Merge pull request #7 from frheault/limit_executor

Copy executor routine from tractoflow
scilus · Apr 8, 2021 · 36b293b · 36b293b
2 parents 3573e08 + ef3928a
commit 36b293b
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diff --git a/USAGE b/USAGE
@@ -7,32 +7,34 @@ nextflow run main.nf --input ... [OPTIONAL_ARGUMENTS]
 
 DESCRIPTION
 
---input=/path/to/[root]              Root folder containing multiple subjects
-
-                                    [root]
-                                    ├── S1
-                                    │   ├── *fa.nii.gz
-                                    │   └── *tracking.trk
-                                    └── S2
-                                        └── *
-
---atlas_config                      Path to json config file
---atlas_anat                        Path to reference anatomy of the atlas
---atlas_directory                   Path of the folder containing all atlases
-
-NOTES
-
-OPTIONAL ARGUMENTS (current value)
---atlas_centroids                       Folder containing centroids (trk) for future tractometry (Must have the same filename as in the atlas_config)
-
---multi_parameters                      Number of executions for the multi-parameters ($multi_parameters)
---minimal_vote_ratio                    Percentage of the vote to obtain in order to be considered valid ($minimal_vote_ratio)
---wb_clustering_thr                     List of distance (mm) for QBx whole brain clustreing ($wb_clustering_thr)
---seeds                                 List of random seeds values for the rng ($seeds)
---outlier_alpha                         Remove spurious streamlines based on shape ($outlier_alpha)
-
---register_processes                    Number of processes for registration task ($register_processes).
---rbx_processes                         Number of processes for bundle recognition task ($rbx_processes).
+    --input=/path/to/[root]              Root folder containing multiple subjects
+
+                                        [root]
+                                        ├── S1
+                                        │   ├── *fa.nii.gz
+                                        │   └── *tracking.trk
+                                        └── S2
+                                            └── *
+
+    --atlas_config                      Path to json config file
+    --atlas_anat                        Path to reference anatomy of the atlas
+    --atlas_directory                   Path of the folder containing all atlases
+
+    NOTES
+
+    OPTIONAL ARGUMENTS (current value)
+    --atlas_centroids                       Folder containing centroids (trk) for future tractometry (Must have the same filename as in the atlas_config)
+
+    --multi_parameters                      Number of executions for the multi-parameters ($multi_parameters)
+    --minimal_vote_ratio                    Percentage of the vote to obtain in order to be considered valid ($minimal_vote_ratio)
+    --wb_clustering_thr                     List of distance (mm) for QBx whole brain clustreing ($wb_clustering_thr)
+    --seeds                                 List of random seeds values for the rng ($seeds)
+    --outlier_alpha                         Remove spurious streamlines based on shape ($outlier_alpha)
+
+    --register_processes                    Number of processes for registration task ($register_processes).
+    --rbx_processes                         Number of processes for bundle recognition task ($rbx_processes).
+    --processes                             The number of parallel processes to launch ($cpu_count).
+                                            Only affects the local scheduler.
 
 Use '-C config_file.config' to specify a non-default configuration file.
 The '-C config_file.config' must be inserted after the nextflow call

diff --git a/nextflow.config b/nextflow.config
@@ -28,6 +28,19 @@ params {
         params.rbx_memory_limit='8 GB'
 }
 
+if(params.processes) {
+    if(params.processes > Runtime.runtime.availableProcessors()) {
+        throw new RuntimeException("Number of processes higher than available CPUs.")
+    }
+    else if(params.processes < 1) {
+        throw new RuntimeException("When set, number of processes must be >= 1 " +
+                                   "and smaller or equal to the number of CPUs.")
+    }
+    else {
+        executor.$local.cpus = params.processes
+    }
+}
+
 singularity.autoMounts = true
 
 profiles {