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37 #include "gromacs/legacyheaders/gmx_thread_affinity.h"
46 #ifdef HAVE_SCHED_AFFINITY
48 # include <sys/syscall.h>
51 #include "thread_mpi/threads.h"
53 #include "gromacs/legacyheaders/copyrite.h"
54 #include "gromacs/legacyheaders/gmx_cpuid.h"
55 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
56 #include "gromacs/legacyheaders/md_logging.h"
57 #include "gromacs/legacyheaders/typedefs.h"
58 #include "gromacs/legacyheaders/types/commrec.h"
59 #include "gromacs/legacyheaders/types/hw_info.h"
60 #include "gromacs/utility/basenetwork.h"
61 #include "gromacs/utility/cstringutil.h"
62 #include "gromacs/utility/fatalerror.h"
63 #include "gromacs/utility/gmxomp.h"
64 #include "gromacs/utility/smalloc.h"
67 get_thread_affinity_layout(FILE *fplog,
69 const gmx_hw_info_t * hwinfo,
71 int pin_offset, int * pin_stride,
72 const int **locality_order)
74 int nhwthreads, npkg, ncores, nhwthreads_per_core, rc;
77 const int * hwthread_id;
78 gmx_bool bPickPinStride;
82 gmx_fatal(FARGS, "Negative thread pinning offset requested");
86 gmx_fatal(FARGS, "Negative thread pinning stride requested");
89 rc = gmx_cpuid_topology(hwinfo->cpuid_info, &nhwthreads, &npkg, &ncores,
91 &pkg_id, &core_id, &hwthread_id, locality_order);
95 /* topology information not available or invalid, ignore it */
96 nhwthreads = hwinfo->nthreads_hw_avail;
97 *locality_order = NULL;
101 /* We don't know anything about the hardware, don't pin */
102 md_print_warn(cr, fplog,
103 "NOTE: No information on available cores, thread pinning disabled.");
109 if (nthreads > nhwthreads)
111 /* We are oversubscribing, don't pin */
112 md_print_warn(NULL, fplog,
113 "NOTE: Oversubscribing the CPU, will not pin threads");
118 if (pin_offset + nthreads > nhwthreads)
120 /* We are oversubscribing, don't pin */
121 md_print_warn(NULL, fplog,
122 "WARNING: Requested offset too large for available cores, thread pinning disabled.");
128 /* do we need to choose the pinning stride? */
129 bPickPinStride = (*pin_stride == 0);
133 if (rc == 0 && pin_offset + nthreads*nhwthreads_per_core <= nhwthreads)
135 /* Put one thread on each physical core */
136 *pin_stride = nhwthreads_per_core;
140 /* We don't know if we have SMT, and if we do, we don't know
141 * if hw threads in the same physical core are consecutive.
142 * Without SMT the pinning layout should not matter too much.
143 * so we assume a consecutive layout and maximally spread out"
144 * the threads at equal threads per core.
145 * Note that IBM is the major non-x86 case with cpuid support
146 * and probably threads are already pinned by the queuing system,
147 * so we wouldn't end up here in the first place.
149 *pin_stride = (nhwthreads - pin_offset)/nthreads;
154 /* Check the placement of the thread with the largest index to make sure
155 * that the offset & stride doesn't cause pinning beyond the last hardware thread. */
156 if (pin_offset + (nthreads-1)*(*pin_stride) >= nhwthreads)
158 /* We are oversubscribing, don't pin */
159 md_print_warn(NULL, fplog,
160 "WARNING: Requested stride too large for available cores, thread pinning disabled.");
168 fprintf(fplog, "Pinning threads with a%s logical core stride of %d\n",
169 bPickPinStride ? "n auto-selected" : " user-specified",
176 /* Set CPU affinity. Can be important for performance.
177 On some systems (e.g. Cray) CPU Affinity is set by default.
178 But default assigning doesn't work (well) with only some ranks
179 having threads. This causes very low performance.
180 External tools have cumbersome syntax for setting affinity
181 in the case that only some ranks have threads.
182 Thus it is important that GROMACS sets the affinity internally
183 if only PME is using threads.
186 gmx_set_thread_affinity(FILE *fplog,
188 gmx_hw_opt_t *hw_opt,
189 const gmx_hw_info_t *hwinfo)
191 int nth_affinity_set, thread0_id_node,
192 nthread_local, nthread_node, nthread_hw_max, nphyscore;
194 const int *locality_order;
197 if (hw_opt->thread_affinity == threadaffOFF)
203 /* If the tMPI thread affinity setting is not supported encourage the user
204 * to report it as it's either a bug or an exotic platform which we might
205 * want to support. */
206 if (tMPI_Thread_setaffinity_support() != TMPI_SETAFFINITY_SUPPORT_YES)
208 /* we know Mac OS & BlueGene do not support setting thread affinity, so there's
209 no point in warning the user in that case. In any other case
210 the user might be able to do something about it. */
211 #if !defined(__APPLE__) && !defined(__bg__)
212 md_print_warn(NULL, fplog,
213 "NOTE: Cannot set thread affinities on the current platform.");
214 #endif /* __APPLE__ */
218 /* threads on this MPI process or TMPI thread */
219 if (cr->duty & DUTY_PP)
221 nthread_local = gmx_omp_nthreads_get(emntNonbonded);
225 nthread_local = gmx_omp_nthreads_get(emntPME);
228 /* map the current process to cores */
230 nthread_node = nthread_local;
232 if (PAR(cr) || MULTISIM(cr))
234 /* We need to determine a scan of the thread counts in this
239 MPI_Comm_split(MPI_COMM_WORLD,
240 gmx_physicalnode_id_hash(), cr->rank_intranode,
242 MPI_Scan(&nthread_local, &thread0_id_node, 1, MPI_INT, MPI_SUM, comm_intra);
243 /* MPI_Scan is inclusive, but here we need exclusive */
244 thread0_id_node -= nthread_local;
245 /* Get the total number of threads on this physical node */
246 MPI_Allreduce(&nthread_local, &nthread_node, 1, MPI_INT, MPI_SUM, comm_intra);
247 MPI_Comm_free(&comm_intra);
251 if (hw_opt->thread_affinity == threadaffAUTO &&
252 nthread_node != hwinfo->nthreads_hw_avail)
254 if (nthread_node > 1 && nthread_node < hwinfo->nthreads_hw_avail)
256 md_print_warn(cr, fplog,
257 "NOTE: The number of threads is not equal to the number of (logical) cores\n"
258 " and the -pin option is set to auto: will not pin thread to cores.\n"
259 " This can lead to significant performance degradation.\n"
260 " Consider using -pin on (and -pinoffset in case you run multiple jobs).\n");
267 if (hw_opt->core_pinning_offset != 0)
269 offset = hw_opt->core_pinning_offset;
270 md_print_info(cr, fplog, "Applying core pinning offset %d\n", offset);
273 rc = get_thread_affinity_layout(fplog, cr, hwinfo,
275 offset, &hw_opt->core_pinning_stride,
280 /* Incompatible layout, don't pin, warning was already issued */
284 /* Set the per-thread affinity. In order to be able to check the success
285 * of affinity settings, we will set nth_affinity_set to 1 on threads
286 * where the affinity setting succeded and to 0 where it failed.
287 * Reducing these 0/1 values over the threads will give the total number
288 * of threads on which we succeeded.
290 nth_affinity_set = 0;
291 #pragma omp parallel num_threads(nthread_local) reduction(+:nth_affinity_set)
293 int thread_id, thread_id_node;
295 gmx_bool setaffinity_ret;
297 thread_id = gmx_omp_get_thread_num();
298 thread_id_node = thread0_id_node + thread_id;
299 index = offset + thread_id_node*hw_opt->core_pinning_stride;
300 if (locality_order != NULL)
302 core = locality_order[index];
309 setaffinity_ret = tMPI_Thread_setaffinity_single(tMPI_Thread_self(), core);
311 /* store the per-thread success-values of the setaffinity */
312 nth_affinity_set = (setaffinity_ret == 0);
316 fprintf(debug, "On rank %2d, thread %2d, index %2d, core %2d the affinity setting returned %d\n",
317 cr->nodeid, gmx_omp_get_thread_num(), index, core, setaffinity_ret);
321 if (nth_affinity_set > nthread_local)
325 sprintf(msg, "Looks like we have set affinity for more threads than "
326 "we have (%d > %d)!\n", nth_affinity_set, nthread_local);
331 /* check & warn if some threads failed to set their affinities */
332 if (nth_affinity_set != nthread_local)
334 char sbuf1[STRLEN], sbuf2[STRLEN];
336 /* sbuf1 contains rank info, while sbuf2 OpenMP thread info */
337 sbuf1[0] = sbuf2[0] = '\0';
338 /* Only add rank info if we have more than one rank. */
342 #ifdef GMX_THREAD_MPI
343 sprintf(sbuf1, "In tMPI thread #%d: ", cr->nodeid);
344 #else /* GMX_LIB_MPI */
345 sprintf(sbuf1, "In MPI process #%d: ", cr->nodeid);
350 if (nthread_local > 1)
352 sprintf(sbuf2, "for %d/%d thread%s ",
353 nthread_local - nth_affinity_set, nthread_local,
354 nthread_local > 1 ? "s" : "");
357 md_print_warn(NULL, fplog,
358 "NOTE: %sAffinity setting %sfailed. This can cause performance degradation.\n"
359 " If you think your settings are correct, ask on the gmx-users list.",
366 /* Check the process affinity mask and if it is found to be non-zero,
367 * will honor it and disable mdrun internal affinity setting.
368 * Note that this will only work on Linux as we use a GNU feature.
371 gmx_check_thread_affinity_set(FILE *fplog,
373 gmx_hw_opt_t *hw_opt,
374 int gmx_unused nthreads_hw_avail,
375 gmx_bool bAfterOpenmpInit)
377 #ifdef HAVE_SCHED_AFFINITY
378 cpu_set_t mask_current;
379 int i, ret, cpu_count, cpu_set;
383 gmx_bool bAllSet_All;
387 if (!bAfterOpenmpInit)
389 /* Check for externally set OpenMP affinity and turn off internal
390 * pinning if any is found. We need to do this check early to tell
391 * thread-MPI whether it should do pinning when spawning threads.
392 * TODO: the above no longer holds, we should move these checks later
394 if (hw_opt->thread_affinity != threadaffOFF)
397 if (!gmx_omp_check_thread_affinity(&message))
399 /* TODO: with -pin auto we should only warn when using all cores */
400 md_print_warn(cr, fplog, "%s", message);
402 hw_opt->thread_affinity = threadaffOFF;
406 /* With thread-MPI this is needed as pinning might get turned off,
407 * which needs to be known before starting thread-MPI.
408 * With thread-MPI hw_opt is processed here on the master rank
409 * and passed to the other ranks later, so we only do this on master.
415 #ifndef GMX_THREAD_MPI
420 #ifdef HAVE_SCHED_GETAFFINITY
421 if (hw_opt->thread_affinity == threadaffOFF)
423 /* internal affinity setting is off, don't bother checking process affinity */
427 CPU_ZERO(&mask_current);
428 if ((ret = sched_getaffinity(0, sizeof(cpu_set_t), &mask_current)) != 0)
430 /* failed to query affinity mask, will just return */
433 fprintf(debug, "Failed to query affinity mask (error %d)", ret);
438 /* Before proceeding with the actual check, make sure that the number of
439 * detected CPUs is >= the CPUs in the current set.
440 * We need to check for CPU_COUNT as it was added only in glibc 2.6. */
442 if (nthreads_hw_avail < CPU_COUNT(&mask_current))
446 fprintf(debug, "%d hardware threads detected, but %d was returned by CPU_COUNT",
447 nthreads_hw_avail, CPU_COUNT(&mask_current));
451 #endif /* CPU_COUNT */
454 for (i = 0; (i < nthreads_hw_avail && i < CPU_SETSIZE); i++)
456 bAllSet = bAllSet && (CPU_ISSET(i, &mask_current) != 0);
460 MPI_Allreduce(&bAllSet, &bAllSet_All, 1, MPI_INT, MPI_LAND, MPI_COMM_WORLD);
461 bAllSet = bAllSet_All;
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 */