Development Environment / Linux Commands

This documentation provides a summary of useful Linux commands that may be used during StateMod development.

Introduction
Shell Scripts
Linux Command Summary

Introduction

The StateMod development environment uses MinGW, which provides a Linux environment within Windows desktop. The MinGW environment is provided as a command line terminal window that displays a prompt and responds to typed commands. Use the Windows Start / MSYS2 / MINGW64 menu to open a window to run Linux commands.

Links to internet documentation are provided in the following.

Shell Scripts

In addition to commands, the StateMod development environment makes use of shell scripts for bash and sh command "shells". These scripts typically have extension .bash and .sh to avoid confusion with other Windows files, but the file extension is not required by Linux.

Programs to run are located by checking the PATH environment variable. This concept is similar on Windows and Linux. To display the PATH, type:

echo $PATH

or, to see all environment variables:

printenv

If a program or shell script to be run is not found in the PATH, it can be run by typing the relative or full path to the file. If the file is in the current folder, it may be necessary to run with ./scriptname because the current folder (.) is often not included in the PATH for security reasons.

Linux Command Summary

The following table lists common commands that are used during development. Some commands are built into the shell program and others are separate programs. Some commands (e.g., cygpath) are available in MinGW and Git Bash environments but will not be available in full Linux environments). Linux provides many commands to perform common tasks. Commands may operate on more than one file, specified as multiple file separated by spaces or use * as wildcard in names. Click on the command name below for additional documentation.

Linux Programs used in the StateMod Development Environment

Linux Command	Similar in Windows	Description
`cat`	`type`	Print the contents of a file, for example: `cat filenme`
`cd`	`cd`	Change directory (folder), for example: `cd` - change to user's home folder `cd folder` - change to the specified folder `cd ..` - change to the parent folder of the current folder `cd ../..` - change up two folder levels
`clear`	`cls`	Clear the terminal of output, useful when want to start a clean sequence of commands.
`cygpath`	`cygpath`	Convert between Linux and Windows file paths, for example: `cygpath -w ~` - print the Windows location of Linux user's home folder `cygpath -w /some/path` - print the Windows location of a Linux folder
`ls`	`dir`	List files, for example: `ls -l` - long listing `ls -la` - list all files including hidden files (hidden files have name that start with a period), long output `ls folder/path` - list the contents of a folder given its path
`mkdir`	`mkdir`	Make a new directory (folder), for example: `mkdir newfolder`
`pwd`	`cd`	Print the present working directory (folder). Although the prompt often shows the directory, it may only show part of the full path.
`rm`	`del`	Remove one or more files, for example: `rm *.log`
`rmdir`	`rmdir`	Remove one or more directories (folders), for example: `rmdir folder`
`which`	`where`	Find where a program exists on the system by searching the `PATH` environment variable, for example: `which gfortran`