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Copy pathAFS_ctmc_petsc.c
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AFS_ctmc_petsc.c
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#include <petscksp.h>
#include "AFS.h"
#include "AFS_ctmc_petsc.h"
#include "im_clam.h"
#include "sparseExp.h"
#include "cs.h"
#include "AFS_ctmc.h"
#include "nlopt.h"
#include "adkGSL.h"
#include <gsl/gsl_linalg.h>
#include <gsl/gsl_rng.h>
#include <gsl/gsl_cblas.h>
#include <gsl/gsl_blas.h>
//Functions for jointly computing CTMC transitions and embedded chain
//this function fills two petsc matrices: 1) embedded Discrete MC trans Mat, 2) CTMC trans mat
// also fills the rates vector
void fillPetscTransMats(afsStateSpace *S, double *topol, int *moveType, int *nzCount,
int *dim1, int *dim2, double theta1, double theta2, double mig1, double mig2, Mat *DTMC, Mat *CTMC, gsl_vector *rates){
int i, j,k, newnz, abcount=0;
int N = S->nstates,abFlag;
double c0r[N],c1r[N],m0r[N],m1r[N],totR[N],rowSums[N], tmp;;
gsl_vector_set_zero(rates);
//set rates vector
for(i=0;i<N;i++){
c0r[i] = S->states[i]->aCounts[0] * (S->states[i]->aCounts[0]-1) / theta1 ;
if(theta2 == 0)
c1r[i] = 0.0;
else
c1r[i] = S->states[i]->aCounts[1] * (S->states[i]->aCounts[1]-1) / theta2;
m0r[i] = S->states[i]->aCounts[0] * mig1 ;
m1r[i] = S->states[i]->aCounts[1] * mig2 ;
totR[i] = c0r[i] + c1r[i] + m0r[i] + m1r[i];
rowSums[i] = 0.0;
if(S->states[i]->nalleles > 1 && c0r[i] >= 0 && c1r[i] >= 0 && totR[i] != 0.0)
gsl_vector_set(rates,i,1.0/totR[i]);
else
gsl_vector_set(rates,i,0);
}
newnz=0;
for(k=0;k<*nzCount;k++){
i = dim1[k];
j= dim2[k];
// printf("i: %d, j:%d, movetype: %d\n",i,j,moveType[k]);
if(S->states[i]->nalleles ==1 || S->states[j]->nalleles ==1 )abFlag=1;
// if(S->states[i]->nalleles ==1 )abFlag=1;
else abFlag = 0;
switch(moveType[k]){
case 0: //coal pop0
if(totR[i]==0)tmp=0;
else tmp = c0r[i] / totR[i] * topol[k];
MatSetValue(*CTMC,i,j,tmp*totR[i],INSERT_VALUES);
rowSums[i] += tmp* totR[i];
if(abFlag==0)MatSetValue(*DTMC,i,j,tmp,INSERT_VALUES);
break;
case 1: //coal pop1
if(totR[i]==0)tmp=0;
else tmp = c1r[i] / totR[i] * topol[k];
MatSetValue(*CTMC,i,j,tmp*totR[i],INSERT_VALUES);
rowSums[i] += tmp* totR[i];
if(abFlag==0)MatSetValue(*DTMC,i,j,tmp,INSERT_VALUES);
break;
case 2: //mig pop0
if(totR[i]==0)tmp=0;
else tmp = m0r[i] / totR[i] * topol[k];
MatSetValue(*CTMC,i,j,tmp*totR[i],INSERT_VALUES);
rowSums[i] += tmp* totR[i];
if(abFlag==0)MatSetValue(*DTMC,i,j,tmp,INSERT_VALUES);
break;
case 3: //mig pop1
if(totR[i]==0)tmp=0;
else tmp = m1r[i] / totR[i] * topol[k];
MatSetValue(*CTMC,i,j,tmp*totR[i],INSERT_VALUES);
rowSums[i] += tmp* totR[i];
if(abFlag==0)MatSetValue(*DTMC,i,j,tmp,INSERT_VALUES);
break;
case -1:
abcount+=1;
break;
}
}
newnz=*nzCount ;
//now add diagonal elements; topol pre-set to -1
for(k=0;k<N;k++){
if((rowSums[k]) != 0.0){
MatSetValue(*CTMC,k,k,0.0-rowSums[k],INSERT_VALUES);
newnz++;
}
MatSetValue(*DTMC,k,k,0.0,INSERT_VALUES);
}
*nzCount = newnz;
/* Assemble the matrix */
MatAssemblyBegin(*CTMC,MAT_FINAL_ASSEMBLY);
MatAssemblyEnd(*CTMC,MAT_FINAL_ASSEMBLY);
MatAssemblyBegin(*DTMC,MAT_FINAL_ASSEMBLY);
MatAssemblyEnd(*DTMC,MAT_FINAL_ASSEMBLY);
}
//fillPetscCsparseTransMats--this function fills one petsc matrix with CTMC transmat and returns pointer to CSparse matrix for DTMC trans mat
// also fills the rates vector
//note that the DTMC matrix needs to be cleared before entry to this function and compressed afterward.
struct cs_di_sparse * fillPetscCsparseTransMats(afsStateSpace *S, double *topol, int *moveType, int *nzCount,
int *dim1, int *dim2, double theta1, double theta2, double mig1, double mig2, Mat *CTMC, gsl_vector *rates){
int i, j,k, newnz, abcount=0;
int N = S->nstates,abFlag;
double c0r[N],c1r[N],m0r[N],m1r[N],totR[N],rowSums[N], tmp;;
struct cs_di_sparse *triplet, *tmat;
//allocate new cs_sparse obj
triplet = cs_spalloc(N, N, *nzCount + N , 1, 1); //alloc sparse mat with extra space for nonzero identity mats
gsl_vector_set_zero(rates);
//set rates vector
for(i=0;i<N;i++){
c0r[i] = S->states[i]->aCounts[0] * (S->states[i]->aCounts[0]-1) / theta1 ;
if(theta2 == 0)
c1r[i] = 0.0;
else
c1r[i] = S->states[i]->aCounts[1] * (S->states[i]->aCounts[1]-1) / theta2;
m0r[i] = S->states[i]->aCounts[0] * mig1 ;
m1r[i] = S->states[i]->aCounts[1] * mig2 ;
totR[i] = c0r[i] + c1r[i] + m0r[i] + m1r[i];
rowSums[i] = 0.0;
if(S->states[i]->nalleles > 1 && c0r[i] >= 0 && c1r[i] >= 0 && totR[i] != 0.0)
gsl_vector_set(rates,i,1.0/totR[i]);
else
gsl_vector_set(rates,i,0);
}
newnz=0;
for(k=0;k<*nzCount;k++){
i = dim1[k];
j= dim2[k];
// printf("i: %d, j:%d, movetype: %d\n",i,j,moveType[k]);
if(S->states[i]->nalleles ==1 || S->states[j]->nalleles ==1 )abFlag=1;
// if(S->states[i]->nalleles ==1 )abFlag=1;
else abFlag = 0;
switch(moveType[k]){
case 0: //coal pop0
if(totR[i]==0)tmp=0;
else tmp = c0r[i] / totR[i] * topol[k];
// printf("here--- i:%d j:%d tmp*totR[i]:%f",i,j,tmp*totR[i]);
MatSetValue(*CTMC,i,j,tmp*totR[i],INSERT_VALUES);
rowSums[i] += tmp* totR[i];
if(abFlag==0)cs_entry(triplet,i,j,tmp);
break;
case 1: //coal pop1
if(totR[i]==0)tmp=0;
else tmp = c1r[i] / totR[i] * topol[k];
MatSetValue(*CTMC,i,j,tmp*totR[i],INSERT_VALUES);
rowSums[i] += tmp* totR[i];
if(abFlag==0)cs_entry(triplet,i,j,tmp);
break;
case 2: //mig pop0
if(totR[i]==0)tmp=0;
else tmp = m0r[i] / totR[i] * topol[k];
MatSetValue(*CTMC,i,j,tmp*totR[i],INSERT_VALUES);
rowSums[i] += tmp* totR[i];
if(abFlag==0)cs_entry(triplet,i,j,tmp);
break;
case 3: //mig pop1
if(totR[i]==0)tmp=0;
else tmp = m1r[i] / totR[i] * topol[k];
MatSetValue(*CTMC,i,j,tmp*totR[i],INSERT_VALUES);
rowSums[i] += tmp* totR[i];
if(abFlag==0)cs_entry(triplet,i,j,tmp);
break;
case -1:
abcount+=1;
break;
}
}
newnz=*nzCount ;
//now add diagonal elements; topol pre-set to -1
for(k=0;k<N;k++){
if((rowSums[k]) != 0.0){
MatSetValue(*CTMC,k,k,0.0-rowSums[k],INSERT_VALUES);
newnz++;
}
}
*nzCount = newnz;
/* Assemble the matrix */
MatAssemblyBegin(*CTMC,MAT_FINAL_ASSEMBLY);
MatAssemblyEnd(*CTMC,MAT_FINAL_ASSEMBLY);
tmat = cs_compress(triplet);
cs_spfree(triplet);
return(tmat);
}
//fillPetscCsparseTransMats_prealloc--this function fills one petsc matrix with CTMC transmat and returns pointer to CSparse matrix for DTMC trans mat
// also fills the rates vector
struct cs_di_sparse * fillPetscCsparseTransMats_prealloc(afsStateSpace *S, double *topol, int *moveType, int *nzCount,
int *dim1, int *dim2, double theta1, double theta2, double mig1, double mig2,
Mat *CTMC, gsl_vector *rates, struct cs_di_sparse *triplet){
int i, j,k, newnz, abcount=0;
int N = S->nstates,abFlag;
double *c0r,*c1r,*m0r,*m1r,*totR,*rowSums, tmp;
struct cs_di_sparse *tmat;
c0r = malloc(sizeof(double)*N);
c1r = malloc(sizeof(double)*N);
m0r = malloc(sizeof(double)*N);
m1r = malloc(sizeof(double)*N);
totR = malloc(sizeof(double)*N);
rowSums = malloc(sizeof(double)*N);
gsl_vector_set_zero(rates);
//set rates vector
for(i=0;i<N;i++){
c0r[i] = S->states[i]->aCounts[0] * (S->states[i]->aCounts[0]-1) / theta1 ;
if(theta2 == 0)
c1r[i] = 0.0;
else
c1r[i] = S->states[i]->aCounts[1] * (S->states[i]->aCounts[1]-1) / theta2;
m0r[i] = S->states[i]->aCounts[0] * mig1 ;
m1r[i] = S->states[i]->aCounts[1] * mig2 ;
totR[i] = c0r[i] + c1r[i] + m0r[i] + m1r[i];
rowSums[i] = 0.0;
if(S->states[i]->nalleles > 1 && c0r[i] >= 0 && c1r[i] >= 0 && totR[i] != 0.0)
gsl_vector_set(rates,i,1.0/totR[i]);
else
gsl_vector_set(rates,i,0);
}
newnz=0;
for(k=0;k<*nzCount;k++){
i = dim1[k];
j= dim2[k];
// printf("i: %d, j:%d, movetype: %d\n",i,j,moveType[k]);
if(S->states[i]->nalleles ==1 || S->states[j]->nalleles ==1 )abFlag=1;
// if(S->states[i]->nalleles ==1 )abFlag=1;
else abFlag = 0;
switch(moveType[k]){
case 0: //coal pop0
if(totR[i]==0)tmp=0;
else tmp = c0r[i] / totR[i] * topol[k];
// printf("here--- i:%d j:%d tmp*totR[i]:%f",i,j,tmp*totR[i]);
MatSetValue(*CTMC,i,j,tmp*totR[i],INSERT_VALUES);
rowSums[i] += tmp* totR[i];
if(abFlag==0)cs_entry(triplet,i,j,tmp);
break;
case 1: //coal pop1
if(totR[i]==0)tmp=0;
else tmp = c1r[i] / totR[i] * topol[k];
MatSetValue(*CTMC,i,j,tmp*totR[i],INSERT_VALUES);
rowSums[i] += tmp* totR[i];
if(abFlag==0)cs_entry(triplet,i,j,tmp);
break;
case 2: //mig pop0
if(totR[i]==0)tmp=0;
else tmp = m0r[i] / totR[i] * topol[k];
MatSetValue(*CTMC,i,j,tmp*totR[i],INSERT_VALUES);
rowSums[i] += tmp* totR[i];
if(abFlag==0)cs_entry(triplet,i,j,tmp);
break;
case 3: //mig pop1
if(totR[i]==0)tmp=0;
else tmp = m1r[i] / totR[i] * topol[k];
MatSetValue(*CTMC,i,j,tmp*totR[i],INSERT_VALUES);
rowSums[i] += tmp* totR[i];
if(abFlag==0)cs_entry(triplet,i,j,tmp);
break;
case -1:
abcount+=1;
break;
}
}
newnz=*nzCount ;
//now add diagonal elements; topol pre-set to -1
for(k=0;k<N;k++){
if((rowSums[k]) != 0.0){
MatSetValue(*CTMC,k,k,0.0-rowSums[k],INSERT_VALUES);
newnz++;
}
}
*nzCount = newnz;
/* Assemble the matrix */
MatAssemblyBegin(*CTMC,MAT_FINAL_ASSEMBLY);
MatAssemblyEnd(*CTMC,MAT_FINAL_ASSEMBLY);
tmat = cs_compress(triplet);
free(c0r);
free(c1r);
free(m0r);
free(m1r);
free(totR);
free(rowSums);
return(tmat);
}
//calcLogAFS_IM -- returns the expects log AFS from an IM model
void calcLogAFS_IM(void * p){
struct clam_lik_params * params = (struct clam_lik_params *) p;
PetscInt i,j, N = params->stateSpace->nstates;
cs *spMat, *mt, *tmpMat ;
double timeV, sum, thetaA, theta2, mig1, mig2;
PetscInt Na;
gsl_vector *tmpStates;
css *S ;
csn *NN ;
PetscInt n,Ntmp ;
double *xx;
PetscInt iStart,iEnd, *idx;
const PetscInt *idx2;
PetscScalar *tmpArray;
const PetscScalar *tmpArrayC;
PetscErrorCode ierr;
MFNConvergedReason reason;
//initialize some vectors
gsl_vector_set_zero(params->rates);
MatZeroEntries(params->C);
MatZeroEntries(params->C2);
tmpStates = gsl_vector_alloc(N);
Ntmp=N;
Na=params->Na;
//For straight MLE the paramVector takes the form [N2,NA,m1,m2,t]
theta2 = gsl_vector_get(params->paramVector,0);
thetaA = gsl_vector_get(params->paramVector,1);
mig1 = gsl_vector_get(params->paramVector,2);
mig2 = gsl_vector_get(params->paramVector,3);
timeV = gsl_vector_get(params->paramVector,4);
// printf("params-> %f %f %f %f %f\n",theta2,thetaA,mig1,mig2,timeV);
// printf("nnz %d nnzA%d \n",params->nnz,params->nnzA);
//fill transMat
// tmpMat = fillPetscCsparseTransMats_prealloc(params->stateSpace, params->top, params->move, ¶ms->nnz,
// params->dim1, params->dim2, 1, theta2, mig1, mig2, ¶ms->C, params->rates,params->triplet);
tmpMat = fillPetscCsparseTransMats(params->stateSpace, params->top, params->move, ¶ms->nnz,
params->dim1, params->dim2, 1, theta2, mig1, mig2, ¶ms->C, params->rates);
//using CSparse
// S = (I-P)^-1
//add negative ident
// ident = cs_spalloc(N,N,N,1,1);
// for(i=0;i<N;i++) cs_entry(ident,i,i,1);
// eye = cs_compress(ident);
spMat = cs_add(params->eye,tmpMat,1.0,-1.0);
//cs_print_adk(spMat);
mt = cs_transpose(spMat,1);
//cs_print_adk(mt);
n = mt->n ;
S = cs_sqr (0, mt, 0) ; /* ordering and symbolic analysis */
NN = cs_lu (mt, S, 1e-12) ; /* numeric LU factorization */
xx = cs_malloc (n, sizeof (double)) ; /* get workspace */
MatGetOwnershipRange(params->denseMat1,&iStart,&iEnd);
PetscMalloc1(N,&idx);
for(j=0;j<N;j++) idx[j]=j;
////Compute Entire Inverse Mat
for(j=iStart;j<iEnd;j++){
//create unit array for solve
for(i=0; i<N; i++)params->b[i] = 0.0;
params->b[j]=1.0;
//factor outside loop leads to ~40x speedup
cs_ipvec (NN->pinv, params->b, xx, n) ; /* x = b(p) */
cs_lsolve (NN->L, xx) ; /* x = L\x */
cs_usolve (NN->U, xx) ; /* x = U\x */
cs_ipvec (S->q, xx, params->b, n) ; /* b(q) = x */
// if(!rank)printf("row %d\n",j);
MatSetValues(params->denseMat1,1,&j,N,idx,params->b,INSERT_VALUES);
}
MatAssemblyBegin(params->denseMat1,MAT_FINAL_ASSEMBLY);
MatAssemblyEnd(params->denseMat1,MAT_FINAL_ASSEMBLY);
//temporary clean up
free(xx);
cs_spfree(spMat);
cs_spfree(mt);
// cs_spfree(ident);
// cs_spfree(eye);
cs_spfree(tmpMat);
cs_nfree(NN);
cs_sfree(S);
PetscFree(idx);
// MatView(params->denseMat1,PETSC_VIEWER_STDOUT_WORLD);
//broadcast the invMat[0,] as vector to each processor
if(params->rank==0){
MatGetRow(params->denseMat1,0,&N,&idx2,&tmpArrayC);
for (j = 0; j < N; j++) params->b[j] = tmpArrayC[j];
MatRestoreRow(params->denseMat1,0,&Ntmp,&idx2,&tmpArrayC); //have to use Ntmp here as MatRestoreRow does something funky
}
MPI_Bcast(params->b,N,MPI_DOUBLE,0,PETSC_COMM_WORLD);
//Get Island Time 0-INF Unnormal
gsl_matrix_set_zero(params->expAFS);
fillExpectedAFS_unnorm(params->stateSpace, params->b,params->rates,params->expAFS);
// printf("////////////////////Island Time 0 - INF unnormalized\n");
// for(i=0;i< (params->n1+1) ;i++){
// for(j=0;j< (params->n2+1);j++){
// printf("%.5f ",gsl_matrix_get(params->expAFS,i,j));
// }
// printf("\n");
// }
//Matrix Exponentiation to get state vector at time t
//SLEPC Stuff ahead!
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create the solver and set various options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Set operator matrix, the function to compute, and other options
*/
//transpose
MatTranspose(params->C,MAT_REUSE_MATRIX,¶ms->C);
ierr = MFNSetOperator(params->mfn,params->C);CHKERRV(ierr);
/*
Set solver parameters at runtime
*/
ierr = MFNSetScaleFactor(params->mfn,timeV); CHKERRV(ierr);
ierr = MFNSetFromOptions(params->mfn);CHKERRV(ierr);
/* set v = e_1 */
ierr = MatGetVecs(params->C,PETSC_NULL,¶ms->y);CHKERRV(ierr);
ierr = MatGetVecs(params->C,¶ms->v, PETSC_NULL);CHKERRV(ierr);
ierr = VecSetValue(params->v,0,1.0,INSERT_VALUES);CHKERRV(ierr);
ierr = VecAssemblyBegin(params->v);CHKERRV(ierr);
ierr = VecAssemblyEnd(params->v);CHKERRV(ierr);
ierr = MFNSolve(params->mfn,params->v,params->y);CHKERRV(ierr);
ierr = MFNGetConvergedReason(params->mfn,&reason);CHKERRV(ierr);
if (reason!=MFN_CONVERGED_TOL) ierr = 1; CHKERRV(ierr);
//retranspose for later use
MatTranspose(params->C,MAT_REUSE_MATRIX,¶ms->C);
//state vector at time t stored in y
//scatter y and store in expoArray
VecScatterCreateToAll(params->y,¶ms->ctx,¶ms->v_seq);
VecScatterBegin(params->ctx,params->y,params->v_seq,INSERT_VALUES,SCATTER_FORWARD);
VecScatterEnd(params->ctx,params->y,params->v_seq,INSERT_VALUES,SCATTER_FORWARD);
VecGetArray(params->v_seq,&tmpArray);
for (j = 0; j < N; j++){
params->expoArray[j] = tmpArray[j];
//printf("%.5f\n",expoArray[j]);
}
VecRestoreArray(params->v_seq,&tmpArray);
VecScatterDestroy(¶ms->ctx);
VecDestroy(¶ms->v_seq);
VecDuplicate(params->y,¶ms->x);
//VecView(y, PETSC_VIEWER_STDOUT_WORLD);
MatMultTranspose(params->denseMat1,params->y,params->x);
VecScatterCreateToAll(params->x,¶ms->ctx,¶ms->v_seq);
VecScatterBegin(params->ctx,params->x,params->v_seq,INSERT_VALUES,SCATTER_FORWARD);
VecScatterEnd(params->ctx,params->x,params->v_seq,INSERT_VALUES,SCATTER_FORWARD);
VecGetArray(params->v_seq,&tmpArray);
for (j = 0; j < N; j++){
params->b[j] = tmpArray[j];
//printf("rank %d expoArray[%d]:%.5f\n",rank,j,expoArray[j]);
//printf("rank %d b[%d]:%.5f\n",rank,j,b[j]);
}
VecRestoreArray(params->v_seq,&tmpArray);
VecScatterDestroy(¶ms->ctx);
VecDestroy(¶ms->v_seq);
fillExpectedAFS_unnorm(params->stateSpace, params->b,params->rates,params->expAFS2);
//now subtract older AFS (t_t - t_INF) from total AFS (t_0 - t_INF)
/////////////////
///////
gsl_matrix_sub(params->expAFS,params->expAFS2);
//////////////////////
//Final phase, collapse popns, reset rates
//now collapse populations
//state vector at time t stored in st[] for largerStateSpace; use reverseMap
for(i=0;i<N;i++)params->st[i]=0.0;
for(i=0;i<N;i++){params->st[params->map[i]]+=params->expoArray[i];
// printf("expoArray[%d]:%f\n",i,expoArray[i]);
}
for(i=0; i<params->reducedStateSpace->nstates; i++){
VecSetValue(params->ancStateVec,i,params->st[params->reverseMap[i]],INSERT_VALUES );
}
//Re-Fill trans mats for Ancestral Params
params->nnzA = coalMarkovChainTopologyMatrix_sparse(params->reducedStateSpace,params->topA,params->moveA, params->dim1A, params->dim2A);
tmpMat=fillPetscCsparseTransMats(params->reducedStateSpace, params->topA, params->moveA, ¶ms->nnzA,
params->dim1A, params->dim2A, thetaA, 0, 0, 0, ¶ms->C2, params->rates);
//////////////////////
//
// S = (I-P)^-1
//
/////////
//////
//add negative ident
// ident = cs_spalloc(Na,Na,Na,1,1);
// for(i=0;i<Na;i++) cs_entry(ident,i,i,1);
// eye = cs_compress(ident);
spMat = cs_add(params->eyeAnc,tmpMat,1.0,-1.0);
//cs_print_adk(spMat);
mt = cs_transpose(spMat,1);
//VecView(y,PETSC_VIEWER_STDOUT_WORLD);
n = mt->n ;
S = cs_sqr (0, mt, 0) ; /* ordering and symbolic analysis */
NN = cs_lu (mt, S, 1e-12) ; /* numeric LU factorization */
xx = cs_malloc (n, sizeof (double)) ; /* get workspace */
MatGetOwnershipRange(params->denseMat2,&iStart,&iEnd);
// printf("here\n");
PetscFree(idx);
PetscMalloc1(Na,&idx);
for(j=0;j<Na;j++) idx[j]=j;
////Compute Entire Inverse Mat
for(j=iStart;j<iEnd;j++){
//create unit array for solve
for(i=0; i<Na; i++)params->b[i] = 0.0;
params->b[j]=1.0;
//factor outside loop leads to ~40x speedup
cs_ipvec (NN->pinv, params->b, xx, n) ; /* x = b(p) */
cs_lsolve (NN->L, xx) ; /* x = L\x */
cs_usolve (NN->U, xx) ; /* x = U\x */
cs_ipvec (S->q, xx, params->b, n) ; /* b(q) = x */
// if(!rank)printf("row %d\n",j);
MatSetValues(params->denseMat2,1,&j,Na,idx,params->b,INSERT_VALUES);
}
MatAssemblyBegin(params->denseMat2,MAT_FINAL_ASSEMBLY);
MatAssemblyEnd(params->denseMat2,MAT_FINAL_ASSEMBLY);
free(xx);
MatMultTranspose(params->denseMat2,params->ancStateVec,params->ancResVec);
VecScatterCreateToAll(params->ancResVec,¶ms->ctx,¶ms->v_seq);
VecScatterBegin(params->ctx,params->ancResVec,params->v_seq,INSERT_VALUES,SCATTER_FORWARD);
VecScatterEnd(params->ctx,params->ancResVec,params->v_seq,INSERT_VALUES,SCATTER_FORWARD);
VecGetArray(params->v_seq,&tmpArray);
for (j = 0; j < Na; j++){
params->expoArray[j] = tmpArray[j];
//printf("%.5f\n",expoArray[j]);
}
VecRestoreArray(params->v_seq,&tmpArray);
VecScatterDestroy(¶ms->ctx);
VecDestroy(¶ms->v_seq);
//get contribution starting at st
gsl_matrix_set_zero(params->expAFS2);
fillExpectedAFS_unnorm(params->reducedStateSpace, params->expoArray,params->rates,params->expAFS2);
// printf("////////////////////--Ancestral bit\n");
// for(i=0;i< (n1+1) ;i++){
// for(j=0;j< (n2+1);j++){
// printf("%.5f ",gsl_matrix_get(expAFS2,i,j));
// }
// printf("\n");
// }
//if(params->rank==0)printf("////////////////////normalized IM:\n");
gsl_matrix_add(params->expAFS,params->expAFS2);
sum = matrixSumDouble(params->expAFS);
gsl_matrix_scale(params->expAFS, 1.0 / sum);
params->meanTreeLength = sum;
// for(i=0;i< (params->n1+1) ;i++){
// for(j=0;j< (params->n2+1);j++){
// if(params->rank==0)printf("%.5f ",gsl_matrix_get(params->expAFS,i,j));
// }
// if(params->rank==0)printf("\n");
// }
//
//clean up
PetscFree(idx);
VecDestroy(¶ms->y);
VecDestroy(¶ms->x);
VecDestroy(¶ms->v);
PetscFree(tmpArray);
cs_spfree(spMat);
cs_spfree(mt);
// cs_spfree(ident);
// cs_spfree(eye);
cs_spfree(tmpMat);
gsl_vector_free(tmpStates);
cs_nfree(NN);
cs_sfree(S);
}
//calcLogAFS_IM_allPETSC -- returns the expects log AFS from an IM model; only uses PETSC
void calcLogAFS_IM_allPETSC(void * p){
struct clam_lik_params * params = (struct clam_lik_params *) p;
PetscInt i,j, N = params->stateSpace->nstates;
cs *spMat, *mt, *ident, *eye, *tmpMat ;
double timeV, sum, thetaA, theta2, mig1, mig2;
PetscInt Na;
gsl_vector *tmpStates;
css *S ;
csn *NN ;
PetscInt n,Ntmp ;
double *xx;
PetscInt iStart,iEnd, *idx;
const PetscInt *idx2;
PetscScalar *tmpArray;
PetscScalar negOne = -1.0;
// PetscScalar one = 1.0;
const PetscScalar *tmpArrayC;
PetscErrorCode ierr;
IS perm,iperm;
MatFactorInfo info;
MFNConvergedReason reason;
//initialize some vectors
gsl_vector_set_zero(params->rates);
MatZeroEntries(params->C);
MatZeroEntries(params->C2);
MatZeroEntries(params->D);
tmpStates = gsl_vector_alloc(N);
Ntmp=N;
Na=params->Na;
//For straight MLE the paramVector takes the form [N2,NA,m1,m2,t]
theta2 = gsl_vector_get(params->paramVector,0);
thetaA = gsl_vector_get(params->paramVector,1);
mig1 = gsl_vector_get(params->paramVector,2);
mig2 = gsl_vector_get(params->paramVector,3);
timeV = gsl_vector_get(params->paramVector,4);
// printf("params-> %f %f %f %f %f\n",theta2,thetaA,mig1,mig2,timeV);
// printf("nnz %d nnzA%d \n",params->nnz,params->nnzA);
//fill transMat
fillPetscTransMats(params->stateSpace, params->top, params->move, ¶ms->nnz,
params->dim1, params->dim2, 1, theta2, mig1, mig2, ¶ms->D, ¶ms->C, params->rates);
//using CSparse
// S = (I-P)^-1
//subtract DTMC mat from identity
MatZeroEntries(params->D_copy);
MatCopy(params->ident,params->D_copy,DIFFERENT_NONZERO_PATTERN);
MatAXPY(params->D_copy,negOne,params->D,DIFFERENT_NONZERO_PATTERN);
// MatTranspose(params->D_copy,MAT_REUSE_MATRIX,¶ms->D);
ierr = MatGetOrdering(params->D_copy, MATORDERINGNATURAL, &perm, &iperm);
ierr = MatFactorInfoInitialize(&info);
ierr = MatGetFactor(params->D_copy,MATSOLVERSUPERLU_DIST,MAT_FACTOR_LU,¶ms->F);
PetscInt icntl_7 = 5;
//ierr = MatMumpsSetIcntl(params->F,7,icntl_7);
info.fill = 5.0;
ierr = MatLUFactorSymbolic(params->F,params->D_copy,perm,iperm,&info);
ierr = MatLUFactorNumeric(params->F,params->D_copy,&info);
//ierr = MatLUFactor(params->D_copy, perm, iperm, &info);
////Compute Entire Inverse Mat
ierr = MatMatSolve(params->F,params->denseIdent,params->denseMat1);
//MatView(params->denseMat1,PETSC_VIEWER_STDOUT_SELF);
// MatGetOwnershipRange(params->denseMat1,&iStart,&iEnd);
// PetscMalloc1(N,&idx);
// for(j=0;j<N;j++) idx[j]=j;
// for(j=0;j<N;j++){
// //create unit array for solve
// VecZeroEntries(params->bInv);
// VecZeroEntries(params->xInv);
// VecSetValue(params->bInv,j,one,INSERT_VALUES);
// VecAssemblyBegin(params->bInv);
// VecAssemblyEnd(params->bInv);
//
// KSPSolve(params->ksp,params->bInv,params->xInv);
// VecGetValues(params->x,N,idx,hold);
// MatSetValues(params->denseMat1,1,&j,N,idx,hold,INSERT_VALUES);
// }
// MatAssemblyBegin(params->denseMat1,MAT_FINAL_ASSEMBLY);
// MatAssemblyEnd(params->denseMat1,MAT_FINAL_ASSEMBLY);
// //temporary clean up
// // free(xx);
// // cs_spfree(spMat);
// // cs_spfree(mt);
// // cs_spfree(ident);
// // cs_spfree(eye);
// // cs_spfree(tmpMat);
// // cs_nfree(NN);
// // cs_sfree(S);
// PetscFree(idx);
// KSPDestroy(¶ms->ksp);
// MatView(params->denseMat1,PETSC_VIEWER_STDOUT_WORLD);
MatDestroy(¶ms->F);
//broadcast the invMat[0,] as vector to each processor
if(params->rank==0){
MatGetRow(params->denseMat1,0,&N,&idx2,&tmpArrayC);
for (j = 0; j < N; j++) params->b[j] = tmpArrayC[j];
MatRestoreRow(params->denseMat1,0,&Ntmp,&idx2,&tmpArrayC); //have to use Ntmp here as MatRestoreRow does something funky
}
MPI_Bcast(params->b,N,MPI_DOUBLE,0,PETSC_COMM_WORLD);
//Get Island Time 0-INF Unnormal
gsl_matrix_set_zero(params->expAFS);
fillExpectedAFS_unnorm(params->stateSpace, params->b,params->rates,params->expAFS);
// printf("////////////////////Island Time 0 - INF unnormalized\n");
// for(i=0;i< (params->n1+1) ;i++){
// for(j=0;j< (params->n2+1);j++){
// printf("%.5f ",gsl_matrix_get(params->expAFS,i,j));
// }
// printf("\n");
// }
//Matrix Exponentiation to get state vector at time t
//SLEPC Stuff ahead!
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create the solver and set various options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Set operator matrix, the function to compute, and other options
*/
//transpose
MatTranspose(params->C,MAT_REUSE_MATRIX,¶ms->C);
ierr = MFNSetOperator(params->mfn,params->C);CHKERRV(ierr);
/*
Set solver parameters at runtime
*/
ierr = MFNSetScaleFactor(params->mfn,timeV); CHKERRV(ierr);
ierr = MFNSetFromOptions(params->mfn);CHKERRV(ierr);
/* set v = e_1 */
ierr = MatGetVecs(params->C,PETSC_NULL,¶ms->y);CHKERRV(ierr);
ierr = MatGetVecs(params->C,¶ms->v, PETSC_NULL);CHKERRV(ierr);
ierr = VecSetValue(params->v,0,1.0,INSERT_VALUES);CHKERRV(ierr);
ierr = VecAssemblyBegin(params->v);CHKERRV(ierr);
ierr = VecAssemblyEnd(params->v);CHKERRV(ierr);
ierr = MFNSolve(params->mfn,params->v,params->y);CHKERRV(ierr);
ierr = MFNGetConvergedReason(params->mfn,&reason);CHKERRV(ierr);
if (reason!=MFN_CONVERGED_TOL) ierr = 1; CHKERRV(ierr);
//retranspose for later use
MatTranspose(params->C,MAT_REUSE_MATRIX,¶ms->C);
//state vector at time t stored in y
//scatter y and store in expoArray
VecScatterCreateToAll(params->y,¶ms->ctx,¶ms->v_seq);
VecScatterBegin(params->ctx,params->y,params->v_seq,INSERT_VALUES,SCATTER_FORWARD);
VecScatterEnd(params->ctx,params->y,params->v_seq,INSERT_VALUES,SCATTER_FORWARD);
VecGetArray(params->v_seq,&tmpArray);
for (j = 0; j < N; j++){
params->expoArray[j] = tmpArray[j];
//printf("%.5f\n",expoArray[j]);
}
VecRestoreArray(params->v_seq,&tmpArray);
VecScatterDestroy(¶ms->ctx);
VecDestroy(¶ms->v_seq);
VecDuplicate(params->y,¶ms->x);
//VecView(y, PETSC_VIEWER_STDOUT_WORLD);
MatMultTranspose(params->denseMat1,params->y,params->x);
VecScatterCreateToAll(params->x,¶ms->ctx,¶ms->v_seq);
VecScatterBegin(params->ctx,params->x,params->v_seq,INSERT_VALUES,SCATTER_FORWARD);
VecScatterEnd(params->ctx,params->x,params->v_seq,INSERT_VALUES,SCATTER_FORWARD);
VecGetArray(params->v_seq,&tmpArray);
for (j = 0; j < N; j++){
params->b[j] = tmpArray[j];
//printf("rank %d expoArray[%d]:%.5f\n",rank,j,expoArray[j]);
//printf("rank %d b[%d]:%.5f\n",rank,j,b[j]);
}
VecRestoreArray(params->v_seq,&tmpArray);
VecScatterDestroy(¶ms->ctx);
VecDestroy(¶ms->v_seq);
fillExpectedAFS_unnorm(params->stateSpace, params->b,params->rates,params->expAFS2);
//now subtract older AFS (t_t - t_INF) from total AFS (t_0 - t_INF)
/////////////////
///////
gsl_matrix_sub(params->expAFS,params->expAFS2);
//////////////////////
//Final phase, collapse popns, reset rates
//now collapse populations
//state vector at time t stored in st[] for largerStateSpace; use reverseMap
for(i=0;i<N;i++)params->st[i]=0.0;
for(i=0;i<N;i++){params->st[params->map[i]]+=params->expoArray[i];
// printf("expoArray[%d]:%f\n",i,expoArray[i]);
}
for(i=0; i<params->reducedStateSpace->nstates; i++){
VecSetValue(params->ancStateVec,i,params->st[params->reverseMap[i]],INSERT_VALUES );
}
//Re-Fill trans mats for Ancestral Params
params->nnzA = coalMarkovChainTopologyMatrix_sparse(params->reducedStateSpace,params->topA,params->moveA, params->dim1A, params->dim2A);
tmpMat=fillPetscCsparseTransMats(params->reducedStateSpace, params->topA, params->moveA, ¶ms->nnzA,
params->dim1A, params->dim2A, thetaA, 0, 0, 0, ¶ms->C2, params->rates);
//////////////////////
//
// S = (I-P)^-1
//
/////////
//////
//add negative ident
ident = cs_spalloc(Na,Na,Na,1,1);
for(i=0;i<Na;i++) cs_entry(ident,i,i,1);
eye = cs_compress(ident);
spMat = cs_add(eye,tmpMat,1.0,-1.0);
//cs_print_adk(spMat);
mt = cs_transpose(spMat,1);
//VecView(y,PETSC_VIEWER_STDOUT_WORLD);
n = mt->n ;
S = cs_sqr (0, mt, 0) ; /* ordering and symbolic analysis */
NN = cs_lu (mt, S, 1e-12) ; /* numeric LU factorization */
xx = cs_malloc (n, sizeof (double)) ; /* get workspace */
MatGetOwnershipRange(params->denseMat2,&iStart,&iEnd);
// printf("here\n");
// PetscFree(idx);
PetscMalloc1(Na,&idx);
for(j=0;j<Na;j++) idx[j]=j;
////Compute Entire Inverse Mat
for(j=iStart;j<iEnd;j++){
//create unit array for solve
for(i=0; i<Na; i++)params->b[i] = 0.0;
params->b[j]=1.0;
//factor outside loop leads to ~40x speedup
cs_ipvec (NN->pinv, params->b, xx, n) ; /* x = b(p) */
cs_lsolve (NN->L, xx) ; /* x = L\x */
cs_usolve (NN->U, xx) ; /* x = U\x */
cs_ipvec (S->q, xx, params->b, n) ; /* b(q) = x */
// if(!rank)printf("row %d\n",j);
MatSetValues(params->denseMat2,1,&j,Na,idx,params->b,INSERT_VALUES);
}
MatAssemblyBegin(params->denseMat2,MAT_FINAL_ASSEMBLY);
MatAssemblyEnd(params->denseMat2,MAT_FINAL_ASSEMBLY);
free(xx);
MatMultTranspose(params->denseMat2,params->ancStateVec,params->ancResVec);
VecScatterCreateToAll(params->ancResVec,¶ms->ctx,¶ms->v_seq);
VecScatterBegin(params->ctx,params->ancResVec,params->v_seq,INSERT_VALUES,SCATTER_FORWARD);
VecScatterEnd(params->ctx,params->ancResVec,params->v_seq,INSERT_VALUES,SCATTER_FORWARD);
VecGetArray(params->v_seq,&tmpArray);
for (j = 0; j < Na; j++){
params->expoArray[j] = tmpArray[j];
//printf("%.5f\n",expoArray[j]);
}
VecRestoreArray(params->v_seq,&tmpArray);
VecScatterDestroy(¶ms->ctx);
VecDestroy(¶ms->v_seq);
//get contribution starting at st
gsl_matrix_set_zero(params->expAFS2);
fillExpectedAFS_unnorm(params->reducedStateSpace, params->expoArray,params->rates,params->expAFS2);
// printf("////////////////////--Ancestral bit\n");
// for(i=0;i< (n1+1) ;i++){
// for(j=0;j< (n2+1);j++){
// printf("%.5f ",gsl_matrix_get(expAFS2,i,j));
// }
// printf("\n");
// }
//if(params->rank==0)printf("////////////////////normalized IM:\n");
gsl_matrix_add(params->expAFS,params->expAFS2);
sum = matrixSumDouble(params->expAFS);
gsl_matrix_scale(params->expAFS, 1.0 / sum);
// for(i=0;i< (params->n1+1) ;i++){
// for(j=0;j< (params->n2+1);j++){
// if(params->rank==0)printf("%.5f ",gsl_matrix_get(params->expAFS,i,j));
// }
// if(params->rank==0)printf("\n");
// }
//
//clean up
PetscFree(idx);
VecDestroy(¶ms->y);
VecDestroy(¶ms->x);
VecDestroy(¶ms->v);
ierr = ISDestroy(&perm);
ierr = ISDestroy(&iperm);
PetscFree(tmpArray);
cs_spfree(spMat);
cs_spfree(mt);
cs_spfree(ident);
cs_spfree(eye);
cs_spfree(tmpMat);
gsl_vector_free(tmpStates);
cs_nfree(NN);
cs_sfree(S);
}
double calcLikNLOpt(unsigned n, const double *point, double *gradients, void *p){
int i,j;
struct clam_lik_params * params = (struct clam_lik_params *) p;
double localNNZ = params->nnz;
double output = 666.0;
double lik=0.0;
double x[5];
for(i = 0;i<5;i++) x[i] = point[i];
MPI_Bcast(x,5,MPI_DOUBLE,0,PETSC_COMM_WORLD);
for(i = 0;i<5;i++) gsl_vector_set(params->paramVector, i, x[i]);
//fill in the expAFS table
calcLogAFS_IM(p);
params->nnz = localNNZ;
//compute lik
for(i=0;i<params->obsData->size1;i++){
for(j=0;j<params->obsData->size2;j++){
if (gsl_matrix_get(params->expAFS,i,j) > 0.0) //corners of AFS are zero prob
lik += gsl_matrix_get(params->obsData,i,j) * (log(gsl_matrix_get(params->expAFS,i,j)));
}
}
output = -1.0* lik;
MPI_Bcast(&output,1,MPI_DOUBLE,0,PETSC_COMM_WORLD);
if(params->rank == 0 && vbse){
for(i = 0;i<5;i++) printf("x[%d]: %lf\t",i,x[i]);
printf("lik: %lf\n",lik);
}
params->fEvals += 1;
// gsl_matrix_prettyPrint(params->expAFS);
return(output);
}
double calcLikNLOpt_gradients(unsigned n, const double *point, double *gradients, void *p){
int i,j;
//struct clam_lik_params * params = (struct clam_lik_params *) p;
//double localNNZ = params->nnz;
double output = 666.0;
double lik=0.0;
double newF;
double x[5];
double temp[5];
double epsilon=1e-5;
for(i = 0;i<5;i++) x[i] = point[i];
MPI_Bcast(x,5,MPI_DOUBLE,0,PETSC_COMM_WORLD);
lik = calcLikNLOpt(n, point, NULL, p);
if (gradients != NULL){
for(i=0; i<n ;i++){
for( j=0; j< n; j++)
temp[j] = x[j];
temp[i] += epsilon;
newF = calcLikNLOpt(n,temp,NULL,p);
gradients[i] = (newF - lik)/epsilon;
}
}
output = lik;
MPI_Bcast(&output,1,MPI_DOUBLE,0,PETSC_COMM_WORLD);
// gsl_matrix_prettyPrint(params->expAFS);