From 5c50e5b378a3240ce8ea07ef1fa2d4fce80eea79 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Tue, 20 Dec 2016 11:46:58 +0100
Subject: [PATCH] Embryo of code for openMP parallelization of LCS alignment
 but deactivated for now because can't make it compile with cython/clang

---
 python/obitools3/commands/lcs.pyx | 18 ++++++++++++++----
 src/obi_align.c                   | 12 +++++++++++-
 src/obi_align.h                   |  3 ++-
 3 files changed, 27 insertions(+), 6 deletions(-)

diff --git a/python/obitools3/commands/lcs.pyx b/python/obitools3/commands/lcs.pyx
index 8a8bea9..1591fd8 100644
--- a/python/obitools3/commands/lcs.pyx
+++ b/python/obitools3/commands/lcs.pyx
@@ -147,6 +147,13 @@ def addOptions(parser):
                        default=False,
                        help="Sequence counts are written in the output view. Default: they are not written.")
 
+    group.add_argument('--thread-count','-p',   # TODO should probably be in a specific option group
+                       action="store", dest="align:threadcount",
+                       metavar='<THREAD COUNT>',
+                       default=1,
+                       type=int,
+                       help="Number of threads to use for the computation. Default: one.")
+
 
 cpdef align(str dms_n, 
             str input_view_1_n, str output_view_n,
@@ -157,7 +164,8 @@ cpdef align(str dms_n,
             double threshold=0.0, bint normalize=True, 
             int reference=0, bint similarity_mode=True,
             bint print_seq=False, bint print_count=False,
-            comments="") :
+            comments="",
+            int thread_count=1) :
                  
     cdef OBIDMS d         
     d = OBIDMS(dms_n)
@@ -172,7 +180,8 @@ cpdef align(str dms_n,
                                     str2bytes(comments), \
                                     print_seq, \
                                     print_count, \
-                                    threshold, normalize, reference, similarity_mode) < 0 :
+                                    threshold, normalize, reference, similarity_mode,
+                                    thread_count) < 0 :
             raise Exception("Error aligning sequences")
     else :
         if obi_lcs_align_two_columns(d._pointer, \
@@ -216,8 +225,9 @@ def run(config):
           similarity_mode  = config['align']['similarity'],  \
           print_seq        = config['align']['printseq'],  \
           print_count      = config['align']['printcount'], \
-          comments         = comments)
-      
+          comments         = comments, \
+          thread_count     = config['align']['threadcount'])
+
     print("Done.")
 
     
diff --git a/src/obi_align.c b/src/obi_align.c
index 97f6d4c..3fa3678 100644
--- a/src/obi_align.c
+++ b/src/obi_align.c
@@ -9,6 +9,10 @@
  * @brief Functions handling LCS sequence alignments.
  */
 
+//#define OMP_SUPPORT // TODO
+#ifdef OMP_SUPPORT
+#include <omp.h>
+#endif
 
 #include <stdlib.h>
 #include <stdio.h>
@@ -389,7 +393,8 @@ int obi_lcs_align_one_column(OBIDMS_p dms, const char* seq_view_name, const char
 							 const char* id_column_name,
 					         const char* output_view_name, const char* output_view_comments,
 							 bool print_seq, bool print_count,
-						     double threshold, bool normalize, int reference, bool similarity_mode)
+						     double threshold, bool normalize, int reference, bool similarity_mode,
+							 int thread_count)
 {
 	index_t         i, j, k;
 	index_t         seq_count;
@@ -537,6 +542,11 @@ int obi_lcs_align_one_column(OBIDMS_p dms, const char* seq_view_name, const char
 
 	seq_count = (seq_view->infos)->line_count;
 
+	#ifdef OMP_SUPPORT
+	omp_set_num_threads(thread_count);
+	#pragma omp parallel for
+	#endif
+
 	for (i=0; i < (seq_count - 1); i++)
 	{
 		if (i%100 == 0)
diff --git a/src/obi_align.h b/src/obi_align.h
index 68048bd..98da4da 100644
--- a/src/obi_align.h
+++ b/src/obi_align.h
@@ -92,7 +92,8 @@ int obi_lcs_align_one_column(OBIDMS_p dms,
 							 const char* id_column_name,
 					         const char* output_view_name, const char* output_view_comments,
 							 bool print_seq, bool print_count,
-						     double threshold, bool normalize, int reference, bool similarity_mode);
+						     double threshold, bool normalize, int reference, bool similarity_mode,
+							 int thread_count);
 
 
 /**