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sge

This profile configures Snakemake to run on (Sun) Grid Engine.

Setup

Deploy profile

To deploy this profile, run

mkdir -p ~/.config/snakemake
cd ~/.config/snakemake
cookiecutter https://github.com/Snakemake-Profiles/sge.git

Then, you can run Snakemake with

snakemake --profile sge ...

Cookiecutter options

  • profile_name : A name to address the profile via the --profile Snakemake option.
  • cluster_config : Path to a YAML or JSON configuration file analogues to the Snakemake --cluster-config option. This is also used to define custom resources on the SGE cluster.

Default snakemake arguments

Default arguments to snakemake maybe adjusted in the <profile path>/config.yaml file.

Cluster Files

Per rule configuration can be defined in a cluster file and passed in using --cluser-config. This is a yaml file where the key is the rule name followed by a list of SGE settings to add or override settings set in the profile. You can also add options to the __default__ config. NOTE that these are ADDED to the default and will be inheritted by any named rules.

An example local cluster config file (cluster.yaml) looks like:

__default__
	q: private.q
	
rule1:
	gpu:1
	
rule2:
	time: "4:0:0"

which will be used by specifying snakemake --profile sge --cluster-config cluster.yaml.

Parsing arguments to SGE (qsub)

Arguments are overridden in the following order, aliases are also defined and can be defined :

  1. QSUB_DEFAULTS in sge-submit.py
  2. Profile cluster_config file __default__ entries
  3. Snakefile threads and resources (time, mem)
  4. Profile cluster_config file entries
  5. --cluster-config parsed to Snakemake (deprecated since Snakemake 5.10)

Resource and option mapping

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.

Notes

Custom SGE resources can be specified in __resources__ only in the profile folder (i.e. any __resources__ in a local --cluster-config cluster.yaml will be ignored, but you can request the resources defined in the global profile). Custom resources are specified as a YAML dictionary where the key is the resource name as defined in SGE and the values are any aliases you want to use for this resource. The key will always be avaiable as a name even if you don't specifiy it as an alias. If a key already exists in the resource list the the aliases are just appended to that resource.

For example:

__resources__:
  coproc_v100: 
    - "gpu"
    - "nvidia_gpu"

Allows you to request with coproc_v100=1, gpu=1 or nvidia_gpu=1 in the cluster config files or snakemake rule resources all of which will actually set -l coproc_v100=1 for qsub.

Memory (s_vmem, h_vmem and aliases) must be given in megabytes (NOTE: this is to support snakemake version >= 7 which sets a default mem_mb resource. In older versions of the grid engine profile the memory was in gigabytes).

Custom SGE options can be specified in __options__ in the profile folder in the same way as resources.

For example:

__options__:
  jc: 
    - "jc"
    - "job_class"

A full list of the default supported SGE options and resource requests with their aliases is:

SGE Option Accepted aliases
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_mb, mem, memory, virtual_memory
s_fsize s_fsize, soft_file_size
h_fsize h_fsize, disk_mb, file_size

Non Requestable Resources

On some cluster configurations some resources may be non-requestable.