HPC Resources at W&M and ...How To Use Them February 5 th , 2016 Eric J. Walter ● What is HPC? ● HPC ticket system ● What hardware is available? ● Linux Shell / Text editors ● How to find out about software that is available? ● Software Modules ● HPC file systems ● Using the batch system
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HPC Resources at W&M and How To Use Them file Vim Tutorials Nano homepage. Logging into HPC machines Must use Secure Shell client (SSH)
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HPC Resources at W&M and ...How To Use Them
February 5th, 2016
Eric J. Walter
● What is HPC?● HPC ticket system ● What hardware is available?● Linux Shell / Text editors● How to find out about software that is available?● Software Modules● HPC file systems● Using the batch system
Logging into HPC machinesMust use Secure Shell client (SSH)● Linux / Mac built-in (terminal)● Windows – SSH Secure Shell Client / PuTTY
[ewalter@particle ~]$ ssh hurricane.sciclone.wm.eduPassword: Last login: Tue Feb 2 13:57:59 2016 from particle.hpc.wm.edu-------------------------------------------------------------------------------- William and Mary Information Technology / SciClone Cluster...1 [hurricane]
Questions to ask yourself:
● Am I on or off campus? If you are off-campus – log into stat.wm.edu first using your W&M username and password
● Is my username the same as my current machine?If it is different use: ssh <username>@<host>.<domain>
● Do I need graphics?If yes, then log in with -X
Questions to ask yourself:
● Am I on or off campus? If you are off-campus – log into stat.wm.edu first using your W&M username and password
● Is my username the same as my current machine?If it is different use: ssh <username>@<host>.<domain>
● Do I need graphics?If yes, then log in with -X
Software Modules
http://www.hpc.wm.edu/SciCloneTutorials/ModuleBasics - online module help
This means that startup is controlled by .cshrc.rhel6-xeon for hurricane
Can use module load and unload commands for current shell. Best to use startup
Wiki
URL: www.hpc.wm.edu/SciClone/Home
Software
FACT: Software is requested and installed more quickly than documentation can be writtenSubmit a ticket for any software requests. Please make sure you need the software.
HPC Filesystems / Backup3 types of filesystems:
home – backed up nightly ; small used for input files and code, etc.data – backed up weekly ; large files ; medium term storagescratch – NOT backed up ; large output files short term storage
/sciclone/data20 is our fastest fileserver currently – gets a lot of useUse local scratch if you can!
CompilersAll platforms have GNU and Portland C/C++/FORTRAN compilersCheck the Tutorials - Subcluster Essentials / Using XX pages for what flags are suggested for optimization.
Important to know what the isa of the target processor is.
Available HPC hardware and software
http://www.hpc.wm.edu/SciClone/Home - Wiki homepage
http://www.hpc.wm.edu/SciClone/Software - Software list (out of date)http://www.hpc.wm.edu/SciCloneTutorials/ModuleBasics - Software modules
Use this command if you want to allow group access to your home, scrXX, and dataXX directories
HPC default umask is 077
How do I change the initial permissions that files and folders are given when created:
You need to edit your .cshrc file in your home directory and add: umaskumask 077 files get “-rw-------” folders get “drwx------” umask 027 files get “-rw-r-----” folders get “drwxr-x---” umask 022 files get “-rw-r--r--” folders get “drwxr-xr-x”
What groups are I in?: groups52 [hurricane] groups ewalterewalter : hpcf wmall hpcstaff www seadas vasp sysadmin wm hpcadmin wheel hpsmh
My primary (default) group is hpcf and the rest are secondary
Change a group associated with a file or directory: chgrp 54 [hurricane] ls -ld projectdrwx------ 2 ewalter hpcf 512 Aug 18 20:47 project55 [hurricane] chgrp hpcstaff project56 [hurricane] ls -ld projectdrwx------ 2 ewalter hpcstaff 512 Aug 18 20:47 project