Pawsey Nimbus Cloud Configuration
nf-core pipelines have been successfully run on the Nimbus cloud at Pawsey Supercomputing Centre.
Currently profiles for various instance flavours, Singularity, and Docker are supported. This config has been developed for the ‘Pawsey Bio - Ubuntu 22.04 - 2023-03’ image. Instructions for setting up your instance with an image are here. Nextflow (v22.10.6), Singularity (v3.8.7), and Docker (v20.10.16) are pre-installed on the ‘Pawsey Bio - Ubuntu 22.04 - 2023-03’ image.
Profiles
Specifying instance flavour
Profiles for various standard instance flavours are available in this config. Please select a profile based on the flavour (i.e. CPUs, and RAM it has access to):
- c2r8: 2 CPU cores, 8 Gb RAM
- c4r16: 4 CPU cores, 16 Gb RAM
- c8r32: 8 CPU cores, 32 Gb RAM
- c16r64: 16 CPU cores, 64 Gb RAM
For example, to run the nimbus profile on the c2r8 flavour with Singularity, specify:
-profile pawsey_nimbus,singularity,c2r8Specifying container management tool
Profiles for both Singularity and Docker are available. To run the nimbus profile with Singularity, specify:
-profile pawsey_nimbus,singularityTo run the nimbus profile with Docker, specify:
-profile pawsey_nimbus,dockerRecommendations
Pawsey recommend storing cached nf-core container images on your attached external data volume. By default your Singularity cache directory will be /home/ubuntu/singularity. You can override this using the NXF_SINGULARITY_CACHEDIR= environmental variable to change the default cache directory.
Config file
// profile for Nimbus cloud at Pawsey
params {
config_profile_description = 'Pawsey Nimbus cloud profile'
config_profile_contact = '@marcodelapierre & @SarahBeecroft'
config_profile_url = 'https://support.pawsey.org.au/documentation/display/US/Nimbus+for+Bioinformatics'
}
process {
cache = 'lenient'
}
profiles {
// To use singularity, use nextflow run -profile pawsey_nimbus,singularity
singularity {
singularity {
enabled = true
autoMounts = true
}
}
// To use docker, use nextflow run -profile pawsey_nimbus,docker
docker {
docker {
enabled = true
}
}
c2r8 {
params {
max_cpus = 2
max_memory = '6.GB'
}
process {
resourceLimits = [
memory: 6.GB,
cpus: 2
]
}
}
c4r16 {
params {
max_cpus = 4
max_memory = '14.GB'
}
process {
resourceLimits = [
memory: 14.GB,
cpus: 4
]
}
}
c8r32 {
params {
max_cpus = 8
max_memory = '30.GB'
}
process {
resourceLimits = [
memory: 30.GB,
cpus: 8
]
}
}
c16r64 {
params {
max_cpus = 16
max_memory = '62.GB'
}
process {
resourceLimits = [
memory: 62.GB,
cpus: 16
]
}
}
}
contact
