https://github.com/nosolls/geos-singularity
Singularity containers for using GEOS fixtures.
https://github.com/nosolls/geos-singularity
climate-model climate-modeling singularity singularity-containers
Last synced: 5 months ago
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Singularity containers for using GEOS fixtures.
- Host: GitHub
- URL: https://github.com/nosolls/geos-singularity
- Owner: nosolls
- Created: 2020-08-04T14:59:00.000Z (almost 6 years ago)
- Default Branch: main
- Last Pushed: 2022-04-12T21:06:11.000Z (about 4 years ago)
- Last Synced: 2024-01-29T10:18:23.771Z (over 2 years ago)
- Topics: climate-model, climate-modeling, singularity, singularity-containers
- Homepage:
- Size: 16.6 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# GEOS fixtures in Singularity
These files are various definition files for using GEOSfvdycore and GEOSgcm within Singularity. Most are on the Singularity library. There are constant changes to GEOS, so these may not build because of that.
### Which files are which?
Files ending in:
`b.def` : Indicates the container that installs the base libraries
`fvy.def` : Indicates the container that installs GEOSfvdycore
`gcm.def` : Indicates the container that installs GEOSgcm
### How do I use these?
When using the containers for GEOSfvdycore and GEOSgcm, the install directories are located at `/GEOSfvdycore` and `/GEOSgcm` inside their containers respectively. Documentation for running GEOSgcm can be found at the [GEOS-5 wiki](https://geos5.org/wiki/index.php?title=GEOS_GCM_Quick_Start#Running_GEOS_GCM). Running GEOSfvdycore is a similar process.
You go to `/installdirectory/install/bin` for one of them, and then use their setup scripts to create an experiment directory. GEOSfvdycore has `fv3_setup` and GEOSgcm has `gcm_setup`. If you want to run an experimental directory you made with slurm and singularity, you can create a slurm script and use something like:
```
singularity exec image.sif experimentdirectory/./fv3.j
```
### It takes time to convert to a sandbox with each run. Is there a way around this?
You should convert your `.sif` file to a sandbox and use that for each run, especially if you use a container multiple times.
```
singularity build -s yoursandbox/ yourimage.sif
```
Now you can use that sandbox for runs instead of the image. This will save time in converting the image and having to clean it. You do not need the original `.sif` file for the sandbox.
### Do I have to make changes to the run script for these containers to work with slurm?
If you want to change the amount of tasks the run script specifies or use multiple nodes, then yes. A specified amount of tasks (`ntasks`) will already be made once an experiment directory is created, and you should ideally go by these conditions for your slurm script. However, if you'd like to change these values, the variables `FV_NX` and `FV_NY` in the runscript will have to be changed to what number of nodes / number of cores you'd like.