Merge release-5-0 into master

[alexxy/gromacs.git] / src / programs / mdrun / runner.c

diff --git a/src/programs/mdrun/runner.c b/src/programs/mdrun/runner.c
index bf6fd312e787196968de98aefe4dd1b863af4a1d..d023c6b026ca523a9a98d8a16a159e2a062e3a00 100644 (file)
--- a/src/programs/mdrun/runner.c
+++ b/src/programs/mdrun/runner.c
@@ -37,17 +37,16 @@
 #ifdef HAVE_CONFIG_H
 #include <config.h>
 #endif
+
+#include <assert.h>
 #include <signal.h>
 #include <stdlib.h>
+#include <string.h>
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif
-#include <string.h>
-#include <assert.h>
 
 #include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
 #include "copyrite.h"
 #include "force.h"
 #include "mdrun.h"
@@ -73,22 +72,24 @@
 #include "gmx_detect_hardware.h"
 #include "gmx_omp_nthreads.h"
 #include "gromacs/gmxpreprocess/calc_verletbuf.h"
-#include "gmx_fatal_collective.h"
 #include "membed.h"
 #include "macros.h"
 #include "gmx_thread_affinity.h"
 #include "inputrec.h"
+#include "main.h"
 
+#include "gromacs/essentialdynamics/edsam.h"
 #include "gromacs/fileio/tpxio.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/mdlib/nbnxn_search.h"
 #include "gromacs/mdlib/nbnxn_consts.h"
-#include "gromacs/timing/wallcycle.h"
-#include "gromacs/utility/gmxmpi.h"
-#include "gromacs/utility/gmxomp.h"
-#include "gromacs/swap/swapcoords.h"
-#include "gromacs/essentialdynamics/edsam.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"
 #include "gromacs/pulling/pull_rotation.h"
+#include "gromacs/swap/swapcoords.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
 
 #ifdef GMX_FAHCORE
 #include "corewrap.h"
@@ -1212,29 +1213,14 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
         }
     }
 
-    /* Check for externally set OpenMP affinity and turn off internal
-     * pinning if any is found. We need to do this check early to tell
-     * thread-MPI whether it should do pinning when spawning threads.
-     * TODO: the above no longer holds, we should move these checks down
-     */
-    gmx_omp_check_thread_affinity(fplog, cr, hw_opt);
-
     /* Check and update the hardware options for internal consistency */
     check_and_update_hw_opt_1(hw_opt, SIMMASTER(cr));
 
+    /* Early check for externally set process affinity. */
+    gmx_check_thread_affinity_set(fplog, cr,
+                                  hw_opt, hwinfo->nthreads_hw_avail, FALSE);
     if (SIMMASTER(cr))
     {
-#ifdef GMX_THREAD_MPI
-        /* Early check for externally set process affinity.
-         * With thread-MPI this is needed as pinning might get turned off,
-         * which needs to be known before starting thread-MPI.
-         * With thread-MPI hw_opt is processed here on the master rank
-         * and passed to the other ranks later, so we only do this on master.
-         */
-        gmx_check_thread_affinity_set(fplog,
-                                      NULL,
-                                      hw_opt, hwinfo->nthreads_hw_avail, FALSE);
-#endif
 
 #ifdef GMX_THREAD_MPI
         if (cr->npmenodes > 0 && hw_opt->nthreads_tmpi <= 0)