Computerome 2.0 Configuration
To use, run the pipeline with -profile computerome. This will download and launch the computerome.config which has been pre-configured with a setup suitable for the Computerome cluster.
Using the Computerome config profile
Before running the pipeline you will need to load Nextflow using the environment module system (this can be done with e.g. module load tools Nextflow/<VERSION> where VERSION is e.g. 20.10).
To use, run the pipeline with -profile computerome (one hyphen).
This will download and launch the computerome.config which has been pre-configured with a setup suitable for the Computerome servers.
It will enable Nextflow to manage the pipeline jobs via the Torque job scheduler.
Using this profile, Singularity image(s) containing required software(s) will be downloaded before execution of the pipeline.
Recent version of Nextflow also support the environment variable NXF_SINGULARITY_CACHEDIR which can be used to supply images. The computerome configuration uses your project’s scratch folder as the cachedir if not specified.
In addition to this config profile, you will also need to specify a Computerome project id.
You can do this with the --project flag (two hyphens) when launching Nextflow.
For example:
# Launch a nf-core pipeline with the computerome profile for the project id ab00002
$ nextflow run nf-core/<PIPELINE> -profile computerome --project ab00002 [...]NB: If you’re not sure what your Computerome project ID is, try running
groups.
Remember to use -bg to launch Nextflow in the background, so that the pipeline doesn’t exit if you leave your terminal session.
Alternatively, you can also launch Nextflow in a screen or a tmux session.
About Computerome 2.0
The Danish National Supercomputer for Life Sciences (a.k.a. Computerome) is installed at the DTU National Lifescience Center at Technical University of Denmark.
The computer hardware is funded with grants from Technical University of Denmark (DTU), University of Copenhagen (KU) and Danish e-infrastructure Cooperation (DeiC) - also, it is the official Danish ELIXIR Node.
Computerome 1.0 was opened in November 2014 at #121 on TOP500 Supercomputing Sites.
The current setup, Computerome 2.0, was opened in 2019. It’s compute resources consists of 31760 CPU cores with 210 TeraBytes of memory, connected to 17 PetaBytes of High-performance storage,
Config file
//Profile config names for nf-core/configs
params {
config_profile_description = 'Computerome 2.0 cluster profile provided by nf-core/configs.'
config_profile_contact = 'Marc Trunjer Kusk Nielsen (@marcmtk)'
config_profile_url = 'https://www.computerome.dk/'
project = null
cache_dir = "/home/projects/${params.project}/scratch"
schema_ignore_params = "project,cache_dir,genomes,modules"
validationSchemaIgnoreParams = "project,cache_dir,genomes,modules,schema_ignore_params"
//Thin nodes with 192GB and Fat nodes with ~1500GB. Torque should be allowed to handle this
max_memory = 1500.GB
max_cpus = 40
//There is no max walltime on the cluster, but a week seems sensible if not directly specified
max_time = 168.h
}
singularity {
enabled = true
autoMounts = true
cacheDir = params.cache_dir
}
process {
resourceLimits = [
memory: 1500.GB,
cpus: 40,
time: 168.h
]
beforeScript = "module load tools singularity/3.8.0; export _JAVA_OPTIONS=-Djava.io.tmpdir=${params.cache_dir}"
executor = 'pbs'
queueSize = 2000
clusterOptions = "-A ${params.project} -W group_list=${params.project}"
}
executor
contact
