static void PrintDlgUpdate(
paramGroup_p pg,
int inx,
void * valueP )
{
if ( inx < 0 ) return;
if ( pg->paramPtr[inx].context == (void*)1 )
DoPrintScale();
else if ( pg->paramPtr[inx].context == (void*)2 )
PrintUpdate( inx );
ParamControlActive( &printPG, I_RULER, currPrintGrid.angle == 0 );
}
void ContinueExecution()
{
static BOOL pageflipping = 0; //?
const double fUsecPerSec = 1.e6;
#if 1
const UINT nExecutionPeriodUsec = 1000; // 1.0ms
// const UINT nExecutionPeriodUsec = 100; // 0.1ms
const double fExecutionPeriodClks = g_fCurrentCLK6502 * ((double)nExecutionPeriodUsec / fUsecPerSec);
#else
const double fExecutionPeriodClks = 1800.0;
const UINT nExecutionPeriodUsec = (UINT) (fUsecPerSec * (fExecutionPeriodClks / g_fCurrentCLK6502));
#endif
//
bool bScrollLock_FullSpeed = g_uScrollLockToggle
? g_bScrollLock_FullSpeed
: (GetKeyState(VK_SCROLL) < 0);
g_bFullSpeed = ( (g_dwSpeed == SPEED_MAX) ||
bScrollLock_FullSpeed ||
(DiskIsSpinning() && enhancedisk && !Spkr_IsActive() && !MB_IsActive()) );
if(g_bFullSpeed)
{
// Don't call Spkr_Mute() - will get speaker clicks
MB_Mute();
SysClk_StopTimer();
g_nCpuCyclesFeedback = 0; // For the case when this is a big -ve number
}
else
{
// Don't call Spkr_Demute()
MB_Demute();
SysClk_StartTimerUsec(nExecutionPeriodUsec);
}
//
int nCyclesToExecute = (int) fExecutionPeriodClks + g_nCpuCyclesFeedback;
if(nCyclesToExecute < 0)
nCyclesToExecute = 0;
DWORD dwExecutedCycles = CpuExecute(nCyclesToExecute);
g_dwCyclesThisFrame += dwExecutedCycles;
//
cyclenum = dwExecutedCycles;
DiskUpdatePosition(dwExecutedCycles);
JoyUpdatePosition();
VideoUpdateVbl(g_dwCyclesThisFrame);
SpkrUpdate(cyclenum);
sg_SSC.CommUpdate(cyclenum);
PrintUpdate(cyclenum);
//
const DWORD CLKS_PER_MS = (DWORD)g_fCurrentCLK6502 / 1000;
emulmsec_frac += dwExecutedCycles;
if(emulmsec_frac > CLKS_PER_MS)
{
emulmsec += emulmsec_frac / CLKS_PER_MS;
emulmsec_frac %= CLKS_PER_MS;
}
//
// DETERMINE WHETHER THE SCREEN WAS UPDATED, THE DISK WAS SPINNING,
// OR THE KEYBOARD I/O PORTS WERE BEING EXCESSIVELY QUERIED THIS CLOCKTICK
VideoCheckPage(0);
BOOL screenupdated = VideoHasRefreshed();
BOOL systemidle = 0; //(KeybGetNumQueries() > (clockgran << 2)); // && (!ranfinegrain); // TO DO
if(screenupdated)
pageflipping = 3;
//
if(g_dwCyclesThisFrame >= dwClksPerFrame)
{
g_dwCyclesThisFrame -= dwClksPerFrame;
if(g_nAppMode != MODE_LOGO)
{
VideoUpdateFlash();
static BOOL anyupdates = 0;
static DWORD lastcycles = 0;
static BOOL lastupdates[2] = {0,0};
anyupdates |= screenupdated;
//
lastcycles = cumulativecycles;
if ((!anyupdates) && (!lastupdates[0]) && (!lastupdates[1]) && VideoApparentlyDirty())
{
VideoCheckPage(1);
static DWORD lasttime = 0;
DWORD currtime = GetTickCount();
if ((!g_bFullSpeed) ||
(currtime-lasttime >= (DWORD)((graphicsmode || !systemidle) ? 100 : 25)))
{
VideoRefreshScreen();
lasttime = currtime;
}
screenupdated = 1;
}
lastupdates[1] = lastupdates[0];
lastupdates[0] = anyupdates;
anyupdates = 0;
if (pageflipping)
pageflipping--;
}
MB_EndOfVideoFrame();
}
//
if(!g_bFullSpeed)
{
SysClk_WaitTimer();
#if DBG_CALC_FREQ
if(g_nPerfFreq)
{
QueryPerformanceCounter((LARGE_INTEGER*)&nTime1);
LONGLONG nTimeDiff = nTime1 - nTime0;
double fTime = (double)nTimeDiff / (double)(LONGLONG)g_nPerfFreq;
g_fDbg[g_nIdx] = fTime;
g_nIdx = (g_nIdx+1) & (MAX_CNT-1);
g_fMeanPeriod = 0.0;
for(UINT n=0; n<MAX_CNT; n++)
g_fMeanPeriod += g_fDbg[n];
g_fMeanPeriod /= (double)MAX_CNT;
g_fMeanFreq = 1.0 / g_fMeanPeriod;
}
#endif
}
}
int main (int argc, char *argv[])
{
/*data--------- */
int *Geno; /*NUMINDSxLINES: genotypes */
float *R; /*NUMINDS */
float *Mapdistance; /*NUMLOCI */
float *Phase; /*NUMLOCI*NUMINDS */
int *Phasemodel=NULL; /*NUMINDS */
char *Markername; /*GENELEN*NUMLOCI */
struct IND *Individual; /*NUMINDS: records for each individual */
int *Translation; /*NUMLOCIxMAXALLELES: value of each coded allele */
int *NumAlleles; /*NUMLOCI: number of alleles at each locus */
/* only used for recessive or inbreeding models: */
int *PreGeno=
NULL; /*NUMINDSxLINESxNUMLOCI; diploid genotype if recessive alleles */
int *Recessive=
NULL; /*NUMLOCI recessive allele at each locus, or -1 if there is none */
/*Basic parameters */
int *Z; /*NUMINDSx2xNUMLOCI: Z=pop of origin for each allele */
int *Z1;
float *Q; /*NUMINDSxMAXPOPS: Q=ancestry of individuals */
float *P; /*NUMLOCIxMAXPOPSxMAXALLELES: P=population allele freqs */
float *Epsilon; /*NUMLOCIxMAXALLELES: Dirichlet parameter for allele
frequencies. This is either LAMBDA (if uncorrelated), or
ancestral allele freqs if they are correlated */
float *Fst; /*MAXPOPS: Factor multiplied by epsilon under the Fst model */
float *Alpha; /*MAXPOPS: Dirichlet parameter for degree of admixture.
Start this at ALPHA, and possibly change
(if INFERALPHA==1) */
float *lambda; /*Dirichlet prior parameter for allele frequencies;
start this at LAMBDA, and update if INFERLAMBDA*/
float *sumlambda;
/*Summaries */
int *NumLociPop; /*NUMINDSxMAXPOPS: Number of alleles from each pop (by ind) */
float *PSum; /*NUMLOCIxMAXPOPSxMAXALLELES: sum of AlFreqs */
float *QSum; /*NUMINDSxMAXPOPS: sum of Ancestries */
float *FstSum; /*MAXPOPS: Sum of Fst */
float *SumEpsilon=
NULL; /*NUMLOCIxMAXALLELES: sum of ancestral allele freqs*/
float *sumAlpha; /*MAXPOPS*/
float *sumR; /*NUMINDS */
float *varR; /*NUMINDS */
float recomblikelihood=0.0;
float *like; /*current likelihood value */
float *sumlikes; /*sum of likelihood values */
float *sumsqlikes; /*sum of squared likelihoods */
int *popflags; /*The populationflags of individuals*/
unsigned int *randGens;
/*Melissa added 7/12/07 for calculating DIC*/
float *sumIndLikes, *indLikesNorm;
int *AncestDist=
NULL; /*NUMINDS*MAXPOPS*NUMBOXES histogram of Q values */
float *UsePopProbs=
NULL; /*NUMINDS*MAXPOPS*(GENSBACK+1) This is used when the
population info is used. It stores the probability that an
individual has each of a specified set of ancestry amounts */
/*loop variables-------------- */
int rep; /*MCMC iterations so far */
int savefreq; /*frequency of saving to file */
int ind;
/*Melissa's new variables added 7/12/07 to use priors based on sampling location*/
float *LocPrior=NULL, *sumLocPrior=NULL, LocPriorLen=0;
/* ======================= GPU Structure ======================== */
/*Dict to that keeps track of CL info */
/*CLDict *clDict = NULL;*/
float * randomArr; /* array of random numbers */
int POPFLAGINDS = 0;
float invsqrtnuminds;
/* enum BUFFER buffers[5]; */
/* char *names[5]; */
/* size_t sizes[5]; */
/* void *dests[5]; */
float *reduceresult;
int *Numafrompopscl;
int *Numlocipopscl;
if (signal(SIGINT, catch_function) == SIG_ERR) {
fputs("An error occurred while setting a signal handler.\n", stderr);
return EXIT_FAILURE;
}
clDict = malloc(sizeof (*clDict));
sumlikes = calloc(1,sizeof(float));
sumsqlikes = calloc(1,sizeof(float));
like = calloc(1,sizeof(float));
/*=====Code for getting started=============================*/
Welcome (stdout); /*welcome */
GetParams (0,argc,argv); /*read in parameter values */
CheckParamCombinations(); /*check that some parameter combinations are valid*/
Mapdistance = calloc (NUMLOCI, sizeof (float));
Phase = calloc (NUMLOCI * NUMINDS, sizeof (float));
if (LINES ==2 && PHASED ==0) {
Phasemodel=calloc(NUMINDS,sizeof(int));
for (ind=0; ind<NUMINDS; ind++) {
if (MARKOVPHASE) {
Phasemodel[ind]=0;
} else {
Phasemodel[ind]=1;
}
}
}
lambda=calloc(MAXPOPS, sizeof (float));
sumlambda=calloc(MAXPOPS, sizeof (float));
Markername = calloc (GENELEN*NUMLOCI, sizeof (char));
Geno = calloc (LINES * NUMLOCI * NUMINDS, sizeof (int));
if (RECESSIVEALLELES) {
PreGeno = calloc (LINES * NUMLOCI * NUMINDS, sizeof (int));
Recessive = calloc (NUMLOCI, sizeof (int));
if (PreGeno == NULL || Recessive == NULL) {
printf ("Error (3) in assigning memory\n");
Kill ();
}
}
Individual = calloc (NUMINDS, sizeof (struct IND));
if (Geno == NULL || Individual == NULL || Mapdistance == NULL
|| Markername == NULL) {
printf ("Error in assigning memory (not enough space?)\n");
Kill ();
}
Randomize(RANDOMIZE, &SEED);
/*read in data file */
if (RECESSIVEALLELES) {
ReadInputFile(PreGeno, Mapdistance, Markername, Individual, Phase, Recessive);
} else {
ReadInputFile (Geno, Mapdistance, Markername, Individual, Phase, Recessive);
}
if (RECESSIVEALLELES) {
MAXALLELES = FindMaxAlleles (PreGeno, Recessive);
} else {
MAXALLELES = FindMaxAlleles (Geno, Recessive);
}
/*=============set aside memory space=====================*/
Translation = calloc (NUMLOCI * MAXALLELES, sizeof (int));
NumAlleles = calloc (NUMLOCI, sizeof (int));
Z = calloc (NUMINDS * LINES * NUMLOCI, sizeof (int));
Z1 = calloc (NUMINDS * LINES * NUMLOCI, sizeof (int));
Q = calloc (NUMINDS * MAXPOPS, sizeof (float));
P = calloc (NUMLOCI * MAXPOPS * MAXALLELES, sizeof (float));
R = calloc (NUMINDS, sizeof (float));
sumR = calloc (NUMINDS, sizeof (float));
varR = calloc (NUMINDS, sizeof (float));
Epsilon = calloc (NUMLOCI * MAXALLELES, sizeof (float));
if (FREQSCORR) {
SumEpsilon = calloc (NUMLOCI * MAXALLELES, sizeof (float));
}
Fst = calloc (MAXPOPS, sizeof (float));
FstSum = calloc (MAXPOPS, sizeof (float));
NumLociPop = calloc (NUMINDS * MAXPOPS, sizeof (int));
PSum = calloc (NUMLOCI * MAXPOPS * MAXALLELES, sizeof (float));
QSum = calloc (NUMINDS * MAXPOPS, sizeof (float));
if (ANCESTDIST) {
AncestDist = calloc (NUMINDS * MAXPOPS * NUMBOXES, sizeof (int));
}
if (USEPOPINFO) {
UsePopProbs = calloc (NUMINDS * MAXPOPS * (GENSBACK + 1), sizeof (float));
}
/*Melissa added 7/12/07*/
if (LOCDATA>0 || LOCISPOP) {
GetNumLocations(Individual);
}
/*Allocate the LocPrior vector.
For no-admixture, it contains r, and the vectors nu and gamma.
For admixture, it contains gamma. The alphas_locals are stored with alpha global*/
if (LOCPRIOR) {
if (NOADMIX) {
LocPriorLen = 1+MAXPOPS*(NUMLOCATIONS+1);
} else {
LocPriorLen=1;
}
LocPrior = malloc(LocPriorLen*sizeof(float));
sumLocPrior = malloc(LocPriorLen*sizeof(float));
}
if (LOCPRIOR && NOADMIX==0) {
Alpha = malloc(MAXPOPS*(NUMLOCATIONS+1)*sizeof(float));
sumAlpha = malloc(MAXPOPS*(NUMLOCATIONS+1)*sizeof(float));
} else {
Alpha = calloc(MAXPOPS, sizeof (float));
sumAlpha = calloc(MAXPOPS, sizeof (float));
}
/* this is for DIC */
sumIndLikes = malloc(NUMINDS*sizeof(float));
indLikesNorm = malloc(NUMINDS*sizeof(float));
if ((Translation == NULL) || (NumAlleles == NULL) || (Z == NULL)
|| (Z1 == NULL) || (Q == NULL) ||
(P == NULL) || (R == NULL) || (sumR == NULL) || (varR == NULL)
|| (Epsilon == NULL) ||
(Fst == NULL) || (NumLociPop == NULL) ||
(PSum == NULL) || (QSum == NULL) || (FstSum == NULL) ||
((ANCESTDIST) && (AncestDist == NULL)) ||
((USEPOPINFO) && (UsePopProbs == NULL))||(Alpha == NULL)||(sumAlpha==NULL)||
((FREQSCORR) && (SumEpsilon == NULL)) ||
(LocPriorLen>0 && (LocPrior==NULL || sumLocPrior==NULL)) ||
sumIndLikes==NULL || indLikesNorm==NULL) {
printf ("Error in assigning memory (not enough space?)\n");
FreeAll(Mapdistance, Phase, Phasemodel, lambda, sumlambda, Markername, Geno,
PreGeno, Recessive,
Individual, Translation, NumAlleles, Z, Z1, Q, P, R, sumR, varR, Epsilon,
SumEpsilon,
Fst, FstSum, NumLociPop, PSum, QSum, AncestDist, UsePopProbs, LocPrior,
sumLocPrior, Alpha, sumAlpha, sumIndLikes, indLikesNorm, clDict);
Kill ();
}
/*=========done setting aside memory space=====================*/
/*initialize variables and arrays */
Initialization (Geno, PreGeno, Individual, Translation, NumAlleles, Z, Z1,
Epsilon, SumEpsilon,
Fst, PSum, Q, QSum, FstSum, AncestDist, UsePopProbs, Alpha,
sumAlpha, sumR, varR, sumlikes, sumsqlikes, &savefreq, R, lambda,
sumlambda,Phase,Recessive, LocPrior, sumLocPrior, LocPriorLen, sumIndLikes,
indLikesNorm, clDict);
/* ==================== GPU Structure ==================== */
/*Allocate an array of random numbers. Primarily used so that we can compare
CL implementation to the original */
randomArr = calloc(RANDSIZE,sizeof(float));
randGens = calloc(NUMRANDGENS,sizeof(unsigned int));
Numafrompopscl = calloc(NUMLOCI*MAXPOPS*MAXALLELES,sizeof(int));
Numlocipopscl = calloc(NUMINDS*MAXPOPS,sizeof(int));
/* ====== OpenCL initialized ====== */
printf ("\n\n--------------------------------------\n\n");
printf ("Finished initialization; starting MCMC \n");
printf ("%d iterations + %d burnin\n\n", NUMREPS, BURNIN);
/*=====Main MCMC loop=======================================*/
writeBuffer(clDict,Numafrompopscl,sizeof(int) * NUMLOCI*MAXPOPS*MAXALLELES,NUMAFROMPOPSCL,"NumAFromPops");
writeBuffer(clDict,Numlocipopscl,sizeof(int)*NUMINDS*MAXPOPS,NUMLOCIPOPSCL,"NUMLOCIPOPS");
/* init buffers on GPU */
writeBuffer(clDict,P,sizeof(float) * PSIZE,PCL,"P");
writeBuffer(clDict,Z,sizeof(int)*ZSIZE,ZCL,"Z");
writeBuffer(clDict,Q, sizeof(float) * QSIZE,QCL, "Q");
writeBuffer(clDict,NumAlleles,sizeof(int) * NUMLOCI,NUMALLELESCL,"NumAlleles");
writeBuffer(clDict,lambda,sizeof(float) * MAXPOPS,LAMBDACL,"LAMBDA");
if(!RECESSIVEALLELES){
writeBuffer(clDict,Geno,sizeof(int)*GENOSIZE,GENOCL,"Geno");
}
popflags = calloc(NUMINDS,sizeof(int));
for(ind = 0; ind < NUMINDS;ind++){
popflags[ind] = Individual[ind].PopFlag;
if (!((USEPOPINFO) && (Individual[ind].PopFlag))) {
POPFLAGINDS++;
}
}
printf("Setting updatealpha arg\n");
setKernelArgExplicit(clDict,UpdateAlphaKernel,sizeof(int),&POPFLAGINDS,7);
printf("Setting invsqrtnuminds arg\n");
invsqrtnuminds = 1.0/sqrt(NUMINDS);
setKernelArgExplicit(clDict,NonIndUpdateEpsilonKernel,sizeof(float),&invsqrtnuminds,6);
writeBuffer(clDict,popflags,sizeof(int)*NUMINDS,POPFLAGCL,"popflags");
writeBuffer(clDict,Alpha,sizeof(float) *MAXPOPS,ALPHACL,"Alpha");
reduceresult = calloc(NUMINDS*NUMLOCI*MAXGROUPS,sizeof(float));
if(reduceresult == NULL){
printf("Failed to allocate reduce result\n");
}
printf("Writing reduce results\n");
writeBuffer(clDict,reduceresult,sizeof(float)*MAXGROUPS*NUMINDS*NUMLOCI,REDUCERESULTSCL,"result");
printf("Done writing reduce results\n");
writeBuffer(clDict,sumAlpha, sizeof(float) * MAXPOPS,ALPHASUMCL, "alphasum");
writeBuffer(clDict,sumlambda, sizeof(float) * MAXPOPS,LAMBDASUMCL, "lambdasum");
writeBuffer(clDict,like, sizeof(float),LIKECL, "like");
writeBuffer(clDict,sumsqlikes, sizeof(float),SUMSQLIKESCL, "sumsqlikes");
writeBuffer(clDict,sumlikes, sizeof(float),SUMLIKESCL, "sumlikes");
writeBuffer(clDict,QSum, sizeof(float) * QSIZE,QSUMCL, "qsum");
writeBuffer(clDict,PSum, sizeof(float) * PSIZE,PSUMCL, "psum");
writeBuffer(clDict,SumEpsilon, sizeof(float) * NUMLOCI*MAXALLELES,EPSILONSUMCL, "epssum");
if(ANCESTDIST){
writeBuffer(clDict,AncestDist, sizeof(int)*NUMINDS*MAXPOPS*NUMBOXES,ANCESTDISTCL, "ancest dist");
}
if (FREQSCORR) {
writeBuffer(clDict,Fst,sizeof(float) * MAXPOPS,FSTCL,"FST");
writeBuffer(clDict,FstSum, sizeof(float) * MAXPOPS,FSTSUMCL, "fstsum");
writeBuffer(clDict,Epsilon,sizeof(float) * NUMLOCI*MAXALLELES,EPSILONCL,
"EPSILON");
}
/*printf("%d, %d\n",INFERALPHA,INFERLAMBDA);*/
/*printf("%d\n",USEPOPINFO);*/
/*printf("%d\n",RECESSIVEALLELES);*/
/*printf("%d\n",LINKAGE);*/
/*printf("%d\n",COMPUTEPROB);*/
/*printf("%d\n",POPALPHAS);*/
/*printf("%d\n",NOADMIX);*/
/*printf("%d\n",LOCPRIOR);*/
/*handleCLErr(1,clDict,"heyhey");*/
/*Initialize Q */
initQ(Q);
initRandGens(clDict,randGens);
finishWaitList(clDict);
printf("Waitlist finished!\n");
for (rep = 0; rep < (NUMREPS + BURNIN); rep++) {
breakP(clDict);
/*FillArrayWithRandomCL(clDict,randomArr,NUMLOCI*MAXALLELES*MAXPOPS*MAXRANDOM);*/
/*FillArrayWithRandom(randomArr,NUMLOCI*MAXALLELES*MAXPOPS*MAXRANDOM);*/
/*FillArrayWithRandom(randomArr,RANDSIZE);*/
/* if(DEBUGCOMPARE) { */
/* readBuffer(clDict,randomArr, */
/* sizeof(float) * NUMLOCI*MAXALLELES*MAXPOPS*MAXRANDOM,RANDCL, */
/* "randomArr"); */
/* comparePCLandP(clDict,P,Epsilon, Fst, NumAlleles, Geno, Z, */
/* lambda, Individual, randomArr); */
/* } */
/* if (USEWORKINGCL) { */
/* clear buffer */
writeBuffer(clDict,Numafrompopscl,sizeof(int) * NUMLOCI*MAXPOPS*MAXALLELES,NUMAFROMPOPSCL,"NumAFromPops");
UpdatePCL (clDict,P, Epsilon, Fst, NumAlleles, Geno, Z, lambda,
Individual,
randomArr);
/* } else { */
/* readBuffer(clDict,randomArr, */
/* sizeof(float) * NUMLOCI*MAXALLELES*MAXPOPS*MAXRANDOM,RANDCL, */
/* "randomArr"); */
/* UpdateP (P, Epsilon, Fst, NumAlleles, Geno, Z, lambda, Individual, */
/* randomArr); */
/* } */
/* Update Q */
/*FillArrayWithRandomCL(clDict,randomArr,NUMINDS+NUMINDS*MAXRANDOM);*/
if (LINKAGE && rep >= ADMBURNIN) {
UpdateQMetroRecombine (Geno, Q, Z, P, Alpha, rep,
Individual, Mapdistance, R, Phase,Phasemodel,randomArr);
} else {
writeBuffer(clDict,Numlocipopscl,sizeof(int)*NUMINDS*MAXPOPS,NUMLOCIPOPSCL,"NUMLOCIPOPS");
UpdateQCL (clDict,Geno, PreGeno, Q, P, Z, Alpha, rep, Individual, UsePopProbs,
Recessive, LocPrior,randomArr);
}
if (LOCPRIOR && UPDATELOCPRIOR) {
UpdateLocPrior(Q, LocPrior, Alpha, Individual);
}
if (RECESSIVEALLELES) {
UpdateGeno (PreGeno, Geno, P, Z, Recessive, NumAlleles, Q);
writeBuffer(clDict,Geno,sizeof(int) * GENOSIZE,GENOCL,"Geno");
/*The Zs are not correct after UpdateGeno, until UpdateZ is run */
}
if (LINKAGE && rep > ADMBURNIN) {
if (!INDIVIDUALR) {
recomblikelihood = UpdateZandSingleR(Z, Q, P, Geno,
R, Mapdistance, rep, Phase, Z1,Phasemodel, rep+1 > BURNIN? sumIndLikes : NULL,
indLikesNorm);
} else {
recomblikelihood = UpdateZandR(Z, Q, P, Geno, R,
Mapdistance, rep, Phase, Z1,Phasemodel, rep+1 > BURNIN ? sumIndLikes:NULL,
indLikesNorm);
}
} else {
/*FillArrayWithRandomCL(clDict,randomArr,NUMINDS*NUMLOCI*LINES);*/
/* if (DEBUGCOMPARE) { */
/* readBuffer(clDict,randomArr, */
/* sizeof(float) * NUMINDS*NUMLOCI*LINES,RANDCL, */
/* "randomArr"); */
/* compareZCLandZ(clDict,Z,Q,P,Geno,randomArr); */
/* } */
/* if (USEWORKINGCL) { */
UpdateZCL (clDict,Z, Q, P, Geno,randomArr);
/* Not needed */
/*readBuffer(clDict,Z,sizeof(int)*ZSIZE,ZCL,"Z");*/
/* } else { */
/* readBuffer(clDict,randomArr, */
/* sizeof(float) * NUMINDS*NUMLOCI*LINES,RANDCL, */
/* "randomArr"); */
/* UpdateZ (Z, Q, P, Geno,randomArr); */
/* } */
/* printf("done updatez alpha[2]=%e\n", Alpha[2]); */
}
if (LOCPRIOR && NOADMIX==0) {
UpdateAlphaLocPrior(Q, Alpha, LocPrior, Individual);
} else if (INFERALPHA) {
UpdateAlphaCL (clDict,Q, Alpha, Individual, rep,POPFLAGINDS);
/* readBuffer(clDict,Q, sizeof(float) * QSIZE,QCL, "Q"); */
/* readBuffer(clDict,Alpha, sizeof(float) * MAXPOPS,ALPHACL, "alpha"); */
/* UpdateAlpha(Q, Alpha, Individual, rep); */
/* writeBuffer(clDict,Alpha, sizeof(float) * MAXPOPS,ALPHACL, "alpha"); */
}
if (INFERLAMBDA) {
readBuffer(clDict,P,sizeof(float) * PSIZE,PCL,"P");
if (POPSPECIFICLAMBDA) {
UpdatePopLambda(P,lambda,NumAlleles);
} else {
UpdateLambda (P,Epsilon,lambda, NumAlleles);
}
writeBuffer(clDict,lambda,sizeof(float) * MAXPOPS,LAMBDACL,"LAMBDA");
}
if (FREQSCORR) {
UpdateEpsilonCL(clDict,P,Epsilon,Fst,NumAlleles,lambda[0]);
UpdateFstCL (clDict,Epsilon, Fst, P, NumAlleles);
/* readBuffer(clDict,P, sizeof(float) * PSIZE,PCL, "P"); */
/* readBuffer(clDict,Fst,sizeof(float) * MAXPOPS,FSTCL,"FST"); */
/* readBuffer(clDict,Epsilon,sizeof(float) * NUMLOCI*MAXALLELES,EPSILONCL,"eps"); */
/* UpdateEpsilon(P,Epsilon,Fst,NumAlleles,lambda[0]); */
/* UpdateFst (Epsilon, Fst, P, NumAlleles); */
/* writeBuffer(clDict,Epsilon,sizeof(float) * NUMLOCI*MAXALLELES,EPSILONCL,"eps"); */
/* writeBuffer(clDict,Fst,sizeof(float) * MAXPOPS,FSTCL,"FST"); */
}
/*====book-keeping stuff======================*/
if (rep + 1 > BURNIN) {
/*buffers[0] = PCL;
names[0] = "P"; dests[0] = P; sizes[0] = sizeof(float) * PSIZE;
buffers[1] = QCL;
names[1] = "Q"; dests[1] = Q; sizes[1] = sizeof(float) * QSIZE;
readBuffers(clDict,dests,sizes,buffers,names,2);*/
/*readBuffer(clDict,Alpha, sizeof(float) * MAXPOPS,ALPHACL, "alpha");
if(rep % 100 == 0){
printf("%f",Alpha[0]);
}*/
DataCollectionCL (clDict,Geno, PreGeno, Q, QSum, Z, Z1, P, PSum,
Fst, FstSum, NumAlleles,
AncestDist, Alpha, sumAlpha, sumR, varR, like,
sumlikes, sumsqlikes, R, Epsilon,SumEpsilon,recomblikelihood,
lambda, sumlambda, Recessive, LocPrior, sumLocPrior, LocPriorLen, sumIndLikes,
indLikesNorm, rep);
}
if ((savefreq) && ((rep + 1) > BURNIN)
&& (((rep + 1 - BURNIN) % savefreq) == 0)
&& ((rep + 1) != NUMREPS + BURNIN)) {
/* readBuffer(clDict,Alpha, sizeof(float) * MAXPOPS,ALPHACL, "alpha"); */
readBuffer(clDict,Fst, sizeof(float) * MAXPOPS,FSTCL, "fst");
readBuffer(clDict,sumAlpha, sizeof(float) * MAXPOPS,ALPHASUMCL, "alphasum");
readBuffer(clDict,sumlambda, sizeof(float) * MAXPOPS,LAMBDASUMCL, "lambdasum");
readBuffer(clDict,FstSum, sizeof(float) * MAXPOPS,FSTSUMCL, "fstsum");
readBuffer(clDict,QSum, sizeof(float) * QSIZE,QSUMCL, "Qsum");
readBuffer(clDict,PSum, sizeof(float) * PSIZE,PSUMCL, "Psum");
readBuffer(clDict,SumEpsilon, sizeof(float) * NUMLOCI*MAXALLELES,EPSILONSUMCL, "epssum");
readBuffer(clDict,like, sizeof(float),LIKECL, "like");
readBuffer(clDict,sumlikes, sizeof(float),SUMLIKESCL, "sumlike");
readBuffer(clDict,sumsqlikes, sizeof(float),SUMSQLIKESCL, "sumsqlikes");
OutPutResults (Geno, rep + 1, savefreq, Individual, PSum, QSum,
FstSum, AncestDist, UsePopProbs, *sumlikes,
*sumsqlikes, sumAlpha, sumR, varR,
NumAlleles, Translation, 0, Markername, R,
SumEpsilon,
lambda,sumlambda,sumLocPrior, LocPriorLen,
sumIndLikes, indLikesNorm, argc,argv);
}
if (PRINTLIKES) {
readBuffer(clDict,like, sizeof(float),LIKECL, "like");
PrintLike (*like, rep, Geno, PreGeno, Q, P,recomblikelihood);
}
if (((rep + 1) % UPDATEFREQ) == 0) {
readBuffer(clDict,Alpha, sizeof(float) * MAXPOPS,ALPHACL, "alpha");
readBuffer(clDict,Fst, sizeof(float) * MAXPOPS,FSTCL, "fst");
readBuffer(clDict,like, sizeof(float),LIKECL, "like");
readBuffer(clDict,sumlikes, sizeof(float),SUMLIKESCL, "sumlike");
readBuffer(clDict,sumsqlikes, sizeof(float),SUMSQLIKESCL, "sumsqlikes");
/*readBuffer(clDict,sumAlpha, sizeof(float) * MAXPOPS,ALPHASUMCL, "alphasum");
readBuffer(clDict,sumlambda, sizeof(float) * MAXPOPS,LAMBDASUMCL, "lambdasum");
readBuffer(clDict,FstSum, sizeof(float) * MAXPOPS,FSTSUMCL, "fstsum");
readBuffer(clDict,QSum, sizeof(float) * QSIZE,QSUMCL, "Qsum");
readBuffer(clDict,PSum, sizeof(float) * PSIZE,PSUMCL, "Psum");
readBuffer(clDict,SumEpsilon, sizeof(float) * NUMLOCI*MAXALLELES,EPSILONSUMCL, "epssum");*/
PrintUpdate (rep + 1, Geno, PreGeno, Alpha, Fst, P, Q, *like,
*sumlikes, *sumsqlikes, NumAlleles, R, lambda,Individual,
recomblikelihood, Recessive, LocPrior, LocPriorLen);
}
finishWaitList(clDict);
}
/*====final book-keeping====================================*/
if ((rep % UPDATEFREQ) != 0) {
readBuffer(clDict,Alpha, sizeof(float) * MAXPOPS,ALPHACL, "alpha");
readBuffer(clDict,Fst, sizeof(float) * MAXPOPS,FSTCL, "fst");
readBuffer(clDict,like, sizeof(float),LIKECL, "like");
readBuffer(clDict,sumsqlikes, sizeof(float),SUMSQLIKESCL, "sumsqlikes");
readBuffer(clDict,sumlikes, sizeof(float),SUMLIKESCL, "sumlikes");
/*readBuffer(clDict,sumAlpha, sizeof(float) * MAXPOPS,ALPHASUMCL, "alphasum");
readBuffer(clDict,sumlambda, sizeof(float) * MAXPOPS,LAMBDASUMCL, "lambdasum");
readBuffer(clDict,FstSum, sizeof(float) * MAXPOPS,FSTSUMCL, "fstsum");
readBuffer(clDict,QSum, sizeof(float) * QSIZE,QSUMCL, "Qsum");
readBuffer(clDict,PSum, sizeof(float) * PSIZE,PSUMCL, "Psum");
readBuffer(clDict,SumEpsilon, sizeof(float) * NUMLOCI*MAXALLELES,EPSILONSUMCL, "epssum");*/
PrintUpdate (rep, Geno, PreGeno, Alpha, Fst, P, Q, *like, *sumlikes,
*sumsqlikes, NumAlleles,R, lambda, Individual,recomblikelihood,
Recessive, LocPrior, LocPriorLen);
}
readBuffer(clDict,Alpha, sizeof(float) * MAXPOPS,ALPHACL, "alpha");
readBuffer(clDict,Fst, sizeof(float) * MAXPOPS,FSTCL, "fst");
readBuffer(clDict,sumAlpha, sizeof(float) * MAXPOPS,ALPHASUMCL, "alphasum");
readBuffer(clDict,sumlambda, sizeof(float) * MAXPOPS,LAMBDASUMCL, "lambdasum");
readBuffer(clDict,FstSum, sizeof(float) * MAXPOPS,FSTSUMCL, "fstsum");
readBuffer(clDict,QSum, sizeof(float) * QSIZE,QSUMCL, "Qsum");
readBuffer(clDict,PSum, sizeof(float) * PSIZE,PSUMCL, "Psum");
readBuffer(clDict,SumEpsilon, sizeof(float) * NUMLOCI*MAXALLELES,EPSILONSUMCL, "epssum");
readBuffer(clDict,like, sizeof(float),LIKECL, "like");
readBuffer(clDict,sumsqlikes, sizeof(float),SUMSQLIKESCL, "sumsqlikes");
readBuffer(clDict,sumlikes, sizeof(float),SUMLIKESCL, "sumlikes");
OutPutResults (Geno, rep, savefreq, Individual, PSum, QSum,
FstSum, AncestDist, UsePopProbs,
*sumlikes, *sumsqlikes,
sumAlpha, sumR, varR, NumAlleles, Translation, 1,
Markername, R, SumEpsilon,
lambda,sumlambda,sumLocPrior, LocPriorLen,
sumIndLikes, indLikesNorm,
argc,argv);
/*=====Closing everything down==============================*/
FreeAll(Mapdistance, Phase, Phasemodel, lambda, sumlambda, Markername, Geno,
PreGeno, Recessive,
Individual, Translation, NumAlleles, Z, Z1, Q, P, R, sumR, varR, Epsilon,
SumEpsilon,
Fst, FstSum, NumLociPop, PSum, QSum, AncestDist, UsePopProbs, LocPrior,
sumLocPrior, Alpha, sumAlpha, sumIndLikes, indLikesNorm, clDict);
free(randomArr);
free(randGens);
free(like);
free(sumsqlikes);
free(sumlikes);
free(reduceresult);
printf("Structure seed: %d\n", SEED);
return (0);
}
void ContinueExecution()
{
static BOOL pageflipping = 0; //?
const double fUsecPerSec = 1.e6;
#if 1
const UINT nExecutionPeriodUsec = 1000; // 1.0ms
// const UINT nExecutionPeriodUsec = 100; // 0.1ms
const double fExecutionPeriodClks = g_fCurrentCLK6502 * ((double)nExecutionPeriodUsec / fUsecPerSec);
#else
const double fExecutionPeriodClks = 1800.0;
const UINT nExecutionPeriodUsec = (UINT) (fUsecPerSec * (fExecutionPeriodClks / g_fCurrentCLK6502));
#endif
//
bool bScrollLock_FullSpeed = g_uScrollLockToggle
? g_bScrollLock_FullSpeed
: (GetKeyState(VK_SCROLL) < 0);
g_bFullSpeed = ( (g_dwSpeed == SPEED_MAX) ||
bScrollLock_FullSpeed ||
(DiskIsSpinning() && enhancedisk && !Spkr_IsActive() && !MB_IsActive()) );
if(g_bFullSpeed)
{
// Don't call Spkr_Mute() - will get speaker clicks
MB_Mute();
SysClk_StopTimer();
#ifdef USE_SPEECH_API
g_Speech.Reset(); // TODO: Put this on a timer (in emulated cycles)... otherwise CATALOG cuts out
#endif
g_nCpuCyclesFeedback = 0; // For the case when this is a big -ve number
// Switch to normal priority so that APPLEWIN process doesn't hog machine!
//. EG: No disk in Drive-1, and boot Apple: Windows will start to crawl!
SetPriorityNormal();
}
else
{
// Don't call Spkr_Demute()
MB_Demute();
SysClk_StartTimerUsec(nExecutionPeriodUsec);
// Switch to higher priority, eg. for audio (BUG #015394)
SetPriorityAboveNormal();
}
#ifdef WS_VIDEO
wsVideoNewDirtyRect.ulx = FRAMEBUFFER_W;
wsVideoNewDirtyRect.uly = FRAMEBUFFER_H;
wsVideoNewDirtyRect.lrx = 0;
wsVideoNewDirtyRect.lry = 0;
#endif
//
int nCyclesToExecute = (int) fExecutionPeriodClks + g_nCpuCyclesFeedback;
if(nCyclesToExecute < 0)
nCyclesToExecute = 0;
DWORD dwExecutedCycles = CpuExecute(nCyclesToExecute);
g_dwCyclesThisFrame += dwExecutedCycles;
//
cyclenum = dwExecutedCycles;
DiskUpdatePosition(dwExecutedCycles);
JoyUpdatePosition();
SpkrUpdate(cyclenum);
sg_SSC.CommUpdate(cyclenum);
PrintUpdate(cyclenum);
//
const DWORD CLKS_PER_MS = (DWORD)g_fCurrentCLK6502 / 1000;
emulmsec_frac += dwExecutedCycles;
if(emulmsec_frac > CLKS_PER_MS)
{
emulmsec += emulmsec_frac / CLKS_PER_MS;
emulmsec_frac %= CLKS_PER_MS;
}
#ifdef WS_VIDEO
if (wsVideoNewDirtyRect.lrx > wsVideoNewDirtyRect.ulx)
{
if (wsVideoNewDirtyRect.ulx < wsVideoAllDirtyRect.ulx) wsVideoAllDirtyRect.ulx = wsVideoNewDirtyRect.ulx;
if (wsVideoNewDirtyRect.uly < wsVideoAllDirtyRect.uly) wsVideoAllDirtyRect.uly = wsVideoNewDirtyRect.uly;
if (wsVideoNewDirtyRect.lrx > wsVideoAllDirtyRect.lrx) wsVideoAllDirtyRect.lrx = wsVideoNewDirtyRect.lrx;
if (wsVideoNewDirtyRect.lry > wsVideoAllDirtyRect.lry) wsVideoAllDirtyRect.lry = wsVideoNewDirtyRect.lry;
}
if(g_dwCyclesThisFrame >= dwClksPerFrame)
{
g_dwCyclesThisFrame -= dwClksPerFrame;
wsVideoRefresh();
}
#else
//
// DETERMINE WHETHER THE SCREEN WAS UPDATED, THE DISK WAS SPINNING,
// OR THE KEYBOARD I/O PORTS WERE BEING EXCESSIVELY QUERIED THIS CLOCKTICK
VideoCheckPage(0);
BOOL screenupdated = VideoHasRefreshed();
BOOL systemidle = 0; //(KeybGetNumQueries() > (clockgran << 2)); // && (!ranfinegrain); // TO DO
if(screenupdated)
pageflipping = 3;
//
if(g_dwCyclesThisFrame >= dwClksPerFrame)
{
g_dwCyclesThisFrame -= dwClksPerFrame;
if(g_nAppMode != MODE_LOGO)
{
VideoUpdateFlash();
static BOOL anyupdates = 0;
static DWORD lastcycles = 0;
static BOOL lastupdates[2] = {0,0};
anyupdates |= screenupdated;
//
lastcycles = cumulativecycles;
if ((!anyupdates) && (!lastupdates[0]) && (!lastupdates[1]) && VideoApparentlyDirty())
{
VideoCheckPage(1);
static DWORD lasttime = 0;
DWORD currtime = GetTickCount();
if ((!g_bFullSpeed) ||
(currtime-lasttime >= (DWORD)((g_bGraphicsMode || !systemidle) ? 100 : 25)))
{
VideoRefreshScreen();
lasttime = currtime;
}
screenupdated = 1;
}
lastupdates[1] = lastupdates[0];
lastupdates[0] = anyupdates;
anyupdates = 0;
if (pageflipping)
pageflipping--;
}
MB_EndOfVideoFrame();
}
//
#endif // ifndef WS_VIDEO
if(!g_bFullSpeed)
{
SysClk_WaitTimer();
#if DBG_CALC_FREQ
if(g_nPerfFreq)
{
QueryPerformanceCounter((LARGE_INTEGER*)&nTime1);
LONGLONG nTimeDiff = nTime1 - nTime0;
double fTime = (double)nTimeDiff / (double)(LONGLONG)g_nPerfFreq;
g_fDbg[g_nIdx] = fTime;
g_nIdx = (g_nIdx+1) & (MAX_CNT-1);
g_fMeanPeriod = 0.0;
for(UINT n=0; n<MAX_CNT; n++)
g_fMeanPeriod += g_fDbg[n];
g_fMeanPeriod /= (double)MAX_CNT;
g_fMeanFreq = 1.0 / g_fMeanPeriod;
}
#endif
}
}
void ContinueExecution(void)
{
const double fUsecPerSec = 1.e6;
#if 1
const UINT nExecutionPeriodUsec = 1000; // 1.0ms
// const UINT nExecutionPeriodUsec = 100; // 0.1ms
const double fExecutionPeriodClks = g_fCurrentCLK6502 * ((double)nExecutionPeriodUsec / fUsecPerSec);
#else
const double fExecutionPeriodClks = 1800.0;
const UINT nExecutionPeriodUsec = (UINT) (fUsecPerSec * (fExecutionPeriodClks / g_fCurrentCLK6502));
#endif
//
bool bScrollLock_FullSpeed = sg_PropertySheet.GetScrollLockToggle()
? g_bScrollLock_FullSpeed
: (GetKeyState(VK_SCROLL) < 0);
g_bFullSpeed = ( (g_dwSpeed == SPEED_MAX) ||
bScrollLock_FullSpeed ||
(DiskIsSpinning() && enhancedisk && !Spkr_IsActive() && !MB_IsActive()) );
if (g_bFullSpeed)
{
// Don't call Spkr_Mute() - will get speaker clicks
MB_Mute();
SysClk_StopTimer();
#ifdef USE_SPEECH_API
g_Speech.Reset(); // TODO: Put this on a timer (in emulated cycles)... otherwise CATALOG cuts out
#endif
g_nCpuCyclesFeedback = 0; // For the case when this is a big -ve number
// Switch to normal priority so that APPLEWIN process doesn't hog machine!
//. EG: No disk in Drive-1, and boot Apple: Windows will start to crawl!
SetPriorityNormal();
}
else
{
// Don't call Spkr_Demute()
MB_Demute();
SysClk_StartTimerUsec(nExecutionPeriodUsec);
// Switch to higher priority, eg. for audio (BUG #015394)
SetPriorityAboveNormal();
}
//
int nCyclesToExecute = (int) fExecutionPeriodClks + g_nCpuCyclesFeedback;
if (nCyclesToExecute < 0)
nCyclesToExecute = 0;
DWORD dwExecutedCycles = CpuExecute(nCyclesToExecute);
g_dwCyclesThisFrame += dwExecutedCycles;
//
cyclenum = dwExecutedCycles;
DiskUpdatePosition(dwExecutedCycles);
JoyUpdatePosition();
SpkrUpdate(cyclenum);
sg_SSC.CommUpdate(cyclenum);
PrintUpdate(cyclenum);
//
const DWORD CLKS_PER_MS = (DWORD)g_fCurrentCLK6502 / 1000;
emulmsec_frac += dwExecutedCycles;
if (emulmsec_frac > CLKS_PER_MS)
{
emulmsec += emulmsec_frac / CLKS_PER_MS;
emulmsec_frac %= CLKS_PER_MS;
}
// DETERMINE WHETHER THE SCREEN WAS UPDATED THIS CLOCKTICK
static BOOL anyupdates = 0;
VideoCheckPage(0); // force=0
anyupdates |= VideoHasRefreshed(); // Only called from here. Returns & clears 'hasrefreshed' flag
//
if (g_dwCyclesThisFrame >= dwClksPerFrame)
{
g_dwCyclesThisFrame -= dwClksPerFrame;
VideoUpdateFlash();
static BOOL lastupdates[2] = {0,0};
if (!anyupdates && !lastupdates[0] && !lastupdates[1] && VideoApparentlyDirty())
{
VideoCheckPage(1); // force=1
static DWORD lasttime = 0;
DWORD currtime = GetTickCount();
if ((!g_bFullSpeed) ||
(currtime-lasttime >= (DWORD)(g_bGraphicsMode ? 100 : 25)))
{
VideoRefreshScreen();
lasttime = currtime;
}
}
lastupdates[1] = lastupdates[0];
lastupdates[0] = anyupdates;
anyupdates = 0;
MB_EndOfVideoFrame();
}
//
if (!g_bFullSpeed)
{
SysClk_WaitTimer();
#if DBG_CALC_FREQ
if (g_nPerfFreq)
{
QueryPerformanceCounter((LARGE_INTEGER*)&nTime1);
LONGLONG nTimeDiff = nTime1 - nTime0;
double fTime = (double)nTimeDiff / (double)(LONGLONG)g_nPerfFreq;
g_fDbg[g_nIdx] = fTime;
g_nIdx = (g_nIdx+1) & (MAX_CNT-1);
g_fMeanPeriod = 0.0;
for(UINT n=0; n<MAX_CNT; n++)
g_fMeanPeriod += g_fDbg[n];
g_fMeanPeriod /= (double)MAX_CNT;
g_fMeanFreq = 1.0 / g_fMeanPeriod;
}
#endif
}
}
