Many of us grew up using windows and are used to folders and drive letters. The following may look familiar to people with a Windows computer.
This is a graphical look into your space on the Windows system. Here we can see the folders (subdirectories) Desktop, Downloads, Documents, and Pictures. Files and other folders may be in these. However, on linux systems, all folders are organized in a tree like fashion starting at the root otherwise designated as / (slash). Also, there is no equivalent to a drive letter on Linux like the C: drive on Windows. On monsoon there are two subdirectories (folders) that will be of special interest to you; home and scratch. There are other subdirectories off the root but these two are the ones you will work with at first.
Your home directory is in the home subdirectory off the root (/home). If my username is abc123 then the path notation to my home would be /home/abc123 and similarly your scratch directory will be /scratch/abc123
For example, a visual representation of your scratch area could be:
/scratch/abc123
├── bigdata
│ ├── analysis.sh
│ ├── driver.sh
│ ├── filelist
│ ├── input
│ ├── job_array2.sh
│ ├── job_array3.sh
│ ├── job_array.sh
│ ├── job_depend_driver.sh
│ ├── job_template.sh
│ ├── logs
│ └── output
├── lazyjob.sh
├── lazy.txt
├── logs
├── long.txt
├── lzjob.sh
├── output.txt
├── study1
│ ├── output.txt
│ ├── simplejob.sh
│ └── study1.sh
├── test2.sh
├── test.out
├── test.sh
In this example, there are two subfolder under /scratch/abc123. The two subdirectories are bigdata and study1. Within these subdirectories are files. Subdirectories may also contain other subdirectories and files. As you work on projects on Monsoon it is advised to create subdirectories for each project that you may be working on. Use your home directory for scripts and other files you need to keep long term (just remember the home directory is limited in the amount of space you have) and use the scratch directory for large data files, output, and temporary files.
A few commands you will need to know to navigate are the following
● cd - used to change directory. i.e. cd /scratch/abc123
● mkdir - used to make a directory. You may use a full path like /scratch/abc123/study2 or if you want to make a directory where you have already done a cd you may do - mkdir study2
Working at the command line interface (CLI) on Monsoon will give you the greatest power and most options for doing your research. However, this requires you to learn the commands to do the work you need to do. We do have a graphical user interface (GUI) for Monsoon at ondemand.hpc.nau.edu but that is limited in how complex your research jobs may be.