Useful Unix commands

Below you will find a list of some of the most frequently used commands when using LSNM in a Unix/Linux workstation. Please note that they are not meant to be exhaustive and that some of them apply only if you are located within the NIH computer network.

How to tar and zip a directory prior to copying or transferring:

$ tar -cvzf file_name.tar.gz directory_name

How to unpack and unzip a tar.gz file:

$ tar -xzvf file_name.tar.gz

How to download a file from remote server:

$ scp username@remote.server.com:/home/username/myfile .

How to upload a local file to remote server:

$ scp mylocalfile username@remote.server.com:/home/username

To run a GUI-based program remotely, you need to tunnel the X-windows connection through the SSH connection as follows:

$ ssh -X username@remote.server.com

After pressing <Enter>, you will have to provide your remote server password.

How to execute same command on a number of files using a unix (bash) script loop. Let's say we want to execute

the script 'netgen.py' on all files in current directory with extension 'ws':

$ for file in *.ws; do
$     python netgen.py $file
$ done

How to execute jobs in a remote server and log out without killing those jobs.

First, log in to the remote server using 'ssh' (see above), then execute the command 'screen' to open a virtual screen, then execute your command using 'nohup':

$ nohup python python_script.py &

Now you can disconnect from you screen typing <Ctrl><a><d>, which will disconnect you from the virtual screen. You can log out and later come back to the same virtual screen to check on your job(s) by typing:

$ screen -RD