// File: /workspace/github_cpp_makefile_star2_O3/myudelson[P]hmm-scalable/HMMProblem.cpp
// Function: HMMProblem::BaumWelch()
NUMBER HMMProblem::BaumWelch() {
	NCAT k;
    NUMBER loglik = 0;
	
    //    bool conv_flags[3] = {true, true, true};
	
	//
	// fit all as 1 skill first
	//
    if(this->p->single_skill>0) {
        FitResult fr;
        fr.pO = 0;
        NCAT x;
        FitBit *fb = new FitBit(this->p->nS, this->p->nO, this->p->nK, this->p->nG, this->p->tol, this->p->tol_mode);
        fb->link( this->getPI(0), this->getA(0), this->getB(0), this->p->nSeq, this->p->k_data);// link skill 0 (we'll copy fit parameters to others
        if(this->p->block_fitting[0]!=0) fb->pi = NULL;
        if(this->p->block_fitting[1]!=0) fb->A  = NULL;
        if(this->p->block_fitting[2]!=0) fb->B  = NULL;

        fb->init(FBS_PARm1);
        fb->init(FBS_PARm2);
        fb->init(FBS_GRAD);
        if(this->p->solver==METHOD_CGD) {
            fb->init(FBS_DIR);
            fb->init(FBS_DIRm1);
            fb->init(FBS_GRADm1);
        }

        NCAT* original_ks = Calloc(NCAT, (size_t)this->p->nSeq);
        for(x=0; x<this->p->nSeq; x++) { original_ks[x] = this->p->all_data[x].k; this->p->all_data[x].k = 0; } // save original k's
        fr = BaumWelchBit(fb);
        for(x=0; x<this->p->nSeq; x++) { this->p->all_data[x].k = original_ks[x]; } // restore original k's
        free(original_ks);
        if(!this->p->quiet)
            printf("skill one, seq %4d, dat %8d, iter#%3d p(O|param)= %15.7f >> %15.7f, conv=%d\n",  this->p->nSeq, fr.ndat, fr.iter,fr.pO0,fr.pO,fr.conv);
        if(this->p->single_skill==2) {
            for(NCAT y=0; y<this->sizes[0]; y++) { // copy the rest
                NUMBER *aPI = this->getPI(y);
                NUMBER **aA = this->getA(y);
                NUMBER **aB = this->getB(y);
                cpy3Params(fb->pi, fb->A, fb->B, aPI, aA, aB, this->p->nS, this->p->nO);
            }
        }// force single skill
        delete fb;
    }
	
	//
	// Main fit
	//
    
//    int parallel_now = this->p->parallel==1; //PAR
//    #pragma omp parallel if(parallel_now) //num_threads(2) //PAR
//    {//PAR
//        #pragma omp for schedule(dynamic) reduction(+:loglik) //PAR
        for(k=0; k<this->p->nK; k++) {
            FitBit *fb = new FitBit(this->p->nS, this->p->nO, this->p->nK, this->p->nG, this->p->tol, this->p->tol_mode);
            fb->link(this->getPI(k), this->getA(k), this->getB(k), this->p->k_numg[k], this->p->k_g_data[k]);
            if(this->p->block_fitting[0]!=0) fb->pi = NULL;
            if(this->p->block_fitting[1]!=0) fb->A  = NULL;
            if(this->p->block_fitting[2]!=0) fb->B  = NULL;
            
            fb->init(FBS_PARm1);
            fb->init(FBS_PARm2);
            
            FitResult fr;
            fr = BaumWelchBit(fb);
            delete fb;
            
            if( ( /*(!conv && iter<this->p->maxiter) ||*/ (fr.conv || fr.iter==this->p->maxiter) )) {
                loglik += fr.pO*(fr.pO>0); // reduction'ed
                if(!this->p->quiet)
                    printf("skill %4d, seq %4d, dat %8d, iter#%3d p(O|param)= %15.7f >> %15.7f, conv=%d\n", k,  this->p->k_numg[k], fr.ndat, fr.iter,fr.pO0,fr.pO,fr.conv);
            }
        } // for all skills
//    }//PAR
    return loglik;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x68, %rsp
movq %rdi, 0x8(%rsp)
movq 0x88(%rdi), %rbx
cmpb $0x0, 0x3d(%rbx)
jle 0x148ab
movl $0x110, %edi            # imm = 0x110
callq 0x4210
movq %rax, %r12
movsbl 0x8b8(%rbx), %esi
movsbl 0x8b9(%rbx), %edx
movl 0x8c0(%rbx), %ecx
movl 0x8bc(%rbx), %r8d
movsd 0x28(%rbx), %xmm0
movsbl 0x30(%rbx), %r9d
movq %rax, %rdi
callq 0xa858
movq 0x8(%rsp), %rbx
movq %rbx, %rdi
xorl %esi, %esi
callq 0x11354
movq %rax, %r14
movq %rbx, %rdi
xorl %esi, %esi
callq 0x11370
movq %rax, %r15
movq %rbx, %rdi
xorl %esi, %esi
callq 0x1138c
movq 0x88(%rbx), %rcx
movl 0x8dc(%rcx), %r8d
movq 0x8f0(%rcx), %r9
movq %r12, %rdi
movq %r14, %rsi
movq %r15, %rdx
movq %rax, %rcx
callq 0xac70
movq 0x88(%rbx), %rax
cmpb $0x0, 0x981(%rax)
je 0x14616
movq $0x0, 0x10(%r12)
cmpb $0x0, 0x982(%rax)
je 0x14628
movq $0x0, 0x18(%r12)
cmpb $0x0, 0x983(%rax)
je 0x1463a
movq $0x0, 0x20(%r12)
movq %r12, %rdi
movl $0x2, %esi
callq 0xaf10
movq %r12, %rdi
movl $0x7, %esi
callq 0xaf10
movq %r12, %rdi
movl $0x3, %esi
callq 0xaf10
movq 0x88(%rbx), %rbx
cmpb $0x3, 0x3f(%rbx)
jne 0x146a1
movq %r12, %rdi
movl $0x8, %esi
callq 0xaf10
movq %r12, %rdi
movl $0x6, %esi
callq 0xaf10
movq %r12, %rdi
movl $0x4, %esi
callq 0xaf10
movq 0x8(%rsp), %rax
movq 0x88(%rax), %rbx
movq %r12, 0x18(%rsp)
movslq 0x8dc(%rbx), %r12
movl $0x4, %esi
movq %r12, %rdi
callq 0x4130
movq %rax, %r15
testq %r12, %r12
jle 0x146e7
movq 0x8e8(%rbx), %rax
addq $0x58, %rax
xorl %ecx, %ecx
movl (%rax), %edx
movl %edx, (%r15,%rcx,4)
movl $0x0, (%rax)
incq %rcx
addq $0x60, %rax
cmpq %rcx, %r12
jne 0x146cf
leaq 0x40(%rsp), %r14
movq %r14, %rdi
movq 0x8(%rsp), %rbx
movq %rbx, %rsi
movq 0x18(%rsp), %rdx
callq 0x17aa0
movl (%r14), %ebp
movsd 0x8(%r14), %xmm0
movsd %xmm0, 0x20(%rsp)
movsd 0x18(%r14), %xmm0
movsd %xmm0, 0x10(%rsp)
movl 0x20(%r14), %eax
movl %eax, 0x3c(%rsp)
movl 0x24(%r14), %r13d
movq 0x88(%rbx), %rbx
movslq 0x8dc(%rbx), %r12
testq %r12, %r12
jle 0x1475a
movq 0x8e8(%rbx), %rax
addq $0x58, %rax
xorl %ecx, %ecx
movl (%r15,%rcx,4), %edx
movl %edx, (%rax)
incq %rcx
addq $0x60, %rax
cmpq %rcx, %r12
jne 0x14748
movq %r15, %rdi
callq 0x42a0
cmpb $0x0, 0x3c(%rbx)
jne 0x1479b
leaq 0x1ff87(%rip), %rdi     # 0x346f6
movl %r12d, %esi
movl %r13d, %edx
movl %ebp, %ecx
movsd 0x20(%rsp), %xmm0
movsd 0x10(%rsp), %xmm1
movl 0x3c(%rsp), %r8d
movb $0x2, %al
callq 0x4050
movq 0x8(%rsp), %rax
movq 0x88(%rax), %rbx
cmpb $0x2, 0x3d(%rbx)
movq 0x8(%rsp), %rbx
movq 0x18(%rsp), %r12
jne 0x1488f
cmpl $0x0, 0xc(%rbx)
jle 0x1488f
xorl %r14d, %r14d
movq %rbx, %rdi
movl %r14d, %esi
callq 0x11354
movq %rax, 0x10(%rsp)
movq %rbx, %rdi
movl %r14d, %esi
callq 0x11370
movq %rax, %rbp
movq %rbx, %rdi
movq %r14, 0x20(%rsp)
movl %r14d, %esi
callq 0x1138c
movq %rax, %r15
movq 0x88(%rbx), %rax
movsbq 0x8b8(%rax), %rbx
movsbq 0x8b9(%rax), %r13
movq 0x10(%r12), %rsi
leaq (,%rbx,8), %r14
movq 0x10(%rsp), %rdi
movq %r14, %rdx
callq 0x41c0
testq %rbx, %rbx
jle 0x14878
movq %r15, 0x10(%rsp)
movq 0x18(%r12), %r15
xorl %r12d, %r12d
movq (%rbp,%r12,8), %rdi
movq (%r15,%r12,8), %rsi
movq %r14, %rdx
callq 0x41c0
incq %r12
cmpq %r12, %rbx
jne 0x14830
movq 0x18(%rsp), %r12
movq 0x20(%r12), %r14
shlq $0x3, %r13
xorl %r15d, %r15d
movq 0x10(%rsp), %rbp
movq (%rbp,%r15,8), %rdi
movq (%r14,%r15,8), %rsi
movq %r13, %rdx
callq 0x41c0
incq %r15
cmpq %r15, %rbx
jne 0x1485f
movq 0x20(%rsp), %r14
incl %r14d
movq 0x8(%rsp), %rbx
cmpl 0xc(%rbx), %r14d
jl 0x147bc
movq %r12, %rdi
callq 0xa8fa
movl $0x110, %esi            # imm = 0x110
movq %r12, %rdi
callq 0x4220
movq 0x88(%rbx), %rbx
cmpl $0x0, 0x8c0(%rbx)
jle 0x14a98
xorpd %xmm0, %xmm0
xorl %r14d, %r14d
movsd %xmm0, 0x20(%rsp)
movl $0x110, %edi            # imm = 0x110
callq 0x4210
movq %rax, %r13
movsbl 0x8b8(%rbx), %esi
movsbl 0x8b9(%rbx), %edx
movl 0x8c0(%rbx), %ecx
movl 0x8bc(%rbx), %r8d
movsd 0x28(%rbx), %xmm0
movsbl 0x30(%rbx), %r9d
movq %rax, %rdi
callq 0xa858
movq 0x8(%rsp), %rbx
movq %rbx, %rdi
movl %r14d, %esi
callq 0x11354
movq %rax, %r15
movq %rbx, %rdi
movl %r14d, %esi
callq 0x11370
movq %rax, %r12
movq %rbx, %rdi
movl %r14d, %esi
callq 0x1138c
movq 0x88(%rbx), %rcx
movq 0x8e0(%rcx), %rdx
movq 0x8f8(%rcx), %rcx
movl (%rdx,%r14,4), %r8d
movq (%rcx,%r14,8), %r9
movq %r13, %rdi
movq %r15, %rsi
movq %r12, %rdx
movq %rax, %rcx
callq 0xac70
movq 0x88(%rbx), %rax
cmpb $0x0, 0x981(%rax)
je 0x14971
movq $0x0, 0x10(%r13)
cmpb $0x0, 0x982(%rax)
je 0x14982
movq $0x0, 0x18(%r13)
cmpb $0x0, 0x983(%rax)
je 0x14993
movq $0x0, 0x20(%r13)
movq %r13, %rdi
movl $0x2, %esi
callq 0xaf10
movq %r13, %rdi
movl $0x7, %esi
callq 0xaf10
leaq 0x40(%rsp), %rdi
movq %rbx, %rsi
movq %r13, %rdx
callq 0x17aa0
movl 0x40(%rsp), %ebp
movsd 0x48(%rsp), %xmm0
movsd %xmm0, 0x18(%rsp)
movsd 0x58(%rsp), %xmm0
movsd %xmm0, 0x10(%rsp)
movl 0x60(%rsp), %r12d
movl 0x64(%rsp), %r15d
movq %r13, %rdi
callq 0xa8fa
movl $0x110, %esi            # imm = 0x110
movq %r13, %rdi
callq 0x4220
movq 0x88(%rbx), %rbx
testl %r12d, %r12d
jne 0x14a09
cmpl 0x38(%rbx), %ebp
jne 0x14a79
xorpd %xmm2, %xmm2
movsd 0x10(%rsp), %xmm1
cmpltsd %xmm1, %xmm2
movsd 0x1eed0(%rip), %xmm0    # 0x338f0
andpd %xmm0, %xmm2
mulsd %xmm1, %xmm2
addsd 0x20(%rsp), %xmm2
cmpb $0x0, 0x3c(%rbx)
jne 0x14a7f
movq 0x8e0(%rbx), %rax
movl (%rax,%r14,4), %edx
leaq 0x1fcfd(%rip), %rdi     # 0x34743
movl %r14d, %esi
movl %r15d, %ecx
movl %ebp, %r8d
movsd 0x18(%rsp), %xmm0
movapd %xmm2, 0x20(%rsp)
movl %r12d, %r9d
movb $0x2, %al
callq 0x4050
movapd 0x20(%rsp), %xmm2
movq 0x8(%rsp), %rax
movq 0x88(%rax), %rbx
jmp 0x14a7f
movsd 0x20(%rsp), %xmm2
incq %r14
movslq 0x8c0(%rbx), %rax
movapd %xmm2, %xmm0
cmpq %rax, %r14
jl 0x148bf
jmp 0x14a9c
xorpd %xmm2, %xmm2
movapd %xmm2, %xmm0
addq $0x68, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %rbx
movl $0x110, %esi            # imm = 0x110
movq %r12, %rdi
jmp 0x14ac7
movq %rax, %rbx
movl $0x110, %esi            # imm = 0x110
movq %r13, %rdi
callq 0x4220
movq %rbx, %rdi
callq 0x4430