singularity.md

Running SMND from a container

The SMND project provides a container definition file suitable for creating a singularity container including all the software collection. The container is based on the CentOS 8 packages, but it can be built and run on any Linux x86_64 distribution where the singularity package (version 2.5 or later) is installed.

Building the container

The container has to be built as root user, but it can be built on any system, such as a personal laptop or a virtual machine; after build it can be used, without being root, on any system where the singularity software is installed, such as an HPC cluster.

For building a container, download the Singularity.simc_tools_r8 recipe file from the SMND repository and run:

singularity build ./simc_tools.sif Singularity.simc_tools_r8

This will take some time and require a good internet connection for downloading and installing the software packages and libraries in the container. At the end of the process you will obtain a single big executable file simc_tools.sif (also called "image") containing all the tools and libraries. It can be ported on any system where singularity software is installed.

Downloading a pre-built container

A pre-built container for smnd is available on the SylabsCloud library public service, as an alternative to building it on one's own.

In order to download it you need to install the singularity package version 3.0 or later and pull the container with the command:

singularity pull library://dcesari/default/simctools:simc_tools_r8

obtaining the file simctools_simc_tools_r8.sif (or possibly a file with a different name). It is also possible to download the container interactively through the web interface.

The container on SylabsCloud library is built manually from time to time, so it may not contain the latest versions of the software packages available in the repository as it is the case with a self-built container.

Running executables within the container

To run a tool within the container, you can make the container executable with the chmod +x command and simply launch the container image executable followed by the desired command and arguments, e.g. for vg6d_transform:

./simc_tools.sif vg6d_transform --trans-type=zoom --sub-type=coord \
  --ilon=5. --flon=16. --ilat=40. --flat=48. input.grib output.grib

You can also explicitly run through the singularity command (e.g. in case you need to add command-line arguments to singularity):

singularity exec ./simc_tools.sif vg6d_transform --trans-type=zoom --sub-type=coord \
  --ilon=5. --flon=16. --ilat=40. --flat=48. input.grib output.grib

A frequently needed singularity argument is the -B <directory> (possibly repeated multiple times) which allows to "see" in the container a mount point other than the one containing the user's home directory.

For more information, see the singularity documentation.