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5/8/13: Virtual School Summer Computational Science Courses

The Virtual School of Computational Science and Engineering (VSCSE) is holding two courses this summer. These courses are open to graduate students, post-docs, and young professionals who want to expand their skills with advanced computational resources. The courses are offered at institutions...

How do I use Second Tier Storage from the command line?

To access the MSI second-tier storage, each user must have a set of s3 credentials. The s3 credentials act like a username and password to control access to the storage behind the S3 gateway server called These credientals are automatically generated and stored in a configuration...


MOPAC is a general-purpose semi-empirical molecular orbital package for the study of chemical structures and reactions. MOPAC calculates vibrational spectra, thermodynamic quantities, isotopic substitution effects, and force constants for molecules, radicals, ions and polymers. It can carry these out using methods such as AM1, PM3, and PM6.


The Hadoop Map/Reduce framework harnesses a cluster of machines and executes user defined Map/Reduce jobs across the nodes in the cluster. On itasca, a script exists to create an ephemeral Hadoop cluster on the set of nodes assigned by the scheduler. The script setup_cluster will format a HDFS filesystem on the local scratch disks. This resource is best-suited for application benchmarking, and algorithm testing. All data must be moved to HDFS after the cluster is brought up when the jobs starts. Any data that you wish to save must be moved to your home directory before the job completes. Many...

Functional Genomics of Fusarium graminearum, the Wheat and Barley Scab Fungus


Functional Genomics of Fusarium graminearum, the Wheat and Barley Scab Fungus

Fusarium head blight or scab caused by Fusarium graminearum is a destructive disease of wheat and barley. Infested cereals are reduced in yield and contaminated with harmful mycotoxins. In the past decade, the disease has resulted in billions of dollars of economic loss to United States agriculture. Better understanding of F. graminearum pathogenesis and differentiation is critical because effective fungicides and highly resistant plant varieties are not available for controlling the disease. This group’s goals are to identify and characterize genes important for plant infection and colonization, secondary metabolism, sporulation, and sexual development of F. graminearum by using transcriptome analysis and targeted mutation of selected genes.

One objective of this research is to analyze gene expression profiles of F. graminearum in different infection and colonization stages, in mutants defective in plant infection or toxin production, and in different developmental stages. Genes differentially expressed during specific infection or development processes or in response to mutants will be identified by high throughput cDNA sequencing (RNAseq). The second objective is to experimentally determine the biological functions of selected candidate genes identified in gene expression experiments. Targeted deletion mutants will be generated for genes chosen on the basis of expression profiles and bioinformatics analyses. A third objective will be to assess the presence of Fusarium species and total fungal content of environmental samples using a metagenomic approach. MSI resources are used for storage and analysis of RNAseq data as well as DNA sequence storage and metagenomic analysis of fungi from environmental samples.

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Conceptual Climate Models


Conceptual Climate Models

This researcher is continuing a project develop undergraduate research modules on the mathematics of climate change that can be inserted into a standard course of calculus with differential equations. One such module, Global Warming: A Zonal Energy Balance Model, is availble to the public through a web repository of educational resources sponsored by the Science Education Resource Center (SERC) at Carleton College.

Mathematics has an important role to play in understanding the earth's climate. While controlled physical experiments on climate change are rarely available, mathematical models, computational experiments, and data analysis are the fundamental tools to study the earth’s climate system. The project will focus on zonal energy balance conceptual models of the state of the climate system that are formulated in terms of a mean temperature that varies with latitude and a thermal energy exchange among latitudes by diffusion. Although conceptual models only retain some fundamental features of the climate system, they are capable of reproducing relevant complex phenomena.

This project is supported by the NSF funded Engaging Mathematics Initiative, a partnership organized by faculty colleagues to develop curriculum content aiming at improving mathematics learning by connecting the topics to issues of critical local, national, and global importance. This work will also receive the benefit of the collaboration with colleagues of the Mathematics of Climate Seminar, Department of Mathematics, University of Minnesota, and the “Mathematics and Climate Research Network” (MCRN), a network funded by the National Science Foundation linking researchers across the United States to develop the mathematics needed to better understand the Earth’s climate. One of the objectives of the MCRN is “to prepare and disseminate educational material for the undergraduate- and graduate- level curriculum.

MSI computational resources, such as MATLAB and Python, are used to develop the numerical codes for the modules. The PI's students also use these resources in the implementation of their research projects.

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Bioenergy and Food Safety


Bioenergy and Food Safety

Scum is a rich source of recoverable energy, as it contains greases, vegetable and mineral oil, animal fats, waxes, soaps, food wastes, and plastic materials discharged from households, restaurants, and other animal product industries. The lipid content of scum can be as high as 60%.  The energy store in scum, around 22.3 MJ/kg of dry scum, cannot be utilized if it is disposed of in landfills. Moreover, the disposal of scum increases operation costs in treatment plants. For instance, the Metro plant spends $200,000 a year just in transporting and landfilling scum. Therefore, there is an urgent need to develop a technology for energy recovery and beneficial reuse of scum.

These researchers are developing a novel technology that recovers energy and converts lipid, fatty acid, and soap in scum directly to biodiesel.  The final product has a quality similar to ASTM-grade diesel.  The researchers believe that by utilizing biodiesel derived from scum the wastewater treatment plant can: reduce cost of scum disposal to landfills; reduce petroleum fuel use and cost for fuel purchasing; and reduce GHG emissions by using biofuels. In addition, by diverting scum from landfills the technology could reduce methane emissions that have 25 times more global-warming potential as compared to CO2 in a 100-year's time horizon.  All these benefits are likely to improve the economic and environmental sustainability of the wastewater treatment plant. 

There are still uncertainties to the scum-to-diesel technology. In particular, the environmental performances of this technology have never been evaluated within current literature. When examining the technology, heat, electricity, and chemicals have to be provided for all conversion processes, which will raise environmental impacts, and thus, compromise the environmental benefits obtained in the production of biodiesel.

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mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST . mpiBLAST takes advantage of distributed computational resources, i.e., a cluster, through explicit MPI communication and thereby utilizes all available resources unlike standard NCBI BLAST which can only take advantage of shared-memory multi-processor computers. The primary advantage to using mpiBLAST versus traditional NCBI BLAST is performance. mpiBLAST can increase performance by several orders of magnitude while still retaining identical results as output from NCBI BLAST.

Chenomx NMR Suite

Chenomx NMR suite is an integrated suite of tools that allow you to easily identify and quantify metabolites in NMR spectra. The following products make up Chenomx NMR Suite: Chenomx Profiler Chenomx Profiler offers you a broad range of tools to assist in identifying and quantifying compound concentrations based on data in an NMR spectrum. Using a compound library of over 260 unique spectral signatures together with sophisticated computer-assisted fitting routines, you can accomplish in minutes what would have taken hours or days using manual analysis methods. Chenomx Compound Builder Chenomx...

Use of Vtune for performance optimization



Use of Vtune on different MSI systems

Interactive profiling

Comand-line options

Profiling MPI applications


Intel® VTune™ Amplifier XE 2013 is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java*. It is available on all MSI Linux systems for users to eveluate the performance of your applications (identify and remove the hotspots). The objective is to enable all applications to run efficiently on any MSI systems. Certainly, experienced users can deeply explore each of the performance metrics embedded in Vtune. The performance evaluation process itself can be very benedicial for users to learn and understand  the cutting-edge technologioes available in the HPC world.

Use of Vtune on different systems

The  module vtune  has been set on all systems. One can profile their applications not only through the graphic interface amplxe-gui, but alos by the use  of command-line interface amplxe-cl. The former fits the need of short-time interactive profiling  while the latter is usefulf for collecting infromation during the run-time.  Users who need to do  the Interactive profiling, please go to the section of Find Hotspot for the details.

Table 1: Profiling metrics associated with micro-architecture on differen systems 

System Name Sub-sytem specific features

Itasca - Nehalem processor

General Exploration,  Read Bandwidth; Write Bandwith; Memory Access; Cycles and Ops; Frond End Investigation.

Itasca- Sandy Bridge processor

General Exploration,  Memory Bandwidth; Access contention; Branch Analysis; Client Analysis; Core port Saturation; Cycles and Ops.

Cascade- Knights Corner, phi processor

Lightweight Hotspots; Memory Bandwidth; General exploration

Cascade- Core i7 980x processor

Lightweight Hotspots; Hotspots; Concurrency; Locks and Waits.
Lab Limux workstations Lightweight Hotspots; Hotspots; Concurrency; Locks and Waits.

Comand-line options

The command-line interface amplxe-cl provides users with the convenience to profile a real application. Users need to load the vtune module and specify the analysis type of interests. Here are the basic format:

       module load vtune

       amplxe-cl -collect $analysis_type -result-dir $yourprof_dir -- myApplication

        where $analysis_type is the options that users can chose for analyzing the performance on different sub-sysmtem processor (see the Table 2 for the supported analysis type on different platforms); $yourprof_dir is  the directory in which the profiling information is to save; myApplication is the program that you want to prfile.  After the job finishes, you can view the profiling results by either graphic interface:

       amplxe-gui $yourprof_dir

or the command-line interface:

      amplxe-cl -report  $report_type  -result-dir  $yourprof_dir

        where the $report_type should match the selected $analysis_type 


Table 2 Available Analysis Types for different micro-architectures

 System Name  Options available on different sub-systems
 General     concurrency                    

 Sandy Bridge processor


 phi processor

 Nehalem/Westmere processor     nehalem-cycles-uops         

Please note that the genral analysis-type in Table 2 applies to every platform on which you want to use vtune. One can find the details about one analysis type of particular interest  by

         amplxe-cl --help $analysis_type

For example,

         amplxe-cl --help concurrency



Fortran Applications

C and C++ applications

Profile MPI applications

MPI jobs can be analyzed by using Vtune over the the implementation of Intel MPI. Here are the simplified commands for profling MPI jobs:

module load intel impi vtune

mpirun -r ssh -f $PBS_NODEFILE -np 256 amplxe-cl -collect $analysis_type -result-dir $yourprof_dir ./test > run.out 

After the job runs successfully, one can view the profiling results either graphic or commd-line interface.

Comprehensive information can be found from the software document - Analyzing MPI applications.