From 8919958b4eefcf352558b4036416ff9ac075a36f Mon Sep 17 00:00:00 2001
From: arnaudbore <arnaud.bore@gmail.com>
Date: Fri, 3 Nov 2023 16:07:28 -0400
Subject: [PATCH] cuda to gpu profile

---
 USAGE           |  5 +++--
 main.nf         | 10 +++++++---
 nextflow.config |  2 +-
 3 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/USAGE b/USAGE
index 99c9392..5f67daa 100755
--- a/USAGE
+++ b/USAGE
@@ -194,11 +194,12 @@ OPTIONAL ARGUMENTS (current value)
 --processes                                 The number of parallel processes to launch ($cpu_count).
                                             Only affects the local scheduler.
 
-AVAILABLE PROFILES (using -profile option (e.g. -profile use_cuda,fully_reproducible))
+AVAILABLE PROFILES (using -profile option (e.g. -profile use_gpu,fully_reproducible))
 
 macos                                       When this profile is used, TractoFlow will modify a parameter (scratch) for MacOS users.
 
-use_cuda                                    When this profile is used, TractoFlow will use eddy_cuda for Eddy process.
+use_gpu                                     When this profile is used, TractoFlow will use eddy_cuda for Eddy process.
+                                            If local tracking is also enabled, Tractoflow will use the gpu implementation of scil_compute_local_tracking.py.
                                             This feature is available with NVidia GPUs only. Without this profile, TractoFlow will run eddy_openmp.
 
 fully_reproducible                          When this profile is used, all the parameters will be set to have 100% reproducible results.
diff --git a/main.nf b/main.nf
index 8cf9143..b4b0e7b 100644
--- a/main.nf
+++ b/main.nf
@@ -355,6 +355,10 @@ if (params.bids && workflow.profile.contains("ABS") && !params.fs){
     error "Error ~ --bids parameter cannot be run with Atlas Based Segmentation (ABS) profile"
 }
 
+if (workflow.profile.containes("use_gpu")){
+    warning ""
+}
+
 (dwi, gradients, t1, readout_encoding) = in_data
     .map{sid, rev_flag, bvals, bvecs, dwi, t1, readout, encoding -> [tuple(sid, rev_flag, dwi),
                                         tuple(sid, rev_flag, bvals, bvecs),
@@ -375,9 +379,9 @@ if (params.eddy_cmd == "eddy_cpu" && params.processes_eddy == 1 && params.run_ed
 number_rev_dwi
     .subscribe{a -> if (a>0)
     error "Error ~ You have some subjects with a reverse encoding DWI.\n" + 
-          "Eddy will take forever to run with this configuration. \nPlease add " +
-          "-profile use_cuda with a GPU environnement OR increase the number of processes " + 
-          "for this task (--processes_eddy) to be able to analyse this data."}
+          "Eddy will take forever to run with this configuration. \nPlease add " + 
+          "-profile use_gpu with a GPU environnement (GPU NVIDIA with cuda) OR increase the number " + 
+          "of processes for this task (--processes_eddy) to be able to analyse this data."}
 }
 
 if (!params.run_topup || !params.run_eddy){
diff --git a/nextflow.config b/nextflow.config
index 445d228..78dd4c7 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -192,7 +192,7 @@ singularity.autoMounts = true
 
 profiles {
 
-    use_cuda {
+    use_gpu {
         singularity.runOptions='--nv'
         docker.runOptions='--gpus all'
         params.eddy_cmd="eddy_cuda10.2"