Set up writable containers: another bio example with Trinity

Overview

Teaching: 10 min
Exercises: 10 min

Questions

Objectives

• Learn how to create and mount a writable overlay filesystem

• Learn how to make a container temporarily writable

Create a persistent overlay filesystem

There can be instances where, rather than reading/writing files in the host filesystem, it would instead come handy to be able to persistently store them inside the container filesystem.
A practical user case is when using a host parallel filesystem such as Lustre to run applications that create a large number (e.g. millions) of small files. This practice creates a huge workload on the metadata servers of the filesystem, degrading its performance. In this context, significant performance benefits can be achieved by reading/writing these files inside the container.

Singularity offers a feature to achieve this, called OverlayFS.

Let us cd into demos/04_trinity:

$ cd $SC19/demos/04_trinity

and then discuss how to use the Linux tools dd and mkfs.ext3 to create and format an empty ext3 file system image, which we will call my_overlay. These tools typically require sudo privileges to run. However, we can bypass this requirement by using the ones provided inside a standard Ubuntu container. The following command looks a bit cumbersome, but is indeed just an idiomatic syntax to achieve our goal:

$ singularity exec library://ubuntu:18.04 bash -c " \
  mkdir -p overlay_tmp/upper && \
  dd if=/dev/zero of=my_overlay count=200 bs=1M && \
  mkfs.ext3 -d overlay_tmp my_overlay && \
  rm -rf overlay_tmp \
  "

200+0 records in
200+0 records out
209715200 bytes (210 MB, 200 MiB) copied, 0.362418 s, 579 MB/s
mke2fs 1.44.1 (24-Mar-2018)
ext2fs_check_if_mount: Can't check if filesystem is mounted due to missing mtab file while determining whether my_overlay is mounted.
Discarding device blocks: done
Creating filesystem with 204800 1k blocks and 51200 inodes
Filesystem UUID: b14f9b2a-188d-4c19-8e6d-38a568f6efe1
Superblock backups stored on blocks:
	8193, 24577, 40961, 57345, 73729

Allocating group tables: done
Writing inode tables: done
Creating journal (4096 blocks): done
Copying files into the device: done
Writing superblocks and filesystem accounting information: done

Here we have wrapped four commands into a single bash call from a container, just for the convenience of running it once. What are the single commands doing?
We are creating (and then deleting at the end) a service directory, overlay_tmp/upper, that will be used by the command mkfs.ext3.
The dd command creates a file named my_overlay, made up of blocks of zeros, namely with count blocks of size bs (the unit here is megabytes); the product count*bs gives the total file size in bytes, in this case corresponding to 200 MB. The command mkfs.ext3 is then used to format the file as a ext3 filesystem image, that will be usable by Singularity. Here we are using the service directory we created, my_overlay, with the flag -d, to tell mkfs we want the filesystem to be owned by the same owner of this directory, i.e. by the current user. If we skipped this option, we would end up with a filesystem that is writable only by root, not very useful.

Mount a persistent overlay filesystem

Let’s give it a go with the persistent filesystem image we have just created. We can mount it at container runtime by using the flag --overlay followed by the image filename:

$ singularity shell --overlay my_overlay library://ubuntu:18.04

Now, every new directory and file that we create from inside the container will be stored in the persistent overlay filesystem. For instance, from the interactive shell we opened let us try:

$ mkdir /australia
$ cd /australia
$ echo perth >wa
$ echo canberra >act
$ exit

Access a pre-existing overlay filesystem

Once exited the container, the newly created directory is not available in the host filesystem. Try and inspect the content of /australia from the host.

Solution

$ ls /australia

ls: /australia: No such file or directory

But, if we run another container and mount the overlay, the files will still be there. Try and ls from inside a container, using the appropriate flag.

Solution

$ singularity exec --overlay my_overlay library://ubuntu:18.04 ls /australia

act wa

Note how the newly created directories and files are persistent, therefore can be re-accessed and re-used in future runs, even by containers instantiated from different images. All we have to do is to mount the filesystem image my_overlay.

Run a Trinity genome assembly from inside the container

A subdirectory in the directory we are in, trinity_test_data/, contains sample inputs for a genome assembly, coming from the Docker/test_data/ subset in the Trinity Github repo.

Create the output directory within an OverlayFS

For this exercise we are going to reuse the file system image file my_overlay.
To begin with, use the Singularity image ubuntu:18.04 to create the directory /trinity_out_dir in the OverlayFS.

Solution

$ singularity exec --overlay my_overlay library://ubuntu:18.04 mkdir /trinity_out_dir

Now, let’s ensure that $SIFPATH is defined, and that the Trinity image from Docker hub, trinityrnaseq/trinityrnaseq:2.8.6, has been correctly downloaded:

$ export SIFPATH=$SC19/demos/sif
$ ls $SIFPATH/trinity*

/home/ubuntu/sc19-containers/demos/sif/trinityrnaseq_2.8.6.sif

Now, we’re going to run a test assembly with our sample dataset, using the directory we just created in the OverlayFS to write the outputs. In this small case, only about a hundred output files are created. However, the Trinity assembly workflow can easily produce up to a million files, making the use of OverlayFS an interesting choice to reduce the workload on a host parallel filesystem.

Run the Trinity workflow

This is the command to be run:

$ Trinity \
  --seqType fq --left trinity_test_data/reads.left.fq.gz  --right trinity_test_data/reads.right.fq.gz \
  --max_memory 1G --CPU 1 --output <OUTPUT-DIRECTORY>

Can you run it using Singularity and OverlayFS? Hint: you will need to specify the appropriate directory for --output.
Expect the run to take approximately 2-3 minutes.

Solution

$ singularity exec --overlay my_overlay $SIFPATH/trinityrnaseq_2.8.6.sif \
  Trinity \
  --seqType fq --left trinity_test_data/reads.left.fq.gz  --right trinity_test_data/reads.right.fq.gz \
  --max_memory 1G --CPU 1 --output /trinity_out_dir

All of our outputs are stored in the OverlayFS, so we need to use a Singularity container to inspect them:

$ singularity exec --overlay my_overlay library://ubuntu:18.04 ls /trinity_out_dir

Trinity.fasta		      both.fa.read_count	       insilico_read_normalization   partitioned_reads.files.list.ok   recursive_trinity.cmds.ok
Trinity.fasta.gene_trans_map  chrysalis			       jellyfish.kmers.fa	     pipeliner.18881.cmds	       right.fa.ok
Trinity.timing		      inchworm.K25.L25.DS.fa	       jellyfish.kmers.fa.histo      read_partitions		       scaffolding_entries.sam
both.fa			      inchworm.K25.L25.DS.fa.finished  left.fa.ok		     recursive_trinity.cmds
both.fa.ok		      inchworm.kmer_count	       partitioned_reads.files.list  recursive_trinity.cmds.completed

Now let’s copy the assembled sequence and transcripts, Trinity.fasta*, in the current directory:

$ singularity exec --overlay my_overlay library://ubuntu:18.04 bash -c 'cp -p /trinity_out_dir/Trinity.fasta* ./'

Note how we’re wrapping the copy command within bash -c; this is to defer the evaluation of the * wildcard to when the container runs the command.

We’ve run the entire workflow within the OverlayFS, and got only the two relevant output files out in the host filesystem!

$ ls -l Trinity.fasta*

-rw-r--r-- 1 ubuntu ubuntu 171507 Nov  4 05:49 Trinity.fasta
-rw-r--r-- 1 ubuntu ubuntu   2818 Nov  4 05:49 Trinity.fasta.gene_trans_map

Ephemeral writable containers

In some situations, you might need your container to be writable not to store persistent output files, but just to write temporary service files.
E.g. this can happen with applications that want to write a dot-file in your home, such as a Python package, or containerised Jupyter notebooks that need to write runtime information under /run.
In this context, a persistent overlay filesystem might require more work than is desired. There are alternative, simpler ways to set this up.

Singularity has a flag for rendering containers from SIF image files ephemerally writable. --writable-tmpfs will allocate a small amount of RAM for this purpose (configured by the sys admins, by default just a bunch of MB), e.g.:

$ singularity exec --writable-tmpfs library://ubuntu:18.04 touch ~/write-to-home

Unless $HOME is bind mounted to the container (for security reasons it shouldn’t be), the newly created file will be gone after the container exits:

$ ls ~/write-to-home

ls: /home/ubuntu/write-to-home: No such file or directory

There are situations where --writable-tmpfs is not usable, in particular if you are trying to write to a directory owned by root, such as /run.
In this case, the solution is to create a host directory and bind mount it as the path you need to write into, e.g.:

$ mkdir ~/my_run
$ singularity exec -B ~/my_run:/run library://ubuntu:18.04 touch /run/running-file

In this case, the file will also persist in the host directory after the container exits.

Key Points

• Use linux tool from a Ubuntu container to create a filesystem image file

• Mount a filesystem image using the flag --overlay

• Make a SIF container ephemerally writable with the flag --writable-tmpfs