omicsx 1.0.2

��cargo :    Compiling omics-simd v0.8.1 (D:\omicsx)

At line:1 char:1

+ cargo test --lib --release 2>&1 > test_output_kernel.txt; Get-Content ...

+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

    + CategoryInfo          : NotSpecified: (   Compiling om...8.1 (D:\omicsx) 

   :String) [], RemoteException

    + FullyQualifiedErrorId : NativeCommandError

 

warning: unused variable: `matrix`

   --> src\alignment\kernel_launcher.rs:123:9

    |

123 |         matrix: &[i32],

    |         ^^^^^^ help: if this is intentional, prefix it with an 

underscore: `_matrix`

    |

    = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by 

default



warning: unused variable: `gap_open`

   --> src\alignment\kernel_launcher.rs:124:9

    |

124 |         gap_open: i32,

    |         ^^^^^^^^ help: if this is intentional, prefix it with an 

underscore: `_gap_open`



warning: unused variable: `gap_extend`

   --> src\alignment\kernel_launcher.rs:125:9

    |

125 |         gap_extend: i32,

    |         ^^^^^^^^^^ help: if this is intentional, prefix it with an 

underscore: `_gap_extend`



warning: variable does not need to be mutable

   --> src\alignment\hmmer3_parser.rs:588:13

    |

588 |         let mut model = HmmerModel {

    |             ----^^^^^

    |             |

    |             help: remove this `mut`

    |

    = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default



warning: variable does not need to be mutable

    --> src\alignment\simd_viterbi.rs:1082:13

     |

1082 |         let mut decoder = ViterbiDecoder::new_dummy();

     |             ----^^^^^^^

     |             |

     |             help: remove this `mut`



warning: unused variable: `a2`

   --> src\alignment\gpu_memory.rs:343:13

    |

343 |         let a2 = pool.allocate(1000).unwrap();

    |             ^^ help: if this is intentional, prefix it with an 

underscore: `_a2`



warning: unused variable: `backend`

   --> src\futures\gpu_jit_compiler.rs:111:23

    |

111 |     fn verify_backend(backend: GpuBackend) -> Result<()> {

    |                       ^^^^^^^ help: if this is intentional, prefix it 

with an underscore: `_backend`



warning: associated function `compute_sw_cpu` is never used

   --> src\alignment\kernel_launcher.rs:120:8

    |

 40 | impl SmithWatermanKernel {

    | ------------------------ associated function in this implementation

...

120 |     fn compute_sw_cpu(

    |        ^^^^^^^^^^^^^^

    |

    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default



warning: associated function `compute_nw_cpu` is never used

   --> src\alignment\kernel_launcher.rs:254:8

    |

180 | impl NeedlemanWunschKernel {

    | -------------------------- associated function in this implementation

...

254 |     fn compute_nw_cpu(

    |        ^^^^^^^^^^^^^^



warning: associated function `execute_viterbi_kernel` is never used

   --> src\alignment\simd_viterbi.rs:309:8

    |

 61 | impl ViterbiDecoder {

    | ------------------- associated function in this implementation

...

309 |     fn execute_viterbi_kernel(

    |        ^^^^^^^^^^^^^^^^^^^^^^



warning: comparison is useless due to type limits

   --> src\futures\tree_refinement.rs:297:17

    |

297 |         assert!(improvements >= 0);

    |                 ^^^^^^^^^^^^^^^^^

    |

    = note: `#[warn(unused_comparisons)]` on by default



warning: comparison is useless due to type limits

   --> src\futures\tree_refinement.rs:328:17

    |

328 |         assert!(improvements >= 0);

    |                 ^^^^^^^^^^^^^^^^^



warning: comparison is useless due to type limits

   --> src\futures\tree_refinement.rs:360:17

    |

360 |         assert!(improvements >= 0);

    |                 ^^^^^^^^^^^^^^^^^



warning: comparison is useless due to type limits

   --> src\futures\phylogeny_parsimony.rs:377:17

    |

377 |         assert!(cost >= 0);

    |                 ^^^^^^^^^



warning: `omics-simd` (lib test) generated 14 warnings (run `cargo fix --lib 

-p omics-simd --tests` to apply 7 suggestions)

    Finished `release` profile [optimized] target(s) in 37.38s

     Running unittests src\lib.rs 

(target\release\deps\omics_simd-e10d7ebebde719eb.exe)



running 251 tests

test alignment::bam::tests::test_bam_file_creation ... ok

test alignment::bam::tests::test_bam_serialization ... ok

test alignment::bam::tests::test_cigar_formatting ... ok

test alignment::bam::tests::test_cigar_parsing ... ok

test alignment::cigar_gen::tests::test_hmm_cigar_generation ... ok

test alignment::cuda_kernels::tests::test_grid_calculation ... ok

test alignment::bam::tests::test_sequence_encoding ... ok

test alignment::bam::tests::test_valid_utf8_roundtrip ... ok

test alignment::gpu_kernels::tests::test_multi_gpu_distribution ... ok

test alignment::cigar_gen::tests::test_cigar_generation ... ok

test alignment::cigar_gen::tests::test_cigar_parsing ... ok

test alignment::cuda_kernels::tests::test_cuda_compute_capability ... ok

test alignment::cuda_kernels::tests::test_kernel_config ... ok

test alignment::bam::tests::test_invalid_utf8_in_reference_name ... ok

test alignment::cuda_kernels::tests::test_shared_memory_size ... ok

test alignment::cuda_runtime::tests::test_device_detection ... ok

test alignment::cuda_kernels::tests::test_time_estimation ... ok

test alignment::gpu_dispatcher::tests::test_gpu_dispatcher_creation ... ok

test alignment::gpu_dispatcher::tests::test_alignment_strategy_selection ... ok

test alignment::batch::tests::test_batch_with_bandwidth ... ok

test alignment::batch::tests::test_batch_needleman_wunsch ... ok

test alignment::gpu_dispatcher::tests::test_speedup_factors ... ok

test alignment::batch::tests::test_batch_filter_by_score ... ok

test alignment::batch::tests::test_batch_smith_waterman ... ok

test alignment::gpu_kernels::tests::test_gpu_config_default ... ok

test alignment::gpu_kernels::tests::test_memory_pool ... ok

test alignment::cigar_gen::tests::test_cigar_lengths ... ok

test alignment::bam::tests::test_invalid_utf8_in_bam_header ... ok

test alignment::gpu_memory::tests::test_host_device_transfer ... ok

test alignment::bam::tests::test_invalid_utf8_in_read_name ... ok

test alignment::hmmer3_parser::tests::test_evalue_calculation ... ok

test alignment::hmmer3_parser::tests::test_hmmer_model_creation ... ok

test alignment::gpu_dispatcher::tests::test_gpu_memory_estimation ... ok

test alignment::gpu_dispatcher::tests::test_optimization_hints ... ok

test alignment::gpu_memory::tests::test_fragmentation ... ok

test alignment::gpu_memory::tests::test_memory_deallocation ... ok

test alignment::gpu_memory::tests::test_memory_pool_allocation ... ok

test alignment::gpu_memory::tests::test_multilevel_gpu_memory ... ok

test alignment::cuda_kernels::tests::test_multi_gpu_batch ... ok

test alignment::hmmer3_parser::tests::test_hmmer_model_null_model_normalization ... ok

test alignment::hmmer3_parser::tests::test_karlin_evalue_bounds ... ok

test alignment::hmmer3_parser::tests::test_karlin_parameters ... ok

test alignment::hmmer3_parser::tests::test_parse_error_invalid_numeric_score ... ok

test alignment::hmmer3_parser::tests::test_parse_error_special_scores ... ok

test alignment::kernel::avx2::tests::test_avx2_smith_waterman_fallback ... ok

test alignment::kernel::banded::tests::test_banded_fallback_different_lengths ... ok

test alignment::kernel::banded::tests::test_banded_nw_similar_sequences ... ok

test alignment::kernel::banded::tests::test_banded_sw_similar_sequences ... ok

test alignment::kernel::hmm_simd::tests::test_backward_algorithm ... ok

test alignment::kernel::hmm_simd::tests::test_baum_welch_convergence ... ok

test alignment::hmmer3_parser::tests::test_regex_compilation_safety ... ok

test alignment::kernel::hmm_simd::tests::test_baum_welch_iteration ... ok

test alignment::kernel::hmm_simd::tests::test_empty_sequence_error ... ok

test alignment::kernel::hmm_simd::tests::test_forward_algorithm ... ok

test alignment::kernel::hmm_simd::tests::test_forward_backward_consistency ... ok

test alignment::kernel::hmm_simd::tests::test_forward_score_range ... ok

test alignment::kernel::hmm_simd::tests::test_logsumexp_extreme_values ... ok

test alignment::kernel::hmm_simd::tests::test_logsumexp_stability ... ok

test alignment::kernel::hmm_simd::tests::test_logsumexp_zero_values ... ok

test alignment::kernel::hmm_simd::tests::test_long_sequence ... ok

test alignment::kernel::hmm_simd::tests::test_multiple_sequence_alignment ... ok

test alignment::kernel::hmm_simd::tests::test_single_amino_acid ... ok

test alignment::kernel::hmm_simd::tests::test_viterbi_all_amino_acids ... ok

test alignment::kernel::hmm_simd::tests::test_viterbi_backtrack ... ok

test alignment::kernel::hmm_simd::tests::test_viterbi_different_paths ... ok

test alignment::kernel::hmm_simd::tests::test_viterbi_simple ... ok

test alignment::kernel::msa_simd::tests::test_batch_profile_scoring ... ok

test alignment::kernel::msa_simd::tests::test_dirichlet_prior ... ok

test alignment::kernel::msa_simd::tests::test_dirichlet_prior_application ... ok

test alignment::kernel::msa_simd::tests::test_edge_case_invalid_alignment ... ok

test alignment::kernel::msa_simd::tests::test_edge_case_invalid_background ... ok

test alignment::kernel::msa_simd::tests::test_empty_alignment_error ... ok

test alignment::kernel::msa_simd::tests::test_entropy_computation ... ok

test alignment::kernel::msa_simd::tests::test_entropy_conservation ... ok

test alignment::kernel::msa_simd::tests::test_entropy_divergence ... ok

test alignment::kernel::msa_simd::tests::test_henikoff_weights ... ok

test alignment::kernel::msa_simd::tests::test_kl_divergence ... ok

test alignment::kernel::msa_simd::tests::test_long_alignment ... ok

test alignment::kernel::msa_simd::tests::test_profile_alignment_multiple_sequences ... ok

test alignment::kernel::msa_simd::tests::test_profile_scoring ... ok

test alignment::kernel::msa_simd::tests::test_pssm_construction ... ok

test alignment::kernel::msa_simd::tests::test_pssm_diverse_alignment ... ok

test alignment::kernel::msa_simd::tests::test_pssm_identical_sequences ... ok

test alignment::kernel::msa_simd::tests::test_pssm_score_range ... ok

test alignment::kernel::msa_simd::tests::test_pssm_single_sequence ... ok

test alignment::kernel::msa_simd::tests::test_score_frequency ... ok

test alignment::kernel::scalar::tests::test_smith_waterman_scalar ... ok

test alignment::kernel::striped_simd::tests::test_needleman_wunsch_striped ... ok

test alignment::kernel::striped_simd::tests::test_smith_waterman_striped_empty ... ok

test alignment::kernel::striped_simd::tests::test_smith_waterman_striped_match ... ok

test alignment::kernel::striped_simd::tests::test_smith_waterman_striped_single ... ok

test alignment::kernel::striped_simd::tests::test_striped_vs_scalar_consistency ... ok

test alignment::kernel_compiler::tests::test_kernel_cache ... ok

test alignment::kernel_compiler::tests::test_compiler_creation ... ok

test alignment::kernel_compiler::tests::test_kernel_type_names ... ok

test alignment::kernel_compiler::tests::test_source_hash ... ok

test alignment::kernel_launcher::tests::test_needleman_wunsch_kernel_launch ... FAILED

test alignment::kernel_launcher::tests::test_smith_waterman_kernel_empty_sequences ... ok

test alignment::kernel_launcher::tests::test_smith_waterman_kernel_launch ... FAILED

test alignment::kernel_launcher::tests::test_smith_waterman_mismatch ... FAILED

test alignment::profile_dp::tests::test_profile_alignment ... ok

test alignment::profile_dp::tests::test_profile_similarity ... ok

test alignment::profile_dp::tests::test_pssm_creation ... ok

test alignment::simd_viterbi::tests::test_backtrack_generation ... ok

test alignment::simd_viterbi::tests::test_decoder_has_gpu_field ... ok

test alignment::simd_viterbi::tests::test_gpu_dispatcher_initialization ... ok

test alignment::simd_viterbi::tests::test_viterbi_decoder_creation ... ok

test alignment::tests::test_alignment_cigar_generation ... ok

test alignment::tests::test_alignment_result_identity ... ok

test alignment::tests::test_cigar_coalesce ... ok

test alignment::tests::test_cigar_lengths ... ok

test alignment::tests::test_cigar_operations ... ok

test alignment::tests::test_sam_header_generation ... ok

test alignment::tests::test_sam_record_creation ... ok

test alignment::tests::test_sam_record_from_alignment ... ok

test alignment::tests::test_sam_record_to_line ... ok

test alignment::tests::test_smith_waterman ... ok

test alignment::tests::test_smith_waterman_with_cigar ... ok

test futures::cli_file_io::tests::test_batch_processor_creation ... ok

test futures::cli_file_io::tests::test_batch_processor_with_filter ... ok

test futures::cli_file_io::tests::test_file_format_detection ... ok

test futures::cli_file_io::tests::test_parse_fasta_header ... ok

test futures::cli_file_io::tests::test_parse_fastq_header ... ok

test futures::cli_file_io::tests::test_seq_record_creation ... ok

test futures::cli_file_io::tests::test_seq_record_header ... ok

test futures::formats::tests::test_blast_json_export ... ok

test futures::formats::tests::test_blast_json_to_tabular ... ok

test futures::formats::tests::test_blast_tabular_export ... ok

test futures::formats::tests::test_blast_xml_export ... ok

test futures::formats::tests::test_fasta_export ... ok

test futures::formats::tests::test_fasta_wrapping ... ok

test futures::formats::tests::test_gff3_invalid_coordinates ... ok

test futures::formats::tests::test_gff3_line_format ... ok

test futures::formats::tests::test_gff3_record_creation ... ok

test futures::gpu::tests::test_cuda_device_creation ... ok

test futures::gpu::tests::test_data_transfer_size_mismatch ... ok

test futures::gpu::tests::test_cuda_device_detection ... ok

test futures::gpu::tests::test_data_transfer_to_gpu ... ok

test futures::gpu::tests::test_device_creation_produces_unique_ids ... ok

test futures::gpu::tests::test_gpu_memory_allocation ... ok

test futures::gpu::tests::test_hip_device_creation ... ok

test futures::gpu::tests::test_gpu_memory_zero_allocation ... ok

test futures::hmm::tests::test_evalue_computation ... ok

test futures::gpu::tests::test_multi_gpu_execution ... ok

test futures::gpu::tests::test_smith_waterman_empty_sequences ... ok

test futures::gpu::tests::test_vulkan_device_creation ... ok

test futures::gpu_jit_compiler::tests::test_cache_key_generation ... ok

test futures::gpu_jit_compiler::tests::test_compilation_options ... ok

test futures::gpu_jit_compiler::tests::test_jit_compiler_creation ... ok

test futures::gpu_jit_compiler::tests::test_kernel_templates ... ok

test futures::hmm::tests::test_backward_algorithm ... ok

test futures::hmmer3_full_parser::tests::test_database_lookup ... ok

test futures::hmm::tests::test_domain_detection ... ok

test futures::gpu::tests::test_multiple_memory_allocations ... ok

test futures::hmm::tests::test_forward_algorithm ... ok

test futures::hmm::tests::test_hmm_from_msa ... ok

test futures::hmm::tests::test_pfam_loading ... ok

test futures::hmm::tests::test_viterbi_algorithm ... ok

test futures::hmmer3_full_parser::tests::test_database_insertion ... ok

test futures::hmmer3_full_parser::tests::test_model_creation ... ok

test futures::hmmer3_full_parser::tests::test_emission_matrix_parsing ... ok

test futures::hmmer3_full_parser::tests::test_hmmer3_database_creation ... ok

test futures::hmm::tests::test_baum_welch_training ... ok

test futures::hmm::tests::test_forward_backward ... ok

test futures::hmmer3_full_parser::tests::test_model_names ... ok

test futures::hmmer3_full_parser::tests::test_pssm_generation ... ok

test futures::gpu::tests::test_needleman_wunsch_gpu_kernel ... FAILED

test futures::gpu::tests::test_smith_waterman_gpu_kernel ... FAILED

test futures::matrices::tests::test_gonnet_loading ... ok

test futures::matrices::tests::test_hoxd_variants ... ok

test futures::matrices::tests::test_invalid_matrix_dimensions ... ok

test futures::hmmer3_full_parser::tests::test_threshold_checking ... ok

test futures::matrices::tests::test_matrix_symmetry_pam40 ... ok

test futures::matrices::tests::test_matrix_validation_gonnet ... ok

test futures::matrices::tests::test_matrix_validation_pam70 ... ok

test futures::matrices::tests::test_pam40_loading ... ok

test futures::matrices::tests::test_pam70_loading ... ok

test futures::msa::tests::test_align_to_profile ... ok

test futures::matrices::tests::test_pam_variant_loading ... ok

test futures::msa::tests::test_consensus_generation ... ok

test futures::msa::tests::test_conservation_scoring ... ok

test futures::msa::tests::test_distance_matrix_computation ... ok

test futures::msa::tests::test_guide_tree_construction ... ok

test futures::msa::tests::test_profile_building ... ok

test futures::msa::tests::test_progressive_msa ... ok

test futures::msa_profile_alignment::tests::test_consensus_computation ... ok

test futures::msa_profile_alignment::tests::test_gap_identification ... ok

test futures::msa_profile_alignment::tests::test_henikoff_weights ... ok

test futures::msa_profile_alignment::tests::test_pipeline_creation ... ok

test futures::msa_profile_alignment::tests::test_profile_to_profile_alignment ... ok

test futures::msa_profile_alignment::tests::test_profile_to_sequence_alignment ... ok

test futures::pfam::tests::test_bit_score_calculation ... ok

test futures::pfam::tests::test_evalue_calculation ... ok

test futures::pfam::tests::test_evalue_stats_protein ... ok

test futures::pfam::tests::test_pfam_database_creation ... ok

test futures::pfam::tests::test_pvalue_calculation ... ok

test futures::phylogeny::tests::test_ancestral_reconstruction ... ok

test futures::phylogeny::tests::test_bootstrap_analysis ... ok

test futures::phylogeny::tests::test_compute_phylogenetic_distances ... ok

test futures::phylogeny::tests::test_maximum_likelihood ... ok

test futures::phylogeny::tests::test_maximum_parsimony ... ok

test futures::phylogeny::tests::test_neighbor_joining ... ok

test futures::phylogeny::tests::test_newick_format ... ok

test futures::phylogeny::tests::test_rooting_tree ... ok

test futures::phylogeny::tests::test_tree_builder ... ok

test futures::phylogeny::tests::test_tree_statistics ... ok

test futures::phylogeny::tests::test_upgma_tree_building ... ok

test futures::phylogeny_likelihood::tests::test_likelihood_builder_creation ... ok

test futures::phylogeny_likelihood::tests::test_nni_convergence ... ok

test futures::phylogeny_likelihood::tests::test_spr_convergence ... ok

test futures::phylogeny_likelihood::tests::test_topology_search_result_creation ... ok

test futures::phylogeny_likelihood::tests::test_tree_node_creation ... ok

test futures::phylogeny_parsimony::tests::test_ambiguous_states ... ok

test futures::phylogeny_parsimony::tests::test_char_state_creation ... ok

test futures::phylogeny_parsimony::tests::test_char_state_transition ... ok

test futures::phylogeny_parsimony::tests::test_parsimony_scoring ... ok

test futures::phylogeny_parsimony::tests::test_parsimony_tree_builder ... ok

test futures::phylogeny_parsimony::tests::test_state_set_intersection ... ok

test futures::phylogeny_parsimony::tests::test_state_set_union ... ok

test futures::phylogeny_parsimony::tests::test_transition_cost ... ok

test futures::st_jude_bridge::tests::test_alignment_conversion ... ok

test futures::st_jude_bridge::tests::test_bridge_empty_sequence_validation ... ok

test futures::st_jude_bridge::tests::test_bridge_protein_to_st_jude ... ok

test futures::st_jude_bridge::tests::test_bridge_roundtrip_conversion ... ok

test futures::st_jude_bridge::tests::test_bridge_st_jude_to_protein ... ok

test futures::st_jude_bridge::tests::test_clinical_flags ... ok

test futures::st_jude_bridge::tests::test_metadata_preservation ... ok

test futures::st_jude_bridge::tests::test_parsimony_state_creation ... ok

test futures::st_jude_bridge::tests::test_seq_record_to_st_jude ... ok

test futures::st_jude_bridge::tests::test_st_jude_amino_acid_conversion ... ok

test futures::st_jude_bridge::tests::test_taxonomy_id_defaults ... ok

test futures::st_jude_bridge::tests::test_three_letter_codes ... ok

test futures::tree_refinement::tests::test_nni_refinement ... ok

test futures::tree_refinement::tests::test_spr_refinement ... ok

test futures::tree_refinement::tests::test_tree_optimizer ... ok

test protein::tests::test_amino_acid_from_code ... ok

test protein::tests::test_amino_acid_to_code ... ok

test protein::tests::test_protein_creation ... ok

test protein::tests::test_protein_with_metadata ... ok

test scoring::tests::test_affine_penalty ... ok

test scoring::tests::test_blosum45_matrix ... ok

test scoring::tests::test_invalid_penalty ... ok

test scoring::tests::test_blosum80_matrix ... ok

test scoring::tests::test_matrix_symmetry_blosum45 ... ok

test scoring::tests::test_matrix_symmetry_pam70 ... ok

test scoring::tests::test_matrix_type_display ... ok

test scoring::tests::test_pam30_matrix ... ok

test scoring::tests::test_pam70_matrix ... ok

test scoring::tests::test_scoring_matrix ... ok

test futures::gpu::tests::test_device_properties_name_validated ... ok

test futures::gpu::tests::test_gpu_device_properties_non_zero_memory ... ok



failures:



---- alignment::kernel_launcher::tests::test_needleman_wunsch_kernel_launch stdout ----

Error: AlignmentError("CUDA support not compiled (enable 'cuda' feature)")



---- alignment::kernel_launcher::tests::test_smith_waterman_kernel_launch stdout ----

Error: AlignmentError("CUDA support not compiled (enable 'cuda' feature)")



---- alignment::kernel_launcher::tests::test_smith_waterman_mismatch stdout ----

Error: AlignmentError("CUDA support not compiled (enable 'cuda' feature)")



---- futures::gpu::tests::test_needleman_wunsch_gpu_kernel stdout ----

[GPU] Executing Needleman-Wunsch: 4%�4 on Cuda



thread 'futures::gpu::tests::test_needleman_wunsch_gpu_kernel' (13284) panicked at src\futures\gpu.rs:670:14:

Kernel should execute: KernelFailed("NW kernel failed: Alignment error: CUDA support not compiled (enable 'cuda' feature)")

note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace



---- futures::gpu::tests::test_smith_waterman_gpu_kernel stdout ----

[GPU] Executing Smith-Waterman: 4%�4 on Cuda



thread 'futures::gpu::tests::test_smith_waterman_gpu_kernel' (16156) panicked at src\futures\gpu.rs:649:14:

Kernel should execute: KernelFailed("SW kernel failed: Alignment error: CUDA support not compiled (enable 'cuda' feature)")





failures:

    alignment::kernel_launcher::tests::test_needleman_wunsch_kernel_launch

    alignment::kernel_launcher::tests::test_smith_waterman_kernel_launch

    alignment::kernel_launcher::tests::test_smith_waterman_mismatch

    futures::gpu::tests::test_needleman_wunsch_gpu_kernel

    futures::gpu::tests::test_smith_waterman_gpu_kernel



test result: FAILED. 246 passed; 5 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.48s



error: test failed, to rerun pass `--lib`