CLS-IT/bio_tutorial_docu
0
0
Wiki

Update Pmodules

assman_g
2024-06-12 21:33:13 +02:00
parent a4bafe6ea9
commit 530f2200d1
1 changed files with 86 additions and 85 deletions
Download Patch File Download Diff File Expand all files Collapse all files

171
Pmodules.md

@ -1,85 +1,86 @@
## Documentation
Merlin Pmodules documentation: https://lsm-hpce.gitpages.psi.ch/merlin6/using-modules.html
## Important module commands
Below is listed a summary of all available commands:
```bash
module use # show all available PModule Software Groups as well as Release Stages
module avail # to see the list of available software packages provided via pmodules
module use unstable # to get access to a set of packages not fully tested by the community
module load <package>/<version> # to load specific software package with a specific version
module search <string> # to search for a specific software package and its dependencies.
module list # to list which software is loaded in your environment
module purge # unload all loaded packages and clean up the environment
```
### module use/unuse
Without any parameter, `use` **lists** all available PModule **Software Groups and Release Stages**.
```bash
module use
```
When followed by a parameter, `use`/`unuse` invokes/uninvokes a PModule **Software Group** or **Release Stage**.
```bash
module use unstable # Invokes the 'unstable' Release stable
module unuse unstable # Uninvokes the 'unstable' Release stable
```
### module avail
This option **lists** all available PModule **Software Groups and their packages**.
Please run `module avail --help` for further listing options.
### module search
This is used to **search** for **software packages**. By default, if no **Release Stage** or **Software Group** is specified in the options of the `module search` command, it will search from the already invoked *Software Groups* and *Release Stages*. Direct package dependencies will be also showed.
```bash
$ module search openmpi/4.0.5_slurm
Module Release Group Requires
---------------------------------------------------------------------------
openmpi/4.0.5_slurm stable Compiler gcc/8.4.0
openmpi/4.0.5_slurm stable Compiler gcc/9.2.0
openmpi/4.0.5_slurm stable Compiler gcc/9.3.0
openmpi/4.0.5_slurm stable Compiler intel/20.4
$ module load intel/20.4 openmpi/4.0.5_slurm
```
Please run `module search --help` for further search options.
### module load/unload
This loads/unloads specific software packages. Packages might have direct dependencies that need to be loaded first. Most of the dependencies will be automatically loaded.
In the example below, the ``openmpi/4.0.5_slurm`` package will be loaded, however ``gcc/9.3.0`` must be loaded as well as this is a strict dependency. Direct dependencies must be loaded in advance. Users can load multiple packages one by one or at once. This can be useful for instance when loading a package with direct dependencies.
```bash
# Single line
module load gcc/9.3.0 openmpi/4.0.5_slurm
# Multiple line
module load gcc/9.3.0
module load openmpi/4.0.5_slurm
```
#### module purge
This command is an alternative to `module unload`, which can be used to unload **all** loaded module files.
```bash
module purge
```
#### module list
This command lists all your currently loaded modules.
## Documentation
Merlin Pmodules documentation: https://lsm-hpce.gitpages.psi.ch/merlin6/using-modules.html
PSI Pmodules documentation: http://pmodules.gitpages.psi.ch/index.html
## Important module commands
Below is listed a summary of all available commands:
```bash
module use # show all available PModule Software Groups as well as Release Stages
module avail # to see the list of available software packages provided via pmodules
module use unstable # to get access to a set of packages not fully tested by the community
module load <package>/<version> # to load specific software package with a specific version
module search <string> # to search for a specific software package and its dependencies.
module list # to list which software is loaded in your environment
module purge # unload all loaded packages and clean up the environment
```
### module use/unuse
Without any parameter, `use` **lists** all available PModule **Software Groups and Release Stages**.
```bash
module use
```
When followed by a parameter, `use`/`unuse` invokes/uninvokes a PModule **Software Group** or **Release Stage**.
```bash
module use unstable # Invokes the 'unstable' Release stable
module unuse unstable # Uninvokes the 'unstable' Release stable
```
### module avail
This option **lists** all available PModule **Software Groups and their packages**.
Please run `module avail --help` for further listing options.
### module search
This is used to **search** for **software packages**. By default, if no **Release Stage** or **Software Group** is specified in the options of the `module search` command, it will search from the already invoked *Software Groups* and *Release Stages*. Direct package dependencies will be also showed.
```bash
$ module search openmpi/4.0.5_slurm
Module Release Group Requires
---------------------------------------------------------------------------
openmpi/4.0.5_slurm stable Compiler gcc/8.4.0
openmpi/4.0.5_slurm stable Compiler gcc/9.2.0
openmpi/4.0.5_slurm stable Compiler gcc/9.3.0
openmpi/4.0.5_slurm stable Compiler intel/20.4
$ module load intel/20.4 openmpi/4.0.5_slurm
```
Please run `module search --help` for further search options.
### module load/unload
This loads/unloads specific software packages. Packages might have direct dependencies that need to be loaded first. Most of the dependencies will be automatically loaded.
In the example below, the ``openmpi/4.0.5_slurm`` package will be loaded, however ``gcc/9.3.0`` must be loaded as well as this is a strict dependency. Direct dependencies must be loaded in advance. Users can load multiple packages one by one or at once. This can be useful for instance when loading a package with direct dependencies.
```bash
# Single line
module load gcc/9.3.0 openmpi/4.0.5_slurm
# Multiple line
module load gcc/9.3.0
module load openmpi/4.0.5_slurm
```
#### module purge
This command is an alternative to `module unload`, which can be used to unload **all** loaded module files.
```bash
module purge
```
#### module list
This command lists all your currently loaded modules.