Jun Wang hccunledu Outline of Workshop1 Overview of HPC Computing Resources at HCC How to obtain an account at HCC How to login a Linux cluster at HCC How to Copy files tofrom Linux cluster at HCC ID: 427967
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Slide1
HPC at HCCJun Wang
hcc.unl.edu
Outline of Workshop1
Overview of HPC Computing Resources at HCC
How to obtain an account at HCC
How to login a Linux cluster at HCC
How to Copy files to/from Linux cluster at HCC
Commonly Used Linux commands
Change password to your own after first login
How to edit a file using Linux vi editorSlide2
HPC at HCCJun Wang
hcc.unl.edu
Cluster
Overview
Processors
RAM
Connection
Storage
Firefly
720
node
production-mode LINUX cluster
871 (2.8 GHz , 64 bit)
Opteron
, 4-Core Per Node280 2.2 GHz,8-Core Per Node8 GB per node800 MB/secInfinibandinterconnect150 TB shared Panasas storage 6 TB SATA RAID 73 GB per nodeSandhills44 Node Production-mode LINUX cluster1344 cores 2.2 GHz AMD Opteron 612896 cores at 1.9GHz AMD Opteron 616842 Nodes with 128GB per node 2 Nodes with 256GB per nodeQDR InfinibandGigabit Ethernet~1.5TB per nodeRed266 node Production-mode LINUX cluster40x Opteron 226170x Opteron 235443x Xeon E552040x Xeon E5530~2500 Condor job slots1.5-2GB RAM per job slotGigabit Ethernet~2 PB of raw storage spaceTusker106 node Production-mode LINUX clusterOpteron 6272 2.1GHz, 4 CPU/64 cores per node256 GB RAM per nodeQDR Infiniband~350 TB shared Lustre storage ~500GB local scratch
Overview of HPC Computing Resources at HCCSlide3
HPC at HCCJun Wang
hcc.unl.edu
Firefly
Sandhills
Red
TuskerSlide4
HPC at HCCJun Wang
hcc.unl.edu
How to obtain an account at HCC
Group account application for faculty
http://hcc.unl.edu/newusers/newgroup.index.php
User account application for faculty/postdocs/students
http://hcc.unl.edu/newusers/Slide5
HPC at HCCJun Wang
hcc.unl.edu
How to login a Linux cluster at HCC
On PC:
Download putty.exe to your desktop from http://the.earth.li/~sgtatham/putty/latest/x86/putty.exeSlide6
HPC at HCCJun Wang
hcc.unl.edu
How to login a Linux cluster at HCC
On Mac:
Click “Applications”-->”Utilities”-->”Terminal”
Type “ssh YourUserName@tusker.unl.edu”Slide7
HPC at HCCJun Wang
hcc.unl.edu
How to Copy files to/from Linux cluster at HCC
On PC:
Download a free app
WinSCP http://winscp.net/download/winscp514setup.exeInstall it using all default options
Note: You may need to convert
file generated on Windows to Linux format
Type “dos2unix xxx
” in a Linux terminal,
where xxx the file nameSlide8
HPC at HCCJun Wang
hcc.unl.edu
How to Copy files to/from Linux cluster at HCC
On Mac:
Open a terminal and type “
scp -r $PWD/xxx YourUserName@tusker.unl.edu: ” to uploadOpen a terminal and type “scp -r
YourUserName@tusker.unl.edu:xxx ./ ” to downloadSlide9
HPC at HCCJun Wang
hcc.unl.edu
Commonly Used Linux commands
http://www.centos.org/docs/2/rhl-gsg-en-7.2/ch-doslinux.html
Changes
directories: cd /directory/directoryLists
files: lsCopies files: cp
thisfile.txt /home/thisdirectoryMoves files:
mv thisfile.txt /home/thisdirectoryDeletes files:
rm thisfile.txtCreates a directory:
mkdir
directory
View a
file: less thisfile.txtDisplays your present working directory: pwdReset your password: passwdFinds a string of text in a file: grep -i “Phrase” * -RSearch a file in a directory: find /SomeDirectory -name SomeFileName -type f --printExit a terminal: exitDisplays command help: man commandSlide10
HPC at HCCJun Wang
hcc.unl.edu
Change password to your own after first login
Type “
passwd” after login to any HCC cluster
Note: HCC uses LDAP to share users account and password info across all HCC clustersHCC password rule:Password minimum length 8 Minimum
required digit characters 1Minimum required alpha characters 1 Minimum required upper case characters 1Minimum required character categories
1 Minimum token length 1Slide11
HPC at HCCJun Wang
hcc.unl.edu
How to edit a file using Linux vi editor
Type
“vi test-vi” to create a file called test-vi
Press “Enter” key to enter command mode
Press “
i
” key to enter edit mode
Type some charactersSlide12
HPC at HCCJun Wang
hcc.unl.edu
How to edit a file using Linux vi editor
Press “Esc” key to switch to command mode
Type“:
wq” and Press ”Enter” key to save file and exit to command line
Type “q” to quit. Press “
i
” key to re-edit and “Esc” when done. Type “q!” to quit without save or “
wq
” to save and quit
Retype “vi test-vi” to check saved test-viSlide13
HPC at HCCJun Wang
hcc.unl.edu
Thank you for your attention!
Hands-on practice on
zeng-cuda.unl.edu if you do not have a HCC account
Username: workshopCreate your own directorySlide14
HPC at HCCJun Wang
hcc.unl.edu
Familiar with Linux file system
Familiar with Shell environment
Familiar with queuing system How to submit a serial jobHow to submit a MPI parallel job
You may download this ppt file at the newly designed electronics shop websitehttp://
chem.unl.edu/eshop
To be continued: