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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