1. preprocessCore
  2. Commit 0eaf45932825a365990fa83cd1c533b3f7e48692
Browse code

Getting stacksize values that do not conflict with openblas threads

With the introduction of the USE_TLS option in openblas 0.3.4, threads created by packages loading openblas libraries are affected by a glibc bug described here:

https://sourceware.org/bugzilla/show_bug.cgi?id=11787

The ongoing discussion in openblas:

https://github.com/xianyi/OpenBLAS/issues/1936

Example workarounds used by other projects that inspired this one:

https://github.com/rust-lang/rust/issues/6233
https://github.com/rust-lang/rust/pull/11885
https://bugs.openjdk.java.net/browse/JDK-8225498

Francisco D. Morón-Duran authored on 29/07/2019 14:02:51
Showing 4 changed files
src/R_subColSummarize.c
History View file @ 0eaf459
... ... 
@@ -54,6 +54,16 @@ struct loop_data{
54 54 
   int start_row;
55 55 
   int end_row;
56 56 
 };
57 
+
58 
+#ifdef __linux__
59 
+#include <features.h>
60 
+#ifdef __GLIBC__
61 
+#ifdef __GLIBC_PREREQ && __GLIBC_PREREQ(2, 15)
62 
+#define INFER_MIN_STACKSIZE 1
63 
+#endif
64 
+#endif
65 
+#endif
66 
+
57 67 
 #endif
58 68
59 69
... ... 
@@ -108,11 +118,17 @@ SEXP R_subColSummarize_avg_log(SEXP RMatrix, SEXP R_rowIndexList){
108 118 
   double chunk_size_d, chunk_tot_d;
109 119 
   char *nthreads;
110 120 
   pthread_attr_t attr;
121 
+  /* Initialize thread attribute */
122 
+  pthread_attr_init(&attr);
111 123 
   pthread_t *threads;
112 124 
   struct loop_data *args;
113 125 
   void *status;
114 126 
 #ifdef PTHREAD_STACK_MIN
115 
-  size_t stacksize = PTHREAD_STACK_MIN + 0x4000;
127 
+#ifdef INFER_MIN_STACKSIZE
128 
+  size_t stacksize = __pthread_get_minstack(&attr) + sysconf(_SC_PAGE_SIZE);
129 
+#else
130 
+  size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE);
131 
+#endif
116 132 
 #else
117 133 
   size_t stacksize = 0x8000;
118 134 
 #endif
... ... 
@@ -136,8 +152,7 @@ SEXP R_subColSummarize_avg_log(SEXP RMatrix, SEXP R_rowIndexList){
136 152 
   }
137 153 
   threads = (pthread_t *) Calloc(num_threads, pthread_t);
138 154
139 
-  /* Initialize and set thread detached attribute */
140 
-  pthread_attr_init(&attr);
155 
+  /* Set thread detached attribute */
141 156 
   pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
142 157 
   pthread_attr_setstacksize (&attr, stacksize);
143 158 
   /* this code works out how many threads to use and allocates ranges of subColumns to each thread */
... ... 
@@ -276,11 +291,17 @@ SEXP R_subColSummarize_log_avg(SEXP RMatrix, SEXP R_rowIndexList){
276 291 
   double chunk_size_d, chunk_tot_d;
277 292 
   char *nthreads;
278 293 
   pthread_attr_t attr;
294 
+  /* Initialize thread attribute */
295 
+  pthread_attr_init(&attr);
279 296 
   pthread_t *threads;
280 297 
   struct loop_data *args;
281 298 
   void *status;
282 299 
 #ifdef PTHREAD_STACK_MIN
283 
-  size_t stacksize = PTHREAD_STACK_MIN + 0x4000;
300 
+#ifdef INFER_MIN_STACKSIZE
301 
+  size_t stacksize = __pthread_get_minstack(&attr) + sysconf(_SC_PAGE_SIZE);
302 
+#else
303 
+  size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE);
304 
+#endif
284 305 
 #else
285 306 
   size_t stacksize = 0x8000;
286 307 
 #endif
... ... 
@@ -304,8 +325,7 @@ SEXP R_subColSummarize_log_avg(SEXP RMatrix, SEXP R_rowIndexList){
304 325 
   }
305 326 
   threads = (pthread_t *) Calloc(num_threads, pthread_t);
306 327
307 
-  /* Initialize and set thread detached attribute */
308 
-  pthread_attr_init(&attr);
328 
+  /* Set thread detached attribute */
309 329 
   pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
310 330 
   pthread_attr_setstacksize (&attr, stacksize);
311 331
... ... 
@@ -447,11 +467,17 @@ SEXP R_subColSummarize_avg(SEXP RMatrix, SEXP R_rowIndexList){
447 467 
   double chunk_size_d, chunk_tot_d;
448 468 
   char *nthreads;
449 469 
   pthread_attr_t attr;
470 
+  /* Initialize thread attribute */
471 
+  pthread_attr_init(&attr);
450 472 
   pthread_t *threads;
451 473 
   struct loop_data *args;
452 474 
   void *status;
453 475 
 #ifdef PTHREAD_STACK_MIN
454 
-  size_t stacksize = PTHREAD_STACK_MIN + 0x4000;
476 
+#ifdef INFER_MIN_STACKSIZE
477 
+  size_t stacksize = __pthread_get_minstack(&attr) + sysconf(_SC_PAGE_SIZE);
478 
+#else
479 
+  size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE);
480 
+#endif
455 481 
 #else
456 482 
   size_t stacksize = 0x8000;
457 483 
 #endif
... ... 
@@ -475,8 +501,7 @@ SEXP R_subColSummarize_avg(SEXP RMatrix, SEXP R_rowIndexList){
475 501 
   }
476 502 
   threads = (pthread_t *) Calloc(num_threads, pthread_t);
477 503
478 
-  /* Initialize and set thread detached attribute */
479 
-  pthread_attr_init(&attr);
504 
+  /* Set thread detached attribute */
480 505 
   pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
481 506 
   pthread_attr_setstacksize (&attr, stacksize);
482 507
... ... 
@@ -619,11 +644,17 @@ SEXP R_subColSummarize_biweight_log(SEXP RMatrix, SEXP R_rowIndexList){
619 644 
   double chunk_size_d, chunk_tot_d;
620 645 
   char *nthreads;
621 646 
   pthread_attr_t attr;
647 
+  /* Initialize thread attribute */
648 
+  pthread_attr_init(&attr);
622 649 
   pthread_t *threads;
623 650 
   struct loop_data *args;
624 651 
   void *status;
625 652 
 #ifdef PTHREAD_STACK_MIN
626 
-  size_t stacksize = PTHREAD_STACK_MIN + 0x4000;
653 
+#ifdef INFER_MIN_STACKSIZE
654 
+  size_t stacksize = __pthread_get_minstack(&attr) + sysconf(_SC_PAGE_SIZE);
655 
+#else
656 
+  size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE);
657 
+#endif
627 658 
 #else
628 659 
   size_t stacksize = 0x8000;
629 660 
 #endif
... ... 
@@ -648,8 +679,7 @@ SEXP R_subColSummarize_biweight_log(SEXP RMatrix, SEXP R_rowIndexList){
648 679 
   }
649 680 
   threads = (pthread_t *) Calloc(num_threads, pthread_t);
650 681
651 
-  /* Initialize and set thread detached attribute */
652 
-  pthread_attr_init(&attr);
682 
+  /* Set thread detached attribute */
653 683 
   pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
654 684 
   pthread_attr_setstacksize (&attr, stacksize);
655 685 
   /* this code works out how many threads to use and allocates ranges of subColumns to each thread */
... ... 
@@ -790,11 +820,17 @@ SEXP R_subColSummarize_biweight(SEXP RMatrix, SEXP R_rowIndexList){
790 820 
   double chunk_size_d, chunk_tot_d;
791 821 
   char *nthreads;
792 822 
   pthread_attr_t attr;
823 
+  /* Initialize thread attribute */
824 
+  pthread_attr_init(&attr);
793 825 
   pthread_t *threads;
794 826 
   struct loop_data *args;
795 827 
   void *status;
796 828 
 #ifdef PTHREAD_STACK_MIN
797 
-  size_t stacksize = PTHREAD_STACK_MIN + 0x4000;
829 
+#ifdef INFER_MIN_STACKSIZE
830 
+  size_t stacksize = __pthread_get_minstack(&attr) + sysconf(_SC_PAGE_SIZE);
831 
+#else
832 
+  size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE);
833 
+#endif
798 834 
 #else
799 835 
   size_t stacksize = 0x8000;
800 836 
 #endif
... ... 
@@ -818,8 +854,7 @@ SEXP R_subColSummarize_biweight(SEXP RMatrix, SEXP R_rowIndexList){
818 854 
   }
819 855 
   threads = (pthread_t *) Calloc(num_threads, pthread_t);
820 856
821 
-  /* Initialize and set thread detached attribute */
822 
-  pthread_attr_init(&attr);
857 
+  /* Set thread detached attribute */
823 858 
   pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
824 859 
   pthread_attr_setstacksize (&attr, stacksize);
825 860
... ... 
@@ -962,11 +997,17 @@ SEXP R_subColSummarize_median_log(SEXP RMatrix, SEXP R_rowIndexList){
962 997 
   double chunk_size_d, chunk_tot_d;
963 998 
   char *nthreads;
964 999 
   pthread_attr_t attr;
1000 
+  /* Initialize thread attribute */
1001 
+  pthread_attr_init(&attr);
965 1002 
   pthread_t *threads;
966 1003 
   struct loop_data *args;
967 1004 
   void *status;
968 1005 
 #ifdef PTHREAD_STACK_MIN
969 
-  size_t stacksize = PTHREAD_STACK_MIN + 0x4000;
1006 
+#ifdef INFER_MIN_STACKSIZE
1007 
+  size_t stacksize = __pthread_get_minstack(&attr) + sysconf(_SC_PAGE_SIZE);
1008 
+#else
1009 
+  size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE);
1010 
+#endif
970 1011 
 #else
971 1012 
   size_t stacksize = 0x8000;
972 1013 
 #endif
... ... 
@@ -990,8 +1031,7 @@ SEXP R_subColSummarize_median_log(SEXP RMatrix, SEXP R_rowIndexList){
990 1031 
   }
991 1032 
   threads = (pthread_t *) Calloc(num_threads, pthread_t);
992 1033
993 
-  /* Initialize and set thread detached attribute */
994 
-  pthread_attr_init(&attr);
1034 
+  /* Set thread detached attribute */
995 1035 
   pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
996 1036 
   pthread_attr_setstacksize (&attr, stacksize);
997 1037
... ... 
@@ -1132,11 +1172,17 @@ SEXP R_subColSummarize_log_median(SEXP RMatrix, SEXP R_rowIndexList){
1132 1172 
   double chunk_size_d, chunk_tot_d;
1133 1173 
   char *nthreads;
1134 1174 
   pthread_attr_t attr;
1175 
+  /* Initialize thread attribute */
1176 
+  pthread_attr_init(&attr);
1135 1177 
   pthread_t *threads;
1136 1178 
   struct loop_data *args;
1137 1179 
   void *status;
1138 1180 
 #ifdef PTHREAD_STACK_MIN
1139 
-  size_t stacksize = PTHREAD_STACK_MIN + 0x4000;
1181 
+#ifdef INFER_MIN_STACKSIZE
1182 
+  size_t stacksize = __pthread_get_minstack(&attr) + sysconf(_SC_PAGE_SIZE);
1183 
+#else
1184 
+  size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE);
1185 
+#endif
1140 1186 
 #else
1141 1187 
   size_t stacksize = 0x8000;
1142 1188 
 #endif
... ... 
@@ -1160,8 +1206,7 @@ SEXP R_subColSummarize_log_median(SEXP RMatrix, SEXP R_rowIndexList){
1160 1206 
   }
1161 1207 
   threads = (pthread_t *) Calloc(num_threads, pthread_t);
1162 1208
1163 
-  /* Initialize and set thread detached attribute */
1164 
-  pthread_attr_init(&attr);
1209 
+  /* Set thread detached attribute */
1165 1210 
   pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
1166 1211 
   pthread_attr_setstacksize (&attr, stacksize);
1167 1212
... ... 
@@ -1301,11 +1346,17 @@ SEXP R_subColSummarize_median(SEXP RMatrix, SEXP R_rowIndexList){
1301 1346 
   double chunk_size_d, chunk_tot_d;
1302 1347 
   char *nthreads;
1303 1348 
   pthread_attr_t attr;
1349 
+  /* Initialize thread attribute */
1350 
+  pthread_attr_init(&attr);
1304 1351 
   pthread_t *threads;
1305 1352 
   struct loop_data *args;
1306 1353 
   void *status;
1307 1354 
 #ifdef PTHREAD_STACK_MIN
1308 
-  size_t stacksize = PTHREAD_STACK_MIN + 0x4000;
1355 
+#ifdef INFER_MIN_STACKSIZE
1356 
+  size_t stacksize = __pthread_get_minstack(&attr) + sysconf(_SC_PAGE_SIZE);
1357 
+#else
1358 
+  size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE);
1359 
+#endif
1309 1360 
 #else
1310 1361 
   size_t stacksize = 0x8000;
1311 1362 
 #endif
... ... 
@@ -1329,8 +1380,7 @@ SEXP R_subColSummarize_median(SEXP RMatrix, SEXP R_rowIndexList){
1329 1380 
   }
1330 1381 
   threads = (pthread_t *) Calloc(num_threads, pthread_t);
1331 1382
1332 
-  /* Initialize and set thread detached attribute */
1333 
-  pthread_attr_init(&attr);
1383 
+  /* Set thread detached attribute */
1334 1384 
   pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
1335 1385 
   pthread_attr_setstacksize (&attr, stacksize);
1336 1386
... ... 
@@ -1475,11 +1525,17 @@ SEXP R_subColSummarize_medianpolish_log(SEXP RMatrix, SEXP R_rowIndexList){
1475 1525 
   double chunk_size_d, chunk_tot_d;
1476 1526 
   char *nthreads;
1477 1527 
   pthread_attr_t attr;
1528 
+  /* Initialize thread attribute */
1529 
+  pthread_attr_init(&attr);
1478 1530 
   pthread_t *threads;
1479 1531 
   struct loop_data *args;
1480 1532 
   void *status;
1481 1533 
 #ifdef PTHREAD_STACK_MIN
1482 
-  size_t stacksize = PTHREAD_STACK_MIN + 0x4000;
1534 
+#ifdef INFER_MIN_STACKSIZE
1535 
+  size_t stacksize = __pthread_get_minstack(&attr) + sysconf(_SC_PAGE_SIZE);
1536 
+#else
1537 
+  size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE);
1538 
+#endif
1483 1539 
 #else
1484 1540 
   size_t stacksize = 0x8000;
1485 1541 
 #endif
... ... 
@@ -1507,8 +1563,7 @@ SEXP R_subColSummarize_medianpolish_log(SEXP RMatrix, SEXP R_rowIndexList){
1507 1563 
   }
1508 1564 
   threads = (pthread_t *) Calloc(num_threads, pthread_t);
1509 1565
1510 
-  /* Initialize and set thread detached attribute */
1511 
-  pthread_attr_init(&attr);
1566 
+  /* Set thread detached attribute */
1512 1567 
   pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
1513 1568 
   pthread_attr_setstacksize (&attr, stacksize);
1514 1569
... ... 
@@ -1650,11 +1705,17 @@ SEXP R_subColSummarize_medianpolish(SEXP RMatrix, SEXP R_rowIndexList){
1650 1705 
   double chunk_size_d, chunk_tot_d;
1651 1706 
   char *nthreads;
1652 1707 
   pthread_attr_t attr;
1708 
+  /* Initialize thread attribute */
1709 
+  pthread_attr_init(&attr);
1653 1710 
   pthread_t *threads;
1654 1711 
   struct loop_data *args;
1655 1712 
   void *status;
1656 1713 
 #ifdef PTHREAD_STACK_MIN
1657 
-  size_t stacksize = PTHREAD_STACK_MIN + 0x4000;
1714 
+#ifdef INFER_MIN_STACKSIZE
1715 
+  size_t stacksize = __pthread_get_minstack(&attr) + sysconf(_SC_PAGE_SIZE);
1716 
+#else
1717 
+  size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE);
1718 
+#endif
1658 1719 
 #else
1659 1720 
   size_t stacksize = 0x8000;
1660 1721 
 #endif
... ... 
@@ -1678,8 +1739,7 @@ SEXP R_subColSummarize_medianpolish(SEXP RMatrix, SEXP R_rowIndexList){
1678 1739 
   }
1679 1740 
   threads = (pthread_t *) Calloc(num_threads, pthread_t);
1680 1741
1681 
-  /* Initialize and set thread detached attribute */
1682 
-  pthread_attr_init(&attr);
1742 
+  /* Set thread detached attribute */
1683 1743 
   pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
1684 1744 
   pthread_attr_setstacksize (&attr, stacksize);
1685 1745
src/R_subrcModel_interfaces.c
History View file @ 0eaf459
... ... 
@@ -51,6 +51,16 @@ struct loop_data{
51 51 
   int start_row;
52 52 
   int end_row;
53 53 
 };
54 
+
55 
+#ifdef __linux__
56 
+#include <features.h>
57 
+#ifdef __GLIBC__
58 
+#ifdef __GLIBC_PREREQ && __GLIBC_PREREQ(2, 15)
59 
+#define INFER_MIN_STACKSIZE 1
60 
+#endif
61 
+#endif
62 
+#endif
63 
+
54 64 
 #endif
55 65
56 66
... ... 
@@ -165,11 +175,17 @@ SEXP R_sub_rcModelSummarize_medianpolish(SEXP RMatrix, SEXP R_rowIndexList){
165 175 
   double chunk_size_d, chunk_tot_d;
166 176 
   char *nthreads;
167 177 
   pthread_attr_t attr;
178 
+  /* Initialize thread attribute */
179 
+  pthread_attr_init(&attr);
168 180 
   pthread_t *threads;
169 181 
   struct loop_data *args;
170 182 
   void *status;
171 183 
 #ifdef PTHREAD_STACK_MIN
172 
-  size_t stacksize = PTHREAD_STACK_MIN + 0x4000;
184 
+#ifdef INFER_MIN_STACKSIZE
185 
+  size_t stacksize = __pthread_get_minstack(&attr) + sysconf(_SC_PAGE_SIZE);
186 
+#else
187 
+  size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE);
188 
+#endif
173 189 
 #else
174 190 
   size_t stacksize = 0x8000;
175 191 
 #endif
... ... 
@@ -211,8 +227,7 @@ SEXP R_sub_rcModelSummarize_medianpolish(SEXP RMatrix, SEXP R_rowIndexList){
211 227 
   }
212 228 
   threads = (pthread_t *) Calloc(num_threads, pthread_t);
213 229
214 
-  /* Initialize and set thread detached attribute */
215 
-  pthread_attr_init(&attr);
230 
+  /* Set thread detached attribute */
216 231 
   pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
217 232 
   pthread_attr_setstacksize (&attr, stacksize);
218 233
... ... 
@@ -480,11 +495,17 @@ SEXP R_sub_rcModelSummarize_plm(SEXP RMatrix, SEXP R_rowIndexList, SEXP PsiCode,
480 495 
   double chunk_size_d, chunk_tot_d;
481 496 
   char *nthreads;
482 497 
   pthread_attr_t attr;
498 
+  /* Initialize thread attribute */
499 
+  pthread_attr_init(&attr);
483 500 
   pthread_t *threads;
484 501 
   struct loop_data *args;
485 502 
   void *status;
486 503 
 #ifdef PTHREAD_STACK_MIN
487 
-  size_t stacksize = PTHREAD_STACK_MIN + 0x4000;
504 
+#ifdef INFER_MIN_STACKSIZE
505 
+  size_t stacksize = __pthread_get_minstack(&attr) + sysconf(_SC_PAGE_SIZE);
506 
+#else
507 
+  size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE);
508 
+#endif
488 509 
 #else
489 510 
   size_t stacksize = 0x8000;
490 511 
 #endif
... ... 
@@ -532,8 +553,7 @@ SEXP R_sub_rcModelSummarize_plm(SEXP RMatrix, SEXP R_rowIndexList, SEXP PsiCode,
532 553 
   }
533 554 
   threads = (pthread_t *) Calloc(num_threads, pthread_t);
534 555
535 
-  /* Initialize and set thread detached attribute */
536 
-  pthread_attr_init(&attr);
556 
+  /* Set thread detached attribute */
537 557 
   pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
538 558 
   pthread_attr_setstacksize (&attr, stacksize);
539 559
src/qnorm.c
History View file @ 0eaf459
... ... 
@@ -110,6 +110,16 @@ struct loop_data{
110 110 
   int start_col;
111 111 
   int end_col;
112 112 
 };
113 
+
114 
+#ifdef __linux__
115 
+#include <features.h>
116 
+#ifdef __GLIBC__
117 
+#ifdef __GLIBC_PREREQ && __GLIBC_PREREQ(2, 15)
118 
+#define INFER_MIN_STACKSIZE 1
119 
+#endif
120 
+#endif
121 
+#endif
122 
+
113 123 
 #endif
114 124
115 125 
 /*****************************************************************************************************
... ... 
@@ -486,11 +496,17 @@ int qnorm_c_l(double *data, size_t rows, size_t cols){
486 496 
   double chunk_size_d, chunk_tot_d;
487 497 
   char *nthreads;
488 498 
   pthread_attr_t attr;
499 
+  /* Initialize thread attribute */
500 
+  pthread_attr_init(&attr);
489 501 
   pthread_t *threads;
490 502 
   struct loop_data *args;
491 503 
   void *status;
492 504 
 #ifdef PTHREAD_STACK_MIN
493 
-  size_t stacksize = PTHREAD_STACK_MIN + 0x4000;
505 
+#ifdef INFER_MIN_STACKSIZE
506 
+  size_t stacksize = __pthread_get_minstack(&attr);
507 
+#else
508 
+  size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE);
509 
+#endif
494 510 
 #else
495 511 
   size_t stacksize = 0x8000;
496 512 
 #endif
... ... 
@@ -510,8 +526,7 @@ int qnorm_c_l(double *data, size_t rows, size_t cols){
510 526 
   }
511 527 
   threads = (pthread_t *) Calloc(num_threads, pthread_t);
512 528
513 
-  /* Initialize and set thread detached attribute */
514 
-  pthread_attr_init(&attr);
529 
+  /* Set thread detached attribute */
515 530 
   pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
516 531 
   pthread_attr_setstacksize (&attr, stacksize);
517 532
... ... 
@@ -1597,11 +1612,17 @@ int qnorm_c_using_target_l(double *data, size_t rows, size_t cols, double *targe
1597 1612 
   double chunk_size_d, chunk_tot_d;
1598 1613 
   char *nthreads;
1599 1614 
   pthread_attr_t attr;
1615 
+  /* Initialize thread attribute */
1616 
+  pthread_attr_init(&attr);
1600 1617 
   pthread_t *threads;
1601 1618 
   struct loop_data *args;
1602 1619 
   void *status;
1603 1620 
 #ifdef PTHREAD_STACK_MIN
1604 
-  size_t stacksize = PTHREAD_STACK_MIN + 0x4000;
1621 
+#ifdef INFER_MIN_STACKSIZE
1622 
+  size_t stacksize = __pthread_get_minstack(&attr) + sysconf(_SC_PAGE_SIZE);
1623 
+#else
1624 
+  size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE);
1625 
+#endif
1605 1626 
 #else
1606 1627 
   size_t stacksize = 0x8000;
1607 1628 
 #endif
... ... 
@@ -1631,9 +1652,7 @@ int qnorm_c_using_target_l(double *data, size_t rows, size_t cols, double *targe
1631 1652 
   }
1632 1653 
   threads = (pthread_t *) Calloc(num_threads, pthread_t);
1633 1654
1634 
-  /* Initialize and set thread detached attribute */
1635 
-
1636 
-  pthread_attr_init(&attr);
1655 
+  /* Set thread detached attribute */
1637 1656 
   pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
1638 1657 
   pthread_attr_setstacksize (&attr, stacksize);
1639 1658
... ... 
@@ -1890,11 +1909,17 @@ int qnorm_c_determine_target_l(double *data, size_t rows, size_t cols, double *t
1890 1909 
   double chunk_size_d, chunk_tot_d;
1891 1910 
   char *nthreads;
1892 1911 
   pthread_attr_t attr;
1912 
+  /* Initialize thread attribute */
1913 
+  pthread_attr_init(&attr);
1893 1914 
   pthread_t *threads;
1894 1915 
   struct loop_data *args;
1895 1916 
   void *status;
1896 1917 
 #ifdef PTHREAD_STACK_MIN
1897 
-  size_t stacksize = PTHREAD_STACK_MIN + 0x4000;
1918 
+#ifdef INFER_MIN_STACKSIZE
1919 
+  size_t stacksize = __pthread_get_minstack(&attr) + sysconf(_SC_PAGE_SIZE);
1920 
+#else
1921 
+  size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE);
1922 
+#endif
1898 1923 
 #else
1899 1924 
   size_t stacksize = 0x8000;
1900 1925 
 #endif
... ... 
@@ -1910,8 +1935,7 @@ int qnorm_c_determine_target_l(double *data, size_t rows, size_t cols, double *t
1910 1935 
   }
1911 1936 
   threads = (pthread_t *) Calloc(num_threads, pthread_t);
1912 1937
1913 
-  /* Initialize and set thread detached attribute */
1914 
-  pthread_attr_init(&attr);
1938 
+  /* Set thread detached attribute */
1915 1939 
   pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
1916 1940 
   pthread_attr_setstacksize (&attr, stacksize);
1917 1941
... ... 
@@ -2484,11 +2508,17 @@ int qnorm_c_determine_target_via_subset_l(double *data, size_t rows, size_t cols
2484 2508 
   double chunk_size_d, chunk_tot_d;
2485 2509 
   char *nthreads;
2486 2510 
   pthread_attr_t attr;
2511 
+  /* Initialize thread attribute */
2512 
+  pthread_attr_init(&attr);
2487 2513 
   pthread_t *threads;
2488 2514 
   struct loop_data *args;
2489 2515 
   void *status;
2490 2516 
 #ifdef PTHREAD_STACK_MIN
2491 
-  size_t stacksize = PTHREAD_STACK_MIN + 0x4000;
2517 
+#ifdef INFER_MIN_STACKSIZE
2518 
+  size_t stacksize = __pthread_get_minstack(&attr) + sysconf(_SC_PAGE_SIZE);
2519 
+#else
2520 
+  size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE);
2521 
+#endif
2492 2522 
 #else
2493 2523 
   size_t stacksize = 0x8000;
2494 2524 
 #endif
... ... 
@@ -2504,8 +2534,7 @@ int qnorm_c_determine_target_via_subset_l(double *data, size_t rows, size_t cols
2504 2534 
   }
2505 2535 
   threads = (pthread_t *) Calloc(num_threads, pthread_t);
2506 2536
2507 
-  /* Initialize and set thread detached attribute */
2508 
-  pthread_attr_init(&attr);
2537 
+  /* Set thread detached attribute */
2509 2538 
   pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
2510 2539 
   pthread_attr_setstacksize (&attr, stacksize);
2511 2540
... ... 
@@ -2988,11 +3017,17 @@ int qnorm_c_using_target_via_subset_l(double *data, size_t rows, size_t cols, in
2988 3017 
   double chunk_size_d, chunk_tot_d;
2989 3018 
   char *nthreads;
2990 3019 
   pthread_attr_t attr;
3020 
+  /* Initialize thread attribute */
3021 
+  pthread_attr_init(&attr);
2991 3022 
   pthread_t *threads;
2992 3023 
   struct loop_data *args;
2993 3024 
   void *status;
2994 3025 
 #ifdef PTHREAD_STACK_MIN
2995 
-  size_t stacksize = PTHREAD_STACK_MIN + 0x4000;
3026 
+#ifdef INFER_MIN_STACKSIZE
3027 
+  size_t stacksize = __pthread_get_minstack(&attr) + sysconf(_SC_PAGE_SIZE);
3028 
+#else
3029 
+  size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE);
3030 
+#endif
2996 3031 
 #else
2997 3032 
   size_t stacksize = 0x8000;
2998 3033 
 #endif
... ... 
@@ -3022,9 +3057,7 @@ int qnorm_c_using_target_via_subset_l(double *data, size_t rows, size_t cols, in
3022 3057 
   }
3023 3058 
   threads = (pthread_t *) Calloc(num_threads, pthread_t);
3024 3059
3025 
-  /* Initialize and set thread detached attribute */
3026 
-
3027 
-  pthread_attr_init(&attr);
3060 
+  /* Set thread detached attribute */
3028 3061 
   pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
3029 3062 
   pthread_attr_setstacksize (&attr, stacksize);
3030 3063
src/rma_background4.c
History View file @ 0eaf459
... ... 
@@ -58,6 +58,16 @@ struct loop_data{
58 58 
   size_t start_col;
59 59 
   size_t end_col;
60 60 
 };
61 
+
62 
+#ifdef __linux__
63 
+#include <features.h>
64 
+#ifdef __GLIBC__
65 
+#ifdef __GLIBC_PREREQ &&  __GLIBC_PREREQ(2, 15)
66 
+#define INFER_MIN_STACKSIZE 1
67 
+#endif
68 
+#endif
69 
+#endif
70 
+
61 71 
 #endif
62 72
63 73
... ... 
@@ -347,11 +357,17 @@ void rma_bg_correct(double *PM, size_t rows, size_t cols){
347 357 
   double chunk_size_d, chunk_tot_d;
348 358 
   char *nthreads;
349 359 
   pthread_attr_t attr;
360 
+  /* Initialize thread attribute */
361 
+  pthread_attr_init(&attr);
350 362 
   pthread_t *threads;
351 363 
   struct loop_data *args;
352 364 
   void *status;
353 365 
 #ifdef PTHREAD_STACK_MIN
354 
-  size_t stacksize = PTHREAD_STACK_MIN + 0x4000;
366 
+#ifdef INFER_MIN_STACKSIZE
367 
+  size_t stacksize = __pthread_get_minstack(&attr) + sysconf(_SC_PAGE_SIZE);
368 
+#else
369 
+  size_t stacksize = PTHREAD_STACK_MIN + sysconf(_SC_PAGE_SIZE);
370 
+#endif
355 371 
 #else
356 372 
   size_t stacksize = 0x8000;
357 373 
 #endif
... ... 
@@ -369,8 +385,7 @@ void rma_bg_correct(double *PM, size_t rows, size_t cols){
369 385 
   }
370 386 
   threads = (pthread_t *) Calloc(num_threads, pthread_t);
371 387
372 
-  /* Initialize and set thread detached attribute */
373 
-  pthread_attr_init(&attr);
388 
+  /* Set thread detached attribute */
374 389 
   pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
375 390 
   pthread_attr_setstacksize (&attr, stacksize);
376 391 
   /* this code works out how many threads to use and allocates ranges of columns to each thread */