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https://github.com/NVIDIA/ngc-container-environment-modules

Environment modules for NGC containers
https://github.com/NVIDIA/ngc-container-environment-modules

lmod ngc singularity

Last synced: 27 days ago
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Environment modules for NGC containers

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README 

        
# NGC Container Environment Modules



NGC container environment modules are lightweight wrappers that make

it possible to transparently use [NGC

containers](https://ngc.nvidia.com) as environment modules.



- Use familiar environment module commands, ensuring a minimal

  learning curve or change to existing workflows



- Leverage all the benefits of containers, including portability and

  reproducibility



- Take advantage of the optimized HPC and Deep Learning containers

  from NGC



## Synopsis



```

$ git clone https://github.com/NVIDIA/ngc-container-environment-modules

$ module use $(pwd)/ngc-container-environment-modules

$ module load gromacs

$ gmx

```



The `gmx` command on the host is transparently mapped into the GROMACS

container. If the container image is not already present, then the

image will be pulled and cached on first use.  Since Singularity

automatically mounts `$HOME`, `/tmp`, and the current working

directory into the container, the container environment modules provide

nearly transparent access to NGC containers.



Note: Add the path to the NGC container environment modules to

`MODULEPATH` to skip the `module use` step.



## Prerequisites



- [Lmod](https://lmod.readthedocs.io/en/latest/)

- [Singularity](https://sylabs.io/guides/latest/user-guide/) 3.4.1 or later



## Modification



The NGC container environment modules are a reference. It is expected

that they will need some modification for the local environment.



Some of the expected changes are:



1. The name of the Singularity module. The container environment

   modules try to load the `Singularity` module (note the capital

   'S'). Set the `NGC_SINGULARITY_MODULE` environment variable if the

   local Singularity module is named differently (set it to `none` if

   no Singularity module is required).



2. Module conflicts. The container environment modules set module

   conflicts based on the commands mapped into the container. Sites

   may want to modify the list of conflicting modules to prevent

   conflicts between containers or other environment modules.



3. Container image cache. The container environment modules can either

   pull NGC container images as needed or use a library of

   pre-downloaded container images. Sites may wish to modify the

   modules to only support one of these modes. Sites may also want to

   hard-code the path to the library of pre-downloaded container

   images rather than using the `NGC_IMAGE_DIR` environment variable.



4. Mount additional directories into the containers. Sites may have

   filesystems that should be visible to all user processes, such as a

   `/scratch` filesystem or a set of shared datasets. In this case,

   set `SINGULARITY_BINDPATH`, either globally, or in the container

   environment modules.



## Examples



### Basic



Download a [GROMACS benchmark](http://ftp.gromacs.org/pub/benchmarks/)

to run this example.



```

$ module load gromacs/2020.2

$ gmx mdrun -ntmpi 1 -ntomp 40 -v -pin on -nb gpu --pme gpu --resetstep 12000 -nsteps 20000 -nstlist 400 -noconfout -s topol.tpr

```



### Interactive



```

$ module load pytorch/20.02-py3

$ python3

>>> import torch

>>> x = torch.randn(2,3)

```



### Jupyter notebooks



```

$ module load rapidsai

$ jupyter notebook --ip 0.0.0.0 --no-browser --notebook-dir /rapids/notebooks

```



### Multi-node MPI



Download the LAMMPS [Lennard Jones

fluid](https://lammps.sandia.gov/inputs/in.lj.txt) dataset to run this

example.



```

$ module load lammps/15Jun2020

$ mpirun -n 2 lmp -in in.lj.txt -var x 8 -var y 8 -var z 8 -k on g 2 -sf kk -pk kokkos cuda/aware on neigh full comm device binsize 2.8

```