Environment

Lmod

Lmod is a Lua based module system that helps manage the user environment (PATH, LD_LIBRARY_PATH etc.) through module files. It supports hierarchical MODULEPATH. We use Lmod to provide and manage different versions of libraries compiled by different combinations of compilers and MPI libraries.

Some useful module commands

Command	Description
module avail	List available modules in MODULEPATH
module list	List active modules in the user environment
module load [module]	Load a module file in the users environment
module unload [module]	Remove a loaded module from the user environment
module swap [module1] [module2]	Replace module1 with module2
module purge	Remove all modules from the user environment
module use [-a] [path]	Prepend or Append path to MODULEPATH
module unuse [path]	Remove path from MODULEPATH

Like many other commands in Linux, you can use man module or module --help to find more instructions on how to use it. See also here for a user guide for Lmod.

Modules on this machine

On this machine, we adopt the naming convention described here and module hierarchy described here. Running module avail gives the following three levels of modules.

------------------------------- /public/apps/module/modulefiles/mpi/gcc/12.3/openmpi/4.1 --------------------------------
   esmf/8.5.0    fftw/3.3.10    hdf5/1.14.1    netcdf/4.9.2    pio/1.10.1    pnetcdf/1.12.3

----------------------------------- /public/apps/module/modulefiles/compiler/gcc/12.3 -----------------------------------
   openmpi/4.1 (L)    zlib/1.2.13

----------------------------------------- /public/apps/module/modulefiles/core ------------------------------------------
   R/4.3.1        anaconda3/2023.07-2    cmake/3.27.4 (L)    intel/2023.2    julia/1.9.3  (D)    nvidia/23.7
   StdEnv  (L)    cdo/2.2.1              gcc/12.3     (L)    julia/1.6.7     matlab/2018a

  Where:
   L:  Module is loaded
   D:  Default Module

The three levels of modules from bottom to top are core modules, modules compiled with a specific compiler, and modules compiled with a specific combination of compiler/MPI, respectively. The compiler/MPI combination of gcc/12.3 and openmpi/4.1 is automatically loaded when logging in the system (managed by a standard set of modules StdEnv, read more here). To use other compilers, e.g., the Intel compiler, simply run module swap gcc intel and openmpi compiled with Intel compiler will automatically be swapped and reloaded. Currently, we have the GNU Compiler Collection (gcc), Intel oneAPI Toolkits (intel), and Nvidia HPC SDK (including the PGI compiler; nvidia) installed on the system, but only OpenMPI (openmpi) is supported at this moment. All libraries are compiled using these combinations of compiler/MPI.