Add QRAFT end-to-end batched uncapped NNI outputs on uDance 199k

.gitattributes

@@ -65,3 +65,5 @@ runs/texas-2026-10-02/outputs/astralx_outputs/t_400000_g_1000_sb_0.000001_spmin_
 runs/texas-2026-10-02/results/logs/stelarx-t500000-g1000-R1.log filter=lfs diff=lfs merge=lfs -text
 runs/texas-2026-10-02/results/udance/199k-batch-nni/qraft-nni-test3 filter=lfs diff=lfs merge=lfs -text
 runs/texas-2026-10-02/results/udance/199k-batch-nni/nni.trace filter=lfs diff=lfs merge=lfs -text
+udance/qraft_outputs/batch-nni/nni.trace filter=lfs diff=lfs merge=lfs -text
+udance/qraft_outputs/batch-nni/qraft-nni-test3 filter=lfs diff=lfs merge=lfs -text

udance/qraft_outputs/batch-nni/README.txt

@@ -0,0 +1,6 @@
+QRAFT end to end on the pruned uDance gene trees (gt199k-pruned.tre, 380 genes, 199,330 taxa) with
+batched, uncapped NNI and no support gate: measurement build qraft-nni-test3 (branch
+measure/nni-cap-angio; byte-identical to QRAFT 38d32f1 with default settings) run with
+QRAFT_NNI_BATCH=1 QRAFT_NNI_MAX_MOVES=10000000 QRAFT_NNI_MAX_SUPPORT_DROP=1e9, 64 threads on the
+CPUs 0-31,64-95 of the Texas run box, 1 GiB stacks. nni.trace: one line per accepted move
+(moves, pass, gain, total gain, seconds since NNI started). exit=0 wall=30252 s peak_rss_kb=15965448

udance/qraft_outputs/batch-nni/nni.trace

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:601fe8873b43deb473693a866be116b5c794aa2ce2978f123c0316f24b1f0442
+size 19560027

udance/qraft_outputs/batch-nni/out-qraft.stats.json

@@ -0,0 +1,129 @@
+{
+  "genes": 380,
+  "taxa": 199330,
+  "workers": 64,
+  "progress": "off",
+  "divide": true,
+  "divide_score": "quartet",
+  "bipartition_test": true,
+  "bipartition_test_available": false,
+  "bipartition_test_coefficient": 0.05,
+  "bipartition_test_crossover": 10000,
+  "bipartition_test_proposals": 1,
+  "bipartition_test_anchor_pairs": 1,
+  "bipartition_test_threshold": null,
+  "regraft_score": "raw",
+  "nni": true,
+  "subproblems": 94840,
+  "completed_subproblems": 94840,
+  "max_depth": 8347,
+  "max_active_taxa": 199330,
+  "taxon_registry_ns": 896869199,
+  "taxon_registry_physical_labels": 59891336,
+  "taxon_registry_unique_labels": 199330,
+  "taxon_registry_sort_items": 199330,
+  "gene_index_ns": 836352057,
+  "startup_ns": 43620370735,
+  "mre_distinct_splits": 12454368,
+  "mre_accepted_splits": 158892,
+  "mre_count_ns": 4947739964,
+  "mre_assembly_ns": 36247907248,
+  "starting_tree_index_builds": 1,
+  "starting_tree_index_nodes": 358223,
+  "candidate_sets": 94840,
+  "candidates": 64142678,
+  "bipartitions_scored": 64128068,
+  "bipartition_score_ns": 21863497947553,
+  "bipartition_test_index_ns": 26036995,
+  "bipartition_test_ns": 0,
+  "bipartition_tests": 0,
+  "bipartition_test_accepts": 0,
+  "bipartition_test_rejects": 0,
+  "bipartition_test_negative_accepts": 0,
+  "bipartition_test_max_negative_gap_twice_k": 0,
+  "bipartition_test_singletons": 0,
+  "bipartition_test_distance_queries": 0,
+  "regraft_calls": 189680,
+  "regraft_vertices": 108916018,
+  "regraft_edge_ties": 3173,
+  "regraft_ns": 23669798763669,
+  "nni_edges_scored": 15970166,
+  "nni_full_score_passes": 15,
+  "nni_local_score_passes": 768,
+  "nni_local_edges_scored": 9990356,
+  "nni_moves_accepted": 375289,
+  "nni_support_stops": 0,
+  "nni_split_support_ns": 4598719517,
+  "nni_ns": 10946894604491,
+  "active_taxa_entries": 593023062,
+  "active_taxa_index_entries": 593023062,
+  "query_tree_selected_leaves": 109280768,
+  "query_tree_lca_queries": 109185928,
+  "query_tree_retained_nodes": 173568412,
+  "gene_set_scoring_calls": 162859,
+  "gene_set_scoring_nodes": 97541319290,
+  "hdt_builds": 62183960,
+  "hdt_build_ns": 21806193958349,
+  "hdt_queries": 68111951650,
+  "hdt_recolor_ops": 580029200832,
+  "hdt_nodes_recomputed": 1398951362411,
+  "extract_scratch_peak_bytes": 14619784,
+  "contract_scratch_peak_bytes": 45481013,
+  "state_arena_peak_bytes": 1016527128,
+  "worker_total_peak_bytes": 1046985173,
+  "max_scoring_source_taxa": 199330,
+  "scoring_source_inflation_violations": 0,
+  "child_gene_set_reuses": 127757,
+  "child_gene_set_attempts": 94839,
+  "child_gene_set_accepts": 61923,
+  "child_gene_set_heavy_reuses": 32916,
+  "child_gene_set_pair_violations": 0,
+  "child_gene_set_input_nodes": 89180320647,
+  "child_gene_set_output_nodes": 42747059158,
+  "child_gene_set_max_accepted_ratio_ppm": 750000,
+  "child_gene_set_ns": 2364753071206,
+  "live_child_gene_sets": 0,
+  "max_child_gene_sets": 3231,
+  "live_child_gene_set_slots": 0,
+  "max_child_gene_set_slots": 794814,
+  "max_child_gene_set_bytes": 2016895304,
+  "serial_children": 73477,
+  "parallel_children": 21363,
+  "parallel_child_budget_rejections": 0,
+  "parallel_child_size_rejections": 0,
+  "max_parallel_child_slots": 199330,
+  "recursion_calls": 189681,
+  "recursion_nonbase_calls": 94840,
+  "recursion_max_depth": 8348,
+  "recursion_taxon_mass": 109480098,
+  "recursion_split_tests": 109280768,
+  "recursion_partition_moves": 109280768,
+  "recursion_balanced_splits": 16323,
+  "recursion_skewed_splits": 14610,
+  "recursion_tree_node_visits": 218196786,
+  "recursion_radix_entries": 874129264,
+  "recursion_radix_bucket_ops": 179271680,
+  "recursion_unique_taxa": 109280768,
+  "recursion_root_gene_set_nodes": 86948496,
+  "recursion_root_gene_set_entries": 510487880,
+  "live_payload": 0,
+  "peak_payload": 2649194552,
+  "live_taxa": 0,
+  "peak_taxa": 199330,
+  "live_continuation_taxa": 0,
+  "peak_continuation_taxa": 377,
+  "live_gene_set_nodes": 0,
+  "peak_gene_set_nodes": 428564316,
+  "live_gene_set_entries": 0,
+  "peak_gene_set_entries": 2218699576,
+  "live_gene_set_taxa": 0,
+  "peak_gene_set_taxa": 794814,
+  "live_tree_nodes": 0,
+  "peak_tree_nodes": 781336,
+  "live_tree_adjacencies": 0,
+  "peak_tree_adjacencies": 1562668,
+  "live_taxon_scratch": 0,
+  "peak_taxon_scratch": 390670,
+  "accounting_violations": 0,
+  "complexity_contract_satisfied": true
+}

udance/qraft_outputs/batch-nni/qraft-nni-test3

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f5ae90a484feebf8a10048edccc21eb432a609f3cf8c322494704bb9e13fe2e1
+size 5418504

udance/qraft_outputs/batch-nni/rf-summary.txt

@@ -0,0 +1,3 @@
+full: shared_taxa=199330 estimate_splits=199327 reference_splits=199327 common=131454 rf=0.340511 fn=0.340511 fp=0.340511
+--min-length 1e-6: shared_taxa=199330 estimate_splits=199327 reference_splits=73806 common=61737 rf=0.375411 fn=0.163523 fp=0.690273
+--min-length 1e-6 --min-support 0.9: shared_taxa=199330 estimate_splits=199327 reference_splits=63599 common=57837 rf=0.369373 fn=0.090599 fp=0.709839

udance/qraft_outputs/batch-nni/time.log

@@ -0,0 +1,23 @@
+	Command being timed: "taskset -c 0-31,64-95 /workspace/udance/qraft-nni-test3 -i /workspace/phylogeny/data/udance/gt199k-pruned.tre -o /workspace/phylo-bench/results/runbox/udance/199k-batch-nni/out-qraft.tre --stats-json /workspace/phylo-bench/results/runbox/udance/199k-batch-nni/out-qraft.stats.json --no-progress -t 64"
+	User time (seconds): 1450706.29
+	System time (seconds): 79181.47
+	Percent of CPU this job got: 5057%
+	Elapsed (wall clock) time (h:mm:ss or m:ss): 8:24:11
+	Average shared text size (kbytes): 0
+	Average unshared data size (kbytes): 0
+	Average stack size (kbytes): 0
+	Average total size (kbytes): 0
+	Maximum resident set size (kbytes): 15965448
+	Average resident set size (kbytes): 0
+	Major (requiring I/O) page faults: 17
+	Minor (reclaiming a frame) page faults: 11953943082
+	Voluntary context switches: 6214726
+	Involuntary context switches: 28773493
+	Swaps: 0
+	File system inputs: 1402160
+	File system outputs: 43288
+	Socket messages sent: 0
+	Socket messages received: 0
+	Signals delivered: 0
+	Page size (bytes): 4096
+	Exit status: 0