently all UM-CCS resources, clusters, storage and back up system run from this facility and
serves all major campuses of UM.
Equipment
Advanced Computing
UM maintains one of the largest centralized academic cyber infrastructures in the country with numerous
assets.
The Advanced Computing Team has been in operation since 2007. Over that time, the core was grown
from zero advanced computing cyerinfrastructure to a regional high-performance computing environment that
currently supports more than 1,500 users, 220 TFlops of computational power, and more than 3 Petabytes of
disk storage. The center’s latest system acquisition, an IBM IDataPlex system, was ranked at number 389 on
the November 2012 Top 500 Supercomputer Sites list.
At present, CCS maintains several clusters and application servers:
Pegasus – CentOS 6.5 based batch/interactive compute cluster consisting of:
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10,000 cores. IBM IDataPlex/Blade system
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Diverse operating environments (Intel Xeon, Intel Phi, AMD processors)
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19TB of RAM
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Dedicated graphical nodes (Pegasus-gui)
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Dedicated data transfer nodes with direct connection to I2 (Aspera, GridFTP, SFTP)
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250+ programs, compilers, and libraries
Jabberwocky – CentOS 6.5 based interactive visualization cluster
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184 cores
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1 TB RAM
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Graphical access from all nodes
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Firewalled access to all resources
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1 PB+ of storage
Elysium – CentOS 6.5 based secure data processing cluster (HIPAA/IRB compliant)
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32 cores
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128 GB RAM
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Separate VLAN
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Restricted access (MAC authentication/user ACL’s enforced)
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Full auditing and attestation
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500 TB
DAVID (Distributed Access for Visualization and Interaction with Data) Cloud –
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32 cores
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128 GB RAM
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CIFS/NFS/FTP/HTTP access
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500 TB
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Data Storage
CCS offers an integrated storage environment for both structured (relational) and unstructured (flat file) data.
These systems are specifically tuned for CCS’ data type and application requirements, whether they are serial
access or highly parallelized. Each investigator or group has access to its own area and can present his or her
data through a service-oriented architecture (SOA) model. Researchers can share their data via access control
lists (ACLs), which ensure data integrity and security while allowing flexibility for collaboration.
CCS offers structured data services through the most common relational database formats, including: Oracle,
MySQL, and PostgreSQL. Investigators and project teams can access their space through SOA and utilize
their resources with the support of an integrated backend infrastructure.
The CCS flat file storage environment is built as a multi-tier solution combining high-speed storage with dense
high capacity storage in a tiered architecture, all supported by IBM’s GPFS. Our HPC/Global tier (700TB) is
available on all compute nodes. This storage is designed for massively parallel work and has been clocked at
157,000 IOP/sec and over 20 GB/sec bandwidth.
Our standard tier of storage (2.8 PB) is designed for general-purpose data storage, analysis, and presentation
of data to collaborators both within and without the University of Miami. All tier 2 storage is available from all
systems including our visualization cluster. Several data management tools are available for tier 2 storage
including public presentation, long-term archive, deduplication, encryption, and HSM.
Our archival tier of storage (2.5 PB) leverages several platforms for keeping critical data safe. By using a
combination of tape and disk technologies, we are able to reduce restore times significantly while still ensuring
data integrity.
HPC Core Expertise
The HPC team has in-depth experience in various scientific research areas with extensive experience in
parallelizing or distributing codes written in Fortran, C, Java, Perl, Python and R. The team is active in
contributing to Open Source software efforts including: R, Python, the Linux Kernel, Torque, Maui, XFS and
GFS. The team also specializes in scheduling software (LSF) to optimize the efficiency of the HPC systems
and adapt codes to the CCS environment. The HPC core has expertise in parallelizing code using both MPI
and OpenMP depending on the programming paradigm. CCS has contributed several parallelization efforts
back to the community in projects such as R, WRF, and HYCOM.
The core specializes in implementing and porting open source codes to CCS’ environment and often
contributes changes back to the community. CCS currently supports more than 300 applications and optimized
libraries on its computing environment. The core personnel are experts in implementing and designing
solutions in the three different variants of Unix. CCS also maintains industry research partnerships with IBM,
Schrodinger, Open Eye, and DDN.
Software
HPC users have a complete software suite at their fingertips, including standard scientific libraries and
numerous optimized libraries and algorithms tuned for the computing environment. All programs and
algorithms are implemented in 64-bit mode in order to address large memory problems, and also offer
compatible 32-bit libraries and algorithms. In addition, the LSF grid scheduling process maximizes the
efficiency of the computational resources. Increased efficiency translates into the faster execution of programs,
which provides researchers faster access to more resources. By utilizing the full suite of LSF tools we are able
to provide both batch and interactive workloads while still retaining workload management features.
For more details about our HPC infrastructure, please visit our pages on this website at
http://www.ccs.miami.edu/hpc
Other Resources
Bioinformatics
CCS’ Computational Biology and Bioinformatics Program (CBBP) was established to conduct research and
offer services and training in the management and analysis of biological and medical/health record data. The
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program’s mission is to spearhead bioinformatics capacity at the University of Miami for all biological and
medical applications. This includes data management, data mining, and data analysis capacities. The CBBP
aims to achieve this mission through infrastructure, education, and expertise. In particular, CBBP provides an
online portal for bioinformatics databases and web tools, and offers a number of data analysis services. CBBP
are concomitantly leading educational and training initiatives in bioinformatics analysis, and nourishing these
activities with high impact bioinformatics research.
Bioinformatics Data Analysis
The team provides data analysis training and expertise at a three levels, consulting, preliminary data
generation, and fully collaborative, based on the time and complexity of the service requested. The analyses
are undertaken by skilled analysts, and overseen by experienced faculty. The group has been working mostly
with microarray data and next generation sequencing data, and the analytical services include, but are not
limited to, the following:
• gene expression analysis for transcriptome profiling and/or gene regulatory network building,
• prognostics and/or diagnostic biomarker discovery,
• microRNA target analysis,
• copy number variant analysis, in this context we are testing the few existing algorithms and developing new
ones for accurate and unambiguous discovery of copy number variation in the human genome,
• genome or transcriptome assembly from next generation sequencing data, and its visualization,
• SNP functionality analysis,
• other projects include merging or correlating data from various data types for a holistic view of a particular
pathway or disease process.
Advanced Data Mining
The Center’s Data Mining Research Group provides advanced data mining expertise and capabilities to further
explore high dimensional data. The following are examples of the expertise areas covered by our faculty.
• Classification, which appears essentially in every subject area that involves collection of data of different
types, such as disease diagnosis based on clinical and laboratory data. Methods include regression (linear and
logistic), artificial neural nets (ANN), k-nearest neighborhood (KNN), support vector machines (SVM), Bayesian
networks, decision trees and others.
• Clustering, which is used to partition the input data points into mutually similar groupings, such that data
points from different groups are not similar. Methods include KMeans, hierarchical clustering, and selforganizing map (SOM), and are often accompanied by space decomposition methods to offer low dimensional
representations of high dimensional data space. Methods of space decomposition include principal component
analysis (PCA), independent component analysis (IDA), multidimensional scaling (MDA), Isomap, and manifold
learning. Advanced topics in clustering include multifold clustering, graphical models, and semi-supervised
clustering.
• Association data mining, which finds frequent combinations of attributes in databases of categorical
attributes. The frequent combinations can be then used to develop prediction of categorical values.
• Analysis of sequential data involves mostly biological sequence and includes such diverse topics as
extraction of common patterns in genomic sequences for motif discovery, sequence comparison for haplotype
analysis, alignment of sequences, and phylogeny reconstruction.
• Text mining, particularly in terms of extracting information from published papers, thus transforming
documents to vectors of relatively low dimension to enable the use of data mining methods mentioned above.
Visualization
The Visualization program conducts both theoretical and applied research in the general areas of Machine
Vision and Learning, and specifically in
(i) computer vision and image processing,
(ii) machine learning,
(iii) biomedical image analysis, and
(iv) computational biology and neuroscience.
The goal is to provide expertise n this area to develop novel fully automated methods that can provide
robustness, accuracy and computational efficiency. The program works towards finding better solutions to
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existing open problems in the above areas, as well as exploring different scientific fields where our research
can provide useful interpretation, quantification and modeling.
Cheminformatics
CCS has a sophisticated cheminformatics and compute infrastructure with a significant level of support from
the institution. CCS facilitates scientific interactions and enables efficient research using informatics and
computational approaches. A variety of departments and centers at the University use high content and high
throughout screening approaches – The Miami Project to Cure Paralysis, the Diabetes Research Institute, the
Cancer Center, Bascom Palmer Eye Institute, the Dept. of Surgery, the John P. Hussman Institute for Human
Genomics.
Cheminformatics and computational chemistry tools—running on HPC Linux cluster and high performance
application server.
• SciTegic Pipeline Pilot—visual work-flow-based programming environment (data pipelining); broad
cheminformatics, reporting / visualization, modeling capabilities; integration of applications, databases,
algorithms, data.
• Leadscope Enterprise—integrated cheminformatics data mining and visualization environment; unique
chemical perception (~27K custom keys; user extensions); various algorithms, HTS analysis, SAR / R-group
analysis, data modeling.
• ChemAxon Tools and Applications—cheminformatics software applications and tools; wide variety of
cheminformatics functionality.
• Spotfire—highly interactive visualization and data analysis environment, various statistical algorithms with
chemical structure visualization, HTS and SAR analysis.
• Open Eye ROCS, FRED, OMEGA, EON, etc. implemented on Linux cluster – suite of powerful applications
and tool kits for high-throughput 3D manipulation of chemical structures, modeling of shape, electrostatics,
protein-ligand interactions and various other aspects of structure- and ligand-based design; also includes
powerful cheminformatics 2D structure tools.
• Schrodinger Glide, Prime, Macromodel, and various other tools implemented on Linux Cluster—powerful
state of the art docking, protein modeling and structure prediction tools and visualization.
• Desmond implemented on Linux Cluster—powerful state of the art explicit solvent molecular dynamics.
• TIP workgroup—powerful environment for global analysis of protein structures, binding sites, binding
interactions; implemented automated homology modeling, binding site prediction, structure and site
comparison for amplification of known protein structure space.
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