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