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42 #include "types/commrec.h"
44 #include "gmx_fatal.h"
49 #include "gromacs/utility/smalloc.h"
57 static const t_nrnb_data nbdata[eNRNB] = {
58 /* These are re-used for different NB kernels, since there are so many.
59 * The actual number of flops is set dynamically.
61 { "NB VdW [V&F]", 1 },
63 { "NB Elec. [V&F]", 1 },
64 { "NB Elec. [F]", 1 },
65 { "NB Elec. [W3,V&F]", 1 },
66 { "NB Elec. [W3,F]", 1 },
67 { "NB Elec. [W3-W3,V&F]", 1 },
68 { "NB Elec. [W3-W3,F]", 1 },
69 { "NB Elec. [W4,V&F]", 1 },
70 { "NB Elec. [W4,F]", 1 },
71 { "NB Elec. [W4-W4,V&F]", 1 },
72 { "NB Elec. [W4-W4,F]", 1 },
73 { "NB VdW & Elec. [V&F]", 1 },
74 { "NB VdW & Elec. [F]", 1 },
75 { "NB VdW & Elec. [W3,V&F]", 1 },
76 { "NB VdW & Elec. [W3,F]", 1 },
77 { "NB VdW & Elec. [W3-W3,V&F]", 1 },
78 { "NB VdW & Elec. [W3-W3,F]", 1 },
79 { "NB VdW & Elec. [W4,V&F]", 1 },
80 { "NB VdW & Elec. [W4,F]", 1 },
81 { "NB VdW & Elec. [W4-W4,V&F]", 1 },
82 { "NB VdW & Elec. [W4-W4,F]", 1 },
84 { "NB Generic kernel", 1 },
85 { "NB Generic charge grp kernel", 1 },
86 { "NB Generic AdResS kernel", 1 },
87 { "NB Free energy kernel", 1 },
88 { "NB All-vs-all", 1 },
89 { "NB All-vs-all, GB", 1 },
91 { "Pair Search distance check", 9 }, /* nbnxn pair dist. check */
92 /* nbnxn kernel flops are based on inner-loops without exclusion checks.
93 * Plain Coulomb runs through the RF kernels, except with CUDA.
94 * invsqrt is counted as 6 flops: 1 for _mm_rsqt_ps + 5 for iteration.
95 * The flops are equal for plain-C, x86 SIMD and CUDA, except for:
96 * - plain-C kernel uses one flop more for Coulomb-only (F) than listed
97 * - x86 SIMD LJ geom-comb.rule kernels (fastest) use 2 more flops
98 * - x86 SIMD LJ LB-comb.rule kernels (fast) use 3 (8 for F+E) more flops
99 * - GPU always does exclusions, which requires 2-4 flops, but as invsqrt
100 * is always counted as 6 flops, this roughly compensates.
102 { "NxN RF Elec. + LJ [F]", 38 }, /* nbnxn kernel LJ+RF, no ener */
103 { "NxN RF Elec. + LJ [V&F]", 54 },
104 { "NxN QSTab Elec. + LJ [F]", 41 }, /* nbnxn kernel LJ+tab, no en */
105 { "NxN QSTab Elec. + LJ [V&F]", 59 },
106 { "NxN Ewald Elec. + LJ [F]", 66 }, /* nbnxn kernel LJ+Ewald, no en */
107 { "NxN Ewald Elec. + LJ [V&F]", 107 },
108 { "NxN LJ [F]", 33 }, /* nbnxn kernel LJ, no ener */
109 { "NxN LJ [V&F]", 43 },
110 { "NxN RF Electrostatics [F]", 31 }, /* nbnxn kernel RF, no ener */
111 { "NxN RF Electrostatics [V&F]", 36 },
112 { "NxN QSTab Elec. [F]", 34 }, /* nbnxn kernel tab, no ener */
113 { "NxN QSTab Elec. [V&F]", 41 },
114 { "NxN Ewald Elec. [F]", 61 }, /* nbnxn kernel Ewald, no ener */
115 { "NxN Ewald Elec. [V&F]", 84 },
116 /* The switch function flops should be added to the LJ kernels above */
117 { "NxN LJ add F-switch [F]", 12 }, /* extra cost for LJ F-switch */
118 { "NxN LJ add F-switch [V&F]", 22 },
119 { "NxN LJ add P-switch [F]", 27 }, /* extra cost for LJ P-switch */
120 { "NxN LJ add P-switch [V&F]", 20 },
121 { "NxN LJ add LJ Ewald [F]", 36 }, /* extra cost for LJ Ewald */
122 { "NxN LJ add LJ Ewald [V&F]", 33 },
123 { "1,4 nonbonded interactions", 90 },
124 { "Born radii (Still)", 47 },
125 { "Born radii (HCT/OBC)", 183 },
126 { "Born force chain rule", 15 },
127 { "All-vs-All Still radii", 1 },
128 { "All-vs-All HCT/OBC radii", 1 },
129 { "All-vs-All Born chain rule", 1 },
130 { "Calc Weights", 36 },
132 { "Spread Q Bspline", 2 },
134 { "Gather F Bspline", 6 },
136 { "Convolution", 4 },
139 { "Reset In Box", 3 },
145 { "FENE Bonds", 58 },
146 { "Tab. Bonds", 62 },
147 { "Restraint Potential", 86 },
148 { "Linear Angles", 57 },
150 { "G96Angles", 150 },
151 { "Quartic Angles", 160 },
152 { "Tab. Angles", 169 },
154 { "Impropers", 208 },
155 { "RB-Dihedrals", 247 },
156 { "Four. Dihedrals", 247 },
157 { "Tab. Dihedrals", 227 },
158 { "Dist. Restr.", 200 },
159 { "Orient. Restr.", 200 },
160 { "Dihedral Restr.", 200 },
161 { "Pos. Restr.", 50 },
162 { "Flat-bottom posres", 50 },
163 { "Angle Restr.", 191 },
164 { "Angle Restr. Z", 164 },
165 { "Morse Potent.", 83 },
166 { "Cubic Bonds", 54 },
168 { "Polarization", 59 },
169 { "Anharmonic Polarization", 72 },
170 { "Water Pol.", 62 },
171 { "Thole Pol.", 296 },
174 { "Ext.ens. Update", 54 },
181 { "Constraint-V", 8 },
182 { "Shake-Init", 10 },
183 { "Constraint-Vir", 24 },
185 { "Virtual Site 2", 23 },
186 { "Virtual Site 3", 37 },
187 { "Virtual Site 3fd", 95 },
188 { "Virtual Site 3fad", 176 },
189 { "Virtual Site 3out", 87 },
190 { "Virtual Site 4fd", 110 },
191 { "Virtual Site 4fdn", 254 },
192 { "Virtual Site N", 15 },
193 { "Mixed Generalized Born stuff", 10 }
196 static void pr_two(FILE *out, int c, int i)
200 fprintf(out, "%c0%1d", c, i);
204 fprintf(out, "%c%2d", c, i);
208 static void pr_difftime(FILE *out, double dt)
210 int ndays, nhours, nmins, nsecs;
211 gmx_bool bPrint, bPrinted;
213 ndays = dt/(24*3600);
214 dt = dt-24*3600*ndays;
220 bPrint = (ndays > 0);
224 fprintf(out, "%d", ndays);
226 bPrint = bPrint || (nhours > 0);
231 pr_two(out, 'd', nhours);
235 fprintf(out, "%d", nhours);
238 bPrinted = bPrinted || bPrint;
239 bPrint = bPrint || (nmins > 0);
244 pr_two(out, 'h', nmins);
248 fprintf(out, "%d", nmins);
251 bPrinted = bPrinted || bPrint;
254 pr_two(out, ':', nsecs);
258 fprintf(out, "%ds", nsecs);
263 void init_nrnb(t_nrnb *nrnb)
267 for (i = 0; (i < eNRNB); i++)
273 void cp_nrnb(t_nrnb *dest, t_nrnb *src)
277 for (i = 0; (i < eNRNB); i++)
279 dest->n[i] = src->n[i];
283 void add_nrnb(t_nrnb *dest, t_nrnb *s1, t_nrnb *s2)
287 for (i = 0; (i < eNRNB); i++)
289 dest->n[i] = s1->n[i]+s2->n[i];
293 void print_nrnb(FILE *out, t_nrnb *nrnb)
297 for (i = 0; (i < eNRNB); i++)
301 fprintf(out, " %-26s %10.0f.\n", nbdata[i].name, nrnb->n[i]);
306 void _inc_nrnb(t_nrnb *nrnb, int enr, int inc, char gmx_unused *file, int gmx_unused line)
310 printf("nrnb %15s(%2d) incremented with %8d from file %s line %d\n",
311 nbdata[enr].name, enr, inc, file, line);
315 /* Returns in enr is the index of a full nbnxn VdW kernel */
316 static gmx_bool nrnb_is_nbnxn_vdw_kernel(int enr)
318 return (enr >= eNR_NBNXN_LJ_RF && enr <= eNR_NBNXN_LJ_E);
321 /* Returns in enr is the index of an nbnxn kernel addition (LJ modification) */
322 static gmx_bool nrnb_is_nbnxn_kernel_addition(int enr)
324 return (enr >= eNR_NBNXN_ADD_LJ_FSW && enr <= eNR_NBNXN_ADD_LJ_EWALD_E);
327 void print_flop(FILE *out, t_nrnb *nrnb, double *nbfs, double *mflop)
330 double mni, frac, tfrac, tflop;
331 const char *myline = "-----------------------------------------------------------------------------";
334 for (i = 0; (i < eNR_NBKERNEL_ALLVSALLGB); i++)
336 if (strstr(nbdata[i].name, "W3-W3") != NULL)
338 *nbfs += 9e-6*nrnb->n[i];
340 else if (strstr(nbdata[i].name, "W3") != NULL)
342 *nbfs += 3e-6*nrnb->n[i];
344 else if (strstr(nbdata[i].name, "W4-W4") != NULL)
346 *nbfs += 10e-6*nrnb->n[i];
348 else if (strstr(nbdata[i].name, "W4") != NULL)
350 *nbfs += 4e-6*nrnb->n[i];
354 *nbfs += 1e-6*nrnb->n[i];
358 for (i = 0; (i < eNRNB); i++)
360 tflop += 1e-6*nrnb->n[i]*nbdata[i].flop;
365 fprintf(out, "No MEGA Flopsen this time\n");
370 fprintf(out, "\n\tM E G A - F L O P S A C C O U N T I N G\n\n");
375 fprintf(out, " NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels\n");
376 fprintf(out, " RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table\n");
377 fprintf(out, " W3=SPC/TIP3p W4=TIP4p (single or pairs)\n");
378 fprintf(out, " V&F=Potential and force V=Potential only F=Force only\n\n");
380 fprintf(out, " %-32s %16s %15s %7s\n",
381 "Computing:", "M-Number", "M-Flops", "% Flops");
382 fprintf(out, "%s\n", myline);
386 for (i = 0; (i < eNRNB); i++)
388 mni = 1e-6*nrnb->n[i];
389 /* Skip empty entries and nbnxn additional flops,
390 * which have been added to the kernel entry.
392 if (mni > 0 && !nrnb_is_nbnxn_kernel_addition(i))
396 flop = nbdata[i].flop;
397 if (nrnb_is_nbnxn_vdw_kernel(i))
399 /* Possibly add the cost of an LJ switch/Ewald function */
400 for (j = eNR_NBNXN_ADD_LJ_FSW; j <= eNR_NBNXN_ADD_LJ_EWALD; j += 2)
404 /* Select the force or energy flop count */
405 e_kernel_add = j + ((i - eNR_NBNXN_LJ_RF) % 2);
407 if (nrnb->n[e_kernel_add] > 0)
409 flop += nbdata[e_kernel_add].flop;
414 frac = 100.0*mni*flop/tflop;
418 fprintf(out, " %-32s %16.6f %15.3f %6.1f\n",
419 nbdata[i].name, mni, mni*flop, frac);
425 fprintf(out, "%s\n", myline);
426 fprintf(out, " %-32s %16s %15.3f %6.1f\n",
427 "Total", "", *mflop, tfrac);
428 fprintf(out, "%s\n\n", myline);
432 void print_perf(FILE *out, double time_per_thread, double time_per_node,
433 gmx_int64_t nsteps, real delta_t,
434 double nbfs, double mflop)
440 if (time_per_node > 0)
442 fprintf(out, "%12s %12s %12s %10s\n", "", "Core t (s)", "Wall t (s)", "(%)");
443 fprintf(out, "%12s %12.3f %12.3f %10.1f\n", "Time:",
444 time_per_thread, time_per_node, 100.0*time_per_thread/time_per_node);
445 /* only print day-hour-sec format if time_per_node is more than 30 min */
446 if (time_per_node > 30*60)
448 fprintf(out, "%12s %12s", "", "");
449 pr_difftime(out, time_per_node);
453 mflop = mflop/time_per_node;
454 wallclocktime = nsteps*delta_t;
456 if (getenv("GMX_DETAILED_PERF_STATS") == NULL)
458 fprintf(out, "%12s %12s %12s\n",
459 "", "(ns/day)", "(hour/ns)");
460 fprintf(out, "%12s %12.3f %12.3f\n", "Performance:",
461 wallclocktime*24*3.6/time_per_node, 1000*time_per_node/(3600*wallclocktime));
465 fprintf(out, "%12s %12s %12s %12s %12s\n",
466 "", "(Mnbf/s)", (mflop > 1000) ? "(GFlops)" : "(MFlops)",
467 "(ns/day)", "(hour/ns)");
468 fprintf(out, "%12s %12.3f %12.3f %12.3f %12.3f\n", "Performance:",
469 nbfs/time_per_node, (mflop > 1000) ? (mflop/1000) : mflop,
470 wallclocktime*24*3.6/time_per_node, 1000*time_per_node/(3600*wallclocktime));
475 if (getenv("GMX_DETAILED_PERF_STATS") == NULL)
477 fprintf(out, "%12s %14s\n",
479 fprintf(out, "%12s %14.1f\n", "Performance:",
480 nsteps*3600.0/time_per_node);
484 fprintf(out, "%12s %12s %12s %14s\n",
485 "", "(Mnbf/s)", (mflop > 1000) ? "(GFlops)" : "(MFlops)",
487 fprintf(out, "%12s %12.3f %12.3f %14.1f\n", "Performance:",
488 nbfs/time_per_node, (mflop > 1000) ? (mflop/1000) : mflop,
489 nsteps*3600.0/time_per_node);
495 int cost_nrnb(int enr)
497 return nbdata[enr].flop;
500 const char *nrnb_str(int enr)
502 return nbdata[enr].name;
505 static const int force_index[] = {
506 eNR_BONDS, eNR_ANGLES, eNR_PROPER, eNR_IMPROPER,
507 eNR_RB, eNR_DISRES, eNR_ORIRES, eNR_POSRES,
508 eNR_FBPOSRES, eNR_NS,
510 #define NFORCE_INDEX asize(force_index)
512 static const int constr_index[] = {
513 eNR_SHAKE, eNR_SHAKE_RIJ, eNR_SETTLE, eNR_UPDATE, eNR_PCOUPL,
514 eNR_CONSTR_VIR, eNR_CONSTR_V
516 #define NCONSTR_INDEX asize(constr_index)
518 static double pr_av(FILE *log, t_commrec *cr,
519 double fav, double ftot[], const char *title)
527 fav /= cr->nnodes - cr->npmenodes;
528 fprintf(log, "\n %-26s", title);
529 for (i = 0; (i < cr->nnodes); i++)
531 dperc = (100.0*ftot[i])/fav;
532 unb = max(unb, dperc);
534 fprintf(log, "%3d ", perc);
539 fprintf(log, "%6d%%\n\n", perc);
543 fprintf(log, "\n\n");
549 void pr_load(FILE *log, t_commrec *cr, t_nrnb nrnb[])
552 double dperc, unb, uf, us;
558 snew(ftot, cr->nnodes);
559 snew(stot, cr->nnodes);
561 for (i = 0; (i < cr->nnodes); i++)
563 add_nrnb(av, av, &(nrnb[i]));
564 /* Cost due to forces */
565 for (j = 0; (j < eNR_NBKERNEL_ALLVSALLGB); j++)
567 ftot[i] += nrnb[i].n[j]*cost_nrnb(j);
569 for (j = 0; (j < NFORCE_INDEX); j++)
571 ftot[i] += nrnb[i].n[force_index[j]]*cost_nrnb(force_index[j]);
574 for (j = 0; (j < NCONSTR_INDEX); j++)
576 stot[i] += nrnb[i].n[constr_index[j]]*cost_nrnb(constr_index[j]);
579 for (j = 0; (j < eNRNB); j++)
581 av->n[j] = av->n[j]/(double)(cr->nnodes - cr->npmenodes);
584 fprintf(log, "\nDetailed load balancing info in percentage of average\n");
586 fprintf(log, " Type NODE:");
587 for (i = 0; (i < cr->nnodes); i++)
589 fprintf(log, "%3d ", i);
591 fprintf(log, "Scaling\n");
592 fprintf(log, "---------------------------");
593 for (i = 0; (i < cr->nnodes); i++)
595 fprintf(log, "----");
597 fprintf(log, "-------\n");
599 for (j = 0; (j < eNRNB); j++)
604 fprintf(log, " %-26s", nrnb_str(j));
605 for (i = 0; (i < cr->nnodes); i++)
607 dperc = (100.0*nrnb[i].n[j])/av->n[j];
608 unb = max(unb, dperc);
610 fprintf(log, "%3d ", perc);
615 fprintf(log, "%6d%%\n", perc);
624 for (i = 0; (i < cr->nnodes); i++)
629 uf = pr_av(log, cr, fav, ftot, "Total Force");
630 us = pr_av(log, cr, sav, stot, "Total Constr.");
632 unb = (uf*fav+us*sav)/(fav+sav);
636 fprintf(log, "\nTotal Scaling: %.0f%% of max performance\n\n", unb);