From 05e64b7da90314e2c398408112273e96db120d92 Mon Sep 17 00:00:00 2001 From: Sebastian Havens Date: Fri, 16 Aug 2024 12:13:25 +0100 Subject: [PATCH] Improvements to singularity documentation --- docs/source/gettingstarted.md | 26 ++++++++++++++++++-------- 1 file changed, 18 insertions(+), 8 deletions(-) diff --git a/docs/source/gettingstarted.md b/docs/source/gettingstarted.md index ccdfc07..1fb19c8 100644 --- a/docs/source/gettingstarted.md +++ b/docs/source/gettingstarted.md @@ -22,23 +22,33 @@ ``` ```{tab} Singularity -A singularity containter can also be used for running calphy locally or on HPC machines. +A singularity containter can be used for running calphy locally or on HPC machines. The containerised environment contains all of the packages required to run calphy. -The containerised environemnt can be pulled from the repository with: -'singularity pull --arch amd64 library://sebastianhavens/calphy/calphy:latest' -(https://cloud.sylabs.io/library/sebastianhavens/calphy/calphy) +### Downloading the container + +The containerised environemnt can be pulled from the repository with: +`singularity pull --arch amd64 library://sebastianhavens/calphy/calphy:latest` + + +[Calphy image repository](https://cloud.sylabs.io/library/sebastianhavens/calphy/calphy) + +### Ruinning jobs using the container On HPC machines you can usually load the singularity module with: -'module load singularity' if it is not already available. +`module load singularity` if it is not already available. You can initiate calculations using this container with the following line: -'singularity exec --bind $PWD --pwd $PWD {location_of_.sif_image} calphy_kernel -i {input_file} -k 0' -where {location_of_.sif_image} is the file location of the containerlised environment you just pulled and {input_file} is the name of your input file. + +`singularity exec --bind $PWD --pwd $PWD {location_of_.sif_image} calphy_kernel -i {input_file} -k 0` + +where `{location_of_.sif_image}` is the file location of the containerlised environment you just pulled and `{input_file}` is the name of your input file. This line can be placed within a slurm script. -In the calphy input file, the scheduler should be set to local. +In the calphy input file, the scheduler should be set to local.
For parallel calculations to run effectively, the OpenMPI module on the host system must be at least 4.1.2. + +--- ```