LINUX AND HPC REFERENCE

Connecting Working with files Editing files with nano

SSH/SFTP/SCP: login.compute.dundee.ac.uk Command Effect Command Effect
SMB: smb.compute.dundee.ac.uk/cluster cat file Show contents of file nano Open nano with an
Getting Help on STDOUT empty buffer
less file View file one screen nano file.txt Open file.txt in nano
Command Effect
at a time ctrl-o Write-out (save)
man command view man page for head file Show first 10 lines of ctrl-r Read file into current
‘command’ file on STDOUT
man -k term buffer
Search man pages for tail file Show last 10 lines of ctrl-x Exit nano
‘term’ file on STDOUT ctrl-w Search forwards for term
cut -f2 file Output field2 of a tab-
File system operations Univa Grid Engine (UGE)
delimited file file
Command Effect cut -f2 -d’,’ file
Commands
Output field2 of a ‘,’-
pwd Print working directory Command Effect
delimited file file
ls List directory contents qsub script.sh Submit script to queue
grep string file Search file for lines
ls -a Show hidden files qstat Show status of my jobs
containing string
ls -l Long format listing qstat -F -j 12345 Show full status of job id
grep -c string Report number of lines
ls -t Sort by modification file 12345
containing string in
time file qdel 12345 Delete job 12345
ls -S Sort by file size grep -v string qrsh Request interactive job
Search for lines not
ls -r Reverse sort order file qlogin Request X11-
containing string in
cp file1 file2 copy file1 to file2 file eninteracttive job
cp -r dir1 dir2 Recursively copy gzip file Compress file Directives
directory zcat file.gz Shows contents of
file.gz on STDOUT Directive Effect
mv file1 file2 move file1 to file2
gunzip file.gz Decompress file.gz -cwd Start job in current
cd dir Change working
Redirection working directory
directory to ‘dir’ -jc [long|inf] Assign job to job class
cd Change to home dir Command Effect
-j Join STDOUT and
cd - command > out.txt Redirect STDOUT
Change to previous STDERR
of command to
working directory out.txt -mods l_hard Modify mfree resource
mkdir dir Make directory ‘dir’ command 2> err.txt mfree 16G
Redirect STDERR of request of job class
rmdir dir Remove directory -adds l_hard
command to err.txt Add local_free resource
‘dir’ local_free 50G
command1|command2 Pipe STDOUT of request to job class
rmdir -r dir Recursively remove -pe smp 16 Request 16 slot SMP
directory and contents command1 to
command2 STDIN parallel environment