File Commands

ls	directory listing
ls -al	formatted listing with hidden files
cd dir	change directory to dir
cd	change to home
pwd	show current directory
mkdir dir	create a directory dir
rm file	delete file
rm -r dir	delete directory dir
rm -f file	force remove file
rm -rf dir	force remove directory dir (!)
cp file1 file2	copy file1 to file2
cp -r dir1 dir2	copy dir1 to dir2; create dir2 if it doesn't exist
mv file1 file2	rename or move file1 to file2; if file2 is an existing directory, moves file1 into directory file2
ln -s file link	create symbolic link link to file
touch file	create or update file
cat > file	places standard input into file
more file	output the contents of file
head file	output the first 10 lines of file
tail file	output the last 10 lines of file
tail -f file	output the contents of file as it grows, starting with the last 10 lines

Process Management

ps	display your currently active processes
top	display all running processes
kill pid	kill process id pid
killall proc	kill all processes named proc (!)
bg	lists stopped or background jobs; resume a stopped job in the background
fg	brings the most recent job to foreground
fg n	brings job n to the foreground

File Permissions

chmod file	change the permissions of file to ; the format of a is [ugoa...][[+-=][perms...]...], where perms is either zero or more letters from the set rwxXst, or a single letter from the set ugo. ,see man chmod for further details
chmod a+rwx file	change the permissions of file to rwx for everyone
chmod u=rwx,g=rx,o=rx file	change the permissions of file to rwx for owner, and rx for group and world

Working Remotely

ssh user@host	securely connect to remote host host as user user
scp user@host:/home/user/file .	securely copy file /home/user/file on remote host host (as user user) to the current directory
scp file user@host:/home/user/	securely copy (as user user) the file file in the current directory to the directory /home/user/ on the remote host host

LSF Job Submission and Monitoring

bjobs	view status of all jobs currently submitted by user
bjobs -q name	view status of all jobs currently submitted by user to queue name
bjobs -r	view status of all running jobs submitted by user
bqueues	view status of of all queues in the batch system
bsub -q qname command	submit the command to queue qname (command may contain flags, options and arguments)
bsub -q qname -J my_name command	submit the command to queue qname given the name my_name
bsub -q qname -o file command	submit the command to queue qname, LSF will write all command line output (stderr and stdout) to file
bsub < file	submit a job by reading the contents of file
bkill jobid	kill the job with ID jobid by the current user
bkill 0	kill all jobs submitted by the current user
bpeek pid	monitor job pid state
bpeek -f pid	real time monitor job pid state