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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 editor
HPC at HCCJun Wang
hcc.unl.edu
Cluster Overview Processors RAM Connection Storage
Firefly720 node
production-mode LINUX cluster
871 (2.8 GHz , 64 bit)
Opteron, 4-Core Per Node
280 2.2 GHz,8-Core Per Node
8 GB per node800 MB/secInfiniband
interconnect
150 TB shared Panasas storage 6 TB SATA RAID 73 GB per node
Sandhills44 Node
Production-mode LINUX cluster
1344 cores 2.2 GHz AMD Opteron 612896 cores at 1.9GHz AMD Opteron 6168
42 Nodes with 128GB per node
2 Nodes with 256GB per node
QDR InfinibandGigabit Ethernet ~1.5TB per node
Red266 node
Production-mode LINUX cluster
40x Opteron 226170x Opteron 235443x Xeon E552040x Xeon E5530
~2500 Condor job slots
1.5-2GB RAM per job slot Gigabit Ethernet ~2 PB of raw
storage space
Tusker106 node
Production-mode LINUX cluster
Opteron 6272 2.1GHz, 4 CPU/64
cores per node256 GB RAM per
node QDR Infiniband~350 TB shared Lustre storage ~500GB local
scratch
Overview of HPC Computing Resources at HCC
HPC at HCCJun Wang
hcc.unl.edu
Firefly Sandhills
Red Tusker
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/studentshttp://hcc.unl.edu/newusers/
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.exe
HPC at HCCJun Wang
hcc.unl.edu
How to login a Linux cluster at HCC On Mac:Click “Applications”-->”Utilities”-->”Terminal”Type “ssh [email protected]”
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 name
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 [email protected]: ” to uploadOpen a terminal and type “scp -r [email protected]:xxx ./ ” to download
HPC at HCCJun Wang
hcc.unl.edu
Commonly Used Linux commandshttp://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 directoryView 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 command
HPC at HCCJun Wang
hcc.unl.edu
Change password to your own after first loginType “passwd” after login to any HCC clusterNote: 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 1
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 characters
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-vi
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 directory
HPC at HCCJun Wang
hcc.unl.edu
Familiar with Linux file systemFamiliar with Shell environmentFamiliar 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 website
http://chem.unl.edu/eshop
To be continued:
