1、17-April-2007,High Performance Computing Basics,April 17, 2007Dr. David J. Haglin,17-April-2007,Outline,What is the HPC? Where did it come from? How can you get an account on hpc.mnsu.edu? How can you use it for your research? Where do you go from here?,17-April-2007,What is the HPC?,Many AMD Optero
2、n Computers (nodes) in a rack Connected by a high-speed network In the IT Services Secure area (third floor of the library) All nodes run linux http:/www.mnsu.edu/hpc,17-April-2007,What is the HPC?,Head node has 8GB RAM; 7.4 TB of Disk Head node is for doing administrative work and starting long job
3、s The 34 Worker nodes are for doing long computations Each worker has 8GB RAM; 80 GB Hard Disk; 2 dual-core AMD Opteron,17-April-2007,What is the HPC?,Software Installed: GNU languages: C/C+ (gcc/g+), Fortran (gfortran) Message Passing Interface library OpenMPI Software soon to be installed: MATLAB
4、Fluent Portland Group Fortran and C/C+ IMSL Email is “local delivery only”,17-April-2007,Where did it come from?,National Science Foundation Grant MRI Program (Major Research Instrumentation) $140,000 Institutional Equipment funds upgraded machine by adding five nodes PIs: Patrick Tebbe, Rebecca Bat
5、es, David Haglin Proposal focused on a college-wide need for HPC Vendor: PSSC Labs, Inc.,17-April-2007,How can you get an account?,We must submit a final report to NSF after July 31, 2009 Part of the final report must include how much it was used within CSET (and within MSU). We need to track usage
6、(research projects). To get an account, send an email to haglinmnsu.edu with information as described: http:/www.mnsu.edu/hpc/accounts.html Your students can get accounts too! We are very interested in knowing about publications you obtain as a result of using hpc.mnsu.edu.,17-April-2007,Your Resear
7、ch,Okay, so you got an account.Now What?,17-April-2007,Your Research,Learning to use HPC. Learning to use the OpenPBS/Torque job queuing software. Learning to “design” your usage. Tutorials will be maintained at www.mnsu.edu/hpc,17-April-2007,Your Research,Connect to hpc.mnsu.edu (head node) using s
8、sh ssh on unix PuTTY or SSH Windows Client (IT Services) Firewall is pretty tight, may need to request a new opening in the firewall from your location Line-mode (command-line) interface Basic unix commands: http:/www.mnsu.edu/hpc/tutorials/linux_basics.doc,17-April-2007,Your Research,Disks on hpc:,
9、17-April-2007,Your Research,Using OpenPBS/Torque job queuing software: qstat - Inspect current job queue qsub - Add a new job to the queue qdel - Delete one of your jobs from the Q pbsmon.py - See the state of the entire machine xpbsmon - Uses X11 to display machine state firefox localhost/ganglia D
10、etailed information available at: http:/ Research,Designing your usage. Assume you have a program you want to run for different parameter values of 1 through 1000 Ex: $ myProgram -p1 $ myProgram -p2.$ myProgram -p1000,17-April-2007,Your Research,Create 1000 “start scripts” to queue 1000 jobs to the
11、master queue. Start your jobs and monitor their progress Combine results when they are all done. Organize experiments/runs in folders Use scripting languages such as python to generate start scripts.,17-April-2007,Your Research,Input and Output for your jobs: Your script will start on a worker node
12、You can log in to a worker node to see filesystem: ssh n04 df Standard Output and Standard Error are separate Files are written alongside your script when jobs completes No way to monitor progress of your computation,17-April-2007,Your Research,Sample script to run from 501 to 505:,17-April-2007,Where do you go from here?,www.mnsu.edu/hpc is a communication portal Find colleagues who can help Learn more about the capabilities: New software Parallel programming (MPI) Parallel libraries: e.g., ScaLAPACK. Keep this machine computing fast Other ideas?,
