// File: /workspace/github_cpp_makefile_star2_O3/myudelson[P]hmm-scalable/HMMProblemAGK.cpp
// Function: HMMProblemAGK::init(param*)
void HMMProblemAGK::init(struct param *param) {
	this->p = param;
	this->non01constraints = true;
    this->null_obs_ratio = Calloc(NUMBER, (size_t)this->p->nO);
    this->neg_log_lik = 0;
    this->null_skill_obs = 0;
    this->null_skill_obs_prob = 0;
    NPAR nS = this->p->nS, nO = this->p->nO; NCAT nK = this->p->nK, nG = this->p->nG;
    
    NUMBER *a_PI, ** a_A, ** a_B;
    init3Params(a_PI, a_A, a_B, nS, nO);
    //
    // setup params
    //
	NPAR i, j, idx, offset;
	NUMBER sumPI = 0;
	NUMBER sumA[nS];
	NUMBER sumB[nS];
	for(i=0; i<nS; i++) {
		sumA[i] = 0;
		sumB[i] = 0;
	}
    
    // write default parameters first
	// populate PI
	for(i=0; i<((nS)-1); i++) {
		a_PI[i] = this->p->init_params[i];
		sumPI  += this->p->init_params[i];
	}
	a_PI[nS-1] = 1 - sumPI;
	// populate A
	offset = (NPAR)(nS-1);
	for(i=0; i<nS; i++) {
		for(j=0; j<((nS)-1); j++) {
			idx = (NPAR)(offset + i*((nS)-1) + j);
			a_A[i][j] = this->p->init_params[idx];
			sumA[i]  += this->p->init_params[idx];
		}
		a_A[i][((nS)-1)]  = 1 - sumA[i];
	}
	// polupale B
	offset = (NPAR)((nS-1) + nS*(nS-1));
	for(i=0; i<nS; i++) {
		for(j=0; j<((nO)-1); j++) {
			idx = (NPAR)(offset + i*((nO)-1) + j);
			a_B[i][j] = this->p->init_params[idx];
			sumB[i] += this->p->init_params[idx];
		}
		a_B[i][((nO)-1)]  = 1 - sumB[i];
	}
    
    // mass produce PI's/PIg's, A's, B's
    if( this->p->do_not_check_constraints==0 && !checkPIABConstraints(a_PI, a_A, a_B)) {
        fprintf(stderr,"params do not meet constraints.\n");
        exit(1);
    }
    this->pi  = init2D<NUMBER>((NDAT)nK, (NDAT)nS);
    this->A   = init3D<NUMBER>((NDAT)nK, (NDAT)nS, (NDAT)nS);
    this->Ag  = init3D<NUMBER>((NDAT)nG, (NDAT)nS, (NDAT)nS);
    this->B   = init3D<NUMBER>((NDAT)nK, (NDAT)nS, (NDAT)nO);
    NCAT x;
    for(x=0; x<nK; x++) {
        cpy1D<NUMBER>(a_PI, this->pi[x], (NDAT)nS);
        cpy2D<NUMBER>(a_A,  this->A[x],  (NDAT)nS, (NDAT)nS);
        cpy2D<NUMBER>(a_B,  this->B[x],  (NDAT)nS, (NDAT)nO);
    }
    // PIg start with "no-effect" params,PI[i] = 1/nS
    for(x=0; x<nG; x++) {
        for(i=0; i<nS; i++) {
            for(j=0; j<nS; j++)
                this->Ag[x][i][j] = (NUMBER)1/nS;
        }
    }
    // destroy setup params
	free(a_PI);
	free2D<NUMBER>(a_A, (NDAT)nS);
	free2D<NUMBER>(a_B, (NDAT)nS);
	
    // if needs be -- read in init params from a file
    if(param->initfile[0]!=0)
        this->readModel(param->initfile, false /* read and upload but not overwrite*/);
    
    // populate boundaries
	// populate lb*/ub*
	// *PI
    init3Params(this->lbPI, this->lbA, this->lbB, nS, nO);
    init3Params(this->ubPI, this->ubA, this->ubB, nS, nO);
	for(i=0; i<nS; i++) {
		lbPI[i] = this->p->param_lo[i];
		ubPI[i] = this->p->param_hi[i];
	}
	// *A
	offset = nS;
	for(i=0; i<nS; i++)
		for(j=0; j<nS; j++) {
			idx = (NPAR)(offset + i*nS + j);
			lbA[i][j] = this->p->param_lo[idx];
			ubA[i][j] = this->p->param_hi[idx];
		}
	// *B
	offset = (NPAR)(nS + nS*nS);
	for(i=0; i<nS; i++)
		for(j=0; j<nO; j++) {
			idx = (NPAR)(offset + i*nS + j);
			lbB[i][j] = this->p->param_lo[idx];
			ubB[i][j] = this->p->param_hi[idx];
		}
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x88, %rsp
movq %rsi, %r13
movq %rdi, %rbx
movq %rsi, 0x88(%rdi)
movb $0x1, 0x80(%rdi)
movsbq 0x8b9(%rsi), %r15
movl $0x8, %esi
movq %r15, %rdi
callq 0x4130
movq %rax, 0x18(%rbx)
xorpd %xmm0, %xmm0
movupd %xmm0, 0x20(%rbx)
movq $0x0, 0x30(%rbx)
movsbl 0x8b8(%r13), %r12d
movzbl %r12b, %r14d
movl 0x8bc(%r13), %eax
movq %rax, -0x80(%rbp)
movq %r13, -0x98(%rbp)
movl 0x8c0(%r13), %eax
movq %rax, -0x88(%rbp)
leaq -0x68(%rbp), %rsi
leaq -0x60(%rbp), %rdx
leaq -0x58(%rbp), %rcx
movq %rbx, -0x30(%rbp)
movq %rbx, %rdi
movl %r12d, %r8d
movl %r15d, %r9d
callq 0x10fa2
movq %rsp, -0xa0(%rbp)
leal 0xf(,%r14,8), %eax
andl $-0x10, %eax
movq %rsp, %rbx
subq %rax, %rbx
movq %rbx, %rsp
movq %rsp, %r13
subq %rax, %r13
movq %r13, %rsp
movslq %r12d, %rcx
testl %r12d, %r12d
movq %r15, -0x70(%rbp)
movq %r14, -0x50(%rbp)
movq %rcx, -0x38(%rbp)
movq %r12, -0x48(%rbp)
jle 0x1dae6
leal (,%r14,8), %r12d
movq %rbx, %rdi
xorl %esi, %esi
movq %r12, %rdx
callq 0x4120
movq %r13, %rdi
xorl %esi, %esi
movq %r12, %rdx
callq 0x4120
leaq -0x1(%r14), %rax
movq -0x68(%rbp), %rsi
cmpq $0x1, %r14
jne 0x1db01
movl %eax, %ecx
movabsq $0x3ff0000000000000, %rdx # imm = 0x3FF0000000000000
movq %rdx, (%rsi,%rcx,8)
movq -0x38(%rbp), %r12
jmp 0x1db55
movq -0x68(%rbp), %rsi
movabsq $0x3ff0000000000000, %rax # imm = 0x3FF0000000000000
movq %rax, -0x8(%rsi,%rcx,8)
movl %r12d, %r14d
jmp 0x1dc8d
movq -0x30(%rbp), %rcx
movq 0x88(%rcx), %rcx
movq 0x8(%rcx), %rcx
xorpd %xmm0, %xmm0
xorl %edx, %edx
movq -0x38(%rbp), %r12
movsbq %dl, %rdx
movsd (%rcx,%rdx,8), %xmm1
movsd %xmm1, (%rsi,%rdx,8)
addsd %xmm1, %xmm0
incb %dl
movsbl %dl, %edi
cmpl %edi, %eax
jg 0x1db1a
movsd 0x15db3(%rip), %xmm1    # 0x338f0
subsd %xmm0, %xmm1
movsd %xmm1, -0x8(%rsi,%r14,8)
movq %rax, %rcx
cmpb $0x0, -0x48(%rbp)
jle 0x1dc8d
movq -0x30(%rbp), %rdx
movq 0x88(%rdx), %rdx
movq -0x60(%rbp), %rdi
leal -0x1(%r14), %r8d
xorl %r9d, %r9d
movsd 0x15d7d(%rip), %xmm0    # 0x338f0
movl %r8d, %r10d
cmpb $0x1, %r12b
jne 0x1db88
movsd (%rbx,%r9,8), %xmm1
movq (%rdi,%r9,8), %r11
jmp 0x1dbd3
movq 0x8(%rdx), %r15
movq (%rdi,%r9,8), %r11
movsd (%rbx,%r9,8), %xmm1
xorl %r12d, %r12d
leal (%r10,%r12), %r14d
movsbq %r14b, %r14
movsd (%r15,%r14,8), %xmm2
movsbq %r12b, %r12
movsd %xmm2, (%r11,%r12,8)
addsd %xmm2, %xmm1
incb %r12b
movsbl %r12b, %r14d
cmpl %r14d, %eax
jg 0x1db99
movsd %xmm1, (%rbx,%r9,8)
movq -0x70(%rbp), %r15
movq -0x50(%rbp), %r14
movq -0x38(%rbp), %r12
movapd %xmm0, %xmm2
subsd %xmm1, %xmm2
movsd %xmm2, (%r11,%rcx,8)
incq %r9
addb %r8b, %r10b
cmpq %r14, %r9
jne 0x1db76
testb %r12b, %r12b
jle 0x1dc8d
leal -0x1(%r15), %ecx
movq -0x30(%rbp), %rax
movq 0x88(%rax), %rdx
movq -0x58(%rbp), %rdi
movq -0x48(%rbp), %rax
decl %eax
leal 0x1(%r12), %r8d
mulb %r8b
leal -0x1(%r15), %r8d
xorl %r9d, %r9d
cmpb $0x1, %r15b
jle 0x1dc68
movq 0x8(%rdx), %r11
movq (%rdi,%r9,8), %r10
movsd (%r13,%r9,8), %xmm1
xorl %ebx, %ebx
leal (%rax,%rbx), %r14d
movsbq %r14b, %r14
movsd (%r11,%r14,8), %xmm2
movsbq %bl, %rbx
movsd %xmm2, (%r10,%rbx,8)
addsd %xmm2, %xmm1
incb %bl
movsbl %bl, %r14d
cmpl %r14d, %ecx
jg 0x1dc34
movsd %xmm1, (%r13,%r9,8)
movq -0x50(%rbp), %r14
jmp 0x1dc73
movsd (%r13,%r9,8), %xmm1
movq (%rdi,%r9,8), %r10
movapd %xmm0, %xmm2
subsd %xmm1, %xmm2
movsd %xmm2, -0x8(%r10,%r15,8)
incq %r9
addb %r8b, %al
cmpq %r14, %r9
jne 0x1dc1d
movq -0x30(%rbp), %r13
movq 0x88(%r13), %rax
cmpb $0x0, 0x32(%rax)
jne 0x1dcb6
movq -0x60(%rbp), %rdx
movq -0x58(%rbp), %rcx
movq %r13, %rdi
callq 0x10ff0
testb %al, %al
je 0x1e08b
movq -0x88(%rbp), %rbx
movl %ebx, %edi
movl %r14d, %esi
callq 0xbb36
movq %rax, 0x38(%r13)
movl %ebx, %edi
movl %r14d, %esi
movl %r14d, %edx
callq 0xcaae
movq %rax, 0x40(%r13)
movq -0x80(%rbp), %rdi
movl %r14d, %esi
movl %r14d, %edx
callq 0xcaae
movq %rax, 0x90(%r13)
movl %ebx, %edi
movl %r14d, -0x3c(%rbp)
movl %r14d, %esi
movl %r15d, %edx
callq 0xcaae
movq %rax, 0x48(%r13)
testl %ebx, %ebx
jle 0x1dde1
movq -0x38(%rbp), %rax
leaq (,%rax,8), %rdx
movl -0x3c(%rbp), %r12d
movq -0x70(%rbp), %rax
leaq (,%rax,8), %rax
movq %rax, -0xa8(%rbp)
xorl %ecx, %ecx
movq %rdx, -0x90(%rbp)
movq -0x68(%rbp), %rsi
movq 0x38(%r13), %rax
movq %rcx, -0x78(%rbp)
movq (%rax,%rcx,8), %rdi
callq 0x41c0
cmpb $0x0, -0x48(%rbp)
jle 0x1ddc2
movq -0x60(%rbp), %r14
movq -0x30(%rbp), %rax
movq 0x40(%rax), %rax
movq -0x78(%rbp), %rcx
movq (%rax,%rcx,8), %r15
xorl %r13d, %r13d
movq -0x90(%rbp), %rbx
movq (%r15,%r13,8), %rdi
movq (%r14,%r13,8), %rsi
movq %rbx, %rdx
callq 0x41c0
incq %r13
cmpq %r13, %r12
jne 0x1dd74
movq -0x58(%rbp), %r14
movq -0x30(%rbp), %rax
movq 0x48(%rax), %rax
movq -0x78(%rbp), %rcx
movq (%rax,%rcx,8), %r15
xorl %r13d, %r13d
movq -0xa8(%rbp), %rbx
movq (%r15,%r13,8), %rdi
movq (%r14,%r13,8), %rsi
movq %rbx, %rdx
callq 0x41c0
incq %r13
cmpq %r13, %r12
jne 0x1ddaa
movq -0x78(%rbp), %rcx
incq %rcx
cmpq -0x88(%rbp), %rcx
movq -0x30(%rbp), %r13
movq -0x90(%rbp), %rdx
jne 0x1dd3b
movq -0x80(%rbp), %r10
testl %r10d, %r10d
movq -0x70(%rbp), %r12
movq -0x50(%rbp), %r14
movq -0x48(%rbp), %r15
jle 0x1dee7
movsbl %r15b, %eax
xorps %xmm1, %xmm1
cvtsi2sd %eax, %xmm1
movsd 0x15ae3(%rip), %xmm0    # 0x338f0
divsd %xmm1, %xmm0
leaq -0x1(%r14), %rax
movq %rax, %xmm1
pshufd $0x44, %xmm1, %xmm1     # xmm1 = xmm1[0,1,0,1]
leal 0x8(,%r14,8), %eax
andl $0x7f0, %eax            # imm = 0x7F0
xorl %ecx, %ecx
movdqa 0x16a5a(%rip), %xmm2    # 0x34890
movdqa 0x16a62(%rip), %xmm3    # 0x348a0
pxor %xmm3, %xmm1
pcmpeqd %xmm4, %xmm4
movdqa 0x16a62(%rip), %xmm5    # 0x348b0
testb %r14b, %r14b
jle 0x1dedb
movq 0x90(%r13), %rdx
movq (%rdx,%rcx,8), %rdx
xorl %esi, %esi
movq (%rdx,%rsi,8), %rdi
xorl %r8d, %r8d
movdqa %xmm2, %xmm6
movdqa %xmm6, %xmm7
pxor %xmm3, %xmm7
movdqa %xmm7, %xmm8
pcmpgtd %xmm1, %xmm8
pcmpeqd %xmm1, %xmm7
pshufd $0xf5, %xmm7, %xmm9     # xmm9 = xmm7[1,1,3,3]
pand %xmm8, %xmm9
pshufd $0xf5, %xmm8, %xmm7     # xmm7 = xmm8[1,1,3,3]
por %xmm9, %xmm7
movd %xmm7, %r9d
notl %r9d
testb $0x1, %r9b
je 0x1deaf
movsd %xmm0, (%rdi,%r8)
pxor %xmm4, %xmm7
pextrw $0x4, %xmm7, %r9d
testb $0x1, %r9b
je 0x1dec6
movsd %xmm0, 0x8(%rdi,%r8)
paddq %xmm5, %xmm6
addq $0x10, %r8
cmpq %r8, %rax
jne 0x1de6f
incq %rsi
cmpq %r14, %rsi
jne 0x1de64
incq %rcx
cmpq %r10, %rcx
jne 0x1de4e
movq -0x68(%rbp), %rdi
callq 0x42a0
movq -0x60(%rbp), %rdi
movl -0x3c(%rbp), %ebx
movl %ebx, %esi
callq 0xa5dd
movq -0x58(%rbp), %rdi
movl %ebx, %esi
callq 0xa5dd
movq -0x98(%rbp), %rsi
cmpb $0x0, 0x6c(%rsi)
je 0x1df24
addq $0x6c, %rsi
movq %r13, %rdi
xorl %edx, %edx
callq 0x11182
leaq 0x50(%r13), %rsi
leaq 0x58(%r13), %rdx
leaq 0x60(%r13), %rcx
movq %r13, %rdi
movq -0x38(%rbp), %rbx
movl %ebx, %r8d
movl %r12d, %r9d
callq 0x10fa2
leaq 0x68(%r13), %rsi
leaq 0x70(%r13), %rdx
leaq 0x78(%r13), %rcx
movq %r13, %rdi
movl %r15d, %r8d
movl %r12d, %r9d
callq 0x10fa2
testb %bl, %bl
jle 0x1e075
movq 0x88(%r13), %rcx
movq 0x18(%rcx), %rax
movq 0x20(%rcx), %rcx
movq 0x50(%r13), %rdx
movq 0x68(%r13), %rsi
xorl %edi, %edi
movsd (%rax,%rdi,8), %xmm0
movsd %xmm0, (%rdx,%rdi,8)
movsd (%rcx,%rdi,8), %xmm0
movsd %xmm0, (%rsi,%rdi,8)
incq %rdi
cmpq %rdi, %r14
jne 0x1df7d
testb %r14b, %r14b
jle 0x1e075
movq 0x88(%r13), %rsi
movq 0x58(%r13), %rax
movq 0x70(%r13), %rcx
movq 0x18(%rsi), %rdx
movq 0x20(%rsi), %rsi
xorl %r8d, %r8d
movq %r14, %rdi
movq (%rax,%r8,8), %r9
movq (%rcx,%r8,8), %r10
incq %r8
xorl %r11d, %r11d
leal (%rdi,%r11), %ebx
movsbq %bl, %rbx
movsd (%rdx,%rbx,8), %xmm0
movsd %xmm0, (%r9,%r11,8)
movsd (%rsi,%rbx,8), %xmm0
movsd %xmm0, (%r10,%r11,8)
incq %r11
cmpq %r11, %r14
jne 0x1dfcd
addq %r14, %rdi
cmpq %r14, %r8
jne 0x1dfbf
testb %r15b, %r15b
jle 0x1e075
movq 0x88(%r13), %rcx
movq 0x60(%r13), %rdx
movq 0x78(%r13), %rsi
movzbl %r12b, %edi
movq -0x38(%rbp), %r8
incb %r8b
movl %r14d, %eax
mulb %r8b
movzbl %al, %eax
xorl %r8d, %r8d
testb %r12b, %r12b
jle 0x1e066
movq 0x18(%rcx), %r9
movq 0x20(%rcx), %r10
movq (%rdx,%r8,8), %r11
movq (%rsi,%r8,8), %rbx
xorl %r14d, %r14d
leal (%rax,%r14), %r15d
movsbq %r15b, %r15
movsd (%r9,%r15,8), %xmm0
movsd %xmm0, (%r11,%r14,8)
movsd (%r10,%r15,8), %xmm0
movsd %xmm0, (%rbx,%r14,8)
incq %r14
cmpq %r14, %rdi
jne 0x1e03e
incq %r8
movq -0x50(%rbp), %r9
addq %r9, %rax
cmpq %r9, %r8
jne 0x1e026
movq -0xa0(%rbp), %rsp
leaq -0x28(%rbp), %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x4e27