// File: /workspace/github_cpp_makefile_star2_O1/myudelson[P]hmm-scalable/HMMProblemSlicedAB.cpp
// Function: HMMProblemSlicedAB::BaumWelch()
NUMBER HMMProblemSlicedAB::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;
        FitBitSlicedAB *fb = new FitBitSlicedAB(this->p->nS, this->p->nO, this->p->nK, this->p->nG, this->p->nZ, 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);
                cpy1D<NUMBER>(fb->pi, aPI, this->p->nS);
                cpy3D<NUMBER>(fb->A,  this->getA(y), this->p->nZ, this->p->nS, this->p->nS);
                cpy3D<NUMBER>(fb->B,  this->getB(y), this->p->nZ, 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++) {
            FitResult fr;
            fr.iter = 0;
            fr.pO0  = 0.0;
            fr.pO   = 0.0;
            fr.conv = 0; // converged
            fr.ndat = 0;
            for(NPAR z=0; z<this->p->nZ; z++) {
                FitBitSlicedAB *fb = new FitBitSlicedAB(this->p->nS, this->p->nO, this->p->nK, this->p->nG, this->p->nZ, 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 || z>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_loc;
                fr_loc = BaumWelchBit(fb);
                fr.iter+=fr_loc.iter;
                fr.conv+=fr_loc.conv;
                fr.pO0=(z==0)?fr_loc.pO0:0;
                fr.pO =(z==(this->p->nZ-1))?fr_loc.pO:0;
                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 $0x78, %rsp
movq %rdi, %r14
movq 0x88(%rdi), %rbx
cmpb $0x0, 0x3d(%rbx)
jle 0x2780f
movl $0xf8, %edi
callq 0x4210
movq %rax, %r13
movsbl 0x8b8(%rbx), %esi
movsbl 0x8b9(%rbx), %edx
movl 0x8c0(%rbx), %ecx
movl 0x8bc(%rbx), %r8d
movsbl 0x8c8(%rbx), %r9d
movsd 0x28(%rbx), %xmm0
movsbl 0x30(%rbx), %eax
movl %eax, (%rsp)
movq %r13, %rdi
callq 0xcb4c
movq %r14, %rdi
xorl %esi, %esi
callq 0x25c26
movq %rax, %r15
movq %r14, %rdi
xorl %esi, %esi
callq 0x25c42
movq %rax, %r12
movq %r14, %rdi
xorl %esi, %esi
callq 0x25c62
movq 0x88(%r14), %rcx
movl 0x8dc(%rcx), %r8d
movq 0x8f0(%rcx), %r9
movq %r13, %rdi
movq %r15, %rsi
movq %r12, %rdx
movq %rax, %rcx
callq 0xd010
movq 0x88(%r14), %rax
cmpb $0x0, 0x981(%rax)
je 0x27526
movq $0x0, 0x10(%r13)
cmpb $0x0, 0x982(%rax)
je 0x27537
movq $0x0, 0x18(%r13)
cmpb $0x0, 0x983(%rax)
je 0x27548
movq $0x0, 0x20(%r13)
movq %r13, %rdi
movl $0x2, %esi
callq 0xd392
movq %r13, %rdi
movl $0x7, %esi
callq 0xd392
movq %r13, %rdi
movl $0x3, %esi
callq 0xd392
movq 0x88(%r14), %rax
cmpb $0x3, 0x3f(%rax)
jne 0x275a3
movq %r13, %rdi
movl $0x8, %esi
callq 0xd392
movq %r13, %rdi
movl $0x6, %esi
callq 0xd392
movq %r13, %rdi
movl $0x4, %esi
callq 0xd392
movq %r13, 0x10(%rsp)
movq 0x88(%r14), %rbx
movslq 0x8dc(%rbx), %r12
movl $0x4, %esi
movq %r12, %rdi
callq 0x4130
movq %rax, %r15
testq %r12, %r12
jle 0x275f0
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 0x275d8
leaq 0x50(%rsp), %r12
movq %r12, %rdi
movq %r14, %rsi
movq 0x10(%rsp), %rdx
callq 0x296dc
movl (%r12), %ebp
movsd 0x8(%r12), %xmm0
movsd %xmm0, 0x20(%rsp)
movsd 0x18(%r12), %xmm0
movsd %xmm0, 0x18(%rsp)
movl 0x20(%r12), %eax
movl %eax, 0x30(%rsp)
movl 0x24(%r12), %r13d
movq 0x88(%r14), %rbx
movslq 0x8dc(%rbx), %r12
testq %r12, %r12
jle 0x27663
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 0x27651
movq %r15, %rdi
callq 0x42a0
cmpb $0x0, 0x3c(%rbx)
jne 0x27698
leaq 0xdfee(%rip), %rdi      # 0x35666
movl %r12d, %esi
movl %r13d, %edx
movl %ebp, %ecx
movsd 0x20(%rsp), %xmm0
movsd 0x18(%rsp), %xmm1
movl 0x30(%rsp), %r8d
movb $0x2, %al
callq 0x4050
movq 0x88(%r14), %rax
cmpb $0x2, 0x3d(%rax)
jne 0x277f5
cmpl $0x0, 0xc(%r14)
jle 0x277f5
xorl %r15d, %r15d
movq %r14, 0x38(%rsp)
movq %r14, %rdi
movl %r15d, %esi
callq 0x25c26
movq 0x10(%rsp), %rbx
movq 0x10(%rbx), %rsi
movq 0x88(%r14), %rcx
movsbq 0x8b8(%rcx), %rdx
shlq $0x3, %rdx
movq %rax, %rdi
callq 0x41c0
movq 0x18(%rbx), %rbx
movq %r14, %rdi
movq %r15, 0x18(%rsp)
movl %r15d, %esi
callq 0x25c42
movq %rax, %r12
movq 0x88(%r14), %rax
movsbq 0x8c8(%rax), %rcx
movq %rcx, 0x20(%rsp)
testq %rcx, %rcx
jle 0x2775f
movsbq 0x8b8(%rax), %r15
leaq (,%r15,8), %r13
xorl %ebp, %ebp
testb %r15b, %r15b
jle 0x27755
xorl %r14d, %r14d
movq (%r12,%rbp,8), %rax
movq (%rax,%r14,8), %rdi
movq (%rbx,%rbp,8), %rax
movq (%rax,%r14,8), %rsi
movq %r13, %rdx
callq 0x41c0
incq %r14
cmpq %r14, %r15
jne 0x27735
incq %rbp
cmpq 0x20(%rsp), %rbp
jne 0x2772d
movq 0x10(%rsp), %rax
movq 0x20(%rax), %rbx
movq 0x38(%rsp), %r14
movq %r14, %rdi
movq 0x18(%rsp), %rsi
callq 0x25c62
movq %rax, %r12
movq 0x88(%r14), %rax
movsbq 0x8c8(%rax), %rcx
movq %rcx, 0x20(%rsp)
testq %rcx, %rcx
jle 0x277de
movsbq 0x8b8(%rax), %r15
movsbq 0x8b9(%rax), %r13
shlq $0x3, %r13
xorl %ebp, %ebp
testb %r15b, %r15b
jle 0x277d4
xorl %r14d, %r14d
movq (%r12,%rbp,8), %rax
movq (%rax,%r14,8), %rdi
movq (%rbx,%rbp,8), %rax
movq (%rax,%r14,8), %rsi
movq %r13, %rdx
callq 0x41c0
incq %r14
cmpq %r14, %r15
jne 0x277b4
incq %rbp
cmpq 0x20(%rsp), %rbp
jne 0x277ac
movq 0x18(%rsp), %r15
incl %r15d
movq 0x38(%rsp), %r14
cmpl 0xc(%r14), %r15d
jl 0x276bc
movq 0x10(%rsp), %rbx
movq %rbx, %rdi
callq 0xcbf8
movl $0xf8, %esi
movq %rbx, %rdi
callq 0x4220
movq 0x88(%r14), %rax
cmpl $0x0, 0x8c0(%rax)
jle 0x27aa3
xorpd %xmm3, %xmm3
movq $0x0, 0x10(%rsp)
movq 0x88(%r14), %rbx
cmpb $0x0, 0x8c8(%rbx)
jle 0x27a04
movsd %xmm3, 0x40(%rsp)
xorl %ebp, %ebp
movl $0xffffffff, %r15d      # imm = 0xFFFFFFFF
xorl %r13d, %r13d
movl $0xf8, %edi
callq 0x4210
movq %rax, %r12
movsbl 0x8b8(%rbx), %esi
movsbl 0x8b9(%rbx), %edx
movl 0x8c0(%rbx), %ecx
movl 0x8bc(%rbx), %r8d
movsbl 0x8c8(%rbx), %r9d
movsd 0x28(%rbx), %xmm0
movsbl 0x30(%rbx), %eax
movl %eax, (%rsp)
movq %r12, %rdi
callq 0xcb4c
movl %r13d, 0x18(%rsp)
movl %ebp, 0x20(%rsp)
movq %r14, %rdi
movq 0x10(%rsp), %r13
movl %r13d, %esi
callq 0x25c26
movq %rax, %rbp
movq %r14, %rdi
movl %r13d, %esi
callq 0x25c42
movq %rax, %rbx
movq %r14, %rdi
movl %r13d, %esi
callq 0x25c62
movq 0x88(%r14), %rcx
movq 0x8e0(%rcx), %rdx
movq 0x8f8(%rcx), %rcx
movl (%rdx,%r13,4), %r8d
movq (%rcx,%r13,8), %r9
movq %r12, %rdi
movq %rbp, %rsi
movq %rbx, %rdx
movq %rax, %rcx
callq 0xd010
movq 0x88(%r14), %rax
cmpl $-0x1, %r15d
jne 0x27912
cmpb $0x0, 0x981(%rax)
je 0x2791b
movq $0x0, 0x10(%r12)
cmpb $0x0, 0x982(%rax)
movl 0x20(%rsp), %ebp
movl 0x18(%rsp), %r13d
je 0x27936
movq $0x0, 0x18(%r12)
cmpb $0x0, 0x983(%rax)
je 0x27948
movq $0x0, 0x20(%r12)
movq %r12, %rdi
movl $0x2, %esi
callq 0xd392
movq %r12, %rdi
movl $0x7, %esi
callq 0xd392
leaq 0x50(%rsp), %rdi
movq %r14, %rsi
movq %r12, %rdx
callq 0x296dc
movsd 0x58(%rsp), %xmm0
movsd %xmm0, 0x30(%rsp)
movsd 0x68(%rsp), %xmm0
movsd %xmm0, 0x48(%rsp)
addl 0x50(%rsp), %r13d
addl 0x70(%rsp), %ebp
movq 0x88(%r14), %rax
movq %r12, %rbx
movsbl 0x8c8(%rax), %r12d
movq %rbx, %rdi
callq 0xcbf8
movl $0xf8, %esi
movq %rbx, %rdi
callq 0x4220
movq 0x88(%r14), %rbx
movsbl 0x8c8(%rbx), %ecx
leal 0x1(%r15), %eax
addl $0x2, %r15d
cmpl %ecx, %r15d
movl %eax, %r15d
jl 0x27855
movsd 0x48(%rsp), %xmm1
testl %eax, %eax
movsd 0x30(%rsp), %xmm2
je 0x279f0
xorpd %xmm2, %xmm2
decl %r12d
cmpl %r12d, %eax
movsd 0x40(%rsp), %xmm3
je 0x27a11
xorpd %xmm1, %xmm1
jmp 0x27a11
xorpd %xmm2, %xmm2
xorpd %xmm1, %xmm1
xorl %r13d, %r13d
xorl %ebp, %ebp
testl %ebp, %ebp
jne 0x27a1b
cmpl 0x38(%rbx), %r13d
jne 0x27a75
xorpd %xmm4, %xmm4
cmpltsd %xmm1, %xmm4
movsd 0xcec4(%rip), %xmm0     # 0x348f0
andpd %xmm0, %xmm4
mulsd %xmm1, %xmm4
addsd %xmm3, %xmm4
cmpb $0x0, 0x3c(%rbx)
jne 0x27a79
movq 0x8e0(%rbx), %rax
movq 0x10(%rsp), %rsi
movl (%rax,%rsi,4), %edx
leaq 0xdc5f(%rip), %rdi      # 0x356b3
xorl %ecx, %ecx
movl %r13d, %r8d
movapd %xmm2, %xmm0
movl %ebp, %r9d
movb $0x2, %al
movapd %xmm4, 0x20(%rsp)
callq 0x4050
movapd 0x20(%rsp), %xmm4
jmp 0x27a79
movapd %xmm3, %xmm4
movq 0x10(%rsp), %rdx
incq %rdx
movq 0x88(%r14), %rax
movslq 0x8c0(%rax), %rax
movapd %xmm4, %xmm3
movq %rdx, 0x10(%rsp)
cmpq %rax, %rdx
jl 0x27830
jmp 0x27aa7
xorpd %xmm4, %xmm4
movapd %xmm4, %xmm0
addq $0x78, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %rbx
movq %r13, %r12
jmp 0x27ac5
movq %rax, %rbx
movl $0xf8, %esi
movq %r12, %rdi
callq 0x4220
movq %rbx, %rdi
callq 0x4430