The command line in a terminal

xeyes

ssh username@machine.domain.ca
ssh saika@alfven.physics.mun.ca

ssh -X saika@alfven.physics.mun.ca
xeyes - check graphics connection
passwd - change password

Some commands for basic filesystem stuff

ls, ls -l, ls -alrt

mkdir, rmdir

cd
cd directory
cd - (go back to directory where you were previously)
cd .. (go up to parent directory of current directory)
cd .  (change to current directory - DOES NOTHING!)
cd / (change to root directory... discuss directory tree)
cd ../../directory  (relative path)
cd /usr/bin (absolute path)

pwd (print working directory)
cp
cp -r (for a directory)
mv
touch
file
rm
rm -r (Careful!)
rm -i

ls -l
Permissions for owner, group, others to read, write and execute
chmod o+w (change so that others can write to file/directory)
chmod +x (anyone can execute file)
chmod 744 -- what the?

Archiving:
tar -zcvf archiveName.tgz Directory1 Dir2 files (to be archived)
tar -cvf archiveName.tar Directory
gzip archiveName.tar

unpacking
tar -zxvf archiveName.tgz
gunzip archiveName.tgz
tar -xvf archiveName.tar

Downloading files:
wget https://www.physics.mun.ca/courses/p3800/PROJECTS/P1/Project1.tgz
wget --no-check-certificate https://www.physics.mun.ca/courses/p3800/PROJECTS/P1/Project1.tgz


alias
alias wg="wget --no-check-certificate"

.bash_profile is used for interactive login shell
.bashrc is used for interactive non-login shell (read every time bash shell is invoked).

put 
alias wg="wget --no-check-certificate"
into .bash_profile
source ~/.bashrc


To submit projects:
# Copy your project directory to alfven.  Don't forget the colon at the end!
scp -r PROJECT1-name username@alfven.physics.mun.ca:
# Log on to alfven
ssh username@alfven.physics.mun.ca
# check that everything for the project runs properly on alfven

# make an archive of your project and copy it to the Submissions folder
tar -zxvf Project1-YourName.tgz PROJECT1-name
cp Project1-YourName.tgz /home/Submissions


editors:
nedit
nano
vi
gedit

mentioned plottting
xmgrace
gnuplot

running, suspending, background, killing
xmgrace
^Z (control-Z)  suspends job
bg (puts job into background)
fg (brings back job into foreground)
^Z (control-Z)
bg
ps
jobs (shows jobs running in background)
kill %1 (or whatever number it is)
xmgrace
^C (tries to kill running job)
xmgrace & (run in backgound from get-go)

Started discussing Project 1.