Legacy SL6 container¶
The legacy container is a way to run applications that were available on our old cluster running Scientific Linux 6.2
The Singularity container /data/containers/sl6/sl6compute.img is available on
Apocrita and is essentially a replica of one of the old compute nodes.
Usage¶
To access a shell or run a script within the container, you will first need to
load the singularity module:
$ module load singularity $ singularity shell /data/containers/sl6/sl6compute.img Singularity~> cat /etc/redhat-release Scientific Linux release 6.2 (Carbon)
Using the module command inside the container will provide access to the
legacy applications. Data files on the cluster filesystem can still be accessed
and written from within the container.
Use qlogin for interactive sessions
Using singularity shell for interactive container sessions can be useful
for initial testing. As with other interactive tasks, these tests should be
performed within qlogin sessions, and not run directly on the login nodes
Singularity~> module avail samtools ---------------- /data/apps/environmentmodules/general ---------------- samtools/0.1.18 samtools/1.1 samtools/1.3.1(default) Singularity~> module load samtools Singularity~> samtools view -b -S -o genome_reads_aligned.bam genome_reads_aligned.sam
Support for parallel applications
While Singularity does allow multi-node parallel jobs with MPI, the legacy versions of MPI are too old to support it. Therefore, we have removed these packages from the container to reduce size and complexity.
Example jobs¶
When running batch jobs, the best approach is to combine all the commands to be
run in the container into a single file, and run it with the singularity
exec command.
Serial jobs¶
Create a file run_commands.sh with the commands that would have been run as a
job script in the legacy environment, making it executable with chmod +x run_commands.sh.
#!/bin/bash module load masurca masurca example.cfg ./assemble.sh
Then prepare your job script according to your resource requirements, to be
run in the usual way with qsub <jobscript>:
#!/bin/bash #$ -cwd #$ -j y #$ -pe smp 1 #$ -l h_rt=1:0:0 #$ -l h_vmem=1G module load singularity singularity exec /data/containers/sl6/sl6compute.img ./run_commands.sh