Accessing ACCRE
| Command
|
Description
|
| ssh vunetid@login.accre.vanderbilt.edu
|
Logging in from a terminal
|
| scp source vunetid@login.accre.vanderbilt.edu:destination
|
Transferring files from your system to ACCRE
|
| scp vunetid@login.accre.vanderbilt.edu:source destination
|
Transferring files from ACCRE to your system
|
Windows/Mac clients
| Client
|
Description
|
| PuTTY
|
SSH client for Windows
|
| WinSCP
|
SCP client for Windows
|
| FileZilla
|
FTP client for Linux, Windows, Mac
|
| Xming/XQuartz
|
X11 server for Windows/Mac
|
Basic Linux file management
| Command
|
Description
|
| man command
|
Displays the manual page for command
|
| 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
|
| ls dir
|
Lists files inside directory dir
|
| rm file
|
Deletes file
|
| mkdir dir
|
Creates an empty directory called dir
|
| rmdir dir
|
Removes an empty directory dir
|
| rm -r dir
|
Removes directory dir and all of its content
|
| cd dir
|
Changes directory to dir
|
| cd ..
|
Changes working directory to parent
|
| cd
|
Changes working directory to home
|
| cp file1 file2
|
Copy file1 into file2
|
| cp file dir
|
Makes a copy of file inside directory dir
|
| mv file1 file2
|
Renames file1 as file2
|
| mv file dir
|
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 on the Internet
|
| unzip file.zip
|
Extracts a ZIP file
|
| tar xzf file.tar.gz
|
Extracts a gz compressed tarball
|
Viewing and editing text files
| Command
|
Description
|
| cat file
|
Prints entire content of file
|
| more file
|
Incrementally displays content of file
|
| less file
|
Similar to more, but with additional features
|
| head file
|
Displays file header
|
| tail file
|
Displays file footer
|
| emacs
|
Extensible and customizable text editor
|
| vim
|
Minimalist yet powerful text editor
|
| nano
|
Simple text editor
|
More advanced file management
| Command
|
Description
|
| chmod
|
Changes read/write/execute permissions
|
| which command
|
Lists the full file path of a command
|
| whereis command
|
Lists possible file paths of a command
|
| du dir
|
Lists size of directory dir and its subdirectories
|
| find
|
Finds files in a directory
|
Aliases and system variables
| Command
|
Description
|
| alias
|
Automatically replaces one command with another
|
| env
|
Lists all system variables
|
| export var=val
|
Create environment variable $var and set value to val
|
| echo
|
Print text to the screen
|
| echo $var
|
Print the value of variable var
|
| .bashrc
|
Define default aliases and system variables
|
Input and output redirection
| Command
|
Description
|
| $(command)
|
Runs the command inside $() first, then inserts the output to the rest of the command. Same as putting grave marks (`) between the command
|
| <
|
Standard input redirection
|
| >
|
Standard output redirection
|
| 2>
|
Standard error redirection
|
| 2>&1
|
Standard error and output redirection
|
| cmd2
|
Pipe command; redirects output of command cmd1 to input of cmd2
|
Filters
| Command
|
Description
|
| wc
|
Word count
|
| grep
|
Gets a regular expression and prints it
|
| sort
|
Sorts 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
|
Cluster directories
| Command
|
Description
|
| /home
|
Backed up nightly
|
| /data
|
Backed up nightly
|
| /dors
|
Backed up nightly
|
| /nobackup
|
Not backed up
|
| /tmp
|
Temporary local storage for I/O intensive tasks
|
Lmod
| Command
|
Description
|
| module avail
|
Shows all available modules
|
| module load module
|
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
|
Lists currently loaded modules
|
| module unload module
|
Removes module from the environment
|
| module purge
|
Removes all modules from the 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 collection
|
Restores modules from collection
|
SLURM
| Command
|
Description
|
| 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
|
| srun
|
Launch parallel job step
|
| sacct
|
Display job accounting information
|
SLURM Directives
| SLURM Directives
|
Description
|
| --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
|
| --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
|
| --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:jobid
|
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
| Variables
|
Description
|
| SLURM_JOBID
|
Job ID
|
| SLURM_SUBMIT_DIR
|
Job submission directory
|
| SLURM_SUBMIT_HOST
|
Name of host from which job was submitted
|
| 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
| Command
|
Description
|
| accre_storage
|
Check storage quota usage
|
| rtracejob jobid
|
Check resources utilization for job jobid
|
| 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
|
Last updated on 01/30/2024
