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Moved mdatom.h from legacyheader/types to mdtypes.
[gromacs.git] / src / gromacs / gmxlib / nrnb.cpp
blob90ed656bd4f1cea61f6893d8b0923a8366382753
1 /*
2 * This file is part of the GROMACS molecular simulation package.
3 *
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
10 *
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
15 *
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19 * Lesser General Public License for more details.
20 *
21 * You should have received a copy of the GNU Lesser General Public
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29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
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35 * the research papers on the package. Check out http://www.gromacs.org.
36 */
37 #include "gmxpre.h"
38
39 #include "gromacs/legacyheaders/nrnb.h"
40
41 #include <cstdlib>
42 #include <cstring>
43
44 #include <algorithm>
45
46 #include "gromacs/legacyheaders/names.h"
47 #include "gromacs/legacyheaders/types/commrec.h"
48 #include "gromacs/legacyheaders/types/nrnb.h"
49 #include "gromacs/utility/arraysize.h"
50 #include "gromacs/utility/smalloc.h"
51
52 typedef struct {
53 const char *name;
54 int flop;
55 } t_nrnb_data;
56
57
58 static const t_nrnb_data nbdata[eNRNB] = {
59 /* These are re-used for different NB kernels, since there are so many.
60 * The actual number of flops is set dynamically.
61 */
62 { "NB VdW [V&F]", 1 },
63 { "NB VdW [F]", 1 },
64 { "NB Elec. [V&F]", 1 },
65 { "NB Elec. [F]", 1 },
66 { "NB Elec. [W3,V&F]", 1 },
67 { "NB Elec. [W3,F]", 1 },
68 { "NB Elec. [W3-W3,V&F]", 1 },
69 { "NB Elec. [W3-W3,F]", 1 },
70 { "NB Elec. [W4,V&F]", 1 },
71 { "NB Elec. [W4,F]", 1 },
72 { "NB Elec. [W4-W4,V&F]", 1 },
73 { "NB Elec. [W4-W4,F]", 1 },
74 { "NB VdW & Elec. [V&F]", 1 },
75 { "NB VdW & Elec. [F]", 1 },
76 { "NB VdW & Elec. [W3,V&F]", 1 },
77 { "NB VdW & Elec. [W3,F]", 1 },
78 { "NB VdW & Elec. [W3-W3,V&F]", 1 },
79 { "NB VdW & Elec. [W3-W3,F]", 1 },
80 { "NB VdW & Elec. [W4,V&F]", 1 },
81 { "NB VdW & Elec. [W4,F]", 1 },
82 { "NB VdW & Elec. [W4-W4,V&F]", 1 },
83 { "NB VdW & Elec. [W4-W4,F]", 1 },
84
85 { "NB Generic kernel", 1 },
86 { "NB Generic charge grp kernel", 1 },
87 { "NB Free energy kernel", 1 },
88 { "NB All-vs-all", 1 },
89 { "NB All-vs-all, GB", 1 },
90
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 GPUs.
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 GPUs, 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.
101 */
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 },
131 { "Spread Q", 6 },
132 { "Spread Q Bspline", 2 },
133 { "Gather F", 23 },
134 { "Gather F Bspline", 6 },
135 { "3D-FFT", 8 },
136 { "Convolution", 4 },
137 { "Solve PME", 64 },
138 { "NS-Pairs", 21 },
139 { "Reset In Box", 3 },
140 { "Shift-X", 6 },
141 { "CG-CoM", 3 },
142 { "Sum Forces", 1 },
143 { "Bonds", 59 },
144 { "G96Bonds", 44 },
145 { "FENE Bonds", 58 },
146 { "Tab. Bonds", 62 },
147 { "Restraint Potential", 86 },
148 { "Linear Angles", 57 },
149 { "Angles", 168 },
150 { "G96Angles", 150 },
151 { "Quartic Angles", 160 },
152 { "Tab. Angles", 169 },
153 { "Propers", 229 },
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 },
167 { "Walls", 31 },
168 { "Polarization", 59 },
169 { "Anharmonic Polarization", 72 },
170 { "Water Pol.", 62 },
171 { "Thole Pol.", 296 },
172 { "Virial", 18 },
173 { "Update", 31 },
174 { "Ext.ens. Update", 54 },
175 { "Stop-CM", 10 },
176 { "P-Coupling", 6 },
177 { "Calc-Ekin", 27 },
178 { "Lincs", 60 },
179 { "Lincs-Mat", 4 },
180 { "Shake", 30 },
181 { "Constraint-V", 8 },
182 { "Shake-Init", 10 },
183 { "Constraint-Vir", 24 },
184 { "Settle", 323 },
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 }
194 };
195
196 static void pr_two(FILE *out, int c, int i)
197 {
198 if (i < 10)
199 {
200 fprintf(out, "%c0%1d", c, i);
201 }
202 else
203 {
204 fprintf(out, "%c%2d", c, i);
205 }
206 }
207
208 static void pr_difftime(FILE *out, double dt)
209 {
210 int ndays, nhours, nmins, nsecs;
211 gmx_bool bPrint, bPrinted;
212
213 ndays = static_cast<int>(dt/(24*3600));
214 dt = dt-24*3600*ndays;
215 nhours = static_cast<int>(dt/3600);
216 dt = dt-3600*nhours;
217 nmins = static_cast<int>(dt/60);
218 dt = dt-nmins*60;
219 nsecs = static_cast<int>(dt);
220 bPrint = (ndays > 0);
221 bPrinted = bPrint;
222 if (bPrint)
223 {
224 fprintf(out, "%d", ndays);
225 }
226 bPrint = bPrint || (nhours > 0);
227 if (bPrint)
228 {
229 if (bPrinted)
230 {
231 pr_two(out, 'd', nhours);
232 }
233 else
234 {
235 fprintf(out, "%d", nhours);
236 }
237 }
238 bPrinted = bPrinted || bPrint;
239 bPrint = bPrint || (nmins > 0);
240 if (bPrint)
241 {
242 if (bPrinted)
243 {
244 pr_two(out, 'h', nmins);
245 }
246 else
247 {
248 fprintf(out, "%d", nmins);
249 }
250 }
251 bPrinted = bPrinted || bPrint;
252 if (bPrinted)
253 {
254 pr_two(out, ':', nsecs);
255 }
256 else
257 {
258 fprintf(out, "%ds", nsecs);
259 }
260 fprintf(out, "\n");
261 }
262
263 void init_nrnb(t_nrnb *nrnb)
264 {
265 int i;
266
267 for (i = 0; (i < eNRNB); i++)
268 {
269 nrnb->n[i] = 0.0;
270 }
271 }
272
273 void cp_nrnb(t_nrnb *dest, t_nrnb *src)
274 {
275 int i;
276
277 for (i = 0; (i < eNRNB); i++)
278 {
279 dest->n[i] = src->n[i];
280 }
281 }
282
283 void add_nrnb(t_nrnb *dest, t_nrnb *s1, t_nrnb *s2)
284 {
285 int i;
286
287 for (i = 0; (i < eNRNB); i++)
288 {
289 dest->n[i] = s1->n[i]+s2->n[i];
290 }
291 }
292
293 void print_nrnb(FILE *out, t_nrnb *nrnb)
294 {
295 int i;
296
297 for (i = 0; (i < eNRNB); i++)
298 {
299 if (nrnb->n[i] > 0)
300 {
301 fprintf(out, " %-26s %10.0f.\n", nbdata[i].name, nrnb->n[i]);
302 }
303 }
304 }
305
306 void _inc_nrnb(t_nrnb *nrnb, int enr, int inc, char gmx_unused *file, int gmx_unused line)
307 {
308 nrnb->n[enr] += inc;
309 #ifdef DEBUG_NRNB
310 printf("nrnb %15s(%2d) incremented with %8d from file %s line %d\n",
311 nbdata[enr].name, enr, inc, file, line);
312 #endif
313 }
314
315 /* Returns in enr is the index of a full nbnxn VdW kernel */
316 static gmx_bool nrnb_is_nbnxn_vdw_kernel(int enr)
317 {
318 return (enr >= eNR_NBNXN_LJ_RF && enr <= eNR_NBNXN_LJ_E);
319 }
320
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)
323 {
324 return (enr >= eNR_NBNXN_ADD_LJ_FSW && enr <= eNR_NBNXN_ADD_LJ_EWALD_E);
325 }
326
327 void print_flop(FILE *out, t_nrnb *nrnb, double *nbfs, double *mflop)
328 {
329 int i, j;
330 double mni, frac, tfrac, tflop;
331 const char *myline = "-----------------------------------------------------------------------------";
332
333 *nbfs = 0.0;
334 for (i = 0; (i < eNR_NBKERNEL_ALLVSALLGB); i++)
335 {
336 if (std::strstr(nbdata[i].name, "W3-W3") != NULL)
337 {
338 *nbfs += 9e-6*nrnb->n[i];
339 }
340 else if (std::strstr(nbdata[i].name, "W3") != NULL)
341 {
342 *nbfs += 3e-6*nrnb->n[i];
343 }
344 else if (std::strstr(nbdata[i].name, "W4-W4") != NULL)
345 {
346 *nbfs += 10e-6*nrnb->n[i];
347 }
348 else if (std::strstr(nbdata[i].name, "W4") != NULL)
349 {
350 *nbfs += 4e-6*nrnb->n[i];
351 }
352 else
353 {
354 *nbfs += 1e-6*nrnb->n[i];
355 }
356 }
357 tflop = 0;
358 for (i = 0; (i < eNRNB); i++)
359 {
360 tflop += 1e-6*nrnb->n[i]*nbdata[i].flop;
361 }
362
363 if (tflop == 0)
364 {
365 fprintf(out, "No MEGA Flopsen this time\n");
366 return;
367 }
368 if (out)
369 {
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");
371 }
372
373 if (out)
374 {
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");
379
380 fprintf(out, " %-32s %16s %15s %7s\n",
381 "Computing:", "M-Number", "M-Flops", "% Flops");
382 fprintf(out, "%s\n", myline);
383 }
384 *mflop = 0.0;
385 tfrac = 0.0;
386 for (i = 0; (i < eNRNB); i++)
387 {
388 mni = 1e-6*nrnb->n[i];
389 /* Skip empty entries and nbnxn additional flops,
390 * which have been added to the kernel entry.
391 */
392 if (mni > 0 && !nrnb_is_nbnxn_kernel_addition(i))
393 {
394 int flop;
395
396 flop = nbdata[i].flop;
397 if (nrnb_is_nbnxn_vdw_kernel(i))
398 {
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)
401 {
402 int e_kernel_add;
403
404 /* Select the force or energy flop count */
405 e_kernel_add = j + ((i - eNR_NBNXN_LJ_RF) % 2);
406
407 if (nrnb->n[e_kernel_add] > 0)
408 {
409 flop += nbdata[e_kernel_add].flop;
410 }
411 }
412 }
413 *mflop += mni*flop;
414 frac = 100.0*mni*flop/tflop;
415 tfrac += frac;
416 if (out != NULL)
417 {
418 fprintf(out, " %-32s %16.6f %15.3f %6.1f\n",
419 nbdata[i].name, mni, mni*flop, frac);
420 }
421 }
422 }
423 if (out)
424 {
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);
429
430 if (nrnb->n[eNR_NBKERNEL_GENERIC] > 0)
431 {
432 fprintf(out,
433 "WARNING: Using the slow generic C kernel. This is fine if you are\n"
434 "comparing different implementations or MD software. Routine\n"
435 "simulations should use a different non-bonded setup for much better\n"
436 "performance.\n\n");
437 }
438 }
439 }
440
441 void print_perf(FILE *out, double time_per_thread, double time_per_node,
442 gmx_int64_t nsteps, double delta_t,
443 double nbfs, double mflop)
444 {
445 double wallclocktime;
446
447 fprintf(out, "\n");
448
449 if (time_per_node > 0)
450 {
451 fprintf(out, "%12s %12s %12s %10s\n", "", "Core t (s)", "Wall t (s)", "(%)");
452 fprintf(out, "%12s %12.3f %12.3f %10.1f\n", "Time:",
453 time_per_thread, time_per_node, 100.0*time_per_thread/time_per_node);
454 /* only print day-hour-sec format if time_per_node is more than 30 min */
455 if (time_per_node > 30*60)
456 {
457 fprintf(out, "%12s %12s", "", "");
458 pr_difftime(out, time_per_node);
459 }
460 if (delta_t > 0)
461 {
462 mflop = mflop/time_per_node;
463 wallclocktime = nsteps*delta_t;
464
465 if (getenv("GMX_DETAILED_PERF_STATS") == NULL)
466 {
467 fprintf(out, "%12s %12s %12s\n",
468 "", "(ns/day)", "(hour/ns)");
469 fprintf(out, "%12s %12.3f %12.3f\n", "Performance:",
470 wallclocktime*24*3.6/time_per_node, 1000*time_per_node/(3600*wallclocktime));
471 }
472 else
473 {
474 fprintf(out, "%12s %12s %12s %12s %12s\n",
475 "", "(Mnbf/s)", (mflop > 1000) ? "(GFlops)" : "(MFlops)",
476 "(ns/day)", "(hour/ns)");
477 fprintf(out, "%12s %12.3f %12.3f %12.3f %12.3f\n", "Performance:",
478 nbfs/time_per_node, (mflop > 1000) ? (mflop/1000) : mflop,
479 wallclocktime*24*3.6/time_per_node, 1000*time_per_node/(3600*wallclocktime));
480 }
481 }
482 else
483 {
484 if (getenv("GMX_DETAILED_PERF_STATS") == NULL)
485 {
486 fprintf(out, "%12s %14s\n",
487 "", "(steps/hour)");
488 fprintf(out, "%12s %14.1f\n", "Performance:",
489 nsteps*3600.0/time_per_node);
490 }
491 else
492 {
493 fprintf(out, "%12s %12s %12s %14s\n",
494 "", "(Mnbf/s)", (mflop > 1000) ? "(GFlops)" : "(MFlops)",
495 "(steps/hour)");
496 fprintf(out, "%12s %12.3f %12.3f %14.1f\n", "Performance:",
497 nbfs/time_per_node, (mflop > 1000) ? (mflop/1000) : mflop,
498 nsteps*3600.0/time_per_node);
499 }
500 }
501 }
502 }
503
504 int cost_nrnb(int enr)
505 {
506 return nbdata[enr].flop;
507 }
508
509 const char *nrnb_str(int enr)
510 {
511 return nbdata[enr].name;
512 }
513
514 static const int force_index[] = {
515 eNR_BONDS, eNR_ANGLES, eNR_PROPER, eNR_IMPROPER,
516 eNR_RB, eNR_DISRES, eNR_ORIRES, eNR_POSRES,
517 eNR_FBPOSRES, eNR_NS,
518 };
519 #define NFORCE_INDEX asize(force_index)
520
521 static const int constr_index[] = {
522 eNR_SHAKE, eNR_SHAKE_RIJ, eNR_SETTLE, eNR_UPDATE, eNR_PCOUPL,
523 eNR_CONSTR_VIR, eNR_CONSTR_V
524 };
525 #define NCONSTR_INDEX asize(constr_index)
526
527 static double pr_av(FILE *log, t_commrec *cr,
528 double fav, double ftot[], const char *title)
529 {
530 int i, perc;
531 double dperc, unb;
532
533 unb = 0;
534 if (fav > 0)
535 {
536 fav /= cr->nnodes - cr->npmenodes;
537 fprintf(log, "\n %-26s", title);
538 for (i = 0; (i < cr->nnodes); i++)
539 {
540 dperc = (100.0*ftot[i])/fav;
541 unb = std::max(unb, dperc);
542 perc = static_cast<int>(dperc);
543 fprintf(log, "%3d ", perc);
544 }
545 if (unb > 0)
546 {
547 perc = static_cast<int>(10000.0/unb);
548 fprintf(log, "%6d%%\n\n", perc);
549 }
550 else
551 {
552 fprintf(log, "\n\n");
553 }
554 }
555 return unb;
556 }
557
558 void pr_load(FILE *log, t_commrec *cr, t_nrnb nrnb[])
559 {
560 int i, j, perc;
561 double dperc, unb, uf, us;
562 double *ftot, fav;
563 double *stot, sav;
564 t_nrnb *av;
565
566 snew(av, 1);
567 snew(ftot, cr->nnodes);
568 snew(stot, cr->nnodes);
569 init_nrnb(av);
570 for (i = 0; (i < cr->nnodes); i++)
571 {
572 add_nrnb(av, av, &(nrnb[i]));
573 /* Cost due to forces */
574 for (j = 0; (j < eNR_NBKERNEL_ALLVSALLGB); j++)
575 {
576 ftot[i] += nrnb[i].n[j]*cost_nrnb(j);
577 }
578 for (j = 0; (j < NFORCE_INDEX); j++)
579 {
580 ftot[i] += nrnb[i].n[force_index[j]]*cost_nrnb(force_index[j]);
581 }
582 /* Due to shake */
583 for (j = 0; (j < NCONSTR_INDEX); j++)
584 {
585 stot[i] += nrnb[i].n[constr_index[j]]*cost_nrnb(constr_index[j]);
586 }
587 }
588 for (j = 0; (j < eNRNB); j++)
589 {
590 av->n[j] = av->n[j]/static_cast<double>(cr->nnodes - cr->npmenodes);
591 }
592
593 fprintf(log, "\nDetailed load balancing info in percentage of average\n");
594
595 fprintf(log, " Type RANK:");
596 for (i = 0; (i < cr->nnodes); i++)
597 {
598 fprintf(log, "%3d ", i);
599 }
600 fprintf(log, "Scaling\n");
601 fprintf(log, "---------------------------");
602 for (i = 0; (i < cr->nnodes); i++)
603 {
604 fprintf(log, "----");
605 }
606 fprintf(log, "-------\n");
607
608 for (j = 0; (j < eNRNB); j++)
609 {
610 unb = 100.0;
611 if (av->n[j] > 0)
612 {
613 fprintf(log, " %-26s", nrnb_str(j));
614 for (i = 0; (i < cr->nnodes); i++)
615 {
616 dperc = (100.0*nrnb[i].n[j])/av->n[j];
617 unb = std::max(unb, dperc);
618 perc = static_cast<int>(dperc);
619 fprintf(log, "%3d ", perc);
620 }
621 if (unb > 0)
622 {
623 perc = static_cast<int>(10000.0/unb);
624 fprintf(log, "%6d%%\n", perc);
625 }
626 else
627 {
628 fprintf(log, "\n");
629 }
630 }
631 }
632 fav = sav = 0;
633 for (i = 0; (i < cr->nnodes); i++)
634 {
635 fav += ftot[i];
636 sav += stot[i];
637 }
638 uf = pr_av(log, cr, fav, ftot, "Total Force");
639 us = pr_av(log, cr, sav, stot, "Total Constr.");
640
641 unb = (uf*fav+us*sav)/(fav+sav);
642 if (unb > 0)
643 {
644 unb = 10000.0/unb;
645 fprintf(log, "\nTotal Scaling: %.0f%% of max performance\n\n", unb);
646 }
647 }
The ultimate molecular dynamics simulation package