introduction to joker - new mexico state university · • enter joker.nmsu.edu in hostname window....
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All About Discovery!New Mexico State Universitynmsu.edu
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Introduction to “Joker”
Cyber Infrastructure Architecture TeamCIA.NMSU.EDU
All About Discovery!New Mexico State Universitynmsu.edu
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What is “Joker”?
• NMSU’s supercomputer. 238 core computer cluster. – Intel E-5 Xeon CPUs and Nvidia K-40 GPUs. – InfiniBand innerconnect.– Linux (CentOS-7) operating system.– Slurm workload manager.– A “head node” and “compute nodes”.
All About Discovery!New Mexico State Universitynmsu.edu
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Head Node -vs- Compute Node
Logically, a Linux cluster looks something like …
User Network Head Node
ComputeNodes
All About Discovery!New Mexico State Universitynmsu.edu
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Head Node
• Login to cluster is usually login to head node.• Launch point for jobs running on the cluster.• Contains tools (e.g. scheduler) necessary to submit
programs to the cluster.• Basically the middle man between the cluster and the
outside network. • Not the place to run computational programs.
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Compute Node
• Used for computational tasks.• Generally not directly accessed by user.• May be accessed if needed.• Interactive and queueing system accessible with slurm.
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Joker Account
• Do you have a “Joker” account?• Why do you need an account?• Where to register for an account?• https://hpc.nmsu.edu/resources/
All About Discovery!New Mexico State Universitynmsu.edu
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Accessing joker.nmsu.edu from within the NMSU domain using a terminal emulator.
• May be accessed by any one of the many SSH terminal programs (such as “PuTTY”).
• Download/run PuTTY (Google “putty ssh” for download URL).
• Enter joker.nmsu.edu in Hostname window.• Click open.
All About Discovery!New Mexico State Universitynmsu.edu
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All About Discovery!New Mexico State Universitynmsu.edu
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Enter your “joker” account username and password when prompted. You will then be in the terminal window ready to go.
All About Discovery!New Mexico State Universitynmsu.edu
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Accessing Joker from outside NMSU’s domain with a terminal emulator.
-“Joker” is not exposed to “outside” connections.-You must first connect using NMSU's VPN service.-The VPN client may be found at “VPN.NMSU.EDU”.-Install and run the client.
All About Discovery!New Mexico State Universitynmsu.edu
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Enter your NMSU Username and Password.Once connected, you may then connect
with a terminal emulator (PuTTY).
All About Discovery!New Mexico State Universitynmsu.edu
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Upload and download files to and fromLinux using sftp.
-Download and install a sftp client (let’s use WinSCP).-Google winscp, go to the site download, installation package.-After install, run the app. and enter the login information.
Note: If “outside” the NMSU domain, you will need toconnect with the VPNclient before the sftp app.
All About Discovery!New Mexico State Universitynmsu.edu
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WinSCP sftp Window
-Local drive on left.-Linux on right.-Windows Explorer functionality (drag and drop, right click options, …)
All About Discovery!New Mexico State Universitynmsu.edu
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Module System
• Modules are not applications, they simply add the application’s environmental variables to your environment.
• Modules are loaded and unloaded.• Allow path definitions to shell environment.• Default compilers, applications, and libraries may be set
by Module commands.
All About Discovery!New Mexico State Universitynmsu.edu
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Module System
• module avail• module load <module name><module name2>• module list• module unload <module name1><module name2>• module clear • module purge
All About Discovery!New Mexico State Universitynmsu.edu
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Module System
• Allows path definitions to shell environment.• Default compilers, applications, and libraries may be set
by Module commands.• Modules are not applications, they simply add the
application’s environmental variables to your environment.
All About Discovery!New Mexico State Universitynmsu.edu
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Installing “R” Worksheet
• A) Install and run R locally.
• B) Load and run R from module.
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The Slurm Scheduler• Job scheduler implemented on Joker.• Basic commands - slurm cheat sheet
sinfosqueuesrunsbatchscancel
• Tutorial– https://hpc.nmsu.edu/hpc-user-guide/using-slurm-on-joker/
All About Discovery!New Mexico State Universitynmsu.edu
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Submit a job to Slurm
• File 1 is the program to run. • File 2 is the Slurm script file. • Submit the job with “sbatch <File 2>”.
All About Discovery!New Mexico State Universitynmsu.edu
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Submit a Job to the Scheduler (slurm)Create 2 files using your favorite editor.File 1
#!/bin/bashecho “Hello World!”
Save it.Change to an executable (chmod +x <File 1>)Run it to verify it works (./<File 1>).
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Submitting to the scheduler Slurm (continued)File 2
#!/bin/bash#SBATCH -n 96srun ./<File 1>srun sleep 20echo “All done sleeping!”
Save it.
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Submitting to the scheduler Slurm (continued)
sinfo (get info about resources) squeue (have a look at the q)
sbatch <File 2> (submit our job)
squeue (see where our job is in the q)
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More information about us and NMSU’s High Performance Computer.
hpc.nmsu.educia.nmsu.edu