nf-core/configs: fub_curta
Freie Universität Berlin HPC cluster (Curta) profile
Freie Universiät Berlin High-Performance Computer (Curta) Configuration
*NB:* In order to run pipelines using this HPC cluster, you must first apply for access here.
This profile is configured to run with Singularity version 1.1.9-1.el7, which is pre-loaded and globally available to all users on the cluster.
Nextflow should be loaded before use. Nextflow version 22.10.6.5844 is installed. The following should be added to your sbatch/SLURM script:
module load Nextflow
Using -profile fub_curta will download fub_curta.config, which has been pre-configured with a setup suitable for the Curta cluster.
Additional Profiles
A profile for deactivating the cleanup of intermediate files is also offered.
debug
This simply turns off automatic clean up of intermediate files, which can be useful for debugging. It is specified with -profile fub_curta,debug.
Publications
If computing time on Curta has contributed to a publication or the completion of a degree course, please send us the corresponding DOI or BibTeX entry and, if possible, an appropriate image to hpc@zedat.fu-berlin.de. This is the ONLY way we can document the usefulness of our service.
The current list of publications is available here.
Please also acknowledge the use of our service in any publications you produce, using the following reporting guidelines, including the DOI 10.17169/refubium-26754.
Acknowledgments
This configuration was refined with Dr. Loris Bennett's help @tardigradus of the HPC Team from the FUB ZEDAT's Scientific Computing Unit.
Config file
// Config profile metadata
params {
config_profile_name = 'FUB Curta'
config_profile_description = 'Freie Universität Berlin HPC cluster (Curta) profile'
config_profile_contact = 'hpc@zedat.fu-berlin.de'
config_profile_url = 'https://www.fu-berlin.de/en/sites/high-performance-computing/index.html'
max_memory = 93.GB
max_time = 14.d
max_cpus = 32
}
// Slurm configuration parameters
process {
scratch = true
executor = 'slurm'
clusterOptions = '--qos=standard'
maxRetries = 2
}
// Singularity parameters
singularity {
enabled = true
autoMounts = true
}
cleanup = true
executor
contact
