Beta Cheat Sheet Guide to General Linux (Bash) and Slurm Commands Head File Print First 10 Lines of File
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Viewing and editing text files cat file Print entire content of file less file Similar to more, but with additional features Beta Cheat Sheet Guide to general Linux (Bash) and Slurm commands head file Print first 10 lines of file tail file Print last 10 lines of file Accessing Beta nano Simple, easy to use text editor Logging in from a terminal (Duo required) vim Minimalist yet powerful text editor ssh [email protected] emacs Extensible and customizable text editor Transferring files between Beta and your system scp source [email protected]:destination Advanced file management scp -r source [email protected]:destination chmod Change read/write/execute permissions scp [email protected]:source destination which cmd List the full file path of a command GUI Clients whereis cmd List all related file paths (binary, source, PuTTY SSH client for Windows 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 val ls -lh Show long, human-readable listing echo $var Print the value of variable $var ls dir List files inside directory dir .bashrc File that defines user aliases and variables rm file Delete file 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 awk Extensive tool for complex filtering tasks extensions, .tar.gz and .tgz) arc-ts.umich.edu/beta Revised 11/2018 Beta directories #SBATCH directives and #PBS counterparts /home/uniqname For use with running jobs, 80 GB quota #SBATCH #PBS Description --job-name==name -N name Job name /tmp Small file reads/writes, deleted after 10 days --account=name -A name Account to charge (test /scratch Large file reads/writes, purged periodically on Beta) /afs Only on login node, 10 GB backed up --partition=name -q name Submit to partition: standard, gpu. Lmod largemem, debug module keyword string Search for module names or --time=dd-hh:mm:ss -l walltime=time Time limit (walltime) descriptions matching string --nodes=count -l nodes=count Number of nodes module spider string Search for modules matching string --tasks-per-node=count -l ppn=count Processes per node module avail Show modules that can be loaded --cpus-per-task=count n/a CPU cores per process now --mem=count -l mem=count 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=count -l pmem=count RAM per CPU core module --gres=gpu:count -l gpus=count GPUs per node module list List currently loaded modules --nodelist=nodes -l nodes=nodes Request nodes module unload module Remove module from environment --array=arrayspec -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=var=val -v var=val Copy env variable collection --depend=var:jobid -W Job dependency states module restore Restore all modules from collection depend=var:jobid (var): after, afterok, collection afterany, afternotok --mail-user=email -M email Email for job alerts Slurm --mail-type=type -m type Email alert types: BEGIN, sbatch filename Submit a job script filename END, NONE, FAIL, REQUEUE squeue -u uniqname Show job queue for user uniqname --nodelist=nodes n/a Preferred nodes scancel jobid Delete job jobid --exclude=nodes n/a Nodes to avoid scontrol hold jobid Hold job jobid scontrol release jobid Release job jobid ARC-TS custom commands sinfo Cluster status my_usage Usage in CPU minutes srun Launch parallel job step my_accounts Show account membership and resource limits sacct Display job accounting information slurm-quota -s Show user disk quota and usage Slurm Environment Variables ARC-TS Documentation & Support SLURM_JOBID Job ID Beta User Guide: https://arc-ts.umich.edu/beta/user-guide SLURM_SUBMIT_DIR Job submission directory Email [email protected] for further Beta support SLURM_SUBMIT_HOST Host from which job was submitted Sensitive data should not be stored or processed on Beta SLURM_JOB_NODELIST Node names allocated to job SLURM_ARRAY_TASK_ID Task ID within job array SLURM_JOB_PARTITION Job partition arc-ts.umich.edu/beta Revised 11/2018 .