Exam March 2019 PDF

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ACCRE Cheat Sheet Guide to Linux, Lmod and SLURM commands

Viewing and editing text files cat filePrint entire content of filename more f  ileIncrementally display content of filename less f  ileSimilar to more, but with additional features

Accessing ACCRE

head f  ileDisplay file header tail f  ileDisplay file footer emacsExtensible and customizable text editor

Logging in from a terminal  login.accre.vanderbilt.edu ssh vunetid@ Transferring files between ACCRE and your system scp source v  unetid@  login.accre.vanderbilt.edu:destination  login.accre.vanderbilt.edu:source  d scp vunetid@  estination

vimMinimalist yet powerful text editor nanoSimple text editor

More advanced file management chmodChanges read/write/execute permissions

Windows/Mac clients: PuTTY SSH client for Windows WinSCPSCP client for Windows FileZilla FTP client for Linux, Windows, Mac

which cmdLists the full file path of a command whereis cmd Lists possible file paths of a command du  dirLists size of directory  dir and its subdirectories

Xming/XQuartz X11 server for Windows/Mac

Basic Linux file management

findFinds files in a directory

Aliases and system variables

man command Displays the manual page for command

aliasAutomatically replace one command with another

pwd Prints out the present working directory lsLists the files in the current directory ls -lh Show long listing of files ls -a Show hidden files as well

envLists all system variables export v  ar = valCreate environment variable $var and set value to val echoPrint text to the screen

ls d  ir Lists files inside directory dir rm  file Deletes file mkdir d  ir Creates empty directory called dir rmdir d  ir Removes empty directory dir

 nd all of its content rm -r d  ir Removes directory dir a cd d  ir Changes directory to dir cd .. Changes working directory to parent

echo $varPrint the value of variable var .bashrc Define default aliases and system variables

Input and output redirection $(command)Runs the command inside $() first, then inserts the output to the rest of the command. Same as putting grave marks (`) between the command

cd Changes working directory to home

Standard output redirection

cp f  ile d  ir Makes a copy of file file inside directory dir

2>Standard error redirection

mv f  ile1 f  ile2 Renames file file1 as file2 mv f  ile d  ir Moves file file inside directory dir cp -i, mv -i Display a warning before copying or moving to an existing file path rm -i Display a warning before removal ~ (tilde)Home directory . (period) Current directory .. (double dot) Parent directory wget  URL Downloads a file from URL in Internet unzip f  ile .zipExtract a ZIP file tar xzf Extract a gz compressed tarball file.tar.gz

2>&1Standard error and output redirection

cmd1 |  cmd2Pipe command; redirects output of command cmd1  to input of cmd2

Filters wcWord count grepGets a regular expression and prints it sortSort input uniqFilter duplicate lines cutCuts specific fields or columns sedStream editor for search and replace awkExtensive tool for complex filtering tasks

vanderbilt.edu/accre ● Hill Center Suite 201 ● 1231 18th Ave. South, Nashville, TN 37212-2807

Revised 3/2019

Cluster directories /home GPFS, backed up nightly /data GPFS, backed up nightly /dors GPFS, backed up nightly /scratch GPFS, higher quotas, not backed up /tmpTemporary local storage for I/O intensive tasks

Lmod

#SBATCH directives (continued) --time= minTime limit; either min or dd-hh:mm:ss --mem= count RAM per node; e.g. 5G --output= file Standard output; defaults to slurm-jobid. out if omitted --error=fileWrite standard error to file --array= arrayspecDefine job array

module availShows all available modules module load  moduleLoads module  in the environment module spider  stringSearches for module names matching string module keyword  stringSearches for modules containing string  in name or description module listList currently loaded modules module unload  moduleRemoves module  from environment module purgeRemoves all modules from environment module save  collectionSaves currently loaded modules to collection module savelist Returns all saved modules collections module describe Get modules in a saved collection module restore Restore modules from collection collection

--gres=gpu: cores GPUs per process --mail-user= emailEmail for job alerts --mail-type= type Email alert types: BEGIN, END, FAIL, REQUEUE, ALL --account= accountAccount to charge --depend= state :j  obidJob dependency. state  = after, afterok, afterany, afternotok --job-name= nameJob name --constrain=attribute Request CPU type: westmere, sandy_bridge, haswell, eight, twelve, sixteen --partition= name Submit to partition: production, debug, maxwell, pascal

SLURM Environment Variables SLURM_JOBID Job ID SLURM_SUBMIT_DIR Job submission directory SLURM_SUBMIT_HOST Name of host from which job was submitted

SLURM sbatch  filenameSubmits a job script filename squeue -u  vunetidShow job queue for user vunetid scancel jobidDeletes the job with jobid scontrol hold  jobidHold job jobid scontrol release  jobidRelease job jobid sinfo Cluster status sallocStarts an interactive job xallocStarts an interactive job with X window support

SLURM_JOB_NODELIST Names of nodes allocated to job SLURM_ARRAY_TASK_ID Task id within job array SLURM_JOB_CPUS_PER_NODE CPU cores per node allocated to job SLURM_NNODESNumber of nodes allocated to job

ACCRE-specific utilities accre_storage Check storage quota usage rtracejob  jobidCheck resources utilization for job jobid q3Get recent jobs by user, group and account

srunLaunch parallel job step sacct Display job accounting information

#SBATCH directives --nodes=count Number of nodes --tasks-per-node= countProcesses per node --ntasks= countTotal processes --cpus-per-task=count CPU cores per process --nodelist=nodes Preferred nodes --exclude= nodesNodes to avoid

qSummary -g  groupQueue summary for group and its users showLimits -g  groupGet resource limits for specific group SlurmActive Show cluster’s CPU/node utilization gpustateShow GPU cluster utilization sinfofeatures Get node availability based on features slurm_groupsList your SLURM group membership

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vanderbilt.edu/accre ● Hill Center Suite 201 ● 1231 18th Ave. South, Nashville, TN 37212-2807

Revised 3/2019...