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Revise module management instructions and examples #203

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44 changes: 17 additions & 27 deletions module_management.md
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Expand Up @@ -16,48 +16,38 @@ Another useful command related to module management is `module spider`. For exam


```bash
----------------------------------------------------------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------------
intel:
----------------------------------------------------------------------------------------------------------------------------------------------------------
Description:
Intel Compiler Family (C/C++/Fortran for x86_64)

--------------------------------------------------------------------------------------------------------------------
Versions:
intel/17.0.3.191
intel/17.0.4.196
intel/17.0.5.239
intel/18.0.0.128
intel/18.0.1.163
intel/18.0.2.199
intel/18.0.4
intel/19.0.5
intel/20.0.4
Other possible modules matches:
abinit-8.2.2-intel-17.0.4-impi-mkl-xz32k53 abinit-8.2.2-intel-18.0.0-impi-mkl-lck65q7 abyss-2.0.2-intel-17.0.4-openmpi-pf2axsd abyss-2.0.2-intel-17.0.4-pf2axsd ...
intel-mkl intel-mpi intel-oneapi-compilers intel-oneapi-mkl intel-oneapi-mpi intel-oneapi-runtime ...

----------------------------------------------------------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------------
To find other possible module matches execute:

$ module -r spider '.*intel.*'

----------------------------------------------------------------------------------------------------------------------------------------------------------
For detailed information about a specific "intel" module (including how to load the modules) use the module's full name.
--------------------------------------------------------------------------------------------------------------------
For detailed information about a specific "intel" package (including how to load the modules) use the module's full na
me.
Note that names that have a trailing (E) are extensions provided by other modules.
For example:

$ module spider intel/18.0.2.199
----------------------------------------------------------------------------------------------------------------------------------------------------------
$ module spider intel/20.0.4
--------------------------------------------------------------------------------------------------------------------
```
This command returns much more detailed information on a module of interest. You can see that there are actually multiple versions of the Intel compilers available for use, as is the case for most software installed on CARC systems.

To see all currently loaded modules use the command `module list`. As an example, lets load the software module for the genome assembler Abyss, and then use `module list`:
To see all currently loaded modules use the command `module list`. As an example, lets load the software module for openmpi and gcc, and then use `module list`:

```bash
module load abyss-2.0.2-intel-18.0.2-openmpi-mag4oti
module list

module load openmpi gcc
Currently Loaded Modules:
1) ncurses-6.0-intel-18.0.2-crfixrx 5) libpciaccess-0.13.5-intel-18.0.2-etjmw6m 9) sparsehash-2.0.3-intel-18.0.2-wkrpmec
2) readline-7.0-intel-18.0.2-v73wsy6 6) hwloc-1.11.8-intel-18.0.2-fjspqwm 10) bzip2-1.0.6-intel-18.0.2-fsqwhjw
3) sqlite-3.21.0-intel-18.0.2-c66lylp 7) openmpi-3.0.0-intel-18.0.2-7ejspct 11) boost-1.66.0-intel-18.0.2-eoio7oh
4) libxml2-2.9.4-intel-18.0.2-gyxifwh 8) libtool-2.4.6-intel-18.0.2-h4zy3we 12) abyss-2.0.2-intel-18.0.2-openmpi-mag4oti
1) gcc/14.1.0-vgbo 2) openmpi/5.0.6-lcny
```
As you can see there are many more modules loaded than just Abyss. These are the libraries and applications that are dependencies of Abyss.

Usually, modules are loaded as part of PBS script and subsequently unloaded automatically after the completion of that Job, so `module avail` and `module load` are the main commands you will be using. However, if you are working on a node interactively you may need to unload modules manually. The command `module unload modulename` will unload modules one at a time, for example `module unload ncurses-6.0-intel-18.0.2-crfixrx` only unloads ncurses but leaves the rest of the modules still loaded. To unload all modules use the command `module purge`.
Usually, modules are loaded as part of Slurm script and subsequently unloaded automatically after the completion of that Job, so `module avail` and `module load` are the main commands you will be using. However, if you are working on a node interactively you may need to unload modules manually. The command `module unload modulename` will unload modules one at a time, for example `module unload ncurses-6.0-intel-18.0.2-crfixrx` only unloads ncurses but leaves the rest of the modules still loaded. To unload all modules use the command `module purge`.