Accessing Host Files with Bind Mounts
It’s possible to create and modify files on the host system from within the container. In fact, that’s exactly what we did in the previous example when we created output files in our home directory.
Let’s be more explicit. Consider this example.
$ singularity shell lolcow.sif
Singularity> echo wutini > ~/jawa.txt
Singularity> cat ~/jawa.txt
wutini
Singularity> exit
$ cat ~/jawa.txt
wutini
Here we shelled into a container and created a file with some text in our home directory. Even after we exited the container, the file still existed. How did this work?
There are several special directories that Singularity bind mounts into your container by default. These include:
$HOME/tmp/proc/sys/dev
You can specify other directories to bind using the --bind option or the environmental variable $SINGULARITY_BINDPATH
Let’s say we want to access a directory called /data from within our container. For this example, we first need to create this new directory with some data on our host system.
$ sudo mkdir /data
$ sudo chown $USER:$USER /data
$ echo 'I am your father' > /data/vader.txt
Now let’s see how bind mounts work. First, let’s list the contents of /data within the container without bind mounting /data on the host system to it.
$ singularity exec lolcow.sif ls -l /data
ls: cannot access '/data': No such file or directory
Nothing there! Now let’s repeat the same command but using the --bind option to bind mount /data into the container.
$ singularity exec --bind /data lolcow.sif ls -l /data
total 4
-rw-rw-r-- 1 student student 17 Mar 2 00:51 vader.txt
Now a /data directory is created in the container and it is bind mounted to the /data directory on the host system.
You can bind mount a source directory of one name on the host system to a destination of another name using a source:destination syntax, and you can bind mount multiple directories as a comma separated string. For instance:
$ singularity shell --bind src1:dest1,src2:dest2,src3:dest3 some.sif
If no colon is present, Singularity assumes the source and destination are identical. To do the same thing with an environment variable, you could do the following:
$ export SINGULARITY_BINDPATH=src1:dest1,src2:dest2,src3:dest3
For a lot more info on how to bind mount host directories to your container, check out the NIH HPC Binding external directories section.