diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index d59e815..f6b86ab 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -30,6 +30,7 @@ jobs: - 'ccga_med' - 'cfc' - 'cfc_dev' + - 'computerome' - 'crick' - 'denbi_qbic' - 'ebc' diff --git a/README.md b/README.md index ae65bc2..7a40140 100644 --- a/README.md +++ b/README.md @@ -102,6 +102,7 @@ Currently documentation is available for the following systems: * [CCGA_DX](docs/ccga_dx.md) * [CCGA_MED](docs/ccga_med.md) * [CFC](docs/cfc.md) +* [Computerome](docs/computerome.md) * [CRICK](docs/crick.md) * [CZBIOHUB_AWS](docs/czbiohub.md) * [DENBI_QBIC](docs/denbi_qbic.md) diff --git a/conf/computerome.config b/conf/computerome.config new file mode 100644 index 0000000..1411127 --- /dev/null +++ b/conf/computerome.config @@ -0,0 +1,29 @@ +//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/$params.project/scratch" + schema_ignore_params = "project,cache_dir" + + //Thin nodes with 192GB and Fat nodes with ~1500GB. Torque should be allowed to handle this + max_memory = 1500.GB + max_cpus = 40 + + //There is no max walltime on the cluster, but a week seems sensible if not directly specified + max_time = 168.h +} + +singularity { + enabled = true + autoMounts = true + cacheDir = params.cache_dir +} + +process { + beforeScript = "module load tools singularity/3.8.0; export _JAVA_OPTIONS=-Djava.io.tmpdir=$params.cache_dir" + executor = 'pbs' + queueSize = 2000 + clusterOptions = "-A $params.project -W group_list=$params.project" +} diff --git a/docs/computerome.md b/docs/computerome.md new file mode 100644 index 0000000..b2e624f --- /dev/null +++ b/docs/computerome.md @@ -0,0 +1,38 @@ +# nf-core/configs: Computerome 2.0 Configuration + +To use, run the pipeline with `-profile computerome`. This will download and launch the [`computerome.config`](../conf/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/` 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`](../conf/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: + +```bash +# Launch a nf-core pipeline with the computerome profile for the project id ab00002 +$ nextflow run nf-core/ -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, diff --git a/nfcore_custom.config b/nfcore_custom.config index 978c65a..da46831 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -23,6 +23,7 @@ profiles { ccga_med { includeConfig "${params.custom_config_base}/conf/ccga_med.config" } cfc { includeConfig "${params.custom_config_base}/conf/cfc.config" } cfc_dev { includeConfig "${params.custom_config_base}/conf/cfc_dev.config" } + computerome { includeConfig "${params.custom_config_base}/conf/computerome.config" } crick { includeConfig "${params.custom_config_base}/conf/crick.config" } czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" } denbi_qbic { includeConfig "${params.custom_config_base}/conf/denbi_qbic.config" }