/*
- *
+ *
* This source code is part of
- *
+ *
* G R O M A C S
- *
+ *
* GROningen MAchine for Chemical Simulations
- *
+ *
* VERSION 3.2.0
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
- *
+ *
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
- *
+ *
* For more info, check our website at http://www.gromacs.org
- *
+ *
* And Hey:
* GROningen Mixture of Alchemy and Childrens' Stories
*/
typedef struct {
- const char *name;
- int flop;
+ const char *name;
+ int flop;
} t_nrnb_data;
{ "NB VdW & Elec. [W4,F]", 1 },
{ "NB VdW & Elec. [W4-W4,V&F]", 1 },
{ "NB VdW & Elec. [W4-W4,F]", 1 },
-
+
{ "NB Generic kernel", 1 },
{ "NB Free energy kernel", 1 },
{ "NB All-vs-all", 1 },
{ "All-vs-All Born chain rule", 1 },
{ "Calc Weights", 36 },
{ "Spread Q", 6 },
- { "Spread Q Bspline", 2 },
+ { "Spread Q Bspline", 2 },
{ "Gather F", 23 },
- { "Gather F Bspline", 6 },
+ { "Gather F Bspline", 6 },
{ "3D-FFT", 8 },
{ "Convolution", 4 },
{ "Solve PME", 64 },
{ "Virtual Site 3fd", 95 },
{ "Virtual Site 3fad", 176 },
{ "Virtual Site 3out", 87 },
- { "Virtual Site 4fd", 110 },
- { "Virtual Site 4fdn", 254 },
+ { "Virtual Site 4fd", 110 },
+ { "Virtual Site 4fdn", 254 },
{ "Virtual Site N", 15 },
- { "Mixed Generalized Born stuff", 10 }
+ { "Mixed Generalized Born stuff", 10 }
};
void init_nrnb(t_nrnb *nrnb)
{
- int i;
+ int i;
- for(i=0; (i<eNRNB); i++)
- nrnb->n[i]=0.0;
+ for (i = 0; (i < eNRNB); i++)
+ {
+ nrnb->n[i] = 0.0;
+ }
}
void cp_nrnb(t_nrnb *dest, t_nrnb *src)
{
- int i;
+ int i;
- for(i=0; (i<eNRNB); i++)
- dest->n[i]=src->n[i];
+ for (i = 0; (i < eNRNB); i++)
+ {
+ dest->n[i] = src->n[i];
+ }
}
void add_nrnb(t_nrnb *dest, t_nrnb *s1, t_nrnb *s2)
{
- int i;
+ int i;
- for(i=0; (i<eNRNB); i++)
- dest->n[i]=s1->n[i]+s2->n[i];
+ for (i = 0; (i < eNRNB); i++)
+ {
+ dest->n[i] = s1->n[i]+s2->n[i];
+ }
}
void print_nrnb(FILE *out, t_nrnb *nrnb)
{
- int i;
+ int i;
- for(i=0; (i<eNRNB); i++)
- if (nrnb->n[i] > 0)
- fprintf(out," %-26s %10.0f.\n",nbdata[i].name,nrnb->n[i]);
+ for (i = 0; (i < eNRNB); i++)
+ {
+ if (nrnb->n[i] > 0)
+ {
+ fprintf(out, " %-26s %10.0f.\n", nbdata[i].name, nrnb->n[i]);
+ }
+ }
}
-void _inc_nrnb(t_nrnb *nrnb,int enr,int inc,char *file,int line)
+void _inc_nrnb(t_nrnb *nrnb, int enr, int inc, char *file, int line)
{
- nrnb->n[enr]+=inc;
+ nrnb->n[enr] += inc;
#ifdef DEBUG_NRNB
- printf("nrnb %15s(%2d) incremented with %8d from file %s line %d\n",
- nbdata[enr].name,enr,inc,file,line);
+ printf("nrnb %15s(%2d) incremented with %8d from file %s line %d\n",
+ nbdata[enr].name, enr, inc, file, line);
#endif
}
-void print_flop(FILE *out,t_nrnb *nrnb,double *nbfs,double *mflop)
+void print_flop(FILE *out, t_nrnb *nrnb, double *nbfs, double *mflop)
{
- int i;
- double mni,frac,tfrac,tflop;
- const char *myline = "-----------------------------------------------------------------------------";
-
- *nbfs = 0.0;
- for(i=0; (i<eNR_NBKERNEL_ALLVSALLGB); i++) {
- if (strstr(nbdata[i].name,"W3-W3") != NULL)
- *nbfs += 9e-6*nrnb->n[i];
- else if (strstr(nbdata[i].name,"W3") != NULL)
- *nbfs += 3e-6*nrnb->n[i];
- else if (strstr(nbdata[i].name,"W4-W4") != NULL)
- *nbfs += 10e-6*nrnb->n[i];
- else if (strstr(nbdata[i].name,"W4") != NULL)
- *nbfs += 4e-6*nrnb->n[i];
- else
- *nbfs += 1e-6*nrnb->n[i];
- }
- tflop=0;
- for(i=0; (i<eNRNB); i++)
- tflop+=1e-6*nrnb->n[i]*nbdata[i].flop;
-
- if (tflop == 0) {
- fprintf(out,"No MEGA Flopsen this time\n");
- return;
- }
- if (out) {
- fprintf(out,"\n\tM E G A - F L O P S A C C O U N T I N G\n\n");
- }
-
- if (out)
- {
- fprintf(out," NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels\n");
- fprintf(out," RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table\n");
- fprintf(out," W3=SPC/TIP3p W4=TIP4p (single or pairs)\n");
- fprintf(out," V&F=Potential and force V=Potential only F=Force only\n\n");
-
- fprintf(out," %-32s %16s %15s %7s\n",
- "Computing:","M-Number","M-Flops","% Flops");
- fprintf(out,"%s\n",myline);
- }
- *mflop=0.0;
- tfrac=0.0;
- for(i=0; (i<eNRNB); i++) {
- mni = 1e-6*nrnb->n[i];
- *mflop += mni*nbdata[i].flop;
- frac = 100.0*mni*nbdata[i].flop/tflop;
- tfrac += frac;
- if (out && mni != 0)
- fprintf(out," %-32s %16.6f %15.3f %6.1f\n",
- nbdata[i].name,mni,mni*nbdata[i].flop,frac);
- }
- if (out) {
- fprintf(out,"%s\n",myline);
- fprintf(out," %-32s %16s %15.3f %6.1f\n",
- "Total","",*mflop,tfrac);
- fprintf(out,"%s\n\n",myline);
- }
-}
+ int i;
+ double mni, frac, tfrac, tflop;
+ const char *myline = "-----------------------------------------------------------------------------";
-void print_perf(FILE *out,double nodetime,double realtime,int nprocs,
- gmx_large_int_t nsteps,real delta_t,
- double nbfs,double mflop,
- int omp_nth_pp)
-{
- real runtime;
+ *nbfs = 0.0;
+ for (i = 0; (i < eNR_NBKERNEL_ALLVSALLGB); i++)
+ {
+ if (strstr(nbdata[i].name, "W3-W3") != NULL)
+ {
+ *nbfs += 9e-6*nrnb->n[i];
+ }
+ else if (strstr(nbdata[i].name, "W3") != NULL)
+ {
+ *nbfs += 3e-6*nrnb->n[i];
+ }
+ else if (strstr(nbdata[i].name, "W4-W4") != NULL)
+ {
+ *nbfs += 10e-6*nrnb->n[i];
+ }
+ else if (strstr(nbdata[i].name, "W4") != NULL)
+ {
+ *nbfs += 4e-6*nrnb->n[i];
+ }
+ else
+ {
+ *nbfs += 1e-6*nrnb->n[i];
+ }
+ }
+ tflop = 0;
+ for (i = 0; (i < eNRNB); i++)
+ {
+ tflop += 1e-6*nrnb->n[i]*nbdata[i].flop;
+ }
- fprintf(out,"\n");
+ if (tflop == 0)
+ {
+ fprintf(out, "No MEGA Flopsen this time\n");
+ return;
+ }
+ if (out)
+ {
+ fprintf(out, "\n\tM E G A - F L O P S A C C O U N T I N G\n\n");
+ }
- if (realtime > 0)
- {
- fprintf(out,"%12s %12s %12s %10s\n","","Core t (s)","Wall t (s)","(%)");
- fprintf(out,"%12s %12.3f %12.3f %10.1f\n","Time:",
- nodetime, realtime, 100.0*nodetime/realtime);
- /* only print day-hour-sec format if realtime is more than 30 min */
- if (realtime > 30*60)
+ if (out)
{
- fprintf(out,"%12s %12s","","");
- pr_difftime(out,realtime);
+ fprintf(out, " NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels\n");
+ fprintf(out, " RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table\n");
+ fprintf(out, " W3=SPC/TIP3p W4=TIP4p (single or pairs)\n");
+ fprintf(out, " V&F=Potential and force V=Potential only F=Force only\n\n");
+
+ fprintf(out, " %-32s %16s %15s %7s\n",
+ "Computing:", "M-Number", "M-Flops", "% Flops");
+ fprintf(out, "%s\n", myline);
}
- if (delta_t > 0)
+ *mflop = 0.0;
+ tfrac = 0.0;
+ for (i = 0; (i < eNRNB); i++)
{
- mflop = mflop/realtime;
- runtime = nsteps*delta_t;
-
- if (getenv("GMX_DETAILED_PERF_STATS") == NULL)
- {
- fprintf(out,"%12s %12s %12s\n",
- "","(ns/day)","(hour/ns)");
- fprintf(out,"%12s %12.3f %12.3f\n","Performance:",
- runtime*24*3.6/realtime,1000*realtime/(3600*runtime));
- }
- else
- {
- fprintf(out,"%12s %12s %12s %12s %12s\n",
- "","(Mnbf/s)",(mflop > 1000) ? "(GFlops)" : "(MFlops)",
- "(ns/day)","(hour/ns)");
- fprintf(out,"%12s %12.3f %12.3f %12.3f %12.3f\n","Performance:",
- nbfs/realtime,(mflop > 1000) ? (mflop/1000) : mflop,
- runtime*24*3.6/realtime,1000*realtime/(3600*runtime));
- }
- }
- else
+ mni = 1e-6*nrnb->n[i];
+ *mflop += mni*nbdata[i].flop;
+ frac = 100.0*mni*nbdata[i].flop/tflop;
+ tfrac += frac;
+ if (out && mni != 0)
+ {
+ fprintf(out, " %-32s %16.6f %15.3f %6.1f\n",
+ nbdata[i].name, mni, mni*nbdata[i].flop, frac);
+ }
+ }
+ if (out)
{
- if (getenv("GMX_DETAILED_PERF_STATS") == NULL)
- {
- fprintf(out,"%12s %14s\n",
- "","(steps/hour)");
- fprintf(out,"%12s %14.1f\n","Performance:",
- nsteps*3600.0/realtime);
- }
- else
- {
- fprintf(out,"%12s %12s %12s %14s\n",
- "","(Mnbf/s)",(mflop > 1000) ? "(GFlops)" : "(MFlops)",
- "(steps/hour)");
- fprintf(out,"%12s %12.3f %12.3f %14.1f\n","Performance:",
- nbfs/realtime,(mflop > 1000) ? (mflop/1000) : mflop,
- nsteps*3600.0/realtime);
- }
+ fprintf(out, "%s\n", myline);
+ fprintf(out, " %-32s %16s %15.3f %6.1f\n",
+ "Total", "", *mflop, tfrac);
+ fprintf(out, "%s\n\n", myline);
+ }
+}
+
+void print_perf(FILE *out, double nodetime, double realtime, int nprocs,
+ gmx_large_int_t nsteps, real delta_t,
+ double nbfs, double mflop,
+ int omp_nth_pp)
+{
+ real runtime;
+
+ fprintf(out, "\n");
+
+ if (realtime > 0)
+ {
+ fprintf(out, "%12s %12s %12s %10s\n", "", "Core t (s)", "Wall t (s)", "(%)");
+ fprintf(out, "%12s %12.3f %12.3f %10.1f\n", "Time:",
+ nodetime, realtime, 100.0*nodetime/realtime);
+ /* only print day-hour-sec format if realtime is more than 30 min */
+ if (realtime > 30*60)
+ {
+ fprintf(out, "%12s %12s", "", "");
+ pr_difftime(out, realtime);
+ }
+ if (delta_t > 0)
+ {
+ mflop = mflop/realtime;
+ runtime = nsteps*delta_t;
+
+ if (getenv("GMX_DETAILED_PERF_STATS") == NULL)
+ {
+ fprintf(out, "%12s %12s %12s\n",
+ "", "(ns/day)", "(hour/ns)");
+ fprintf(out, "%12s %12.3f %12.3f\n", "Performance:",
+ runtime*24*3.6/realtime, 1000*realtime/(3600*runtime));
+ }
+ else
+ {
+ fprintf(out, "%12s %12s %12s %12s %12s\n",
+ "", "(Mnbf/s)", (mflop > 1000) ? "(GFlops)" : "(MFlops)",
+ "(ns/day)", "(hour/ns)");
+ fprintf(out, "%12s %12.3f %12.3f %12.3f %12.3f\n", "Performance:",
+ nbfs/realtime, (mflop > 1000) ? (mflop/1000) : mflop,
+ runtime*24*3.6/realtime, 1000*realtime/(3600*runtime));
+ }
+ }
+ else
+ {
+ if (getenv("GMX_DETAILED_PERF_STATS") == NULL)
+ {
+ fprintf(out, "%12s %14s\n",
+ "", "(steps/hour)");
+ fprintf(out, "%12s %14.1f\n", "Performance:",
+ nsteps*3600.0/realtime);
+ }
+ else
+ {
+ fprintf(out, "%12s %12s %12s %14s\n",
+ "", "(Mnbf/s)", (mflop > 1000) ? "(GFlops)" : "(MFlops)",
+ "(steps/hour)");
+ fprintf(out, "%12s %12.3f %12.3f %14.1f\n", "Performance:",
+ nbfs/realtime, (mflop > 1000) ? (mflop/1000) : mflop,
+ nsteps*3600.0/realtime);
+ }
+ }
}
- }
}
int cost_nrnb(int enr)
{
- return nbdata[enr].flop;
+ return nbdata[enr].flop;
}
const char *nrnb_str(int enr)
{
- return nbdata[enr].name;
+ return nbdata[enr].name;
}
-static const int force_index[]={
- eNR_BONDS, eNR_ANGLES, eNR_PROPER, eNR_IMPROPER,
- eNR_RB, eNR_DISRES, eNR_ORIRES, eNR_POSRES,
- eNR_FBPOSRES, eNR_NS,
+static const int force_index[] = {
+ eNR_BONDS, eNR_ANGLES, eNR_PROPER, eNR_IMPROPER,
+ eNR_RB, eNR_DISRES, eNR_ORIRES, eNR_POSRES,
+ eNR_FBPOSRES, eNR_NS,
};
#define NFORCE_INDEX asize(force_index)
-static const int constr_index[]={
- eNR_SHAKE, eNR_SHAKE_RIJ, eNR_SETTLE, eNR_UPDATE, eNR_PCOUPL,
- eNR_CONSTR_VIR,eNR_CONSTR_V
+static const int constr_index[] = {
+ eNR_SHAKE, eNR_SHAKE_RIJ, eNR_SETTLE, eNR_UPDATE, eNR_PCOUPL,
+ eNR_CONSTR_VIR, eNR_CONSTR_V
};
#define NCONSTR_INDEX asize(constr_index)
-static double pr_av(FILE *log,t_commrec *cr,
- double fav,double ftot[],const char *title)
+static double pr_av(FILE *log, t_commrec *cr,
+ double fav, double ftot[], const char *title)
{
- int i,perc;
- double dperc,unb;
-
- unb=0;
- if (fav > 0) {
- fav /= cr->nnodes - cr->npmenodes;
- fprintf(log,"\n %-26s",title);
- for(i=0; (i<cr->nnodes); i++) {
- dperc=(100.0*ftot[i])/fav;
- unb=max(unb,dperc);
- perc=dperc;
- fprintf(log,"%3d ",perc);
- }
- if (unb > 0) {
- perc=10000.0/unb;
- fprintf(log,"%6d%%\n\n",perc);
+ int i, perc;
+ double dperc, unb;
+
+ unb = 0;
+ if (fav > 0)
+ {
+ fav /= cr->nnodes - cr->npmenodes;
+ fprintf(log, "\n %-26s", title);
+ for (i = 0; (i < cr->nnodes); i++)
+ {
+ dperc = (100.0*ftot[i])/fav;
+ unb = max(unb, dperc);
+ perc = dperc;
+ fprintf(log, "%3d ", perc);
+ }
+ if (unb > 0)
+ {
+ perc = 10000.0/unb;
+ fprintf(log, "%6d%%\n\n", perc);
+ }
+ else
+ {
+ fprintf(log, "\n\n");
+ }
}
- else
- fprintf(log,"\n\n");
- }
- return unb;
+ return unb;
}
-void pr_load(FILE *log,t_commrec *cr,t_nrnb nrnb[])
+void pr_load(FILE *log, t_commrec *cr, t_nrnb nrnb[])
{
- int i,j,perc;
- double dperc,unb,uf,us;
- double *ftot,fav;
- double *stot,sav;
- t_nrnb *av;
-
- snew(av,1);
- snew(ftot,cr->nnodes);
- snew(stot,cr->nnodes);
- init_nrnb(av);
- for(i=0; (i<cr->nnodes); i++) {
- add_nrnb(av,av,&(nrnb[i]));
- /* Cost due to forces */
- for(j=0; (j<eNR_NBKERNEL_ALLVSALLGB); j++)
- ftot[i]+=nrnb[i].n[j]*cost_nrnb(j);
- for(j=0; (j<NFORCE_INDEX); j++)
- ftot[i]+=nrnb[i].n[force_index[j]]*cost_nrnb(force_index[j]);
- /* Due to shake */
- for(j=0; (j<NCONSTR_INDEX); j++) {
- stot[i]+=nrnb[i].n[constr_index[j]]*cost_nrnb(constr_index[j]);
- }
- }
- for(j=0; (j<eNRNB); j++)
- av->n[j]=av->n[j]/(double)(cr->nnodes - cr->npmenodes);
-
- fprintf(log,"\nDetailed load balancing info in percentage of average\n");
-
- fprintf(log," Type NODE:");
- for(i=0; (i<cr->nnodes); i++)
- fprintf(log,"%3d ",i);
- fprintf(log,"Scaling\n");
- fprintf(log,"---------------------------");
- for(i=0; (i<cr->nnodes); i++)
- fprintf(log,"----");
- fprintf(log,"-------\n");
-
- for(j=0; (j<eNRNB); j++) {
- unb=100.0;
- if (av->n[j] > 0) {
- fprintf(log," %-26s",nrnb_str(j));
- for(i=0; (i<cr->nnodes); i++) {
- dperc=(100.0*nrnb[i].n[j])/av->n[j];
- unb=max(unb,dperc);
- perc=dperc;
- fprintf(log,"%3d ",perc);
- }
- if (unb > 0) {
- perc=10000.0/unb;
- fprintf(log,"%6d%%\n",perc);
- }
- else
- fprintf(log,"\n");
- }
- }
- fav=sav=0;
- for(i=0; (i<cr->nnodes); i++) {
- fav+=ftot[i];
- sav+=stot[i];
- }
- uf=pr_av(log,cr,fav,ftot,"Total Force");
- us=pr_av(log,cr,sav,stot,"Total Constr.");
-
- unb=(uf*fav+us*sav)/(fav+sav);
- if (unb > 0) {
- unb=10000.0/unb;
- fprintf(log,"\nTotal Scaling: %.0f%% of max performance\n\n",unb);
- }
-}
+ int i, j, perc;
+ double dperc, unb, uf, us;
+ double *ftot, fav;
+ double *stot, sav;
+ t_nrnb *av;
+
+ snew(av, 1);
+ snew(ftot, cr->nnodes);
+ snew(stot, cr->nnodes);
+ init_nrnb(av);
+ for (i = 0; (i < cr->nnodes); i++)
+ {
+ add_nrnb(av, av, &(nrnb[i]));
+ /* Cost due to forces */
+ for (j = 0; (j < eNR_NBKERNEL_ALLVSALLGB); j++)
+ {
+ ftot[i] += nrnb[i].n[j]*cost_nrnb(j);
+ }
+ for (j = 0; (j < NFORCE_INDEX); j++)
+ {
+ ftot[i] += nrnb[i].n[force_index[j]]*cost_nrnb(force_index[j]);
+ }
+ /* Due to shake */
+ for (j = 0; (j < NCONSTR_INDEX); j++)
+ {
+ stot[i] += nrnb[i].n[constr_index[j]]*cost_nrnb(constr_index[j]);
+ }
+ }
+ for (j = 0; (j < eNRNB); j++)
+ {
+ av->n[j] = av->n[j]/(double)(cr->nnodes - cr->npmenodes);
+ }
+
+ fprintf(log, "\nDetailed load balancing info in percentage of average\n");
+ fprintf(log, " Type NODE:");
+ for (i = 0; (i < cr->nnodes); i++)
+ {
+ fprintf(log, "%3d ", i);
+ }
+ fprintf(log, "Scaling\n");
+ fprintf(log, "---------------------------");
+ for (i = 0; (i < cr->nnodes); i++)
+ {
+ fprintf(log, "----");
+ }
+ fprintf(log, "-------\n");
+
+ for (j = 0; (j < eNRNB); j++)
+ {
+ unb = 100.0;
+ if (av->n[j] > 0)
+ {
+ fprintf(log, " %-26s", nrnb_str(j));
+ for (i = 0; (i < cr->nnodes); i++)
+ {
+ dperc = (100.0*nrnb[i].n[j])/av->n[j];
+ unb = max(unb, dperc);
+ perc = dperc;
+ fprintf(log, "%3d ", perc);
+ }
+ if (unb > 0)
+ {
+ perc = 10000.0/unb;
+ fprintf(log, "%6d%%\n", perc);
+ }
+ else
+ {
+ fprintf(log, "\n");
+ }
+ }
+ }
+ fav = sav = 0;
+ for (i = 0; (i < cr->nnodes); i++)
+ {
+ fav += ftot[i];
+ sav += stot[i];
+ }
+ uf = pr_av(log, cr, fav, ftot, "Total Force");
+ us = pr_av(log, cr, sav, stot, "Total Constr.");
+
+ unb = (uf*fav+us*sav)/(fav+sav);
+ if (unb > 0)
+ {
+ unb = 10000.0/unb;
+ fprintf(log, "\nTotal Scaling: %.0f%% of max performance\n\n", unb);
+ }
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff