Difference between revisions of "Modules and applications"

Revision as of 12:03, 12 October 2021

Modules commands

Here are the most frequently used module commands.

List all modules that match the given module name, e.g., list all available Python

$ module avail python

Load modules, e.g., load GCC 6.3.0 and Python 3.8.5

$ module load gcc/6.3.0 python/3.8.5

List all currently loaded modules

$ module list

Currently Loaded Modules:
 1) StdEnv   2) gcc/6.3.0   3) openblas/0.2.20   4) python/3.8.5

Other commonly used module commands

module                    # get info about module sub-commands
module avail              # List all modules available on the cluster
module key keyword        # list all modules whose description contains keyword
module help name          # get information about module name
module show name          # show what module name does (without loading it)
module unload name        # unload module name
module purge              # unload all modules at once

Where are applications installed?

$ pip install --user packagename

Two software stacks on Euler

$ env2lmod

$ lmod2env

You can set the default software stack to the new one with the command:

$ set_software_stack.sh new

Please note that after setting the default software stack, you need to logout and login again to make the change becoming active.

All new software is installed exclusively in the new software stack, mostly done with SPACK package manager.

The structure of LMOD Modules

$ module load comsol/5.6

$ module load gcc/6.3.0 hdf5/1.10.1

$ module load gcc/6.3.0 openmpi/4.0.2 openblas

Modules for GPUs

In the new software stack, we have installed a Python module which is linked with CUDA, cuDNN and NCCL libraries and contains machine learning / deep learning packages such as scikit-Learn, TensorFlow and Pytorch. This module can be loaded with the following commands:

$ env2lmod
$ module load gcc/6.3.0 python_gpu/3.8.5

The following have been reloaded with a version change:
  1) gcc/4.8.5 => gcc/6.3.0

$ module list

Currently Loaded Modules:
  1) StdEnv            4) cuda/11.0.3    7) python_gpu/3.8.5
  2) gcc/6.3.0         5) cudnn/8.0.5
  3) openblas/0.2.20   6) nccl/2.7.8-1

You can also find and load CUDA, cuDNN and NCCL libraries available on the cluster matching your needs.

 $ env2lmod
 $ module load gcc/6.3.0
 $ module avail cuda

------------- /cluster/apps/lmodules/Compiler/gcc/6.3.0 -------------
  cuda/8.0.61     cuda/9.2.88      cuda/11.0.3 (L)
  cuda/9.0.176    cuda/10.0.130    cuda/11.1.1
  cuda/9.1.85     cuda/10.1.243    cuda/11.2.2 (D)

Application lists

• Euler - New software stack
• Euler - Old software stack
• Most recently installed software

Example

• Python virtual environment

Further reading

• User guide: Setting up your environment
• Setting up a software stack for a research group
• Creating a local module directory
• Unpacking RPM packages in users space