bash shell

open a terminal window to access the command-line (bash shell).

run a program

If a program is in your $PATH (environment variable defined in $HOME/.bashrc), then you can type the program name, and hit return:

$ matlab

If it’s not in your PATH, then email support-neuro@berkeley.edu

common commands

Below are some common commands

navigate:

cd                  go home (to your login directory)
cd ..               go up a parent directory
cd /path/to/dir     go to <dir>
cd path/to/dir      go to path relative to here (no leading slash).

make:

mkdir dirname       make a directory identified by 'dirname'

list:

ls                  list contents of current directory
ls -a               include files with "." (dot files)
ls -l               list contents in long format
ls -lrt             list contents, sort by modified time in reverse order
ls -lR              list contents recursively

info:

file filename       show the content type of 'filename'

view:

cat   filename      show contents of filename
less  filename      show contents of filename one page at a time
head  filename      show first 10 lines of filename
tail  filename      show last 10 lines of filename
head -50 filename   show first 50 lines of filename

move/rename:

mv src dest         rename file; however, if 'dest' is a directory, then 'src' is moved to 'dest'

remove:

rm filename         delete filename
rm -r dir           remove a directory and its contents

search:

find . -name "*.nii"    find files in current directory that end with '.nii'

process management:

pgrep name          print jobs with 'name'
pkill name          kill jobs with 'name' (only your jobs will be terminated).

Show system resources:

top                 show process information on this system
(type 'q' to quit)

Change password:

See: change password

bash shell script

A shell script is a series of commands saved to a file for later execution.

You can create a script with a text editor. Text editors available on the cluster include:

• gedit: simple editor with a graphical interface

• nano: simple editor with a curses-based interface

• emacs: advanced editor with a graphical interface

• vi: advanced editor with a text interface

Below is an example of a script that prints the date, and then sleeps 20 seconds.

1. Start a text editor:

   $ nano
   

2. Enter the following text, and save as ‘simple.sh’:

   #!/bin/sh

   date

   sleep 20

3. Make the script executable:

   $ chmod a+x simple.sh
   

4. Run the command at the shell prompt:

   $ ./simple.sh
   

bash iteration

A common use of shell programming is to perform a task multiple times, iterating over a list.

In this example, we use a ‘for’ loop to run the ‘echo’ command 5 times. As a result, the value of ‘i’ is printed (echo’d) to the screen, where i=1, i=2, i=3, i=4 and i=5. The for loop is terminated with the ‘done’ statement.

You may copy and paste the lines below into a terminal window. Alternatively, copy them into a file, and run it as a shell script:

for i in 1 2 3 4 5; do
    echo "$i"
done

The ‘seq’ command prints a sequence of numbers, and has options to define the increment, pad with zeros, etc. In this example, we evaluate the numbers 0 to 20 by increments of 4:

j=0
for i in `seq 0 4 20`; do
    # print value of i
    echo "i is $i"
    # add i+j
    ((j = $j + $i))
    # print value of j
    echo "j:$j"
done

you may copy and paste the code directly into a terminal window, or copy them into a file, and run it as a shell script. To learn more about seq, run ‘man seq’ (to quit the ‘man’ command, type ‘q’).