# Modules

## What are modules?

- A tool that **simplify** shell initialization and lets users easily modify their environment during the session with modulefiles

- Each modulefile contains the **information** needed to configure the shell for an application. (PATH, LD_LIBRARY_PATH, CPATH, etc.)

- Modules are useful in managing **different versions** of applications. 

- Modules can also be bundled into metamodules that will load an entire **set of different applications**. 

## How to use modules?

> **Module Cheat Sheet**
>
> `module av`
>
> `module av <software>`
>
> `module list`
>
> `module load <software>`
>
> `module unload <software>`
>
> `module swap <loaded_software> <new_software>`
>
> `module purge`

To **check available modules** installed on the cluster:

```
[tutln01@login-prod-01 ~]$ module av
```

Upon login, environment variable **`PATH`** is set for the system to search executables along these paths:

```
[tutln01@login-prod-01 ~]$ echo $PATH
/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/cluster/home/tutln01/bin:/cluster/home/tutln01/.local/bin
```

For example, I would like to use `gcc` compiler, to check what versions of gcc compiler is available, load the version I would like to use, and use it:

```
[tutln01@login-prod-01 ~]$ module av gcc

----------------------------------------------------------- /opt/shared/Modules/modulefiles-rhel6 ------------------------------------------------------------
gcc/4.7.0 gcc/4.9.2 gcc/5.3.0 gcc/7.3.0

-------------------------------------------------------------- /cluster/tufts/hpc/tools/module ---------------------------------------------------------------
gcc/8.4.0 gcc/9.3.0 gcc/11.2.0
```

Use `module list` to **check loaded modules** in current environment:

```
[tutln01@login-prod-01 ~]$ module load gcc/7.3.0
[tutln01@login-prod-01 ~]$ module list
Currently Loaded Modulefiles:
  1) use.own     2) gcc/7.3.0
```

```
[tutln01@login-prod-01 ~]$ which gcc
/opt/shared/gcc/7.3.0/bin/gcc
[tutln01@login-prod-01 ~]$ echo $PATH
/opt/shared/gcc/7.3.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/cluster/home/tutln01/bin:/cluster/home/tutln01/.local/bin
[tutln01@login-prod-01 ~]$ gcc --version
gcc (GCC) 7.3.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
```

**swap a module for another** (doesn't have to be the same software):

```
[tutln01@login-prod-01 ~]$ module swap gcc/7.3.0 gcc/9.3.0 
[tutln01@login-prod-01 ~]$ module list
Currently Loaded Modulefiles:
  1) use.own     2) gcc/9.3.0
```

 **unload loaded modules**:

```
[tutln01@login-prod-01 ~]$ module unload gcc
[tutln01@login-prod-01 ~]$ echo $PATH
/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/cluster/home/tutln01/bin:/cluster/home/tutln01/.local/bin
```

**unload ALL** of the loaded modules:

```
[tutln01@login-prod-01 ~]$ module purge
```



## Install Software/Packages

- [R](https://tufts.box.com/s/qximkv5ke2y4k0vbg6m04m6fc6exh88h) (R command line recommanded), packages need to be reinstalled for each version of R

  - R/4.0.0
    - HPC R repo `/cluster/tufts/hpc/tools/R/4.0.0`
  - R/4.1.1
    - HPC R repo `/cluster/tufts/hpc/tools/R/4.1`
  - R/4.2.0
    - HPC R repo `/cluster/tufts/hpc/tools/R/4.2.0`
  - R/4.3.0
    - HPC R repo `/cluster/tufts/hpc/tools/R/4.3.0`

- [Python](https://tufts.box.com/v/CondaEnvonHPC) (Conda env recommanded)

  - anaconda/3 (older version, source activate)
  - `anaconda/2021.05`, `anaconda/2021.11`, `anaconda/2023.07` (newer version, **source activate**)
  - Use the same version of conda on one conda env every time

- Other software compiled from **source**

  - gcc

  - cmake

  - ... any **dependencies**, load if available, install if not. Some environment variables may need to be set manually.

  - **Follow instructions** (read it through first)

  - Use **"--prefix="** to install in non-standard locations

  - Modify the environment variables !!! (such as PATH, LD_LIBRARY_PATH, CPATH, .etc)

  - You can make a private module for your locally installed software. Here is [HOW](https://tufts.box.com/s/fewt978g2hmmmhskm1n5dg4bj6xt0cdd)

  - OR you can submit a request to tts-research@tufts.edu for the software to be installed globally on the cluster.