Commit ea3ab740 authored by John Cawley's avatar John Cawley

Update environment-and-modules.md PROOFREAD

line 68; is 'module man' a typo?
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## Environment Customization
After logging in, you may want to configure the environment. Write your preferred path definitions, aliases, functions and module loads in the .bashrc file
After logging in, you may want to configure the environment. Write your preferred path definitions, aliases, functions and module loads in the .bashrc file;
```console
$ cat ./bashrc
......@@ -26,63 +26,63 @@ fi
```
!!! note
Do not run commands outputting to standard output (echo, module list, etc) in .bashrc for non-interactive SSH sessions. It breaks fundamental functionality (scp, PBS) of your account! Conside utilization of SSH session interactivity for such commands as stated in the previous example.
Do not run commands outputting to standard output (echo, module list, etc) in .bashrc for non-interactive SSH sessions. It breaks the fundamental functionality (scp, PBS) of your account! Consider utilization of SSH session interactivity for such commands as stated in the previous example.
## Application Modules
In order to configure your shell for running particular application on Anselm we use Module package interface.
In order to configure your shell for running a particular application on Anselm we use Module package interface.
!!! note
The modules set up the application paths, library paths and environment variables for running particular application.
The modules set up the application paths, library paths, and environment variables for running a particular application.
We have also second modules repository. This modules repository is created using tool called EasyBuild. On Salomon cluster, all modules will be build by this tool. If you want to use software from this modules repository, please follow instructions in section [Application Modules Path Expansion](environment-and-modules/#application-modules-path-expansion).
We can also have a second modules repository. This modules repository is created using a tool called EasyBuild. On the Salomon cluster, all modules are built with this tool. If you want to use software from this modules repository, please follow the instructions in the section [Application Modules Path Expansion](environment-and-modules/#application-modules-path-expansion).
The modules may be loaded, unloaded and switched, according to momentary needs.
The modules may be loaded, unloaded, and switched as required.
To check available modules use
To check available modules use;
```console
$ module avail **or** ml av
```
To load a module, for example the octave module use
To load a module, for example the octave module use;
```console
$ module load octave **or** ml octave
```
loading the octave module will set up paths and environment variables of your active shell such that you are ready to run the octave software
loading the octave module will set up paths and the environment variables of your active shell such that you are ready to run the octave software.
To check loaded modules use
To check loaded modules use;
```console
$ module list **or** ml
```
To unload a module, for example the octave module use
To unload a module, for example the octave module use;
```console
$ module unload octave **or** ml -octave
```
Learn more on modules by reading the module man page
Learn more about modules by reading the module man page;
```console
$ man module
```
Following modules set up the development environment
The following modules set up the development environment;
PrgEnv-gnu sets up the GNU development environment in conjunction with the bullx MPI library
PrgEnv-gnu sets up the GNU development environment in conjunction with the bullx MPI library.
PrgEnv-intel sets up the INTEL development environment in conjunction with the Intel MPI library
PrgEnv-intel sets up the INTEL development environment in conjunction with the Intel MPI library.
## Application Modules Path Expansion
All application modules on Salomon cluster (and further) will be build using tool called [EasyBuild](http://hpcugent.github.io/easybuild/ "EasyBuild"). In case that you want to use some applications that are build by EasyBuild already, you have to modify your MODULEPATH environment variable.
All application modules on the Salomon cluster (and further) are built using a tool called [EasyBuild](http://hpcugent.github.io/easybuild/ "EasyBuild"). In the case that you want to use applications that have already been built by EasyBuild, you have to modify your MODULEPATH environment variable.
```console
export MODULEPATH=$MODULEPATH:/apps/easybuild/modules/all/
```
This command expands your searched paths to modules. You can also add this command to the .bashrc file to expand paths permanently. After this command, you can use same commands to list/add/remove modules as is described above.
This command expands your searched paths to modules. You can also add this command to the .bashrc file to expand paths permanently. After this command, you can use the same commands to list/add/remove modules as described above.
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