#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
-#ifdef __linux
+#if defined(HAVE_SCHED_H) && (defined(HAVE_SCHED_GETAFFINITY) || defined(HAVE_SCHED_SETAFFINITY))
#define _GNU_SOURCE
#include <sched.h>
#include <sys/syscall.h>
gmx_mtop_remove_chargegroups(mtop);
}
+/* Check the process affinity mask and if it is found to be non-zero,
+ * will honor it and disable mdrun internal affinity setting.
+ * This function should be called first before the OpenMP library gets
+ * initialized with the last argument FALSE (which will detect affinity
+ * set by external tools like taskset), and later, after the OpenMP
+ * initialization, with the last argument TRUE to detect affinity changes
+ * made by the OpenMP library.
+ *
+ * Note that this will only work on Linux as we use a GNU feature. */
+static void check_cpu_affinity_set(FILE *fplog, const t_commrec *cr,
+ gmx_hw_opt_t *hw_opt, int ncpus,
+ gmx_bool bAfterOpenmpInit)
+{
+#ifdef HAVE_SCHED_GETAFFINITY
+ cpu_set_t mask_current;
+ int i, ret, cpu_count, cpu_set;
+ gmx_bool bAllSet;
+
+ assert(hw_opt);
+ if (!hw_opt->bThreadPinning)
+ {
+ /* internal affinity setting is off, don't bother checking process affinity */
+ return;
+ }
+
+ CPU_ZERO(&mask_current);
+ if ((ret = sched_getaffinity(0, sizeof(cpu_set_t), &mask_current)) != 0)
+ {
+ /* failed to query affinity mask, will just return */
+ if (debug)
+ {
+ fprintf(debug, "Failed to query affinity mask (error %d)", ret);
+ }
+ return;
+ }
+
+ /* Before proceeding with the actual check, make sure that the number of
+ * detected CPUs is >= the CPUs in the current set. */
+ if (ncpus < CPU_COUNT(&mask_current))
+ {
+ if (debug)
+ {
+ fprintf(debug, "%d CPUs detected, but %d was returned by CPU_COUNT",
+ ncpus, CPU_COUNT(&mask_current));
+ }
+ return;
+ }
+
+ bAllSet = TRUE;
+ for (i = 0; (i < ncpus && i < CPU_SETSIZE); i++)
+ {
+ bAllSet = bAllSet && (CPU_ISSET(i, &mask_current) != 0);
+ }
+
+ if (!bAllSet)
+ {
+ if (!bAfterOpenmpInit)
+ {
+ md_print_warn(cr, fplog,
+ "Non-default process affinity set, disabling internal affinity");
+ }
+ else
+ {
+ md_print_warn(cr, fplog,
+ "Non-default process affinity set probably by the OpenMP library, "
+ "disabling internal affinity");
+ }
+ hw_opt->bThreadPinning = FALSE;
+
+ if (debug)
+ {
+ fprintf(debug, "Non-default affinity mask found\n");
+ }
+ }
+ else
+ {
+ if (debug)
+ {
+ fprintf(debug, "Default affinity mask found\n");
+ }
+ }
+#endif /* HAVE_SCHED_GETAFFINITY */
+}
/* Set CPU affinity. Can be important for performance.
On some systems (e.g. Cray) CPU Affinity is set by default.
#endif
#ifdef GMX_OPENMP /* TODO: actually we could do this even without OpenMP?! */
-#ifdef __linux /* TODO: only linux? why not everywhere if sched_setaffinity is available */
+#ifdef HAVE_SCHED_SETAFFINITY
if (hw_opt->bThreadPinning)
{
int thread, nthread_local, nthread_node, nthread_hw_max, nphyscore;
sched_setaffinity((pid_t) syscall (SYS_gettid), sizeof(cpu_set_t), &mask);
}
}
-#endif /* __linux */
+#endif /* HAVE_SCHED_SETAFFINITY */
#endif /* GMX_OPENMP */
}
cr->npmenodes = 0;
}
+ /* 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.
+ */
+ gmx_omp_check_thread_affinity(fplog, cr, hw_opt);
+
#ifdef GMX_THREAD_MPI
/* With thread-MPI inputrec is only set here on the master thread */
if (SIMMASTER(cr))
{
check_and_update_hw_opt(hw_opt,minf.cutoff_scheme);
+#ifdef GMX_THREAD_MPI
+ /* Early check for externally set process affinity. Can't do over all
+ * MPI processes because hwinfo is not available everywhere, but with
+ * thread-MPI it's needed as pinning might get turned off which needs
+ * to be known before starting thread-MPI. */
+ check_cpu_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)
{
}
}
- /* 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.
- */
- gmx_omp_check_thread_affinity(fplog, cr, hw_opt);
-
#ifdef GMX_THREAD_MPI
if (SIMMASTER(cr))
{
gmx_detect_hardware(fplog, hwinfo, cr,
bForceUseGPU, bTryUseGPU, hw_opt->gpu_id);
}
+
+ /* Now do the affinity check with MPI/no-MPI (done earlier with thread-MPI). */
+ check_cpu_affinity_set(fplog, cr,
+ hw_opt, hwinfo->nthreads_hw_avail, FALSE);
#endif
/* now make sure the state is initialized and propagated */
snew(pmedata,1);
}
+ /* Before setting affinity, check whether the affinity has changed
+ * - which indicates that probably the OpenMP library has changed it since
+ * we first checked). */
+ check_cpu_affinity_set(fplog, cr, hw_opt, hwinfo->nthreads_hw_avail, TRUE);
+
/* Set the CPU affinity */
set_cpu_affinity(fplog,cr,hw_opt,nthreads_pme,hwinfo,inputrec);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff