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39 #ifdef HAVE_SCHED_AFFINITY
41 # define _GNU_SOURCE 1
44 # include <sys/syscall.h>
47 #include "gromacs/legacyheaders/gmx_thread_affinity.h"
54 #include "thread_mpi/threads.h"
56 #include "gromacs/legacyheaders/copyrite.h"
57 #include "gromacs/legacyheaders/gmx_cpuid.h"
58 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
59 #include "gromacs/legacyheaders/md_logging.h"
60 #include "gromacs/legacyheaders/typedefs.h"
61 #include "gromacs/legacyheaders/types/commrec.h"
62 #include "gromacs/legacyheaders/types/hw_info.h"
63 #include "gromacs/utility/basenetwork.h"
64 #include "gromacs/utility/cstringutil.h"
65 #include "gromacs/utility/fatalerror.h"
66 #include "gromacs/utility/gmxomp.h"
67 #include "gromacs/utility/smalloc.h"
70 get_thread_affinity_layout(FILE *fplog,
72 const gmx_hw_info_t * hwinfo,
74 int pin_offset, int * pin_stride,
75 const int **locality_order)
77 int nhwthreads, npkg, ncores, nhwthreads_per_core, rc;
80 const int * hwthread_id;
81 gmx_bool bPickPinStride;
85 gmx_fatal(FARGS, "Negative thread pinning offset requested");
89 gmx_fatal(FARGS, "Negative thread pinning stride requested");
92 rc = gmx_cpuid_topology(hwinfo->cpuid_info, &nhwthreads, &npkg, &ncores,
94 &pkg_id, &core_id, &hwthread_id, locality_order);
98 /* topology information not available or invalid, ignore it */
99 nhwthreads = hwinfo->nthreads_hw_avail;
100 *locality_order = NULL;
104 /* We don't know anything about the hardware, don't pin */
105 md_print_warn(cr, fplog,
106 "NOTE: We don't know how many logical cores we have, will not pin threads");
112 if (nthreads > nhwthreads)
114 /* We are oversubscribing, don't pin */
115 md_print_warn(NULL, fplog,
116 "WARNING: Oversubscribing the CPU, will not pin threads");
121 if (pin_offset + nthreads > nhwthreads)
123 /* We are oversubscribing, don't pin */
124 md_print_warn(NULL, fplog,
125 "WARNING: The requested pin offset is too large for the available logical cores,\n"
126 " will not pin threads");
132 /* do we need to choose the pinning stride? */
133 bPickPinStride = (*pin_stride == 0);
137 if (rc == 0 && pin_offset + nthreads*nhwthreads_per_core <= nhwthreads)
139 /* Put one thread on each physical core */
140 *pin_stride = nhwthreads_per_core;
144 /* We don't know if we have SMT, and if we do, we don't know
145 * if hw threads in the same physical core are consecutive.
146 * Without SMT the pinning layout should not matter too much.
147 * so we assume a consecutive layout and maximally spread out"
148 * the threads at equal threads per core.
149 * Note that IBM is the major non-x86 case with cpuid support
150 * and probably threads are already pinned by the queuing system,
151 * so we wouldn't end up here in the first place.
153 *pin_stride = (nhwthreads - pin_offset)/nthreads;
158 /* Check the placement of the thread with the largest index to make sure
159 * that the offset & stride doesn't cause pinning beyond the last hardware thread. */
160 if (pin_offset + (nthreads-1)*(*pin_stride) >= nhwthreads)
162 /* We are oversubscribing, don't pin */
163 md_print_warn(NULL, fplog,
164 "WARNING: The requested pinning stride is too large for the available logical cores,\n"
165 " will not pin threads");
173 fprintf(fplog, "Pinning threads with a%s logical core stride of %d\n",
174 bPickPinStride ? "n auto-selected" : " user-specified",
181 /* Set CPU affinity. Can be important for performance.
182 On some systems (e.g. Cray) CPU Affinity is set by default.
183 But default assigning doesn't work (well) with only some ranks
184 having threads. This causes very low performance.
185 External tools have cumbersome syntax for setting affinity
186 in the case that only some ranks have threads.
187 Thus it is important that GROMACS sets the affinity internally
188 if only PME is using threads.
191 gmx_set_thread_affinity(FILE *fplog,
193 gmx_hw_opt_t *hw_opt,
194 const gmx_hw_info_t *hwinfo)
196 int nth_affinity_set, thread0_id_node,
197 nthread_local, nthread_node, nthread_hw_max, nphyscore;
199 const int *locality_order;
202 if (hw_opt->thread_affinity == threadaffOFF)
208 /* If the tMPI thread affinity setting is not supported encourage the user
209 * to report it as it's either a bug or an exotic platform which we might
210 * want to support. */
211 if (tMPI_Thread_setaffinity_support() != TMPI_SETAFFINITY_SUPPORT_YES)
213 /* we know Mac OS doesn't support setting thread affinity, so there's
214 no point in warning the user in that case. In any other case
215 the user might be able to do something about it. */
217 md_print_warn(NULL, fplog,
218 "Can not set thread affinities on the current platform. On NUMA systems this\n"
219 "can cause performance degradation. If you think your platform should support\n"
220 "setting affinities, contact the GROMACS developers.");
221 #endif /* __APPLE__ */
225 /* threads on this MPI process or TMPI thread */
226 if (cr->duty & DUTY_PP)
228 nthread_local = gmx_omp_nthreads_get(emntNonbonded);
232 nthread_local = gmx_omp_nthreads_get(emntPME);
235 /* map the current process to cores */
237 nthread_node = nthread_local;
239 if (PAR(cr) || MULTISIM(cr))
241 /* We need to determine a scan of the thread counts in this
246 MPI_Comm_split(MPI_COMM_WORLD,
247 gmx_physicalnode_id_hash(), cr->rank_intranode,
249 MPI_Scan(&nthread_local, &thread0_id_node, 1, MPI_INT, MPI_SUM, comm_intra);
250 /* MPI_Scan is inclusive, but here we need exclusive */
251 thread0_id_node -= nthread_local;
252 /* Get the total number of threads on this physical node */
253 MPI_Allreduce(&nthread_local, &nthread_node, 1, MPI_INT, MPI_SUM, comm_intra);
254 MPI_Comm_free(&comm_intra);
258 if (hw_opt->thread_affinity == threadaffAUTO &&
259 nthread_node != hwinfo->nthreads_hw_avail)
261 if (nthread_node > 1 && nthread_node < hwinfo->nthreads_hw_avail)
263 md_print_warn(cr, fplog,
264 "NOTE: The number of threads is not equal to the number of (logical) cores\n"
265 " and the -pin option is set to auto: will not pin thread to cores.\n"
266 " This can lead to significant performance degradation.\n"
267 " Consider using -pin on (and -pinoffset in case you run multiple jobs).\n");
274 if (hw_opt->core_pinning_offset != 0)
276 offset = hw_opt->core_pinning_offset;
277 md_print_info(cr, fplog, "Applying core pinning offset %d\n", offset);
280 rc = get_thread_affinity_layout(fplog, cr, hwinfo,
282 offset, &hw_opt->core_pinning_stride,
287 /* Incompatible layout, don't pin, warning was already issued */
291 /* Set the per-thread affinity. In order to be able to check the success
292 * of affinity settings, we will set nth_affinity_set to 1 on threads
293 * where the affinity setting succeded and to 0 where it failed.
294 * Reducing these 0/1 values over the threads will give the total number
295 * of threads on which we succeeded.
297 nth_affinity_set = 0;
298 #pragma omp parallel num_threads(nthread_local) reduction(+:nth_affinity_set)
300 int thread_id, thread_id_node;
302 gmx_bool setaffinity_ret;
304 thread_id = gmx_omp_get_thread_num();
305 thread_id_node = thread0_id_node + thread_id;
306 index = offset + thread_id_node*hw_opt->core_pinning_stride;
307 if (locality_order != NULL)
309 core = locality_order[index];
316 setaffinity_ret = tMPI_Thread_setaffinity_single(tMPI_Thread_self(), core);
318 /* store the per-thread success-values of the setaffinity */
319 nth_affinity_set = (setaffinity_ret == 0);
323 fprintf(debug, "On rank %2d, thread %2d, index %2d, core %2d the affinity setting returned %d\n",
324 cr->nodeid, gmx_omp_get_thread_num(), index, core, setaffinity_ret);
328 if (nth_affinity_set > nthread_local)
332 sprintf(msg, "Looks like we have set affinity for more threads than "
333 "we have (%d > %d)!\n", nth_affinity_set, nthread_local);
338 /* check & warn if some threads failed to set their affinities */
339 if (nth_affinity_set != nthread_local)
341 char sbuf1[STRLEN], sbuf2[STRLEN];
343 /* sbuf1 contains rank info, while sbuf2 OpenMP thread info */
344 sbuf1[0] = sbuf2[0] = '\0';
345 /* Only add rank info if we have more than one rank. */
349 #ifdef GMX_THREAD_MPI
350 sprintf(sbuf1, "In tMPI thread #%d: ", cr->nodeid);
351 #else /* GMX_LIB_MPI */
352 sprintf(sbuf1, "In MPI process #%d: ", cr->nodeid);
357 if (nthread_local > 1)
359 sprintf(sbuf2, "for %d/%d thread%s ",
360 nthread_local - nth_affinity_set, nthread_local,
361 nthread_local > 1 ? "s" : "");
364 md_print_warn(NULL, fplog,
365 "WARNING: %sAffinity setting %sfailed.\n"
366 " This can cause performance degradation! If you think your setting are\n"
367 " correct, contact the GROMACS developers.",
374 /* Check the process affinity mask and if it is found to be non-zero,
375 * will honor it and disable mdrun internal affinity setting.
376 * Note that this will only work on Linux as we use a GNU feature.
379 gmx_check_thread_affinity_set(FILE *fplog,
381 gmx_hw_opt_t *hw_opt,
382 int gmx_unused nthreads_hw_avail,
383 gmx_bool bAfterOpenmpInit)
385 #ifdef HAVE_SCHED_AFFINITY
386 cpu_set_t mask_current;
387 int i, ret, cpu_count, cpu_set;
392 if (!bAfterOpenmpInit)
394 /* Check for externally set OpenMP affinity and turn off internal
395 * pinning if any is found. We need to do this check early to tell
396 * thread-MPI whether it should do pinning when spawning threads.
397 * TODO: the above no longer holds, we should move these checks later
399 if (hw_opt->thread_affinity != threadaffOFF)
402 if (!gmx_omp_check_thread_affinity(&message))
404 /* TODO: with -pin auto we should only warn when using all cores */
405 md_print_warn(cr, fplog, "%s", message);
407 hw_opt->thread_affinity = threadaffOFF;
411 /* With thread-MPI this is needed as pinning might get turned off,
412 * which needs to be known before starting thread-MPI.
413 * With thread-MPI hw_opt is processed here on the master rank
414 * and passed to the other ranks later, so we only do this on master.
420 #ifndef GMX_THREAD_MPI
425 #ifdef HAVE_SCHED_GETAFFINITY
426 if (hw_opt->thread_affinity == threadaffOFF)
428 /* internal affinity setting is off, don't bother checking process affinity */
432 CPU_ZERO(&mask_current);
433 if ((ret = sched_getaffinity(0, sizeof(cpu_set_t), &mask_current)) != 0)
435 /* failed to query affinity mask, will just return */
438 fprintf(debug, "Failed to query affinity mask (error %d)", ret);
443 /* Before proceeding with the actual check, make sure that the number of
444 * detected CPUs is >= the CPUs in the current set.
445 * We need to check for CPU_COUNT as it was added only in glibc 2.6. */
447 if (nthreads_hw_avail < CPU_COUNT(&mask_current))
451 fprintf(debug, "%d hardware threads detected, but %d was returned by CPU_COUNT",
452 nthreads_hw_avail, CPU_COUNT(&mask_current));
456 #endif /* CPU_COUNT */
459 for (i = 0; (i < nthreads_hw_avail && i < CPU_SETSIZE); i++)
461 bAllSet = bAllSet && (CPU_ISSET(i, &mask_current) != 0);
466 if (hw_opt->thread_affinity == threadaffAUTO)
468 if (!bAfterOpenmpInit)
470 md_print_warn(cr, fplog,
471 "Non-default thread affinity set, disabling internal thread affinity");
475 md_print_warn(cr, fplog,
476 "Non-default thread affinity set probably by the OpenMP library,\n"
477 "disabling internal thread affinity");
479 hw_opt->thread_affinity = threadaffOFF;
483 /* Only warn once, at the last check (bAfterOpenmpInit==TRUE) */
484 if (bAfterOpenmpInit)
486 md_print_warn(cr, fplog,
487 "Overriding thread affinity set outside %s\n",
494 fprintf(debug, "Non-default affinity mask found\n");
501 fprintf(debug, "Default affinity mask found\n");
504 #endif /* HAVE_SCHED_AFFINITY */