Environment Modules¶
With Environment Modules, a variety of software libraries and applications are available for use in the command line interface (CLI). These modules are selectively activated and deactivated with the Environment Module command line utility module.
Module help
As with many other command line tools module help explains the usage of the module command.
Notation¶
Our module naming convention provides an at-a-glance summary of the software provided by the module, its version, and (optionally) the build information. The general format for this naming system is:
[Application Name]/[Application Version]-[Optional Build Information]
For example, Python 3.9.1 is listed as python/3.9.1, Python with version 5.2.0 of the Anaconda package manager is
listed as python/anaconda-5.2.0.
Many of our modules contain build information in the name. This is useful when debugging job errors, as it indicates which compiler and libraries were used to build a version. In general, the syntax for optional build information is:
[Compiler Abbreviation]-[Compiler Version]-[Library Abbreviation]-[Library Version]
A list of compiler and library abbreviations can be found in the following table:
| Name | Abbreviation | Description |
|---|---|---|
| GNU Compiler Collection | g | Open-Source C / C++ / Fortran compilers from the GNU Project |
| Intel Compilers | i | Closed-Source C / C++ / Fortran compilers from Intel |
| OpenMPI | ompi | Open-Source implementation of the Message Passing Interface standard from the OpenMPI Project |
| Intel MPI | impi | Closed-Source implementation of the Message Passing Interface standard from Intel |
For example, Quantum Espresso version 5.2.1 built with GCC 4.8.5 and OpenMPI 1.10.0 would be labeled as
espresso/5.2.1-g-4.8.5-ompi-1.10.0.
Finally, several package names carry additional metadata about their build configuration at the end of the name string. These abbreviations are specific to the application being built, and a table can be found below which lists what they mean:
| Program | Abbreviation | Meaning |
|---|---|---|
| Gromacs | md | Gromacs built with MPI double precision |
| Gromacs | ms | Gromacs built with MPI single precision |
| Gromacs | gms | Gromacs built for use with GPUs (MPI single precision) |
| VASP | nc | VASP built for Non-Collinear calculations |
| VASP | vtst | VASP built with the Transition State Tools from the Henkelman Group |
| VASP | gamma | VASP built to only use gamma-points |
| VASP | gpu | VASP built for use with GPUs |
Putting it all together, if we take the vasp/5.4.4-i-14.0.3.174-impi-5.0.2.044-vtst-gamma module as an example,
we can easily see that this refers to VASP 5.4.4, built with version 14.0.3.174 of the Intel compiler and the Intel MPI
library version 5.0.2.044. Additionally, we can see that this is a gamma-point only version of VASP containing the
Henkelman group's transition state tools.
Legacy Naming Convention¶
Several of the older packages on our system adopt a legacy naming convention. It is similar to the above notation,
except that in order to shorten the name, periods in the version numbers were removed. To protect compatibility with
existing user-made scripts, we have preserved this naming convention. For example, the
espresso/5.2.1-g-4.8.5-ompi-1.10.0 package has a duplicate listing as espresso/521-g-485-ompi-110. We plan for
these packages to be hidden from the output of the module avail command in the future. We discourage the use
of modules with this legacy naming convention in any newly-created job submission scripts. Instead, please use the full,
current naming convention for modules.
List Available Modules¶
The command module avail provides a complete list of the modules made available on our platform. The common stem for the module installation paths is displayed on top of each section listed in the output, whereas the rest of the path name is specified under each listed entry.
We have reproduced the output of this command below listing all currently available modules, for reference purposes. The reader is referred to the software directory overview for an introduction to the codes, libraries and software packages listed here.
```text ---------------------------------------------------------------------------- /export/compute/modulefiles/system ----------------------------------------------------------------------------- emacs/24.5
------------------------------------------------------------------------- /export/compute/modulefiles/applications -------------------------------------------------------------------------- cp2k/4.1-i-14.0.3.174-impi-5.0.2.044 gromacs/2021.5-g-11.2.0-ompi-4.1.1-openblas-0.3.18-gms vasp/5.3.5-g-4.8.5-ompi-1.10.0 cp2k/41-i-174-impi-044 gromacs/2021.5-g-11.2.0-ompi-4.1.1-openblas-0.3.18-md vasp/5.3.5-g-4.8.5-ompi-1.10.0-nc espresso/521-g-485-ompi-110 gromacs/2021.5-g-11.2.0-ompi-4.1.1-openblas-0.3.18-ms vasp/5.3.5-g-4.8.5-ompi-1.10.0-vtst espresso/5.2.1-g-4.8.5-ompi-1.10.0 gromacs/20215-g-11-ompi-411-openblas-0318-gms vasp/535-g-485-ompi-110-nc espresso/5.2.1-i-14.0.3.174-impi-5.0.2.044 gromacs/20215-g-11-ompi-411-openblas-0318-md vasp/535-g-485-ompi-110-vtst espresso/521-i-174-impi-044 gromacs/20215-g-11-ompi-411-openblas-0318-ms vasp/5.3.5-i-14.0.3.174-impi-5.0.2.044 espresso/540-g-485-ompi-110 gromacs/5.1.4-g-4.8.5-ompi-1.10.0-md vasp/5.3.5-i-14.0.3.174-impi-5.0.2.044-nc espresso/5.4.0-g-4.8.5-ompi-1.10.0 gromacs/5.1.4-g-4.8.5-ompi-1.10.0-ms vasp/5.3.5-i-14.0.3.174-impi-5.0.2.044-vtst espresso/5.4.0-i-14.0.3.174-impi-5.0.2.044 gromacs/514-g-485-ompi-110-md vasp/535-i-174-impi-044(default) espresso/540-i-174-impi-044(default) gromacs/514-g-485-ompi-110-ms vasp/535-i-174-impi-044-nc espresso/600-g-485-ompi-110 gromacs/5.1.4-i-14.0.3.174-impi-5.0.2.044-md vasp/535-i-174-impi-044-vtst espresso/6.0.0-g-4.8.5-ompi-1.10.0 gromacs/5.1.4-i-14.0.3.174-impi-5.0.2.044-ms vasp/5.4.4-i-14.0.3.174-impi-5.0.2.044 espresso/6.0.0-i-14.0.3.174-impi-5.0.2.044 gromacs/514-i-174-impi-044-md vasp/5.4.4-i-14.0.3.174-impi-5.0.2.044-gamma espresso/600-i-174-impi-044 gromacs/514-i-174-impi-044-ms vasp/5.4.4-i-14.0.3.174-impi-5.0.2.044-gpu espresso/63-g-485-ompi-110 lammps/1116-g-485-ompi-110 vasp/5.4.4-i-14.0.3.174-impi-5.0.2.044-nc espresso/6.3-g-4.8.5-ompi-1.10.0 lammps/1116-i-174-impi-044 vasp/5.4.4-i-14.0.3.174-impi-5.0.2.044-vtst espresso/6.3-i-14.0.3.174-impi-5.0.2.044 lammps/1218-i-174-impi-044 vasp/5.4.4-i-14.0.3.174-impi-5.0.2.044-vtst-gamma espresso/63-i-174-impi-044 lammps/12Dec2018-i-14.0.3.174-impi-5.0.2.044 vasp/5.4.4-i-14.0.3.174-impi-5.0.2.044-vtst-nc espresso/6.4.1-g-11.2.0-ompi-4.1.1 lammps/2022.01.07-g-11.2.0-ompi-4.1.1-cuda-11.5 vasp/544-i-174-impi-044 espresso/641-g-1120-ompi-411 lammps/5Nov16-g-4.8.5-ompi-1.10.0 vasp/544-i-174-impi-044-gamma espresso/6.5.0-g-11.2.0-ompi-4.1.1 lammps/5Nov16-i-14.0.3.174-impi-5.0.2.044 vasp/544-i-174-impi-044-gpu espresso/650-g-1120-ompi-411 lammps/7Jan2022-g-1120-ompi-411-cuda-115 vasp/544-i-174-impi-044-nc espresso/6.6.0-g-11.2.0-ompi-4.1.1 nwchem/6.6-i-14.0.3.174-impi-5.0.2.044 vasp/544-i-174-impi-044-vtst espresso/660-g-1120-ompi-411 nwchem/66-i-174-impi-044 vasp/544-i-174-impi-044-vtst-gamma espresso/6.7.0-g-11.2.0-ompi-4.1.1 nwchem/702-g-485-ompi-110 vasp/544-i-174-impi-044-vtst-nc espresso/670-g-1120-ompi-411 nwchem/7.0.2-g-4.8.5-ompi-1.10.0 vesta/3.3.8 espresso/6.8.0-g-11.2.0-ompi-4.1.1 nwchem/7.0.2-i-14.0.3.174-impi-5.0.2.044 vmd/1.9.3 espresso/680-g-1120-ompi-411 nwchem/702-i-174-impi-044 vnl-atk/2016.2 gromacs/2018.2-i-14.0.3.174-impi-5.0.2.044-gms p4vasp/0.3.30 wien2k/17.1-i-14.0.3.174-impi-5.0.2.044 gromacs/20182-i-174-impi-044-gms sisso/sisso-1.0-g-11.2.0-ompi-4.1.1-openblas-0.3.18 wien2k/171-i-174-impi-044(default) gromacs/2018.3-i-14.0.3.174-impi-5.0.2.044-gms turbomole/v7.0 xcrysden/1.5.60 gromacs/20183-i-174-impi-044-gms vasp/535-g-485-ompi-110
--------------------------------------------------------------------------- /export/compute/modulefiles/compilers --------------------------------------------------------------------------- gcc/11.2.0(default) gcc/5.4.0 intel/14.0.3.174 intel/i-174(default)
--------------------------------------------------------------------------- /export/compute/modulefiles/libraries --------------------------------------------------------------------------- cuda/11.5(default) mkl/i-11.1.3.174 mpi/impi-044(default) mpi/ompi-110 mpi/ompi-4.1.1 openblas/0.3.18-g-11.2.0 cuda/9.2 mkl/i-174(default) mpi/impi-5.0.2.044 mpi/ompi-1.10 openblas/0.2.18-g-5.4.0 openblas/218-g-540
--------------------------------------------------------------------------- /export/compute/modulefiles/languages --------------------------------------------------------------------------- python/2.7.5 python/3.6.12 python/3.7.9 python/3.8.6(default) python/3.9.1 python/anaconda3-5.2.0 ```
Through the module avail command, the user can also search for available modules, by partially inserting the module's name. This functionality is demonstrated in the example below.
bash
[steve@login.mat3ra.com:~]$ module avail espresso
------------------------------------------------------------------------- /export/compute/modulefiles/applications --------------------------------------------------------------------------
espresso/521-g-485-ompi-110 espresso/540-i-174-impi-044(default) espresso/6.3-i-14.0.3.174-impi-5.0.2.044 espresso/660-g-1120-ompi-411
espresso/5.2.1-g-4.8.5-ompi-1.10.0 espresso/600-g-485-ompi-110 espresso/63-i-174-impi-044 espresso/6.7.0-g-11.2.0-ompi-4.1.1
espresso/5.2.1-i-14.0.3.174-impi-5.0.2.044 espresso/6.0.0-g-4.8.5-ompi-1.10.0 espresso/6.4.1-g-11.2.0-ompi-4.1.1 espresso/670-g-1120-ompi-411
espresso/521-i-174-impi-044 espresso/6.0.0-i-14.0.3.174-impi-5.0.2.044 espresso/641-g-1120-ompi-411 espresso/6.8.0-g-11.2.0-ompi-4.1.1
espresso/540-g-485-ompi-110 espresso/600-i-174-impi-044 espresso/6.5.0-g-11.2.0-ompi-4.1.1 espresso/680-g-1120-ompi-411
espresso/5.4.0-g-4.8.5-ompi-1.10.0 espresso/63-g-485-ompi-110 espresso/650-g-1120-ompi-411
espresso/5.4.0-i-14.0.3.174-impi-5.0.2.044 espresso/6.3-g-4.8.5-ompi-1.10.0 espresso/6.6.0-g-11.2.0-ompi-4.1.1
Actions¶
See the module actions documentation for more information on listing, loading, and resetting software modules.