introduction to the minnesota supercomputing institute · – stadium village (717 building) –...

© 2011 Regents of the University of Minnesota. All rights reserved.

Introduction to the

Minnesota Supercomputing Institutefor Advanced Computational Research

March 13, 2014Sean I. Geronimo Anderson

Nancy Rowemsi.umn.edu > About > Staff


Goals• Introduction to MSI facilities

• How to obtain user access

• Getting started on MSI systems

• Brief introduction to Linux/UNIX and some useful commands

msi.umn.edu > Outreach > Tutorials > Tutorial Materials


MSI at a Glance• Manages approximately 400 software packages and 50 research databases.

• Main data center in Walter Library.

• MSI operates five laboratories on campus, mostly serving the Life Sciences.

• Serves more than 500 PI groups with 3000+ users.

• MSI is an academic unit of the University of Minnesota (under OVPR) with about 45 full time employees & 10 work study students.

• Dedicated resources for serial workflows, database management, and cloud access.


Where Are We?• UMN Twin Cities East Bank, Walter Library,

5th Floor• Main Offices• Two (of Five) Computer Labs• High-Performance Computing Resources


Eligibility• Faculty members at the University of

Minnesota• University of Minnesota academic

professionals • Faculty researchers at other accredited

institutions of post-secondary education in the state of Minnesota


MSI Resources• HPC

– Itasca, Calhoun, Cascade, Koronis (Decommission in March 2014)

• Laboratories

– Stadium Village (717 Building)

– Northrop Mall (Nils Hasselmo and Walter Library)

– St. Paul Campus (Cargill Building)

• Software

– Chemical and Physical Sciences, Engineering, Graphics and Visualization, Life Sciences, Development Tools

• User Services

– Consulting, Tutorials, Code, Porting, Parallelization, Visualization


Access

• System access information is available at

– msi.umn.edu > Access > Sign Up• For current users: msi.umn.edu > MyMSI • For building access, visit MSI reception desk

• Information can be found in the “General Information” page for each lab:

– msi.umn.edu > Resources > Labs• For help, E-mail [email protected] or call x6-0802


Remote Access to MSI lab Linux systems

• Cannot remotely login directly to most machines at MSI

• Three options to connect to MSI lab systems– ssh login.msi.umn.edu– NX - Requires user to download and install client

– GPUT - Requires user to download and install client

• Cannot run software directly from login or NX

• isub

• www.msi.umn.edu/remote-access


HPC ResourcesKoronis: SGI Altix

1140 Intel Nehalem Cores

2.96 TB of memory

Itasca: Hewlett-Packard 3000BL8728 Intel Nehalem Cores

26 TB of memory

Calhoun: SGI Altix XE 13001440 Intel Xeon Clovertown Cores

2.8 TB of memory

Cascade:8 Dell Compute Nodes

32 Nvidia M2070 GPGPUs

GPUT:16 Nvidia GeForce GTX 480 GPUs


Laboratories• Scientific Development and Visualization Laboratory (SDVL)

– Application Development

– Computational Physics

– Workshops• LCSE-MSI Visualization Laboratory (LMVL)

– Virtual Reality

– Large Screen

– Remote Visualization

– Escorted Access

• UMN-TC East Bank, Walter Library


Laboratories (cont'd)• Basic Sciences Computing Laboratory (BSCL)

– Structural Biology, Batch Processing

– Stereoscopic Monitors, Stereoscopic Projection System

– UMN-TC East Bank, Nils Hasselmo Hall• Computational Genetics Laboratory (CGL)

– Bioinformatics, Genomics, Proteomics

– UMN-TC St. Paul, Cargill Building• Biomedical Modeling, Simulation, and Design Laboratory

(BMSDL)

– Drug Design, Molecular Modeling, Computational Chemistry

– UMN-TC East Bank, 717 Building


Software• Approximately 400 software applications

– msi.umn.edu > Resources > Software• Classified into three service levels

– Primary, Ancillary, Minimal

• msi.umn.edu > Resources > Software > Software Service Levels

• Users may install software locally• We can purchase software with justification


Disk Resources• Labs and HPC systems (excluding Koronis) have shared home

directories• Disk space is allocated by group• 50 GB initial quota on Koronis• 150 GB initial quota on HPC systems (with scratch quota of 50

GB)• You may request a quota increase if necessary• PIs may request project space for large data and group

collaboration.• msi.umn.edu > Resources > Storage


Tutorials & Workshops• msi.umn.edu > Outreach > Tutorials

– Free to attend—Sign up in advance, seats fill up fast!

• Introductory: UNIX, Linux, remote computing, job submission, queue policy

• Programming & Scientific Computation: Code parallelization, programming languages, math libraries

• Computational Physics: Fluid dynamics, space physics, structural mechanics, material science

• Computational Chemistry: Quantum chemistry, classical molecular modeling, drug design, cheminformatics

• Computational Biology: Structural biology, computational genomics, proteomics, bioinformatics

• Others by popular demandwww.msi.umn.edu/tutorial


Support

• MSI is dedicated to enabling and improving the quality of computational research at the University of Minnesota.

• Basic research support is made available to researchers at minimal or no cost

• MSI participates with researchers who are seeking funding for projects that require MSI consultants or developers.


Projects• Internal Services

– Assist with long term development projects

– Wide range of project activities

– Tailored to specific research initiatives or development programs

– At cost• External Services

– msi.umn.edu > Services

• MSI requests acknowledgment in publications and grant proposals.


Integrate into Course Work

• Class accounts

– Access to MSI on a semester basis for all students in a course

• Customized workshops and guest lectures

– When our expertise overlaps with your interests (e.g. parallel programming, integration of computational assignments in a field)

• Reserve the LMVL (Virtual Reality)

– Use the stereoscopic capabilities of the visualization lab for high impact structure and model visualization lectures


MSI web pages• MSI home page

– www.msi.umn.edu

• Software– www.msi.umn.edu/sw

• Password reset– www.msi.umn.edu/password

• Tutorials– www.msi.umn.edu/tutorial

• FAQ– msi.umn.edu > Resources > FAQ

http://www.msi.umn.edu/


Questions?• MSI help desk is staffed Monday through

Friday from 8:30 AM – 5:00 PM• Walk-in help is available in Walter 587• Phone x6-0802 (1-612-626-0802)• Email [email protected]

introduction to the minnesota supercomputing institute · – stadium village (717 building) –...

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