Merge pull request #1043 from jen-reeve/reannz_mahuika

Mahuika HPC config

Author: jfy133

.github/CODEOWNERS

@@ -11,3 +11,4 @@
 **/lrz_cm4** @nschan
 **/crg** @joseespinosa
 **/iris** @nikhil
+**/mahuika** @jen-reeve

.github/workflows/main.yml

@@ -129,6 +129,7 @@ jobs:
           - "lugh"
           - "m3c"
           - "maestro"
+          - "mahuika"
           - "mana"
           - "marjorie"
           - "lovelace"

conf/mahuika.config

@@ -0,0 +1,111 @@
+// Mahuika nf-core configuration profile
+params {
+    config_profile_description = 'Mahuika HPC profile provided by nf-core/configs'
+    config_profile_contact     = 'Jennifer Reeve (@jen-reeve)'
+    config_profile_url         = 'https://docs.nesi.org.nz'
+    max_cpus                   = 166
+    max_memory                 = 1024.GB
+    max_time                   = 504.h
+}
+
+env {
+    APPTAINER_TMPDIR="/home/${System.getenv('USER')}/.apptainer/tmp"
+    APPTAINER_CACHEDIR="/home/${System.getenv('USER')}/.apptainer/cache"
+}
+
+process {
+    resourceLimits = [
+        cpus: 166,
+        memory: 1.TB,
+        time: 504.h
+    ]
+    cache = 'lenient'
+    stageInMode = 'symlink'
+    executor = 'slurm'
+    queue = 'genoa,milan'
+    errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
+    maxRetries = 2
+
+    withLabel: 'process_gpu' {
+        clusterOptions = '--gpus-per-node 1'
+        containerOptions = '--nv'
+    }
+}
+
+executor {
+    queueSize = 999
+    submitRateLimit = '60 min'
+}
+
+// Enable use of Apptainer to run containers
+apptainer {
+    enabled = true
+    pullTimeout = '2h'
+    autoMounts = true
+}
+
+cleanup = true
+
+profiles {
+    debug {
+        cleanup = false
+    }
+
+    genoa {
+        process {
+            resourceLimits = [
+                cpus: 166,
+                memory: 1.TB,
+                time: 504.h
+            ]
+            cache = 'lenient'
+            stageInMode = 'symlink'
+            executor = 'slurm'
+            queue = 'genoa'
+            errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
+            maxRetries = 2
+
+            withLabel: 'process_gpu' {
+                clusterOptions = '--gpus-per-node 1'
+                containerOptions = '--nv'
+            }
+        }
+        params {
+            config_profile_description = 'Mahuika HPC genoa partition profile provided by nf-core/configs'
+            config_profile_contact     = 'Jennifer Reeve (@jen-reeve)'
+            config_profile_url         = 'https://docs.nesi.org.nz'
+            max_cpus                   = 166
+            max_memory                 = 1432.GB
+            max_time                   = 504.h
+        }
+    }
+
+    milan {
+        process {
+            resourceLimits = [
+                cpus: 166,
+                memory: 1.TB,
+                time: 504.h
+            ]
+            cache = 'lenient'
+            stageInMode = 'symlink'
+            executor = 'slurm'
+            queue = 'milan'
+            errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
+            maxRetries = 2
+
+            withLabel: 'process_gpu' {
+                clusterOptions = '--gpus-per-node 1'
+                containerOptions = '--nv'
+            }
+        }
+        params {
+            config_profile_description = 'Mahuika HPC milan partition profile provided by nf-core/configs'
+            config_profile_contact     = 'Jennifer Reeve (@jen-reeve)'
+            config_profile_url         = 'https://docs.nesi.org.nz'
+            max_cpus                   = 126
+            max_memory                 = 1024.GB
+            max_time                   = 504.h
+        }
+    }
+}

docs/mahuika.md

@@ -0,0 +1,42 @@
+# nf-core/configs: Mahuika HPC Configuration
+
+nf-core pipelines have been successfully run on the [Mahuika HPC](https://docs.nesi.org.nz/).
+
+To run an nf-core pipeline on Mahuika, run the pipeline with `-profile mahuika`. This will download and launch the [`mahuika.config`](../conf/mahuika.config) which has been pre-configured with a setup suitable for Mahuika. Using this profile, a Docker image containing all of the required software will be downloaded, and converted to an Apptainer image before execution of the pipeline.
+
+## Access to Mahuika
+
+Please be aware that you will need to have a user account and be a member of an active project on Mahuika in order to use this infrastructure. See documentation for details regarding [creating an account](https://docs.nesi.org.nz/Getting_Started/Creating_an_Account/) and [applying for a project](https://docs.nesi.org.nz/Getting_Started/Projects/Applying_for_a_New_Project/) on Mahuika.
+
+## Launch an nf-core pipeline on Mahuika
+
+### Prerequisites
+
+Before running the pipeline you will need to load Nextflow, which is a globally installed module on Mahuika. You can do this by running the commands below:
+
+```bash
+#See what versions are available
+module avail Nextflow
+#Load one of the versions
+module load Nextflow/<version>
+```
+
+### Execution command
+
+```bash
+module load Nextflow/<version>
+
+nextflow run <nf-core_pipeline>/main.nf \
+  -profile mahuika \
+  <additional flags>
+```
+
+### Specifying a partition
+
+By default the `mahuika` profile will use both the Genoa and Milan partitions.
+To specify a partition you can add its name as an additional profile.
+For example, to run exclusively on the Genoa partition `-profile mahuika,genoa`.
+
+### Additional information
+
+More information about running Nextflow on Mahuika can be found on the [Nextflow page in the documentation](https://docs.nesi.org.nz/Software/Available_Applications/Nextflow).

nfcore_custom.config

@@ -262,6 +262,9 @@ profiles {
     maestro {
         includeConfig "${params.custom_config_base}/conf/maestro.config"
     }
+    mahuika {
+        includeConfig "${params.custom_config_base}/conf/mahuika.config"
+    }
     mana {
         includeConfig "${params.custom_config_base}/conf/mana.config"
     }