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Interview: Makenzie Provorse

Makenzie Provorse is a graduate student in Professor Jiali Gao’s ( MSI Fellow ) group in the Department of Chemistry . She entered the University of Minnesota in the fall of 2009 and joined the Gao group in January 2010. She’s been using MSI since then. Ms. Provorse was a finalist at the 2013 MSI...

Maintenance on August 20

posted August 15, 2014 On Wednesday, August 20, 2014, from 4:00am to 5:00pm, MSI systems will be part of a construction downtime and MSI staff will perform scheduled maintenance and upgrades to the network and various systems. The construction will be simultaneously mechanical and electrical work...

This tutorial will help users learn the basics of parallel computation methods, including strategies for collecting calculations together for parallel execution. A brief description of parallel programming using MPI message passing will be given.

This one-day, hands-on workshop provides an introduction on how to write a parallel program using MPI and will help researchers write better and portable parallel codes for distributed-memory Linux clusters.

This tutorial is paired with Analyzing ChIP-Seq Data using Galaxy and will take the user though the same steps but, using the command line versions of the tools used in the Galaxy environment. This tutorial will:

1. Provide a brief introduction to MSI systems.

Python is a modern general purpose programming language that is popular in scientific computing for its readable syntax and extremely rich ecosystem of scientific and mathematical modules.

LATIS: Supporting Research Computing in the Liberal Arts

Abstract: 
<h3 class="red">LATIS: Supporting Research Computing in the Liberal Arts</h3><p>The Liberal Arts Techologies and Innovation Services (LATIS) works to enhance research and scholarship by integrating appropriate technologies into the workflow of faculty, staff, and students. While LATIS is well positioned within the College of Liberal Arts (CLA) to provide the resources, tools, and expertise over infrastructure and software engineering, pedagogy, media, and social science research methods, their mandate is much broader. They strive to engage the broader scientific community in the issues that face the liberal arts, and they encourage their users to view their compute- and data-intensive tasks not only as as an integral component of their study design, but one that could benefit from communities outside of their own.</p><p>Part of this challenge is to convince CLA scholars to view their questions in the light of what HPC can offer, and when appropriate, to bring in the the resources MSI has at its disposal. Accordingly, this Principal Investigator uses MSI access to keeping abreast of the technologies and software MSI supports, to design proof-of-concepts directly on MSI&#39;s infrastructure, to consult with CLA clients on the appropriate use of MSI resources, and to make the transition between LATIS environments and MSI environments as clean as possible.</p><p>Return to this <a href="https://www.msi.umn.edu/pi/cbe7040f8bd5868288db5f1f40417182/10824">PI&#39;s main page</a>.</p>
Group name: 
olsend2

OVPR Announces 2015 Research Infrastructure Investment Program Awards

Several MSI Principal Investigators were selected to receive Research Infrastructure Investment Program Awards for 2015 by the Office of the Vice President for Research. The awards are intended to facilitate interdisciplinary partnerships and strengthen the University’s research infrastructure.

OpenFOAM

Software Description: 

OpenFOAM is an open source software package which is designed to scale well on large distributed memory systems. While originally written for CFD, with it's open source strategy and a large user base OpenFOAM has grown to be a general purpose finite element toolbox.

Software Support Level: 
Secondary Support
Itasca Documentation: 
OpenFOAM v171 is available on Itasca. Several working examples are posted, which illustrate how to run serially, in parallel interactively, and in parallel in the PBS queue. These examples are completely self contained and may be run by simply sourcing a single file. Each one creates it's own run directory into which it copies all inputs, sets the run environment, generates the mesh, does the domain decomposition (for parallel runs), runs ecoFoam (serially, in parallel, or in the PBS queue as appropriate), and merges output (from parallel runs). All these examples are extremely small (~1.3 MB) and run very fast (a few seconds). Hence you can run them in your home directory or on /lustre with no problems. All example scripts and data for these test cases are posted in

    /soft/openfoam/v171/test_cases

To run any of these test cases, just paste one of these lines to your bash shell command prompt on Itasca:

    source /soft/openfoam/v171/test_cases/run_parallel_cavity_small_interactive

    source /soft/openfoam/v171/test_cases/run_parallel_cavity_small_pbs

    source /soft/openfoam/v171/test_cases/run_serial_cavity_quite

    source /soft/openfoam/v171/test_cases/run_serial_cavity_verbose

You can copy any of these scripts to adapt to your simulations. To reproduce the OpenFOAM environment for interactive work, paste this line into your bash shell command prompt on Itasca: 
 

    source /soft/openfoam/v171/set_foam_env
For extensive documentation on OpenFOAM, including detailed descriptions of the many tutorials that came with the install, see the main OpenFOAM web site: http://www.openfoam.com
Software Access Level: 
Open Access
Software Categories: 
Software Interactive/GUI: 
No

FASTA36

Software Description: 

From the software web site:

Although there are a large number of programs in this package, they belong to three groups: (1) Traditional similarity searching programs: fasta36, fastx36, fasty36, tfastx36,tfasty36, ssearch36, ggsearch36, and glsearch36; (2) Programs for searching with short fragments: fasts36, fastf36, tfasts36, tfastf36, and fastm36; (3) A program for finding non-overlapping local align- ments: lalign36. Programs that start with fast search protein databases, while tfast programs search translated DNA databases. Table I gives a brief description of the programs.

In addition, there are several programs included. map db is used to index FASTA format se- quence databases for more efficient scanning. lav2ps and lav2svg plot the .lav files produced by lalign -m 11 as postscript (lav2ps) or SVG (lav2svg) output. 

 

Software Support Level: 
Secondary Support
Itasca Documentation: 

FASTA36 is access from the module command

module load fasta36

This loads MPI versions of the FASTA36 tool set.

A typical invocation would be

 mpirun -np 4 fasta36_mpi -q seq/mgstm1.aa seq/prot_test.lseg

This command will be wrapped within a PBS script.

The module load does not load any query or library files. 

Software Access Level: 
Open Access
Software Categories: 
Lab Documentation: 

FASTA36 is accessed from the module command

module load fasta36

A typical invocation would be

fasta36 -s BP62 query.file library.file

The module load does not load any query or library files. 

 

Software Interactive/GUI: 
No

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