Move _GNU_SOURCE to gmxpre.h

[alexxy/gromacs.git] / src / gromacs / gmxlib / gmx_thread_affinity.c

diff --git a/src/gromacs/gmxlib/gmx_thread_affinity.c b/src/gromacs/gmxlib/gmx_thread_affinity.c
index 8c35b8e7f022c85c5f9e26a4f9e7860d3acec6d1..75e277999be1fcef991d5d14a30d2456a8449214 100644 (file)
--- a/src/gromacs/gmxlib/gmx_thread_affinity.c
+++ b/src/gromacs/gmxlib/gmx_thread_affinity.c
@@ -32,31 +32,33 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-#if defined(HAVE_SCHED_H) && defined(HAVE_SCHED_GETAFFINITY)
-#define _GNU_SOURCE
-#include <sched.h>
-#include <sys/syscall.h>
-#endif
-#include <string.h>
-#include <errno.h>
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/gmx_thread_affinity.h"
+
+#include "config.h"
+
 #include <assert.h>
+#include <errno.h>
 #include <stdio.h>
+#include <string.h>
 
-#include "thread_mpi/threads.h"
+#ifdef HAVE_SCHED_AFFINITY
+#  include <sched.h>
+#  include <sys/syscall.h>
+#endif
 
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "types/hw_info.h"
-#include "copyrite.h"
-#include "gmx_cpuid.h"
-#include "gmx_omp_nthreads.h"
-#include "md_logging.h"
-#include "gmx_thread_affinity.h"
-#include "network.h"
+#include "thread_mpi/threads.h"
 
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/gmx_cpuid.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/hw_info.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxomp.h"
 #include "gromacs/utility/smalloc.h"
@@ -238,7 +240,8 @@ gmx_set_thread_affinity(FILE                *fplog,
          */
         MPI_Comm comm_intra;
 
-        MPI_Comm_split(MPI_COMM_WORLD, gmx_hostname_num(), cr->rank_intranode,
+        MPI_Comm_split(MPI_COMM_WORLD,
+                       gmx_physicalnode_id_hash(), cr->rank_intranode,
                        &comm_intra);
         MPI_Scan(&nthread_local, &thread0_id_node, 1, MPI_INT, MPI_SUM, comm_intra);
         /* MPI_Scan is inclusive, but here we need exclusive */
@@ -373,10 +376,10 @@ void
 gmx_check_thread_affinity_set(FILE            *fplog,
                               const t_commrec *cr,
                               gmx_hw_opt_t    *hw_opt,
-                              int  gmx_unused  ncpus,
+                              int  gmx_unused  nthreads_hw_avail,
                               gmx_bool         bAfterOpenmpInit)
 {
-#ifdef HAVE_SCHED_GETAFFINITY
+#ifdef HAVE_SCHED_AFFINITY
     cpu_set_t mask_current;
     int       i, ret, cpu_count, cpu_set;
     gmx_bool  bAllSet;
@@ -438,19 +441,19 @@ gmx_check_thread_affinity_set(FILE            *fplog,
      * detected CPUs is >= the CPUs in the current set.
      * We need to check for CPU_COUNT as it was added only in glibc 2.6. */
 #ifdef CPU_COUNT
-    if (ncpus < CPU_COUNT(&mask_current))
+    if (nthreads_hw_avail < CPU_COUNT(&mask_current))
     {
         if (debug)
         {
-            fprintf(debug, "%d CPUs detected, but %d was returned by CPU_COUNT",
-                    ncpus, CPU_COUNT(&mask_current));
+            fprintf(debug, "%d hardware threads detected, but %d was returned by CPU_COUNT",
+                    nthreads_hw_avail, CPU_COUNT(&mask_current));
         }
         return;
     }
 #endif /* CPU_COUNT */
 
     bAllSet = TRUE;
-    for (i = 0; (i < ncpus && i < CPU_SETSIZE); i++)
+    for (i = 0; (i < nthreads_hw_avail && i < CPU_SETSIZE); i++)
     {
         bAllSet = bAllSet && (CPU_ISSET(i, &mask_current) != 0);
     }
@@ -495,5 +498,5 @@ gmx_check_thread_affinity_set(FILE            *fplog,
             fprintf(debug, "Default affinity mask found\n");
         }
     }
-#endif /* HAVE_SCHED_GETAFFINITY */
+#endif /* HAVE_SCHED_AFFINITY */
 }