Queues on the HPC¶

To see all available queues in the grid, run bqueues.

QUEUE_NAME      PRIO STATUS          MAX JL/U JL/P JL/H NJOBS  PEND   RUN  SUSP
inter            50  Open:Active       -    -    -    -     0     0     0     0
short            30  Open:Active       -    -    -    -     0     0     0     0
medium           20  Open:Active       -    -    -    -     0     0     0     0
long             10  Open:Active       -    -    -    -     0     0     0     0

Field	Definition
`QUEUE_NAME`	the name of the queue
`PRIO`	the priority of the queue, where higher numbers indicate more important
`STATUS`	if the queue is currently availabale
`MAX`	maximum job limit - this is not set so appears as `-`
`JL/U`	job limit per user - this is not set so appears as `-`
`JL/P`	job limit per processor - this is not set so appears as `-`
`JL/H`	job limit per host - this is not set so appears as `-`
`NJOBS`	total number of jobs currently in the queue
`PEND`	the number of pending jobs in the queue
`RUN`	the number of jobs currently running in the queue
`SUSP`	the numer of suspended jobs in the queue

The `inter` queue¶

The inter queue is for lightweight interactive or GUI tools.

You should use the inter queue when you want to use tools and act immediately upon the output. For example, if you're working with our aggregate VCF files, using bedtools to find the correct chunk, then bcftools to act upon then.

You should also use the inter queue to work with GUI coding tools such as jupyter or Rstudio.

For example, this will start a job on the inter queue, for the project code Bio, using bash.

bsub -q inter -P bio -Is bash

Jobs on the inter queue will keep going until you kill them, even if you close the terminal. You can have a maximum of five jobs running on the inter queue. When you have finished your work, you should kill your job:

bkill <job number>

Batch queues¶

Genomics England HPC batch queues are time based queues (short, medium, long). This means you need to submit the jobs to the queue that reflects the runtime of your job.

Queue name	Description
`short`	This queue is for jobs with maximum RUNTIME of four hours
`medium`	This queue is for jobs with maximum RUNTIME of 24 hours
`long`	This queue is for jobs with unlimited RUNTIME (default to seven days if not specified - or specify the limit as `-W [hours:]minutes` )

We recommend using a script to submit jobs to the batch queues.

Choosing the right queue¶

This decision tree gives some examples of when you might choose which queue. However, every job is different, and in some cases you may need a longer queue than is recommended here.

Make sure include standard output and error files in your run command | -o <path_to/job.%J.out> -e <path_to/job.%J.err>.

If your job has failed, and the .out file states Job killed after reaching LSF run time limit, you should retry your job in a longer queue.

graph LR
  F([Type of job]) --> |interactive| G[interactive queue];
  F --> |batch| A([How many files?]);
  A --> |one| B[short queue];
  A --> |more than one| C([What type of files?]);
  C --> |BAM or CRAM| D[long queue];
  C --> |other| E[medium queue];
  classDef node fill:#FFC6E6,stroke:#FFC6E6,color:#2B2F3B;
  class A,B,C,D,E,F node;

Queues on the HPC¶

The inter queue¶

Batch queues¶

Choosing the right queue¶

The `inter` queue¶