Introduction to the HPCC
Dirk Colbry
Research Specialist
Institute for Cyber Enabled Research
HPCC Online Resources
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www.hpcc.msu.edu – HPCC home
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wiki.hpcc.msu.edu – Public/Private Wiki
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forums.hpcc.msu.edu – User forums
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rt.hpcc.msu.edu – Help desk request tracking
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mon.hpcc.msu.edu – System Monitors
HPCC Cluster Overview
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Linux operating system
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Primary interface is text based though Secure Shell (ssh)
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All Machines in the main cluster are binary compatible (compile
once run anywhere)
Each user has 50Gigs of personal hard drive space.
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Users have access to 33TB of scratch space.
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/mnt/home/username/
/mnt/scratch/username/
A scheduler is used to manage jobs running on the cluster
A submission script is used to tell the scheduler the resources
required and how to run a job
A Module system is used to manage the loading and unloading
of software configurations
gateway
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Access to HPCC is primarily though the
gateway machinie:
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ssh username@hpc.msu.edu
Access to all HPCC services uses MSU username
and password.
HPCC System Diagram
Hardware Time Line
Year
Name
Description
2005
green
1.6GHz Itanium2 (very old)
Cores Memory Total Cores
576
128
128
(shared)
Main Cluster
2005
2007
2008
2009
amd05
intel07
intel08
amd09
Dule-core 2.2GHz AMD Opterons
Quad-core 2.3GHz Xeons
Sun x4450s (Fat Node)
Sun Fire X4600 Opterons (Fat Node)
4
8
16
32
8GB
8GB
64GB
256GB
512
1024
32
128
1696
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We are currently investigating two new
purchases for 2009/2010
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Graphics Processing Unit (GPU) Cluster
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New General Purpose Large Cluster
HPCC System Diagram
Cluster Developer Nodes
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Developer Nodes are accessible from gateway and
used for testing.
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ssh dev-amd05 – Same hardware as amd05
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ssh dev-intel07 – Same hardware as intel07
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ssh dev-amd09 – Same hardware as amd09
We periodically have some test boxes. These include:
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ssh dev-intel09 – 8 core intel Xeon with 24GB of memory
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ssh gfx-000 – Nvidia Graphics Processing Node
Jobs running on the developer nodes should be limited
to two hours of walltime.
Developer nodes are shared by everyone.
HPCC System Diagram
Available Software
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Center Supported Development Software
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Center Supported Research Software
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Intel compilers, openmp, openmpi, mvapich,
totalview, mkl, pathscale, gnu...
Matlab, R, fluent, abaqus, HEEDS, amber, blast, lsdyna, starp...
Center Unsupported Software (module use.cus)
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gromacs, cmake, cuda, imagemagick, java,
openmm, siesta...
Steps in Using the HPCC
1. Connect to HPCC
2. Transfer required input files and source code
3. Determine required software
4. Compile programs (if needed)
5. Test software/programs on a developer node
6. Write a submission script
7. Submit the job
8. Get your results and write a paper!!
Module System
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To maximize the different types of software and
system configurations that are available to the
users. HPCC uses a Module system.
Key Commands
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module avail – show available modules
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module list – list currently loaded modules
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module load modulename – load a module
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module unload modulename – unload a module
Getting Help
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Documentation and User Manual - wiki.hpcc.msu.edu
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User Forums - forums.hpcc.msu.edu
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Contact HPCC and iCER Staff for:
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Reporting System Problems
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HPC Program writing/debugging Consultation
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Help with HPC grant writing
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System Requests
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Other General Questions
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Primary form of contact - www.hpcc.msu.edu/contact
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HPCC Request tracking system – rt.hpcc.msu.edu
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HPCC Phone – (517) 353-9309 9am-5pm
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HPCC Office – Engineering Building 3200 9am-5pm
Next Week - Getting Connected
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Secure Shell - hpc.msu.edu
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Putty
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Windows Secure Shell
X11 Server (windowing)
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xming
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cygwin
File transfers
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Mapped Network Drives - files.hpc.msu.edu