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Great Lakes Cheat Sheet Less File Prints Content of File Page by Page Guide to General L Inux (Bash) a Nd S Lurm C Ommands Head File Print First 10 Lines of File

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Great Lakes Cheat Sheet Less File Prints Content of File Page by Page Guide to General L Inux (Bash) a Nd S Lurm C Ommands Head File Print First 10 Lines of File Viewing and editing text files cat file Print entire content of file Great Lakes Cheat Sheet less file Prints content of file page by page Guide to general L inux (Bash) and S lurm c ommands head file Print first 10 lines of file tail file Print last 10 lines of file Accessing Great Lakes nano Simple, easy to use text editor Logging in from a terminal (Duo required) vim Minimalist yet powerful text editor ssh uniqname @greatlakes.arc-ts.umich.edu emacs Extensible and customizable text editor Transferring files between Great Lakes and your system scp input uniqname@ greatlakes-xfer.arc-ts.umich.edu: output Advanced file management scp -r i nput uniqname@ greatlakes-xfer.arc-ts.umich.edu:o utput scp uniqname@ greatlakes-xfer.arc-ts.umich.edu:i nput output chmod Change read/write/execute permissions which cmd List the full file path of a command GUI Clients PuTTY SSH client for Windows whereis cmd List all related file paths (binary, source, manual, etc.) of a command WinSCP SCP client for Windows du dir List size of directory and its subdirectories FileZilla FTP client for Windows, Mac, and Linux find Find file in a directory Basic Linux file management Aliases and system variables man command Display the manual page for command alias Create shortcut to command pwd Print out the present working directory env Lists all environment variables ls List the files in the current directory export var = val Create environment variable $ var with value ls -lh Show long, human-readable listing val ls dir List files inside directory dir echo $var Print the value of variable $var rm file Delete file .bashrc File that defines user aliases and variables mkdir dir Create empty directory called dir Input and output redirection rmdir dir Remove empty directory dir $( command) Runs command first, then inserts output to the rm -r dir Remove directory dir and all contents rest of the overall command cd dir Change working directory to dir < Standard input redirection cd .. Change working directory to parent > Standard output redirection cd Change working directory to home 2> Standard error redirection ls List the files in the current directory 2>&1 Standard error to standard output redirection cp file1 file2 Copy file1 as file2 cmd1 | cmd2 Pipe the output of cmd1 to cmd2 cp file1 dir Copy file1 into directory dir Filters mv file1 file2 Rename file1 as file2 wc Word, line, and character count mv file1 dir Move file1 into directory dir grep Find and print text matching a regular ~ (tilde) Home directory expression . (period) Current (working) directory sort Sort input .. (2 periods) Parent directory uniq Filter duplicate lines wget URL Download a file from Internet URL cut Cut specific fields or columns unzip file .zip Extract a ZIP file sed Stream editor for search and replace tar xzf file Extract a gzip compressed tarball (common Extensive tool for complex filtering tasks extensions: .tar.gz and .tgz ) awk arc-ts.umich.edu/greatlakes Revised 5/2020 Great Lakes directories #SBATCH directives and #PBS counterparts /home/uniqname For use with running jobs, 80 GB quota #SBATCH #PBS Description /tmp Small file reads/writes, deleted after 10 days --job-name= name -N name Job name /scratch Large file reads/writes, purged periodically --account=n ame -A name Account to charge /afs Only on login node, 10 GB backed up --partition=n ame -q name Submit to partition: standard, gpu. viz, largemem, oncampus, Lmod debug module keyword string Search for module names or --time=d d-hh:mm:ss -l walltime=t ime Time limit (walltime) descriptions matching string --nodes=c ount -l nodes=c ount Number of nodes module spider string Search for modules matching string --tasks-per-node= count -l ppn=c ount Processes per node module avail Show modules that can be loaded --cpus-per-task=c ount n/a CPU cores per process now --mem=c ount -l mem=c ount RAM per node (e.g. module load module Load module in the environment 1000M, 1G) module show module Show the help and variables set by --mem-per-cpu=c ount -l pmem=c ount RAM per CPU core module --gres=gpu: count -l gpus=c ount GPUs per node module list List currently loaded modules --nodelist= nodes -l nodes=n odes Request nodes module unload module Remove module from environment --array=a rrayspec -t arrayspec Define job array module purge Remove all modules from --output=% x-%j.log -o filepath Standard output in run environment directory, formatted: module save collection Save all currently loaded modules to jobName-jobID.log collection --error=% x-%j-E.log -e filepath Standard error log module savelist Return all saved module collections --export=ALL -V Copy environment module describe Return all modules in collection --export=v ar= val -v var= val Copy env variable collection --depend=v ar: jobid -W Job dependency states module restore Restore all modules from collection depend=v ar: jobid ( var ): after, afterok, collection afterany, afternotok --mail-user=e mail -M email Email for job alerts Slurm --mail-type=t ype -m type Email alert types: BEGIN, sbatch filename Submit a job script filename END, NONE, FAIL, REQUEUE squeue -u user OR sq user Show job queue for user --exclude=n odes n/a Nodes to avoid scancel jobid Delete job jobid scontrol hold jobid Hold job jobid ARC-TS custom commands scontrol release jobid Release job jobid my_usage Usage in CPU minutes sinfo Cluster status my_accounts Show account membership and resource limits srun Launch parallel job step home-quota Show home quota and usage per user sacct Display job accounting info Show scratch quota and usage per scratch-quota account_root account Slurm Environment Variables maxwalltime Show walltime available for jobs SLURM_JOBID Job ID (including upcoming maintenance) SLURM_SUBMIT_DIR Job submission directory ARC-TS Documentation & Support SLURM_SUBMIT_HOST Host from which job was submitted GL User Guide: https://arc-ts.umich.edu/greatlakes/user-guide SLURM_JOB_NODELIST Node names allocated to job OnDemand/remote desktop: https://greatlakes.arc-ts.umich.edu SLURM_ARRAY_TASK_ID Task ID within job array Email [email protected] for further Great Lakes support SLURM_JOB_PARTITION Job partition Sensitive data should not be stored or processed on Great Lakes arc-ts.umich.edu/greatlakes Revised 5/2020 .
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