Commit 5c50e5b3 authored by Celine Mercier's avatar Celine Mercier

Embryo of code for openMP parallelization of LCS alignment but

deactivated for now because can't make it compile with cython/clang
parent 9c71b061
......@@ -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.")
......
......@@ -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)
......
......@@ -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);
/**
......
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