This is written for the arc4 cluster at the University of Leeds, but should be general enough to work in most SGE setups.
This profile configures Snakemake to run on (Sun) Grid Engine.
config.yamlcontains default arguments for the profilecluster.yamlcontains default options for grid engine’s qsub
Additional cluster options (including complex resources) can be given in a local yaml file using Snakemake’s --cluster-config flag. This also allows per-rule options. Example use cases would be when a certain rule needs to run in a certain queue or under a certain project or you want to use a complex resource which may not exist in other SGE configurations.
On Linux, place the files into ~/.config/snakemake/sge for snakemake to automatically find the profile.
To use the profile (i.e. to submit tasks as jobs on in an SGE queue) use:
snakemake --profile sge
To also use a local cluster.yaml file in your working directory use;
snakemake --profile sge --cluster-config cluster.yaml
The options are read and overwritten in the following order:
- Default options in
sge-submit.py - Default options in the profile’s
cluster.yamlfile - Resources specified for the rule in the Snakemake file
- Rule specific options in the profile’s
cluster.yamlfile - Default and rule specific options in the cluster config pass with
--cluster-config
To allow more expressive resource requests we map some simple names to the SGE options and resources. These can be used for example in cluster.yaml to make the configuration simpler to read.
| SGE Option | Accepted YAML key names |
|---|---|
| binding | binding |
| cwd | cwd, |
| e | e, error |
| hard | hard, |
| j | j, join |
| m | m, mail_options |
| M | M, email |
| notify | notify, |
| now | now, |
| N | N, name |
| o | o, output |
| P | P, project |
| p | p, priority |
| pe | pe, parallel_environment |
| pty | pty, |
| q | q, queue |
| R | R, reservation |
| r | r, rerun |
| soft | soft, |
| v | v, variable |
| V | V, export_env |
| qname | qname, |
| hostname | hostname, |
| calendar | calendar, |
| min_cpu_interval | min_cpu_interval, |
| tmpdir | tmpdir, |
| seq_no | seq_no, |
| s_rt | s_rt, soft_runtime, soft_walltime |
| h_rt | h_rt, time, runtime, walltime |
| s_cpu | s_cpu, soft_cpu |
| h_cpu | h_cpu, cpu |
| s_data | s_data, soft_data |
| h_data | h_data, data |
| s_stack | s_stack, soft_stack |
| h_stack | h_stack, stack |
| s_core | s_core, soft_core |
| h_core | h_core, core |
| s_rss | s_rss, soft_resident_set_size |
| h_rss | h_rss, resident_set_size |
| slots | slots, |
| s_vmem | s_vmem, soft_memory, soft_virtual_memory |
| h_vmem | h_vmem, mem, memory, virtual_memory |
| s_fsize | s_fsize, soft_file_size |
| h_fsize | h_fsize, file_size |
| nodes | nodes, np |
| coproc_v100 | coproc_v100, gpu |
| node_type | node_type |