Jun Wang
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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 HPC at HCC Jun Wang Overview of HPC Computing Resources at HCC Cluster Firefly Sandhills Red Tusker Overview Processors RAM 871 (2.8 GHz , 64 bit) 720 node Opteron, 4-Core production-mode 8 GB per node Per Node LINUX cluster 280 2.2 GHz, 8-Core Per Node 1344 cores 2.2 GHz 42 Nodes with 44 Node AMD Opteron 6128 128GB per node Production-mode 96 cores at 1.9GHz 2 Nodes with LINUX cluster AMD Opteron 6168 256GB per node 40x Opteron 2261 70x Opteron 2354 266 node 43x Xeon E5520 Production-mode 40x Xeon E5530 LINUX cluster ~2500 Condor job slots 106 node Production-mode LINUX cluster Opteron 6272 2.1GHz, 4 CPU/64 cores per node 1.5-2GB RAM per job slot 256 GB RAM per node Connection Storage 800 MB/sec Infiniband interconnect 150 TB shared Panasas storage 6 TB SATA RAID 73 GB per node QDR Infiniband Gigabit Ethernet ~1.5TB per node Gigabit Ethernet ~2 PB of raw storage space QDR Infiniband ~350 TB shared Lustre storage ~500GB local scratch HPC at HCC Jun Wang Firefly Sandhills Red Tusker HPC at HCC Jun Wang 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/ 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 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” 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.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 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 download 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 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 8 Minimum required digit characters 1 Minimum required alpha characters 1 Minimum required upper case characters 1 Minimum required character categories 1 Minimum token length 1 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 “i” key to enter edit mode Press “Enter” key to enter command mode Type some characters 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 Retype “vi test-vi” to check saved test-vi 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 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 HPC at HCC Jun Wang To be continued: 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
