Merge branch 'omp_bugfix' into dev

Conflicts:
	.gitignore
	iterate_edges.cpp

Author: voutcn

.gitignore

@@ -33,17 +33,4 @@ megahit_iter_k124
 megahit_iter_k61
 megahit_iter_k92
 sdbg_builder_cpu
-test/ecoli_ref-500k.fastq.gz
-test/ecoliMG1655.fa
-test/megahit_out/final.contigs.fa
-test/megahit_out/log
-test/megahit_out/tmp/k21.counting
-test/megahit_out/tmp/k21.final.contigs.fa
-test/megahit_out/tmp/k31.final.contigs.fa
-test/megahit_out/tmp/k41.final.contigs.fa
-test/megahit_out/tmp/k51.final.contigs.fa
-test/megahit_out/tmp/k61.final.contigs.fa
-test/megahit_out/tmp/k71.final.contigs.fa
-test/megahit_out/tmp/k81.final.contigs.fa
-test/megahit_out/tmp/k91.final.contigs.fa
-test/megahit_out/tmp/k99.final.contigs.fa
+test/*

iterate_edges.cpp

@@ -113,6 +113,12 @@ static void ParseOptions(int argc, char *argv[]) {
         if (options.num_cpu_threads == 0) {
             options.num_cpu_threads = omp_get_max_threads();
         }
+        // must set the number of threads before the parallel hash_map declared
+        if (options.num_cpu_threads > 1) {
+            omp_set_num_threads(options.num_cpu_threads - 1);
+        } else {
+            omp_set_num_threads(1);
+        }
     } catch (std::exception &e) {
         std::cerr << e.what() << std::endl;
         std::cerr << "Usage: " << argv[0] << " [options]" << std::endl;
@@ -254,10 +260,15 @@ static void ReadContigsAndBuildHash(IterateGlobalData &globals, bool is_addi_con
     }
 
     pthread_create(&input_thread, NULL, ReadContigsThread, &input_thread_data);
-    omp_set_num_threads(globals.num_cpu_threads - 1);
+    if (globals.num_cpu_threads == 1) {
+        pthread_join(input_thread, NULL);
+    }
 
     while (true) {
-        pthread_join(input_thread, NULL);
+        if (globals.num_cpu_threads > 1) {
+            pthread_join(input_thread, NULL);
+        }
+
         if (packages[input_thread_index].size() == 0) {
             break;
         }
@@ -267,6 +278,10 @@ static void ReadContigsAndBuildHash(IterateGlobalData &globals, bool is_addi_con
         pthread_create(&input_thread, NULL, ReadContigsThread, &input_thread_data);
         ContigPackage &cur_package = packages[input_thread_index ^ 1];
 
+        if (globals.num_cpu_threads == 1) {
+            pthread_join(input_thread, NULL);
+        }
+
         if (!is_addi_contigs) {
 #pragma omp parallel for
             for (unsigned i = 0; i < cur_package.size(); ++i) {
@@ -414,10 +429,16 @@ static void ReadReadsAndProcess(IterateGlobalData &globals) {
     pthread_create(&input_thread, NULL, ReadReadsThread, &input_thread_data);
     globals.iterative_edges.reserve(globals.crusial_kmers.size() * 10);
     AtomicBitVector is_aligned;
-    omp_set_num_threads(globals.num_cpu_threads - 1);
 
-    while (true) {
+    if (globals.num_cpu_threads == 1) {
         pthread_join(input_thread, NULL);
+    }
+
+    while (true) {
+        if (globals.num_cpu_threads > 1) {
+            pthread_join(input_thread, NULL);
+        }
+
         if (packages[input_thread_index].num_of_reads == 0) {
             break;
         }
@@ -428,6 +449,10 @@ static void ReadReadsAndProcess(IterateGlobalData &globals) {
         ReadPackage &cur_package = packages[input_thread_index ^ 1];
         is_aligned.reset(cur_package.num_of_reads);
 
+        if (globals.num_cpu_threads == 1) {
+            pthread_join(input_thread, NULL);
+        }
+
 #pragma omp parallel for
         for (unsigned i = 0; i < (unsigned)cur_package.num_of_reads; ++i) {
             int length = cur_package.length(i);

megahit

@@ -33,7 +33,7 @@ import multiprocessing
 from datetime import datetime, date, time
 
 usage_message = '''
-megahit version: 0.1.3
+megahit version: 0.1.3-bugfix2
 Copyright (c) The University of Hong Kong
 
 Usage:
@@ -191,6 +191,10 @@ def check_opt():
     if low_local_ratio <= 0 or low_local_ratio > 0.5:
         print >> sys.stderr, "low_local_ratio should be in (0, 0.5]."
         exit(1)
+    if num_cpu_threads > multiprocessing.cpu_count():
+        print >> sys.stderr, "Maximum number of available CPU thread is %d." % multiprocessing.cpu_count();
+        print >> sys.stderr, "Number of thread is reset to the %d." % multiprocessing.cpu_count();
+        num_cpu_threads = multiprocessing.cpu_count()
     if num_cpu_threads == 0:
         num_cpu_threads = multiprocessing.cpu_count()
     if num_cpu_threads <= 1:
@@ -579,7 +583,7 @@ def main(argv = None):
         check_bin()
 
         start_time = datetime.now()  
-        print >> sys.stderr, "MEGAHIT version 0.1.3"
+        print >> sys.stderr, "MEAGHIT v0.1.3-bugfix2"
         print >> sys.stderr, "[%s] Start assembly. Number of CPU threads %d." % (start_time.strftime("%c"), num_cpu_threads)
 
         make_out_dir()