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43 #include "types/commrec.h"
45 #include "gmx_fatal.h"
63 static const t_nrnb_data nbdata
[eNRNB
] = {
64 /* These are re-used for different NB kernels, since there are so many.
65 * The actual number of flops is set dynamically.
67 { "NB VdW [V&F]", 1 },
69 { "NB Elec. [V&F]", 1 },
70 { "NB Elec. [F]", 1 },
71 { "NB Elec. [W3,V&F]", 1 },
72 { "NB Elec. [W3,F]", 1 },
73 { "NB Elec. [W3-W3,V&F]", 1 },
74 { "NB Elec. [W3-W3,F]", 1 },
75 { "NB Elec. [W4,V&F]", 1 },
76 { "NB Elec. [W4,F]", 1 },
77 { "NB Elec. [W4-W4,V&F]", 1 },
78 { "NB Elec. [W4-W4,F]", 1 },
79 { "NB VdW & Elec. [V&F]", 1 },
80 { "NB VdW & Elec. [F]", 1 },
81 { "NB VdW & Elec. [W3,V&F]", 1 },
82 { "NB VdW & Elec. [W3,F]", 1 },
83 { "NB VdW & Elec. [W3-W3,V&F]", 1 },
84 { "NB VdW & Elec. [W3-W3,F]", 1 },
85 { "NB VdW & Elec. [W4,V&F]", 1 },
86 { "NB VdW & Elec. [W4,F]", 1 },
87 { "NB VdW & Elec. [W4-W4,V&F]", 1 },
88 { "NB VdW & Elec. [W4-W4,F]", 1 },
90 { "NB Generic kernel", 1 },
91 { "NB Free energy kernel", 1 },
92 { "NB All-vs-all", 1 },
93 { "NB All-vs-all, GB", 1 },
95 { "Pair Search distance check", 9 }, /* nbnxn pair dist. check */
96 /* nbnxn kernel flops are based on inner-loops without exclusion checks.
97 * Plain Coulomb runs through the RF kernels, except with CUDA.
98 * invsqrt is counted as 6 flops: 1 for _mm_rsqt_ps + 5 for iteration.
99 * The flops are equal for plain-C, x86 SIMD and CUDA, except for:
100 * - plain-C kernel uses one flop more for Coulomb-only (F) than listed
101 * - x86 SIMD LJ geom-comb.rule kernels (fastest) use 2 more flops
102 * - x86 SIMD LJ LB-comb.rule kernels (fast) use 3 (8 for F+E) more flops
103 * - GPU always does exclusions, which requires 2-4 flops, but as invsqrt
104 * is always counted as 6 flops, this roughly compensates.
106 { "NxN RF Elec. + VdW [F]", 38 }, /* nbnxn kernel LJ+RF, no ener */
107 { "NxN RF Elec. + VdW [V&F]", 54 },
108 { "NxN QSTab Elec. + VdW [F]", 41 }, /* nbnxn kernel LJ+tab, no en */
109 { "NxN QSTab Elec. + VdW [V&F]", 59 },
110 { "NxN Ewald Elec. + VdW [F]", 66 }, /* nbnxn kernel LJ+Ewald, no en */
111 { "NxN Ewald Elec. + VdW [V&F]", 107 },
112 { "NxN VdW [F]", 33 }, /* nbnxn kernel LJ, no ener */
113 { "NxN VdW [V&F]", 43 },
114 { "NxN RF Electrostatics [F]", 31 }, /* nbnxn kernel RF, no ener */
115 { "NxN RF Electrostatics [V&F]", 36 },
116 { "NxN QSTab Elec. [F]", 34 }, /* nbnxn kernel tab, no ener */
117 { "NxN QSTab Elec. [V&F]", 41 },
118 { "NxN Ewald Elec. [F]", 61 }, /* nbnxn kernel Ewald, no ener */
119 { "NxN Ewald Elec. [V&F]", 84 },
120 { "1,4 nonbonded interactions", 90 },
121 { "Born radii (Still)", 47 },
122 { "Born radii (HCT/OBC)", 183 },
123 { "Born force chain rule", 15 },
124 { "All-vs-All Still radii", 1 },
125 { "All-vs-All HCT/OBC radii", 1 },
126 { "All-vs-All Born chain rule", 1 },
127 { "Calc Weights", 36 },
129 { "Spread Q Bspline", 2 },
131 { "Gather F Bspline", 6 },
133 { "Convolution", 4 },
136 { "Reset In Box", 3 },
142 { "FENE Bonds", 58 },
143 { "Tab. Bonds", 62 },
144 { "Restraint Potential", 86 },
145 { "Linear Angles", 57 },
147 { "G96Angles", 150 },
148 { "Quartic Angles", 160 },
149 { "Tab. Angles", 169 },
151 { "Impropers", 208 },
152 { "RB-Dihedrals", 247 },
153 { "Four. Dihedrals", 247 },
154 { "Tab. Dihedrals", 227 },
155 { "Dist. Restr.", 200 },
156 { "Orient. Restr.", 200 },
157 { "Dihedral Restr.", 200 },
158 { "Pos. Restr.", 50 },
159 { "Angle Restr.", 191 },
160 { "Angle Restr. Z", 164 },
161 { "Morse Potent.", 83 },
162 { "Cubic Bonds", 54 },
164 { "Polarization", 59 },
165 { "Anharmonic Polarization", 72 },
166 { "Water Pol.", 62 },
167 { "Thole Pol.", 296 },
170 { "Ext.ens. Update", 54 },
177 { "Constraint-V", 8 },
178 { "Shake-Init", 10 },
179 { "Constraint-Vir", 24 },
181 { "Virtual Site 2", 23 },
182 { "Virtual Site 3", 37 },
183 { "Virtual Site 3fd", 95 },
184 { "Virtual Site 3fad", 176 },
185 { "Virtual Site 3out", 87 },
186 { "Virtual Site 4fd", 110 },
187 { "Virtual Site 4fdn", 254 },
188 { "Virtual Site N", 15 },
189 { "Mixed Generalized Born stuff", 10 }
193 void init_nrnb(t_nrnb
*nrnb
)
197 for(i
=0; (i
<eNRNB
); i
++)
201 void cp_nrnb(t_nrnb
*dest
, t_nrnb
*src
)
205 for(i
=0; (i
<eNRNB
); i
++)
206 dest
->n
[i
]=src
->n
[i
];
209 void add_nrnb(t_nrnb
*dest
, t_nrnb
*s1
, t_nrnb
*s2
)
213 for(i
=0; (i
<eNRNB
); i
++)
214 dest
->n
[i
]=s1
->n
[i
]+s2
->n
[i
];
217 void print_nrnb(FILE *out
, t_nrnb
*nrnb
)
221 for(i
=0; (i
<eNRNB
); i
++)
223 fprintf(out
," %-26s %10.0f.\n",nbdata
[i
].name
,nrnb
->n
[i
]);
226 void _inc_nrnb(t_nrnb
*nrnb
,int enr
,int inc
,char *file
,int line
)
230 printf("nrnb %15s(%2d) incremented with %8d from file %s line %d\n",
231 nbdata
[enr
].name
,enr
,inc
,file
,line
);
235 void print_flop(FILE *out
,t_nrnb
*nrnb
,double *nbfs
,double *mflop
)
238 double mni
,frac
,tfrac
,tflop
;
239 const char *myline
= "-----------------------------------------------------------------------------";
242 for(i
=0; (i
<eNR_NBKERNEL_ALLVSALLGB
); i
++) {
243 if (strstr(nbdata
[i
].name
,"W3-W3") != NULL
)
244 *nbfs
+= 9e-6*nrnb
->n
[i
];
245 else if (strstr(nbdata
[i
].name
,"W3") != NULL
)
246 *nbfs
+= 3e-6*nrnb
->n
[i
];
247 else if (strstr(nbdata
[i
].name
,"W4-W4") != NULL
)
248 *nbfs
+= 10e-6*nrnb
->n
[i
];
249 else if (strstr(nbdata
[i
].name
,"W4") != NULL
)
250 *nbfs
+= 4e-6*nrnb
->n
[i
];
252 *nbfs
+= 1e-6*nrnb
->n
[i
];
255 for(i
=0; (i
<eNRNB
); i
++)
256 tflop
+=1e-6*nrnb
->n
[i
]*nbdata
[i
].flop
;
259 fprintf(out
,"No MEGA Flopsen this time\n");
263 fprintf(out
,"\n\tM E G A - F L O P S A C C O U N T I N G\n\n");
268 fprintf(out
," NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels\n");
269 fprintf(out
," RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table\n");
270 fprintf(out
," W3=SPC/TIP3p W4=TIP4p (single or pairs)\n");
271 fprintf(out
," V&F=Potential and force V=Potential only F=Force only\n\n");
273 fprintf(out
," %-32s %16s %15s %7s\n",
274 "Computing:","M-Number","M-Flops","% Flops");
275 fprintf(out
,"%s\n",myline
);
279 for(i
=0; (i
<eNRNB
); i
++) {
280 mni
= 1e-6*nrnb
->n
[i
];
281 *mflop
+= mni
*nbdata
[i
].flop
;
282 frac
= 100.0*mni
*nbdata
[i
].flop
/tflop
;
285 fprintf(out
," %-32s %16.6f %15.3f %6.1f\n",
286 nbdata
[i
].name
,mni
,mni
*nbdata
[i
].flop
,frac
);
289 fprintf(out
,"%s\n",myline
);
290 fprintf(out
," %-32s %16s %15.3f %6.1f\n",
291 "Total","",*mflop
,tfrac
);
292 fprintf(out
,"%s\n\n",myline
);
296 void print_perf(FILE *out
,double nodetime
,double realtime
,int nprocs
,
297 gmx_large_int_t nsteps
,real delta_t
,
298 double nbfs
,double mflop
,
307 fprintf(out
,"%12s %12s %12s %10s\n","","Core t (s)","Wall t (s)","(%)");
308 fprintf(out
,"%12s %12.3f %12.3f %10.1f\n","Time:",
309 nodetime
, realtime
, 100.0*nodetime
/realtime
);
310 /* only print day-hour-sec format if realtime is more than 30 min */
311 if (realtime
> 30*60)
313 fprintf(out
,"%12s %12s","","");
314 pr_difftime(out
,realtime
);
318 mflop
= mflop
/realtime
;
319 runtime
= nsteps
*delta_t
;
321 if (getenv("GMX_DETAILED_PERF_STATS") == NULL
)
323 fprintf(out
,"%12s %12s %12s\n",
324 "","(ns/day)","(hour/ns)");
325 fprintf(out
,"%12s %12.3f %12.3f\n","Performance:",
326 runtime
*24*3.6/realtime
,1000*realtime
/(3600*runtime
));
330 fprintf(out
,"%12s %12s %12s %12s %12s\n",
331 "","(Mnbf/s)",(mflop
> 1000) ? "(GFlops)" : "(MFlops)",
332 "(ns/day)","(hour/ns)");
333 fprintf(out
,"%12s %12.3f %12.3f %12.3f %12.3f\n","Performance:",
334 nbfs
/realtime
,(mflop
> 1000) ? (mflop
/1000) : mflop
,
335 runtime
*24*3.6/realtime
,1000*realtime
/(3600*runtime
));
340 if (getenv("GMX_DETAILED_PERF_STATS") == NULL
)
342 fprintf(out
,"%12s %14s\n",
344 fprintf(out
,"%12s %14.1f\n","Performance:",
345 nsteps
*3600.0/realtime
);
349 fprintf(out
,"%12s %12s %12s %14s\n",
350 "","(Mnbf/s)",(mflop
> 1000) ? "(GFlops)" : "(MFlops)",
352 fprintf(out
,"%12s %12.3f %12.3f %14.1f\n","Performance:",
353 nbfs
/realtime
,(mflop
> 1000) ? (mflop
/1000) : mflop
,
354 nsteps
*3600.0/realtime
);
360 int cost_nrnb(int enr
)
362 return nbdata
[enr
].flop
;
365 const char *nrnb_str(int enr
)
367 return nbdata
[enr
].name
;
370 static const int force_index
[]={
371 eNR_BONDS
, eNR_ANGLES
, eNR_PROPER
, eNR_IMPROPER
,
372 eNR_RB
, eNR_DISRES
, eNR_ORIRES
, eNR_POSRES
,
375 #define NFORCE_INDEX asize(force_index)
377 static const int constr_index
[]={
378 eNR_SHAKE
, eNR_SHAKE_RIJ
, eNR_SETTLE
, eNR_UPDATE
, eNR_PCOUPL
,
379 eNR_CONSTR_VIR
,eNR_CONSTR_V
381 #define NCONSTR_INDEX asize(constr_index)
383 static double pr_av(FILE *log
,t_commrec
*cr
,
384 double fav
,double ftot
[],const char *title
)
391 fav
/= cr
->nnodes
- cr
->npmenodes
;
392 fprintf(log
,"\n %-26s",title
);
393 for(i
=0; (i
<cr
->nnodes
); i
++) {
394 dperc
=(100.0*ftot
[i
])/fav
;
397 fprintf(log
,"%3d ",perc
);
401 fprintf(log
,"%6d%%\n\n",perc
);
409 void pr_load(FILE *log
,t_commrec
*cr
,t_nrnb nrnb
[])
412 double dperc
,unb
,uf
,us
;
418 snew(ftot
,cr
->nnodes
);
419 snew(stot
,cr
->nnodes
);
421 for(i
=0; (i
<cr
->nnodes
); i
++) {
422 add_nrnb(av
,av
,&(nrnb
[i
]));
423 /* Cost due to forces */
424 for(j
=0; (j
<eNR_NBKERNEL_ALLVSALLGB
); j
++)
425 ftot
[i
]+=nrnb
[i
].n
[j
]*cost_nrnb(j
);
426 for(j
=0; (j
<NFORCE_INDEX
); j
++)
427 ftot
[i
]+=nrnb
[i
].n
[force_index
[j
]]*cost_nrnb(force_index
[j
]);
429 for(j
=0; (j
<NCONSTR_INDEX
); j
++) {
430 stot
[i
]+=nrnb
[i
].n
[constr_index
[j
]]*cost_nrnb(constr_index
[j
]);
433 for(j
=0; (j
<eNRNB
); j
++)
434 av
->n
[j
]=av
->n
[j
]/(double)(cr
->nnodes
- cr
->npmenodes
);
436 fprintf(log
,"\nDetailed load balancing info in percentage of average\n");
438 fprintf(log
," Type NODE:");
439 for(i
=0; (i
<cr
->nnodes
); i
++)
440 fprintf(log
,"%3d ",i
);
441 fprintf(log
,"Scaling\n");
442 fprintf(log
,"---------------------------");
443 for(i
=0; (i
<cr
->nnodes
); i
++)
445 fprintf(log
,"-------\n");
447 for(j
=0; (j
<eNRNB
); j
++) {
450 fprintf(log
," %-26s",nrnb_str(j
));
451 for(i
=0; (i
<cr
->nnodes
); i
++) {
452 dperc
=(100.0*nrnb
[i
].n
[j
])/av
->n
[j
];
455 fprintf(log
,"%3d ",perc
);
459 fprintf(log
,"%6d%%\n",perc
);
466 for(i
=0; (i
<cr
->nnodes
); i
++) {
470 uf
=pr_av(log
,cr
,fav
,ftot
,"Total Force");
471 us
=pr_av(log
,cr
,sav
,stot
,"Total Constr.");
473 unb
=(uf
*fav
+us
*sav
)/(fav
+sav
);
476 fprintf(log
,"\nTotal Scaling: %.0f%% of max performance\n\n",unb
);