How do I run my program in the background (including the use of 'screen')?

Unix has the ability to run your program in the background. This means that instead of waiting for the program to finish execution, the UNIX shell prompts you again and you can run other commands at the same time that the background process is running. To run the program 'myprog' in background, type:

myprog &

The shell will respond with a number, its process identification number (or PID) and then return to the prompt.

To start a background job in a way that keeps in running even after you logout, there are a few options.

For an R batch job, you can do:

R CMD BATCH --no-save code.R code.log &

More generally, you can use 'nohup'. To keep the program 'myprog' running in background, type:

nohup myprog &

For example, with a Matlab job, where we redirect the output to outfile.txt and the error messages to error.txt:

nohup matlab -nodesktop -nodisplay < infile.m > outfile.txt 2> error.txt &

You may alternatively choose to use GNU screen to run your jobs so that you can leave them running when you logout. Just invoke 'screen' from your shell, type a space or carriage return to dismiss the startup message, then start your job. When you want to detach, type Control-a followed by Control-d. You can then exit from your terminal session. When you want to access your job again, connect to the same machine your job is running on and type 'screen -r'. Note that screen is likely to be more robust than nohup in terms of ensuring your job is not killed by ending a remote login session abruptly (e.g., closing your laptop, losing your wireless connection, etc.).

A few more details on screen. To see a list of available sessions, do 'screen -ls'. To start a session with a specific name, you can do 'screen -S sessionName'. Then to resume a named session, do 'screen -r SessionName'. Or to resume a particular unnamed session, use the name reported by 'screen-ls', e.g., it might look something like 4763.pts-2.beren. If a session is in use, you can forcibly detach it from the other location and attach to it by doing 'screen -d -R sessionName'. To close a session, you can use 'exit' from within the session.