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openmp on j loop (i loop probably better)

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This commit is contained in:
Celine Mercier
2019-05-24 16:51:04 +02:00
parent ed5bb70c80
commit a04588da31
2 changed files with 25 additions and 9 deletions
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2
python/obitools3/commands/clean.pyx
View File

@ -101,7 +101,7 @@ def run(config):
comments = View.print_config(config, "clean", command_line, input_dms_name=[i_dms_name], input_view_name=[i_view_name]) comments = View.print_config(config, "clean", command_line, input_dms_name=[i_dms_name], input_view_name=[i_view_name])
if obi_clean(tobytes(i_dms_name), tobytes(i_view_name), tobytes(config['clean']['sample-tag-name']), tobytes(o_view_name), comments, \ if obi_clean(tobytes(i_dms_name), tobytes(i_view_name), tobytes(config['clean']['sample-tag-name']), tobytes(o_view_name), comments, \
config['clean']['distance'], config['clean']['ratio'], config['clean']['heads-only'], 1) < 0: config['clean']['distance'], config['clean']['ratio'], config['clean']['heads-only'], -1) < 0:
raise Exception("Error running obiclean") raise Exception("Error running obiclean")
# If the input and output DMS are not the same, export result view to output DMS # If the input and output DMS are not the same, export result view to output DMS

32
src/obi_clean.c
View File

@ -9,8 +9,7 @@
* @brief Functions tagging a set of sequences for PCR/sequencing errors identification. * @brief Functions tagging a set of sequences for PCR/sequencing errors identification.
*/ */
//#define OMP_SUPPORT // TODO #ifdef _OPENMP
#ifdef OMP_SUPPORT
#include <omp.h> #include <omp.h>
#endif #endif
@ -209,6 +208,18 @@ int obi_clean(const char* dms_name,
int reference = 0; int reference = 0;
bool similarity_mode = false; bool similarity_mode = false;
bool stop = false;
int max_threads = 1;
#ifdef _OPENMP
max_threads = omp_get_max_threads();
if ((thread_count == -1) || (thread_count > max_threads)) // TODO doc
thread_count = max_threads;
omp_set_num_threads(4);
fprintf(stderr, "Running on %d thread(s)\n", thread_count);
#endif
// Open DMS // Open DMS
dms = obi_dms(dms_name); dms = obi_dms(dms_name);
if (dms == NULL) if (dms == NULL)
@ -414,7 +425,10 @@ int obi_clean(const char* dms_name,
s1_count = sample_count_array[i]; s1_count = sample_count_array[i];
//s1_count = obi_get_int_with_elt_idx_and_col_p_in_view(i_view, sample_column, i, sample); // slower //s1_count = obi_get_int_with_elt_idx_and_col_p_in_view(i_view, sample_column, i, sample); // slower
for (j=i+1; j < seq_count; j++) // TODO parallelize this loop? #pragma omp parallel for shared(i, seq_count, s1_count, sample, blob_array, sample_count_array, alignment_result_array, stop) \
private(j, blob2, s2_count, yes, no, above_threshold, ali_result, score)
for (j=i+1; j < seq_count; j++)
{ {
// Get second sequence // Get second sequence
blob2 = blob_array[j]; blob2 = blob_array[j];
@ -422,7 +436,7 @@ int obi_clean(const char* dms_name,
if (blob2 == NULL) if (blob2 == NULL)
{ {
obidebug(1, "\nError retrieving sequences to align"); obidebug(1, "\nError retrieving sequences to align");
return -1; stop = true;
} }
// Get count for this sample // Get count for this sample
@ -477,22 +491,22 @@ int obi_clean(const char* dms_name,
if (obi_get_char_with_elt_idx_and_col_p_in_view(o_view, status_column, i, sample) == 's') // seq can become head ONLY if it's a singleton if (obi_get_char_with_elt_idx_and_col_p_in_view(o_view, status_column, i, sample) == 's') // seq can become head ONLY if it's a singleton
{ {
if (obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, i, sample, 'h') < 0) if (obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, i, sample, 'h') < 0)
return -1; stop = true;
} }
// Otherwise it's an internal (do nothing) // Otherwise it's an internal (do nothing)
// Label other sequence as internal no matter what // Label other sequence as internal no matter what
if (obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, j, sample, 'i') < 0) if (obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, j, sample, 'i') < 0)
return -1; stop = true;
} }
else // Same thing but with sequences switched else // Same thing but with sequences switched
{ {
if (obi_get_char_with_elt_idx_and_col_p_in_view(o_view, status_column, j, sample) == 's') // seq can become head ONLY if it's a singleton if (obi_get_char_with_elt_idx_and_col_p_in_view(o_view, status_column, j, sample) == 's') // seq can become head ONLY if it's a singleton
{ {
if (obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, j, sample, 'h') < 0) if (obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, j, sample, 'h') < 0)
return -1; stop = true;
} }
if (obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, i, sample, 'i') < 0) if (obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, i, sample, 'i') < 0)
return -1; stop = true;
} }
} }
else if (no == 0) else if (no == 0)
@ -500,6 +514,8 @@ int obi_clean(const char* dms_name,
alignment_result_array[j] = 2; alignment_result_array[j] = 2;
} }
} }
if (stop)
return -1;
} }
// Reset ali result array to 0 // Reset ali result array to 0
memset(alignment_result_array, 0, seq_count); memset(alignment_result_array, 0, seq_count);