Merge pull request #88 from arnaudbore/enh_memory_gpu_processes

[WIP] Increase memory and cpu for eddy and local_tracking processes

main.nf

@@ -97,7 +97,8 @@ if(params.help) {
                 "processes_denoise_t1":"$params.processes_denoise_t1",
                 "processes_eddy":"$params.processes_eddy",
                 "processes_fodf":"$params.processes_fodf",
-                "processes_registration":"$params.processes_registration"]
+                "processes_registration":"$params.processes_registration",
+                "processes_local_tracking":"$params.processes_local_tracking"]
 
     engine = new groovy.text.SimpleTemplateEngine()
     template = engine.createTemplate(usage.text).make(bindings)
@@ -735,7 +736,7 @@ concatenated_dwi_for_eddy
     .set{dwi_gradients_mask_topup_files_for_eddy_topup}
 
 process Eddy_Topup {
-    cpus params.processes_eddy
+    cpus { params.processes_eddy * task.attempt }
     memory { 5.GB * task.attempt }
 
     input:
@@ -799,7 +800,8 @@ dwi_for_eddy
     .set{dwi_gradients_mask_topup_files_for_eddy}
 
 process Eddy {
-    cpus params.processes_eddy
+    cpus { params.processes_eddy * task.attempt }
+    memory { 5.GB * task.attempt }
 
     input:
     set sid, file(dwi), file(bval), file(bvec), file(mask), readout, encoding\
@@ -1879,7 +1881,8 @@ fodf_for_local_tracking
     .set{fodf_maps_for_local_tracking}
 
 process Local_Tracking {
-    cpus 2
+    cpus { params.processes_local_tracking * task.attempt }
+    memory { 5.GB * task.attempt }
 
     input:
     set sid, file(fodf), file(tracking_mask), file(seed)\

nextflow.config

@@ -146,9 +146,10 @@ params {
         processes_brain_extraction_t1=4
         processes_denoise_dwi=4
         processes_denoise_t1=4
-        processes_eddy=1
+        processes_eddy=4
         processes_fodf=4
         processes_registration=4
+        processes_local_tracking=4
 
     //**Tractoflow-ABS**//
         run_tractoflow_abs = false
@@ -189,6 +190,7 @@ if(params.processes) {
 }
 
 singularity.autoMounts = true
+singularity.runOptions = "--no-home"
 
 profiles {
 
@@ -207,6 +209,7 @@ profiles {
         params.processes_eddy=1
         params.processes_fodf=4
         params.processes_registration=1
+        params.processes_local_tracking=1
     }
 
     skip_preprocessing {