Singularity
Using Singularity containers on Sapelo2
The Sapelo2 cluster has the ability to run Singularity containers. Singularity containers are docker like containers that are HPC friendly.
Loading Singularity
Singularity is installed on all compute nodes on Sapelo2. In order to access that executables you have to load the Singularity module.
$ module load Singularity
$ singularity --help
USAGE: singularity [global options...] <command> [command options...] ...
GLOBAL OPTIONS:
-d|--debug Print debugging information
-h|--help Display usage summary
-s|--silent Only print errors
-q|--quiet Suppress all normal output
--version Show application version
-v|--verbose Increase verbosity +1
-x|--sh-debug Print shell wrapper debugging information
GENERAL COMMANDS:
help Show additional help for a command or container
selftest Run some self tests for singularity install
CONTAINER USAGE COMMANDS:
exec Execute a command within container
run Launch a runscript within container
shell Run a Bourne shell within container
test Launch a testscript within container
CONTAINER MANAGEMENT COMMANDS:
apps List available apps within a container
bootstrap *Deprecated* use build instead
build Build a new Singularity container
check Perform container lint checks
inspect Display container's metadata
mount Mount a Singularity container image
pull Pull a Singularity/Docker container to $PWD
COMMAND GROUPS:
image Container image command group
instance Persistent instance command group
CONTAINER USAGE OPTIONS:
see singularity help <command>
For any additional help or support visit the Singularity
website: http://singularity.lbl.gov/
Using BioContainer containers
BioContainers is an open source and community-driven framework which provides system-agnostic executable environments for bioinformatics software. BioContainers framework allows software to be installed and executed under an isolated and controllable environment.
Blast container example
This example is based on the BioContainer example at http://biocontainers.pro/docs/101/running-example/ webpage.
Pulling a container
In order to use a pre built container, one has to "pull" the container from the container registry. The command to pull a blast container from BioContainer docker registry is as below:
$ mkdir /home/raj76/test $ cd /home/raj76/test $ singularity pull docker://biocontainers/blast WARNING: pull for Docker Hub is not guaranteed to produce the WARNING: same image on repeated pull. Use Singularity Registry WARNING: (shub://) to pull exactly equivalent images. Docker image path: index.docker.io/biocontainers/blast:latest Cache folder set to /home/raj76/.singularity/docker [1/1] |===================================| 100.0% Importing: base Singularity environment Importing: /home/raj76/.singularity/docker/sha256:660c48dd555dcbfdfe19c80a30f557ac57a15f595250e67bfad1e5663c1725bb.tar.gz Importing: /home/raj76/.singularity/docker/sha256:4c7380416e7816a5ab1f840482c9c3ca8de58c6f3ee7f95e55ad299abbfe599f.tar.gz Importing: /home/raj76/.singularity/docker/sha256:421e436b5f80d876128b74139531693be9b4e59e4f1081c9a3c379c95094e375.tar.gz Importing: /home/raj76/.singularity/docker/sha256:e4ce6c3651b3a090bb43688f512f687ea6e3e533132bcbc4a83fb97e7046cea3.tar.gz Importing: /home/raj76/.singularity/docker/sha256:be588e74bd348ce48bb7161350f4b9d783c331f37a853a80b0b4abc0a33c569e.tar.gz Importing: /home/raj76/.singularity/docker/sha256:7513e23e94e042f38785a66fba7302331c39e92491ea8057a6d0ec2094fda7c0.tar.gz Importing: /home/raj76/.singularity/docker/sha256:1f1169998bd08c33903c56348ad438f90e69d517d0507b7fba7432decee61eb8.tar.gz Importing: /home/raj76/.singularity/docker/sha256:3c20a4bba592a988108453b44eefbd6fe2022151542b9883221b658145311681.tar.gz Importing: /home/raj76/.singularity/docker/sha256:9bfd0812e2d6aae116904d6c301511ef441b26e766811bcb82528941b416ed1b.tar.gz Importing: /home/raj76/.singularity/docker/sha256:1c6ae521538275a62e5e949c49ca7ca611477d8638df15b6c6ab83b76d01da2f.tar.gz Importing: /home/raj76/.singularity/docker/sha256:7d1b4609c9a59e46ac2c106aa79b4707bd905526df25288f595d90bf01b6e26c.tar.gz Importing: /home/raj76/.singularity/docker/sha256:a8022c247944f5c801b34c391e19aa1792d20b3d55d6a55821cf757c0df43e80.tar.gz Importing: /home/raj76/.singularity/docker/sha256:10c8f0ff4e5a382068d7480f76ce323b131721ae960b880c64ba94f6c856c77a.tar.gz Importing: /home/raj76/.singularity/docker/sha256:a8823f25a74a25d2943097ead4b7a90fc1dadcdd40dce298097ea52fc617981e.tar.gz Importing: /home/raj76/.singularity/docker/sha256:aedae76aecd1555418bdb6d202c3464aebad9c44d366533218fb21b883570d2a.tar.gz Importing: /home/raj76/.singularity/docker/sha256:f3124b62dbfe35c1349d0c38f1df851c0e536a00f15d085e53e3031eff2a94a5.tar.gz Importing: /home/raj76/.singularity/docker/sha256:d3f0d697543a6e83f259022cfa1b74e324b523a7e02057774df35751a5881bc2.tar.gz Importing: /home/raj76/.singularity/metadata/sha256:944beb8dfe363519e9e9ba35cc76ba618aa58d15d1ed941b6a9b0a74fef88746.tar.gz WARNING: Building container as an unprivileged user. If you run this container as root WARNING: it may be missing some functionality. Building Singularity image... Singularity container built: ./blast.simg Cleaning up... Done. Container is at: ./blast.simg $ ls blast.simg $
You now have a blast.simg image that can be used to run blast using Singularity.
Running Blast
$ singularity exec blast.simg blastp -help
This will print the help page for blastp tool. The command singularity exec blast.simg tells singularity that it is going to execute the command that follows inside the blast.simg container.
Downloading the example datasets
Let us download the example datasets to run blast.
$ wget http://www.uniprot.org/uniprot/P04156.fasta $ curl -O ftp://ftp.ncbi.nih.gov/refseq/D_rerio/mRNA_Prot/zebrafish.1.protein.faa.gz $ gunzip zebrafish.1.protein.faa.gz $ ls blast.simg P04156.fasta zebrafish.1.protein.faa
Preparing the database
We need to prepare the zebrafish database with makeblastdb for the search. Before we do that let's understand how to access the Sapelo2 file systems from inside the container. Execute the following command:
$ singularity exec blast.simg df -h Filesystem Size Used Avail Use% Mounted on OverlayFS 1.0M 0 1.0M 0% / /dev/mapper/vg00-lv.root 234G 7.8G 227G 4% /tmp devtmpfs 63G 0 63G 0% /dev tmpfs 63G 428M 63G 1% /dev/shm sn0.storage:/storage/xcluster/home/raj76 97G 24G 74G 25% /home/raj76 tmpfs 16M 8.0K 16M 1% /etc/group
You will see in the output above that my home directory (/home/raj76) is mounted and accessible from inside the container. By default, Singularity mounts the users home directory inside the container. It will also let us mount other directories inside the container.
$ singularity exec -B /db -B /lustre1 -B /lscratch blast.simg df -h Filesystem Size Used Avail Use% Mounted on OverlayFS 1.0M 0 1.0M 0% / /dev/mapper/vg00-lv.root 20G 7.3G 13G 37% /tmp devtmpfs 32G 0 32G 0% /dev tmpfs 32G 0 32G 0% /dev/shm sn0.storage:/storage/xcluster/home/raj76 97G 24G 74G 25% /home/raj76 sn0.storage:/storage/xcluster/db 27T 3.7T 23T 14% /db 10.55.49.1@o2ib:10.55.49.2@o2ib:/csx0009g 452T 361T 87T 81% /lustre1 /dev/mapper/vg00-lv.lscratch 869G 33M 869G 1% /lscratch tmpfs 16M 8.0K 16M 1% /etc/group
In the above example, the -B /db option to the exec command.