1. HCC Workshop August 29, 2014

2. Introduction to LINUX ●Operating system like Windows or OS X (but different) ●OS used by HCC ●Means of communicating with computer ●Command Line Interface (instead of GUI)

3. The Terminal Window After logging in to your account, commands are entered in a terminal window: Working in LINUX, you are always located somewhere in your directory tree. Most common commands: navigating within directory tree, creating, editing, moving and removing files and directories. You are here

4. Your Directories on HCC Computers Work Directory - not backed up /work/ / or just $WORK Use for: temporary scratch space (not long-term storage) I/O for running jobs Home Directory - smaller space than work (quota limited by group) /home/ / or just $HOME Use for: program binaries, source code, configuration files, etc. Your directories are not shared/mounted across all HCC clusters (ie. Tusker and Crane have separate file systems.) “print working directory” “change directory”

5. Other commands to cover Move/rename files: mv Example: mv oldname newname Copy files: cpExample: cp myfile myfilecopy Change the current directory: cdExample: cd mydirectory See contents of the directory:ls See directory contents with more details: ls -l Print working directory:pwd Print file to screen: moreExample: more myfile Merging multiple files: catExample: cat file1 file2 > combinedfile Create empty file:touchExample: touch newfile Search a string in a file:grepExample: grep mystring myfile Compress & decompress files:tar, zip, gzip Remove files: rmExample: rm filetodelete Remove entire directory: rm -rfExample: rm -rf directorytodelete See more at: http://www.comptechdoc.org/os/linux/usersguide/linux_ugbasics.htmlhttp://www.comptechdoc.org/os/linux/usersguide/linux_ugbasics.html

6. Getting Started - Logging in ●Quick start guide for WindowsQuick start guide for Windows ●Quick start guide for Mac/LinuxQuick start guide for Mac/Linux

7. Basic exercise - create directory/file

8. Use Globus Connect to: ●Transfer files between HCC clusters (Tusker, Crane, & Sandhills) ●Transfer files between your laptop/pc and HCC clusters ●Share files with colleagues Globus Connect

9. Getting Started: (HCC-DOCS full instructions)HCC-DOCS full instructions ●Sign up for a Globus accountSign up for a Globus account ●Install Globus Connect Personal on your computerInstall Globus Connect Personal on your computer ●Activate HCC endpoint(s): hcc#tusker, hcc#crane, hcc#sandhillsActivate HCC endpoint(s): ●Log in to Globus account (online) and start making transfersonlinestart making transfers Important: /home is read-only via Globus Connect (transfer from /home, but not to /home ). /work is readable/writable via Globus Connect (can transfer files to and from /work ).

10. Exercise: Transfer files with Globus Option 1: Transfer file with Globus 1.Download example query file to your laptop: Blast query file 2. Transfer file from your laptop to your Crane work directory using Globus Option 2: Copy file into your work directory 1.Log in to crane 2.Copy query file to work with the following command: cp /work/demo/shared/blastexample/query/mouse.query $WORK

11. One editor : nano or any other you prefer Start nano by running ‘nano’. Save: Control + o Exit: Control + x

12. #!/bin/sh #SBATCH --time=00:05:00 #SBATCH --job-name=helloworld #SBATCH --error=helloworld.%J.err #SBATCH --output=helloworld.%J.out #SBATCH --qos=short echo “this is my first slurm job” sleep 30 Exercise - Create submit script Using nano, create the text file to the right. Save it as ‘helloworld.submit’. We will submit it to SLURM later.

13. Cluster Basics ●Every job must be run through a scheduler: Submitting Jobs using SLURM ●Software is managed through the module software: Using Module ●Every user has two directories to use: Where to Put Data

14. Exercise - Submit hello world job

15. Exercise - Run BLAST job ●Use the example mouse.query file we copied using Globus earlier ●Example submit script provided at: /work/demo/shared/blastexample/blast.submit ●Uses small example database

16. Exercise - Run BLAST job