From e48d8f7a62a03b783185fcdb4906fd9d063f9c89 Mon Sep 17 00:00:00 2001
From: Calvin <calvin@EESI>
Date: Thu, 13 Jun 2013 14:51:15 -0400
Subject: use readdir and #omp critical
---
src/c/multifasta_to_otu.c | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
(limited to 'src')
diff --git a/src/c/multifasta_to_otu.c b/src/c/multifasta_to_otu.c
index 6d704dd..62d9222 100644
--- a/src/c/multifasta_to_otu.c
+++ b/src/c/multifasta_to_otu.c
@@ -208,12 +208,10 @@ int main(int argc, char **argv) {
exit(EXIT_FAILURE);
}
- struct dirent result;
-
omp_set_num_threads(jobs);
long done = 0;
printf("Beginning to process samples\n");
-#pragma omp parallel for shared(solutions, sequences, width, result, done)
+ #pragma omp parallel for shared(solutions, sequences, width, done)
for(long i = 0; i < dir_count; i++ ) {
long z = 0;
@@ -225,16 +223,18 @@ int main(int argc, char **argv) {
exit(EXIT_FAILURE);
}
-#pragma omp critical
- readdir_r(input_directory_dh, &result, &directory_entry);
+ #pragma omp critical
+ {
+ directory_entry = readdir(input_directory_dh);
+ strcpy(base_filename, directory_entry->d_name);
+ }
- if(strcmp(directory_entry->d_name, "..") == 0 || strcmp(directory_entry->d_name, ".") == 0) {
+ if(strcmp(base_filename, "..") == 0 || strcmp(base_filename, ".") == 0) {
i--;
continue;
}
// get our base filenames
- strcpy(base_filename, directory_entry->d_name);
filenames[i] = base_filename;
// get our real filename
--
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