Skip to content

Commit 9298812

Browse files
removed old Singularity section
1 parent 9648525 commit 9298812

File tree

1 file changed

+1
-68
lines changed

1 file changed

+1
-68
lines changed

mkdocs-project-dir/docs/Software_Guides/Singularity.md

Lines changed: 1 addition & 68 deletions
Original file line numberDiff line numberDiff line change
@@ -78,77 +78,10 @@ as long as they use a local filesystem and not home or Scratch.
7878
Our default setup uses `$XDG_RUNTIME_DIR` on the local disk of the login nodes, or `$TMPDIR` on a
7979
compute node (local disk on the node, on clusters that are not diskless).
8080

81-
If you try to build a container on a parallel filesystem, it will fail with a number of
81+
If you try to build a container on a parallel filesystem, it may fail with a number of
8282
permissions errors.
8383

8484

85-
## Singularity
86-
87-
Run `singularity --version` to see which version we currently have installed.
88-
89-
90-
!!! important "Singularity update to Apptainer"
91-
On Myriad, we are updating to Singularity to Apptainer. This update will occur on 14th
92-
November during a [planned outage](../Planned_Outages.md)
93-
94-
This update may affect any containers that are currently downloaded, so users will have to test
95-
them to check their workflow still functions correctly after the update. We expect most to work
96-
as before, but cannot confirm this.
97-
98-
A Singularity command that will no longer be available in Apptainer is
99-
`singularity build --remote`. If any of you have workflows that depend on this,
100-
please email [email protected]. We are currently looking into how we would provide
101-
equivalent functionality.
102-
103-
Updates to the other clusters will follow, dates tbc.
104-
105-
106-
### Set up cache locations and bind directories
107-
108-
The cache directories should be set to somewhere in your space so they don't fill up `/tmp` on
109-
the login nodes.
110-
111-
The bindpath mentioned below specifies what directories are made available inside the container -
112-
only your home is bound by default so you need to add Scratch.
113-
114-
You can either use the `singularity-env` environment module for this, or run the commands manually.
115-
116-
```
117-
module load singularity-env
118-
```
119-
120-
or:
121-
122-
```
123-
# Create a .singularity directory in your Scratch
124-
mkdir $HOME/Scratch/.singularity
125-
126-
# Create cache subdirectories we will use / export
127-
mkdir $HOME/Scratch/.singularity/tmp
128-
mkdir $HOME/Scratch/.singularity/localcache
129-
mkdir $HOME/Scratch/.singularity/pull
130-
131-
# Set all the Singularity cache dirs to Scratch
132-
export SINGULARITY_CACHEDIR=$HOME/Scratch/.singularity
133-
export SINGULARITY_TMPDIR=$SINGULARITY_CACHEDIR/tmp
134-
export SINGULARITY_LOCALCACHEDIR=$SINGULARITY_CACHEDIR/localcache
135-
export SINGULARITY_PULLFOLDER=$SINGULARITY_CACHEDIR/pull
136-
137-
# Bind your Scratch directory so it is accessible from inside the container
138-
# and the temporary storage jobs are allocated
139-
export SINGULARITY_BINDPATH=/scratch/scratch/$USER,/tmpdir
140-
```
141-
142-
Different subdirectories are being set for each cache so you can tell which files came from where.
143-
144-
You probably want to add those `export` statements to your `.bashrc` under `# User specific aliases and functions` so those environment variables are always set when you log in.
145-
146-
For more information on these options, have a look at the Singularity documentation:
147-
148-
* [Singularity user guide](https://sylabs.io/guides/3.5/user-guide/index.html)
149-
* [Singularity Bind Paths and Mounts](https://sylabs.io/guides/3.5/user-guide/bind_paths_and_mounts.html)
150-
* [Singularity Build Environment](https://sylabs.io/guides/3.5/user-guide/build_env.html)
151-
15285
## Downloading and running a container
15386

15487
Assuming you want to run an existing container, first you need to pull it from somewhere online that

0 commit comments

Comments
 (0)