Introduction to the Minnesota Supercomputing Institute · – Stadium Village (717 Building) –...
Transcript of 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
© 2011 Regents of the University of Minnesota. All rights reserved.
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
© 2011 Regents of the University of Minnesota. All rights reserved.
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.
© 2011 Regents of the University of Minnesota. All rights reserved.
Where Are We?• UMN Twin Cities East Bank, Walter Library,
5th Floor• Main Offices• Two (of Five) Computer Labs• High-Performance Computing Resources
© 2011 Regents of the University of Minnesota. All rights reserved.
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
© 2011 Regents of the University of Minnesota. All rights reserved.
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
© 2011 Regents of the University of Minnesota. All rights reserved.
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
© 2011 Regents of the University of Minnesota. All rights reserved.
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
© 2011 Regents of the University of Minnesota. All rights reserved.
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
© 2011 Regents of the University of Minnesota. All rights reserved.
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
© 2011 Regents of the University of Minnesota. All rights reserved.
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
© 2011 Regents of the University of Minnesota. All rights reserved.
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
© 2011 Regents of the University of Minnesota. All rights reserved.
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
© 2011 Regents of the University of Minnesota. All rights reserved.
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
© 2011 Regents of the University of Minnesota. All rights reserved.
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.
© 2011 Regents of the University of Minnesota. All rights reserved.
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.
© 2011 Regents of the University of Minnesota. All rights reserved.
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
© 2011 Regents of the University of Minnesota. All rights reserved.
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
© 2011 Regents of the University of Minnesota. All rights reserved.
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]