hcc unl edu HPC at HCC Jun Wang

hcc. unl. edu HPC at HCC Jun Wang Outline of Workshop 1 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 hcc. unl. edu 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 8 GB per node production-mode 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 128 GB per node Production-mode 96 cores at 1. 9 GHz 2 Nodes with LINUX cluster AMD Opteron 6168 256 GB per node 40 x Opteron 2261 70 x Opteron 2354 266 node 43 x Xeon E 5520 Production-mode 40 x Xeon E 5530 LINUX cluster ~2500 Condor job slots 106 node Production-mode LINUX cluster Opteron 6272 2. 1 GHz, 4 CPU/64 cores per node 1. 5 -2 GB 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. 5 TB per node Gigabit Ethernet ~2 PB of raw storage space QDR Infiniband ~350 TB shared Lustre storage ~500 GB local scratch

HPC at HCC hcc. unl. edu Jun Wang Firefly Sandhills Red Tusker

hcc. unl. edu 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/

hcc. unl. edu 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/x 86/putty. exe

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

hcc. unl. edu HPC at HCC Jun Wang How to Copy files to/from Linux cluster at HCC On PC: Download a free app Win. SCP http: //winscp. net/download/winscp 514 setup. exe Install it using all default options Note: You may need to convert file generated on Windows to Linux format Type “dos 2 unix xxx” in a Linux terminal, where xxx the file name

hcc. unl. edu 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 Your. User. Name@tusker. unl. edu: ” to upload Open a terminal and type “scp -r Your. User. Name@tusker. unl. edu: xxx. / ” to download

hcc. unl. edu 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 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 /Some. Directory -name Some. File. Name -type f --print Exit a terminal: exit Displays command help: man command

hcc. unl. edu 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

hcc. unl. edu HPC at HCC Jun Wang How to edit a file using Linux vi editor Type “vi test-vi” to create a file called testvi Press “Enter” key to enter command mode Press “i” key to enter edit mode Type some characters

hcc. unl. edu 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

hcc. unl. edu 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

hcc. unl. edu 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