1. HPC at HCC Jun Wang 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

2. HPC at HCC Jun Wang ClusterOverviewProcessorsRAMConnectionStorage Firefly 720 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 node 800 MB/sec Infiniband interconnect 150 TB shared Panasas storage 6 TB SATA RAID 73 GB per node Sandhills 44 Node Production-mode LINUX cluster 1344 cores 2.2 GHz AMD Opteron 6128 96 cores at 1.9GHz AMD Opteron 6168 42 Nodes with 128GB per node 2 Nodes with 256GB per node QDR Infiniband Gigabit Ethernet ~1.5TB per node Red 266 node Production-mode LINUX cluster 40x Opteron 2261 70x Opteron 2354 43x Xeon E5520 40x Xeon E5530 ~2500 Condor job slots 1.5-2GB RAM per job slot Gigabit Ethernet ~2 PB of raw storage space Tusker 106 node Production-mode LINUX cluster Opteron 6272 2.1GHz, 4 CPU/64 cores per node 256 GB RAM per node QDR Infiniband ~350 TB shared Lustre storage ~500GB local scratch Overview of HPC Computing Resources at HCC

3. HPC at HCC Jun Wang Firefly Sandhills RedTusker

4. HPC at HCC Jun Wang How to obtain an account at HCC Group account application for faculty http://hcc.unl.edu/newusers/newgroup.index.phphttp://hcc.unl.edu/newusers/newgroup.index.php User account application for faculty/postdocs/students http://hcc.unl.edu/newusers/

5. HPC at HCC Jun Wang 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

6. HPC at HCC Jun Wang How to login a Linux cluster at HCC On Mac: Click “Applications”-->”Utilities”-->”Terminal” Type “ssh YourUserName@tusker.unl.edu”

7. HPC at HCC Jun Wang How to Copy files to/from Linux cluster at HCC On PC: Download a free app WinSCP http://winscp.net/download/winscp514setup.exehttp://winscp.net/download/winscp514setup.exe Install 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

8. HPC at HCC Jun Wang 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 upload Open a terminal and type “scp -r YourUserName@tusker.unl.edu:xxx./ ” to downloadYourUserName@tusker.unl.edu:xxx

9. HPC at HCC Jun Wang Commonly Used Linux commands http://www.centos.org/docs/2/rhl-gsg-en-7.2/ch-doslinux.html Changes directories:cd /directory/directory Lists files:ls Copies files: cp thisfile.txt /home/thisdirectory Moves files: mv thisfile.txt /home/thisdirectory Deletes files: rm thisfile.txt Creates a directory: mkdir directory View a file: less thisfile.txt Displays your present working directory: pwd Reset your password:passwd Finds a string of text in a file: grep -i “Phrase” * -R Search a file in a directory:find /SomeDirectory -name SomeFileName -type f --print Exit a terminal:exit Displays command help: man command

10. HPC at HCC Jun Wang 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 clusters HCC password rule: Password minimum length 8Minimum required digit characters 1 Minimum required alpha characters 1Minimum required upper case characters 1 Minimum required character categories 1Minimum token length 1

11. HPC at HCC Jun Wang 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

12. HPC at HCC Jun Wang 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

13. HPC at HCC Jun Wang Thank you for your attention! Hands-on practice on zeng-cuda.unl.edu if you do not have a HCC account Username: workshop Create your own directory

14. HPC at HCC Jun Wang Familiar with Linux file system Familiar with Shell environment Familiar with queuing system How to submit a serial job How 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: