


/*
	thrust::device_vector<char> gene_d(MAX_GENE_STR * num_targets);
	thrust::copy(gene_d.begin(), gene_d.end(), gene.begin());
	thrust::device_vector<char> seq_d(MAX_SEQ_LEN * num_targets);
	thrust::copy(seq_d.begin(), seq_d.end(), seq.begin());

	//int MAX_GENE_STR = 30;
	//thrust::host_vector<char> gene(MAX_GENE_STR * num_targets);
	//thrust::host_vector<char> seq(MAX_SEQ_LEN * num_targets);

	//for(int i=0; i<100; i++){
		h_vec[0] = 'R';
		h_vec[1] = 'T';
	//}
	thrust::device_vector<char> d_vec = h_vec;
	thrust::copy(d_vec.begin(), d_vec.end(), h_vec.begin());


	Indexes *instance_device;
	const unsigned int bytes = sizeof(instance_host);
	cudaMalloc((Indexes**)&instance_device,bytes);
	cudaMemcpy(instance_device,instance_host,bytes,cudaMemcpyHostToDevice);

    //instance_device->buildIndexes();
    //print_target_index(instance_device);

	map<string, string>::iterator it;
	for (it = index_obj->target_sequences.begin(); it != index_obj->target_sequences.end(); ++it) {
		string gene_str = it->first;
		string seq_str = it->second;

		strcpy(gene, gene_str.c_str());
		strcpy(seq, seq_str.c_str());

		cudaMalloc((void**)&gene,bytes);
		cudaMemcpy(instance_device,instance_host,bytes,cudaMemcpyHostToDevice);

	}

*/

/*
    clock_t begin = clock();

    Assembly *assm_obj = new Assembly();
    assm_obj->process();

    clock_t end = clock();
    double elapsed_secs = double(end - begin) / CLOCKS_PER_SEC;
    cout << "time elapsed: " << elapsed_secs << endl;
*/

/*
__host__ __device__  void print_target_index(Indexes *index_obj){
	cout << "1111111111111111" << endl;
	map<string, map<string, vector<int> > >::iterator it;
	map<string, vector<int> >::iterator it_1;

	cout << "222222" << endl;
	for (it = index_obj->sixmer_dic_target.begin(); it != index_obj->sixmer_dic_target.end(); ++it) {
	cout << "333333333" << endl;
	    string key_seq = it->first;
	    map<string, vector<int> > gene_data = it->second;
	    cout << key_seq << " - " ;
	    for (it_1 = gene_data.begin(); it_1 != gene_data.end(); ++it_1) {
		string gene_str = it_1->first;
		vector<int> idx_list = it_1->second;
		cout << gene_str << ":" ;
		if(idx_list.size() == 1)
		    cout << idx_list[0];
		else
		    for(int i=0; i<idx_list.size(); i++)
		        cout << idx_list[i] << ",";
		cout << " ";
	    }
	    cout << endl;
	}
}
*/

	.file	"tmpxft_00203cc1_00000000-6_cuda_snippets.cudafe1.cpp"
	.text
#APP

#NO_APP
	.type	_ZL26__cudaUnregisterBinaryUtilv, @function
_ZL26__cudaUnregisterBinaryUtilv:
.LFB2010:
	.cfi_startproc
	endbr64
	movq	_ZL20__cudaFatCubinHandle(%rip), %rdi
	jmp	__cudaUnregisterFatBinary@PLT
	.cfi_endproc
.LFE2010:
	.size	_ZL26__cudaUnregisterBinaryUtilv, .-_ZL26__cudaUnregisterBinaryUtilv
	.section	.text.startup,"ax",@progbits
	.type	_ZL24__sti____cudaRegisterAllv, @function
_ZL24__sti____cudaRegisterAllv:
.LFB2033:
	.cfi_startproc
	endbr64
	pushq	%rax
	.cfi_def_cfa_offset 16
	leaq	_ZL15__fatDeviceText(%rip), %rdi
	call	__cudaRegisterFatBinary@PLT
	movq	%rax, %rdi
	movq	%rax, _ZL20__cudaFatCubinHandle(%rip)
	call	__cudaRegisterFatBinaryEnd@PLT
	leaq	_ZL26__cudaUnregisterBinaryUtilv(%rip), %rdi
	popq	%rdx
	.cfi_def_cfa_offset 8
	jmp	atexit@PLT
	.cfi_endproc
.LFE2033:
	.size	_ZL24__sti____cudaRegisterAllv, .-_ZL24__sti____cudaRegisterAllv
	.section	.init_array,"aw"
	.align 8
	.quad	_ZL24__sti____cudaRegisterAllv
	.section	.nvFatBinSegment,"aw"
	.align 8
	.type	_ZL15__fatDeviceText, @object
	.size	_ZL15__fatDeviceText, 24
_ZL15__fatDeviceText:
	.long	1180844977
	.long	1
	.quad	fatbinData
	.quad	0
	.local	_ZL20__cudaFatCubinHandle
	.comm	_ZL20__cudaFatCubinHandle,8,8
	.ident	"GCC: (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0"
	.section	.note.GNU-stack,"",@progbits
	.section	.note.gnu.property,"a"
	.align 8
	.long	1f - 0f
	.long	4f - 1f
	.long	5
0:
	.string	"GNU"
1:
	.align 8
	.long	0xc0000002
	.long	3f - 2f
2:
	.long	0x3
3:
	.align 8
4:


#include <hip/hip_runtime.h>



/*
	thrust::device_vector<char> gene_d(MAX_GENE_STR * num_targets);
	thrust::copy(gene_d.begin(), gene_d.end(), gene.begin());
	thrust::device_vector<char> seq_d(MAX_SEQ_LEN * num_targets);
	thrust::copy(seq_d.begin(), seq_d.end(), seq.begin());

	//int MAX_GENE_STR = 30;
	//thrust::host_vector<char> gene(MAX_GENE_STR * num_targets);
	//thrust::host_vector<char> seq(MAX_SEQ_LEN * num_targets);

	//for(int i=0; i<100; i++){
		h_vec[0] = 'R';
		h_vec[1] = 'T';
	//}
	thrust::device_vector<char> d_vec = h_vec;
	thrust::copy(d_vec.begin(), d_vec.end(), h_vec.begin());


	Indexes *instance_device;
	const unsigned int bytes = sizeof(instance_host);
	cudaMalloc((Indexes**)&instance_device,bytes);
	cudaMemcpy(instance_device,instance_host,bytes,cudaMemcpyHostToDevice);

    //instance_device->buildIndexes();
    //print_target_index(instance_device);

	map<string, string>::iterator it;
	for (it = index_obj->target_sequences.begin(); it != index_obj->target_sequences.end(); ++it) {
		string gene_str = it->first;
		string seq_str = it->second;

		strcpy(gene, gene_str.c_str());
		strcpy(seq, seq_str.c_str());

		cudaMalloc((void**)&gene,bytes);
		cudaMemcpy(instance_device,instance_host,bytes,cudaMemcpyHostToDevice);

	}

*/

/*
    clock_t begin = clock();

    Assembly *assm_obj = new Assembly();
    assm_obj->process();

    clock_t end = clock();
    double elapsed_secs = double(end - begin) / CLOCKS_PER_SEC;
    cout << "time elapsed: " << elapsed_secs << endl;
*/

/*
__host__ __device__  void print_target_index(Indexes *index_obj){
	cout << "1111111111111111" << endl;
	map<string, map<string, vector<int> > >::iterator it;
	map<string, vector<int> >::iterator it_1;

	cout << "222222" << endl;
	for (it = index_obj->sixmer_dic_target.begin(); it != index_obj->sixmer_dic_target.end(); ++it) {
	cout << "333333333" << endl;
	    string key_seq = it->first;
	    map<string, vector<int> > gene_data = it->second;
	    cout << key_seq << " - " ;
	    for (it_1 = gene_data.begin(); it_1 != gene_data.end(); ++it_1) {
		string gene_str = it_1->first;
		vector<int> idx_list = it_1->second;
		cout << gene_str << ":" ;
		if(idx_list.size() == 1)
		    cout << idx_list[0];
		else
		    for(int i=0; i<idx_list.size(); i++)
		        cout << idx_list[i] << ",";
		cout << " ";
	    }
	    cout << endl;
	}
}
*/

	.text
	.file	"cuda_snippets.hip"
	.type	__hip_cuid_,@object             # @__hip_cuid_
	.bss
	.globl	__hip_cuid_
__hip_cuid_:
	.byte	0                               # 0x0
	.size	__hip_cuid_, 1

	.ident	"AMD clang version 18.0.0git (https://github.com/RadeonOpenCompute/llvm-project roc-6.3.2 25012 e5bf7e55c91490b07c49d8960fa7983d864936c4)"
	.section	".note.GNU-stack","",@progbits
	.addrsig
	.addrsig_sym __hip_cuid_

	.text
	.p2alignl 7, 3214868480
	.fill 96, 4, 3214868480
	.type	__hip_cuid_,@object             ; @__hip_cuid_
	.section	.bss,"aw",@nobits
	.globl	__hip_cuid_
__hip_cuid_:
	.byte	0                               ; 0x0
	.size	__hip_cuid_, 1

	.ident	"AMD clang version 18.0.0git (https://github.com/RadeonOpenCompute/llvm-project roc-6.3.2 25012 e5bf7e55c91490b07c49d8960fa7983d864936c4)"
	.section	".note.GNU-stack","",@progbits
	.addrsig
	.addrsig_sym __hip_cuid_
	.amdgcn_target "amdgcn-amd-amdhsa--gfx1100"
	.amdgpu_metadata
---
amdhsa.kernels:  []
amdhsa.target:   amdgcn-amd-amdhsa--gfx1100
amdhsa.version:
  - 1
  - 2
...

	.end_amdgpu_metadata
