Simulated outputs: stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/search-space_S1__intersection-method_I1/.stelarx.success

@@ -0,0 +1,2 @@
+exit_code=0
+output=/home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/search-space_S1__intersection-method_I1/.stelarx_run.log

@@ -0,0 +1,151 @@
+=== STELAR-X Monitor Wrapper ===
+Input file:     /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/all_gt.tre
+Output file:    /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+STELAR-X root:  /home/aaniksahaa/research/STELAR-X-2
+STELAR-X opts:  --search-space S1 --intersection-method I1
+Weight method:  smaller-side-traversal
+Time monitor:   true
+GPU monitor:    true
+Notifications:  disabled
+
+=== Building STELAR-X ===
+Build OK -> /home/aaniksahaa/research/STELAR-X-2/build
+Run: ./stelarx -i <rooted-input.tre> -vv --no-build
+=== STELAR-X ===
+Input:       /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/all_gt.tre
+Output:      /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+Build dir:   /home/aaniksahaa/research/STELAR-X-2/build
+Native dir:  /home/aaniksahaa/research/STELAR-X-2/native
+GPU ready:   true
+Java heap:   -Xms256m -Xmx128g
+
+
+  ╔═══════════════════════════════════════════════════════════════╗
+  ║                       STELAR-X  v1.0.0                        ║
+  ╚═══════════════════════════════════════════════════════════════╝
+
+  System  ─────────────────────────────────────────────────────────
+    CPU      16 cores available  →  16 threads configured
+    GPU      NVIDIA GeForce RTX 3050 6GB Laptop GPU  (CC 8.6)  ·  5.7 GB total  ·  5.6 GB free  ✓ CUDA usable
+
+  Run Configuration  ──────────────────────────────────────────────
+
+    Input file                             …/R1/all_gt.tre
+    Output file                            /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+
+    Compute mode                           GPU  (auto-selected CUDA device NVIDIA GeForce RTX 3050 6GB Laptop GPU)
+    CPU threads                            16  (16 available)
+    Tree treatment                         rooted
+    Inference polytomies                   resolve  (deterministic first-pair refinement)
+    Triplet-score polytomies               keep  (always; native input topology)
+
+    Search mode                            local
+    Hash seeds                             2
+    Verbosity                              info
+
+    Weight batching                        auto  (method-specific)
+      VRAM occupancy factor                0.75  →  batch = freeVRAM × factor
+      Tree-walk scratch cap                512 MiB  (automatic simple-tree-walk batches)
+    DP state-space construction memory cap (GPU) (n/a)
+
+  ───────────────────────────────────────────────────────────────
+
+
+  ▶  Phase 1  Parse gene trees  [CPU]
+[  169ms][INFO ] Read 10 lines from /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/all_gt.tre
+[  170ms][INFO ] Registered 10 unique taxa
+     ▸  Parsing trees  [░░░░░░░░░░░░░░░░░░░░░░░░░░░░]  0/10 (0%)  [00:00<?, ?it/s]
     ▸  Parsing trees  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 2134.2it/s]
     ▸  Parsing trees  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 1991.4it/s]
+[  176ms][INFO ] Parsed 10 gene trees in 7 ms
+[  176ms][INFO ] Input binary refinement: no multifurcations detected
+     ✓  8 ms
+        peak RAM (this step): 144 MiB  │  peak RAM (so far): 144 MiB
+
+  ▶  Phase 2  Taxon hashing  [CPU]
+[  228ms][INFO ] Built prefix hash arrays: k=10 trees, m=2 seeds in 0 ms
+     ✓  0 ms
+        peak RAM (this step): 147 MiB  │  peak RAM (so far): 147 MiB
+
+  ▶  Phase 3  Cluster extraction  [CPU]
+     ▸  Cluster extraction  [░░░░░░░░░░░░░░░░░░░░░░░░░░░░]  0/10 (0%)  [00:00<?, ?it/s]
     ▸  Cluster extraction  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 4026.7it/s]
     ▸  Cluster extraction  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 3549.2it/s]
+[  283ms][INFO ] Cluster extraction: 180 candidates -> 28 unique clusters in 3 ms
+     ✓  4 ms
+        peak RAM (this step): 147 MiB  │  peak RAM (so far): 147 MiB
+
+  ▶  Phase 4  Rooted child-partition extraction  [CPU]
+     ▸  Child-partition extraction  [░░░░░░░░░░░░░░░░░░░░░░░░░░░░]  0/10 (0%)  [00:00<?, ?it/s]
     ▸  Child-partition extraction  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 3963.9it/s]
     ▸  Child-partition extraction  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 2942.7it/s]
+[  335ms][INFO ] Rooted partition extraction: 90 internal nodes -> 55 contributing occurrences (35 identically zero skipped) -> 20 unique child partitions in 4 ms
+     ✓  5 ms
+        peak RAM (this step): 147 MiB  │  peak RAM (so far): 147 MiB
+
+  ▶  Phase 5  DP local transitions  [CPU]
+     ▸  Local DP transitions  [░░░░░░░░░░░░░░░░░░░░░░░░░░░░]  0/10 (0%)  [00:00<?, ?it/s]
     ▸  Local DP transitions  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 2992.2it/s]
     ▸  Local DP transitions  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 2598.4it/s]
+[  389ms][INFO ] DP table: 19 clusters with splits, 28 unique splits (90 emitted) in 4 ms
+     ✓  6 ms
+        peak RAM (this step): 147 MiB  │  peak RAM (so far): 147 MiB
+
+  ▶  Phase 6  Weight calculation  [GPU]
+[  446ms][INFO ] Weight accumulation: LONG (exact 64-bit integer)  [taxa=10, genes=10, est. max 2·score ≈ 2.40e+03 within long-safe 1.15e+18].
+[  447ms][INFO ] DP reachability prune: clusters 19/19 reachable (100.0%), splits 28/28 need to be scored (100.0%) — 0 unreachable splits skipped
+[  448ms][INFO ] Weight table: GPU path (smaller-side traversal)  splits=28  uniqueParts=20  trees=10  batching=auto (free-VRAM adaptive, occupancy=75%)
+[STELAR-X GPU] weight accumulator: LONG (exact 64-bit integer)
+[STELAR-X GPU] weight static data uploaded (smaller-side traversal, no prefix sums):
+  orderings :    0.0 MB
+  invIndex  :    0.0 MB
+  parts     :    0.0 MB  (20 unique child partitions × 8 ints)
+  ─────────────────────
+  static total :    0.0 MB   (VRAM free after: 5974.8 MB / 6086.3 MB)
+[STELAR-X GPU] adaptive batch: freeVRAM=5.97 GB, occupancy=75%, usable=4.48 GB, perSplit=48 B → batchSize=28  (numSplits=28, numBatches=1)
+[  551ms][INFO ]   GPU kernel returned in 102 ms
+[  551ms][INFO ] Weight table: 28 splits scored [LONG], maxScore=640, totalScore=2072 in 104 ms
+     ✓  106 ms
+        peak RAM (this step): 158 MiB  │  peak RAM (so far): 158 MiB
+        peak VRAM (this step): 106 MiB  │  peak VRAM (so far): 106 MiB
+
+  ▶  Phase 7  Inference  [CPU]
+[  650ms][INFO ] Inference DP: optimization-objective triplet score = 1127  [long]  (0 ms)
+     ✓  5 ms
+        peak RAM (this step): 156 MiB  │  peak RAM (so far): 158 MiB
+[  700ms][INFO ] Species tree written to /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+[  701ms][INFO ] Final triplet score = 1127  [reused inference DP score; no unresolved input polytomies detected]
+[  703ms][INFO ] Total time: 536 ms
+
+  Run Summary  ──────────────────────────────────────────────────
+
+    Triplet score      1127
+    Running time       0.536 s
+    Max CPU RAM        158 MiB
+    Max GPU VRAM       106 MiB
+
+	Command being timed: "./run.sh --input /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/all_gt.tre --output /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre --search-space S1 --intersection-method I1"
+	User time (seconds): 8.27
+	System time (seconds): 0.52
+	Percent of CPU this job got: 378%
+	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.32
+	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): 257312
+	Average resident set size (kbytes): 0
+	Major (requiring I/O) page faults: 0
+	Minor (reclaiming a frame) page faults: 91739
+	Voluntary context switches: 31213
+	Involuntary context switches: 574
+	Swaps: 0
+	File system inputs: 64
+	File system outputs: 1808
+	Socket messages sent: 0
+	Socket messages received: 0
+	Signals delivered: 0
+	Page size (bytes): 4096
+	Exit status: 0
+
+=== STELAR-X Execution Summary ===
+Status:         SUCCESS
+Running time:   2.327s
+Max CPU RAM:    251.281 MB
+Max GPU VRAM:   109.568 MB
+Triplet score:  1127
+Output exists:  Yes
+Stats saved to: /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx_stats.csv
+Command saved to: /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.command

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/search-space_S1__intersection-method_I1/out-stelarx.command

@@ -0,0 +1,20 @@
+# STELAR-X run command (written by run-stelarx-with-monitor.sh)
+# date:         2026-09-11T14:06:22+0600
+# host:         LOQ
+# stelarx_root: /home/aaniksahaa/research/STELAR-X-2
+# git_commit:   6a20c4d (with uncommitted changes)
+# input:        /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/all_gt.tre
+# output:       /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+# wrapper:      /home/aaniksahaa/research/STELAR-X-2/run-stelarx-with-monitor.sh -i /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/all_gt.tre -o /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre --stelarx-root /home/aaniksahaa/research/STELAR-X-2 --no-notify --opts --search-space\ S1\ --intersection-method\ I1
+# exact STELAR-X invocation (run from stelarx_root):
+cd /home/aaniksahaa/research/STELAR-X-2 && ./run.sh --input /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/all_gt.tre --output /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre --search-space S1 --intersection-method I1
+# exit_code:    0
+# running_time: 2.327s
+# --- simulated-run context (test-stelarx-simulated.sh) ---
+# dataset:      t_10_g_10_sb_0.000001_spmin_100000_spmax_200000
+# replicate:    R1
+# setting:      search-space_S1__intersection-method_I1
+# true tree:    /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/s_tree.trees
+# rf_rate:      0.1429
+# invoked as:   /home/aaniksahaa/research/STELAR-X-2/test-stelarx-simulated.sh -r R1 --simphy-data-dir /home/aaniksahaa/phylogeny/data/simphy/data --no-notify -t 10 -g 10 --sb 0.000001 --spmin 100000 --spmax 200000 --opts --search-space\ S1\ --intersection-method\ I1
+# wrapper cmd:  /home/aaniksahaa/research/STELAR-X-2/run-stelarx-with-monitor.sh -i /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/all_gt.tre -o /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre --stelarx-root /home/aaniksahaa/research/STELAR-X-2 --no-notify --opts --search-space\ S1\ --intersection-method\ I1

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/search-space_S1__intersection-method_I1/out-stelarx.tre

@@ -0,0 +1 @@
+((9,10),((2,((7,4),((3,8),(6,1)))),5));

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/search-space_S1__intersection-method_I1/out-stelarx_stats.csv

@@ -0,0 +1,2 @@
+algorithm,input_file,output_file,running_time_s,max_cpu_mb,max_gpu_mb,optimal_triplet_score,rf_rate,exit_code
+stelar-x,all_gt.tre,out-stelarx.tre,2.327,251.281,109.568,1127,NA,0

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R1/search-space_S1__intersection-method_I1/stat-stelarx.csv

@@ -0,0 +1,2 @@
+alg,setting,num-taxa,gene-trees,replicate,sb,spmin,spmax,rf-rate,optimal-triplet-score,running-time-s,max-cpu-mb,max-gpu-mb
+stelarx,search-space_S1__intersection-method_I1,10,10,R1,0.000001,100000,200000,0.1429,1127,2.327,251.281,109.568

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/search-space_S1__intersection-method_I1/.stelarx.success

@@ -0,0 +1,2 @@
+exit_code=0
+output=/home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/search-space_S1__intersection-method_I1/.stelarx_run.log

@@ -0,0 +1,151 @@
+=== STELAR-X Monitor Wrapper ===
+Input file:     /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/all_gt.tre
+Output file:    /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+STELAR-X root:  /home/aaniksahaa/research/STELAR-X-2
+STELAR-X opts:  --search-space S1 --intersection-method I1
+Weight method:  smaller-side-traversal
+Time monitor:   true
+GPU monitor:    true
+Notifications:  disabled
+
+=== Building STELAR-X ===
+Build OK -> /home/aaniksahaa/research/STELAR-X-2/build
+Run: ./stelarx -i <rooted-input.tre> -vv --no-build
+=== STELAR-X ===
+Input:       /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/all_gt.tre
+Output:      /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+Build dir:   /home/aaniksahaa/research/STELAR-X-2/build
+Native dir:  /home/aaniksahaa/research/STELAR-X-2/native
+GPU ready:   true
+Java heap:   -Xms256m -Xmx128g
+
+
+  ╔═══════════════════════════════════════════════════════════════╗
+  ║                       STELAR-X  v1.0.0                        ║
+  ╚═══════════════════════════════════════════════════════════════╝
+
+  System  ─────────────────────────────────────────────────────────
+    CPU      16 cores available  →  16 threads configured
+    GPU      NVIDIA GeForce RTX 3050 6GB Laptop GPU  (CC 8.6)  ·  5.7 GB total  ·  5.6 GB free  ✓ CUDA usable
+
+  Run Configuration  ──────────────────────────────────────────────
+
+    Input file                             …/R2/all_gt.tre
+    Output file                            /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+
+    Compute mode                           GPU  (auto-selected CUDA device NVIDIA GeForce RTX 3050 6GB Laptop GPU)
+    CPU threads                            16  (16 available)
+    Tree treatment                         rooted
+    Inference polytomies                   resolve  (deterministic first-pair refinement)
+    Triplet-score polytomies               keep  (always; native input topology)
+
+    Search mode                            local
+    Hash seeds                             2
+    Verbosity                              info
+
+    Weight batching                        auto  (method-specific)
+      VRAM occupancy factor                0.75  →  batch = freeVRAM × factor
+      Tree-walk scratch cap                512 MiB  (automatic simple-tree-walk batches)
+    DP state-space construction memory cap (GPU) (n/a)
+
+  ───────────────────────────────────────────────────────────────
+
+
+  ▶  Phase 1  Parse gene trees  [CPU]
+[  159ms][INFO ] Read 10 lines from /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/all_gt.tre
+[  161ms][INFO ] Registered 10 unique taxa
+     ▸  Parsing trees  [░░░░░░░░░░░░░░░░░░░░░░░░░░░░]  0/10 (0%)  [00:00<?, ?it/s]
     ▸  Parsing trees  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 2591.0it/s]
     ▸  Parsing trees  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 2362.5it/s]
+[  166ms][INFO ] Parsed 10 gene trees in 6 ms
+[  166ms][INFO ] Input binary refinement: no multifurcations detected
+     ✓  7 ms
+        peak RAM (this step): 143 MiB  │  peak RAM (so far): 143 MiB
+
+  ▶  Phase 2  Taxon hashing  [CPU]
+[  226ms][INFO ] Built prefix hash arrays: k=10 trees, m=2 seeds in 0 ms
+     ✓  1 ms
+        peak RAM (this step): 146 MiB  │  peak RAM (so far): 146 MiB
+
+  ▶  Phase 3  Cluster extraction  [CPU]
+     ▸  Cluster extraction  [░░░░░░░░░░░░░░░░░░░░░░░░░░░░]  0/10 (0%)  [00:00<?, ?it/s]
     ▸  Cluster extraction  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 9212.8it/s]
     ▸  Cluster extraction  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 7844.5it/s]
+[  278ms][INFO ] Cluster extraction: 180 candidates -> 24 unique clusters in 1 ms
+     ✓  2 ms
+        peak RAM (this step): 146 MiB  │  peak RAM (so far): 146 MiB
+
+  ▶  Phase 4  Rooted child-partition extraction  [CPU]
+     ▸  Child-partition extraction  [░░░░░░░░░░░░░░░░░░░░░░░░░░░░]  0/10 (0%)  [00:00<?, ?it/s]
     ▸  Child-partition extraction  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 8804.0it/s]
     ▸  Child-partition extraction  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 7448.9it/s]
+[  329ms][INFO ] Rooted partition extraction: 90 internal nodes -> 47 contributing occurrences (43 identically zero skipped) -> 13 unique child partitions in 1 ms
+     ✓  2 ms
+        peak RAM (this step): 146 MiB  │  peak RAM (so far): 146 MiB
+
+  ▶  Phase 5  DP local transitions  [CPU]
+     ▸  Local DP transitions  [░░░░░░░░░░░░░░░░░░░░░░░░░░░░]  0/10 (0%)  [00:00<?, ?it/s]
     ▸  Local DP transitions  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 2265.5it/s]
     ▸  Local DP transitions  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 1963.8it/s]
+[  387ms][INFO ] DP table: 15 clusters with splits, 20 unique splits (90 emitted) in 5 ms
+     ✓  7 ms
+        peak RAM (this step): 147 MiB  │  peak RAM (so far): 147 MiB
+
+  ▶  Phase 6  Weight calculation  [GPU]
+[  441ms][INFO ] Weight accumulation: LONG (exact 64-bit integer)  [taxa=10, genes=10, est. max 2·score ≈ 2.40e+03 within long-safe 1.15e+18].
+[  442ms][INFO ] DP reachability prune: clusters 15/15 reachable (100.0%), splits 20/20 need to be scored (100.0%) — 0 unreachable splits skipped
+[  442ms][INFO ] Weight table: GPU path (smaller-side traversal)  splits=20  uniqueParts=13  trees=10  batching=auto (free-VRAM adaptive, occupancy=75%)
+[STELAR-X GPU] weight accumulator: LONG (exact 64-bit integer)
+[STELAR-X GPU] weight static data uploaded (smaller-side traversal, no prefix sums):
+  orderings :    0.0 MB
+  invIndex  :    0.0 MB
+  parts     :    0.0 MB  (13 unique child partitions × 8 ints)
+  ─────────────────────
+  static total :    0.0 MB   (VRAM free after: 5974.8 MB / 6086.3 MB)
+[STELAR-X GPU] adaptive batch: freeVRAM=5.97 GB, occupancy=75%, usable=4.48 GB, perSplit=48 B → batchSize=20  (numSplits=20, numBatches=1)
+[  546ms][INFO ]   GPU kernel returned in 103 ms
+[  546ms][INFO ] Weight table: 20 splits scored [LONG], maxScore=640, totalScore=1965 in 105 ms
+     ✓  106 ms
+        peak RAM (this step): 157 MiB  │  peak RAM (so far): 157 MiB
+        peak VRAM (this step): 106 MiB  │  peak VRAM (so far): 106 MiB
+
+  ▶  Phase 7  Inference  [CPU]
+[  642ms][INFO ] Inference DP: optimization-objective triplet score = 1143  [long]  (0 ms)
+     ✓  1 ms
+        peak RAM (this step): 155 MiB  │  peak RAM (so far): 157 MiB
+[  693ms][INFO ] Species tree written to /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+[  694ms][INFO ] Final triplet score = 1143  [reused inference DP score; no unresolved input polytomies detected]
+[  697ms][INFO ] Total time: 540 ms
+
+  Run Summary  ──────────────────────────────────────────────────
+
+    Triplet score      1143
+    Running time       0.540 s
+    Max CPU RAM        157 MiB
+    Max GPU VRAM       106 MiB
+
+	Command being timed: "./run.sh --input /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/all_gt.tre --output /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre --search-space S1 --intersection-method I1"
+	User time (seconds): 7.51
+	System time (seconds): 0.51
+	Percent of CPU this job got: 369%
+	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.17
+	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): 254668
+	Average resident set size (kbytes): 0
+	Major (requiring I/O) page faults: 0
+	Minor (reclaiming a frame) page faults: 87854
+	Voluntary context switches: 29162
+	Involuntary context switches: 692
+	Swaps: 0
+	File system inputs: 0
+	File system outputs: 1776
+	Socket messages sent: 0
+	Socket messages received: 0
+	Signals delivered: 0
+	Page size (bytes): 4096
+	Exit status: 0
+
+=== STELAR-X Execution Summary ===
+Status:         SUCCESS
+Running time:   2.177s
+Max CPU RAM:    248.699 MB
+Max GPU VRAM:   107.520 MB
+Triplet score:  1143
+Output exists:  Yes
+Stats saved to: /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx_stats.csv
+Command saved to: /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.command

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/search-space_S1__intersection-method_I1/out-stelarx.command

@@ -0,0 +1,20 @@
+# STELAR-X run command (written by run-stelarx-with-monitor.sh)
+# date:         2026-09-11T14:06:25+0600
+# host:         LOQ
+# stelarx_root: /home/aaniksahaa/research/STELAR-X-2
+# git_commit:   6a20c4d (with uncommitted changes)
+# input:        /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/all_gt.tre
+# output:       /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+# wrapper:      /home/aaniksahaa/research/STELAR-X-2/run-stelarx-with-monitor.sh -i /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/all_gt.tre -o /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre --stelarx-root /home/aaniksahaa/research/STELAR-X-2 --no-notify --opts --search-space\ S1\ --intersection-method\ I1
+# exact STELAR-X invocation (run from stelarx_root):
+cd /home/aaniksahaa/research/STELAR-X-2 && ./run.sh --input /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/all_gt.tre --output /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre --search-space S1 --intersection-method I1
+# exit_code:    0
+# running_time: 2.177s
+# --- simulated-run context (test-stelarx-simulated.sh) ---
+# dataset:      t_10_g_10_sb_0.000001_spmin_100000_spmax_200000
+# replicate:    R2
+# setting:      search-space_S1__intersection-method_I1
+# true tree:    /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/s_tree.trees
+# rf_rate:      0.0000
+# invoked as:   /home/aaniksahaa/research/STELAR-X-2/test-stelarx-simulated.sh -r R2 --simphy-data-dir /home/aaniksahaa/phylogeny/data/simphy/data --no-notify -t 10 -g 10 --sb 0.000001 --spmin 100000 --spmax 200000 --opts --search-space\ S1\ --intersection-method\ I1
+# wrapper cmd:  /home/aaniksahaa/research/STELAR-X-2/run-stelarx-with-monitor.sh -i /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/all_gt.tre -o /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre --stelarx-root /home/aaniksahaa/research/STELAR-X-2 --no-notify --opts --search-space\ S1\ --intersection-method\ I1

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/search-space_S1__intersection-method_I1/out-stelarx.tre

@@ -0,0 +1 @@
+((((8,6),(((10,4),9),3)),(7,5)),(2,1));

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/search-space_S1__intersection-method_I1/out-stelarx_stats.csv

@@ -0,0 +1,2 @@
+algorithm,input_file,output_file,running_time_s,max_cpu_mb,max_gpu_mb,optimal_triplet_score,rf_rate,exit_code
+stelar-x,all_gt.tre,out-stelarx.tre,2.177,248.699,107.520,1143,NA,0

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R2/search-space_S1__intersection-method_I1/stat-stelarx.csv

@@ -0,0 +1,2 @@
+alg,setting,num-taxa,gene-trees,replicate,sb,spmin,spmax,rf-rate,optimal-triplet-score,running-time-s,max-cpu-mb,max-gpu-mb
+stelarx,search-space_S1__intersection-method_I1,10,10,R2,0.000001,100000,200000,0.0000,1143,2.177,248.699,107.520

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/search-space_S1__intersection-method_I1/.stelarx.success

@@ -0,0 +1,2 @@
+exit_code=0
+output=/home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/search-space_S1__intersection-method_I1/.stelarx_run.log

@@ -0,0 +1,151 @@
+=== STELAR-X Monitor Wrapper ===
+Input file:     /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/all_gt.tre
+Output file:    /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+STELAR-X root:  /home/aaniksahaa/research/STELAR-X-2
+STELAR-X opts:  --search-space S1 --intersection-method I1
+Weight method:  smaller-side-traversal
+Time monitor:   true
+GPU monitor:    true
+Notifications:  disabled
+
+=== Building STELAR-X ===
+Build OK -> /home/aaniksahaa/research/STELAR-X-2/build
+Run: ./stelarx -i <rooted-input.tre> -vv --no-build
+=== STELAR-X ===
+Input:       /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/all_gt.tre
+Output:      /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+Build dir:   /home/aaniksahaa/research/STELAR-X-2/build
+Native dir:  /home/aaniksahaa/research/STELAR-X-2/native
+GPU ready:   true
+Java heap:   -Xms256m -Xmx128g
+
+
+  ╔═══════════════════════════════════════════════════════════════╗
+  ║                       STELAR-X  v1.0.0                        ║
+  ╚═══════════════════════════════════════════════════════════════╝
+
+  System  ─────────────────────────────────────────────────────────
+    CPU      16 cores available  →  16 threads configured
+    GPU      NVIDIA GeForce RTX 3050 6GB Laptop GPU  (CC 8.6)  ·  5.7 GB total  ·  5.6 GB free  ✓ CUDA usable
+
+  Run Configuration  ──────────────────────────────────────────────
+
+    Input file                             …/R3/all_gt.tre
+    Output file                            /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+
+    Compute mode                           GPU  (auto-selected CUDA device NVIDIA GeForce RTX 3050 6GB Laptop GPU)
+    CPU threads                            16  (16 available)
+    Tree treatment                         rooted
+    Inference polytomies                   resolve  (deterministic first-pair refinement)
+    Triplet-score polytomies               keep  (always; native input topology)
+
+    Search mode                            local
+    Hash seeds                             2
+    Verbosity                              info
+
+    Weight batching                        auto  (method-specific)
+      VRAM occupancy factor                0.75  →  batch = freeVRAM × factor
+      Tree-walk scratch cap                512 MiB  (automatic simple-tree-walk batches)
+    DP state-space construction memory cap (GPU) (n/a)
+
+  ───────────────────────────────────────────────────────────────
+
+
+  ▶  Phase 1  Parse gene trees  [CPU]
+[  159ms][INFO ] Read 10 lines from /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/all_gt.tre
+[  160ms][INFO ] Registered 10 unique taxa
+     ▸  Parsing trees  [░░░░░░░░░░░░░░░░░░░░░░░░░░░░]  0/10 (0%)  [00:00<?, ?it/s]
     ▸  Parsing trees  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 2756.6it/s]
     ▸  Parsing trees  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 2503.5it/s]
+[  165ms][INFO ] Parsed 10 gene trees in 6 ms
+[  165ms][INFO ] Input binary refinement: no multifurcations detected
+     ✓  7 ms
+        peak RAM (this step): 143 MiB  │  peak RAM (so far): 143 MiB
+
+  ▶  Phase 2  Taxon hashing  [CPU]
+[  225ms][INFO ] Built prefix hash arrays: k=10 trees, m=2 seeds in 0 ms
+     ✓  0 ms
+        peak RAM (this step): 146 MiB  │  peak RAM (so far): 146 MiB
+
+  ▶  Phase 3  Cluster extraction  [CPU]
+     ▸  Cluster extraction  [░░░░░░░░░░░░░░░░░░░░░░░░░░░░]  0/10 (0%)  [00:00<?, ?it/s]
     ▸  Cluster extraction  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 3101.3it/s]
     ▸  Cluster extraction  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 2621.8it/s]
+[  283ms][INFO ] Cluster extraction: 180 candidates -> 38 unique clusters in 5 ms
+     ✓  7 ms
+        peak RAM (this step): 146 MiB  │  peak RAM (so far): 146 MiB
+
+  ▶  Phase 4  Rooted child-partition extraction  [CPU]
+     ▸  Child-partition extraction  [░░░░░░░░░░░░░░░░░░░░░░░░░░░░]  0/10 (0%)  [00:00<?, ?it/s]
     ▸  Child-partition extraction  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 3229.8it/s]
     ▸  Child-partition extraction  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 2621.6it/s]
+[  334ms][INFO ] Rooted partition extraction: 90 internal nodes -> 65 contributing occurrences (25 identically zero skipped) -> 32 unique child partitions in 4 ms
+     ✓  5 ms
+        peak RAM (this step): 146 MiB  │  peak RAM (so far): 146 MiB
+
+  ▶  Phase 5  DP local transitions  [CPU]
+     ▸  Local DP transitions  [░░░░░░░░░░░░░░░░░░░░░░░░░░░░]  0/10 (0%)  [00:00<?, ?it/s]
     ▸  Local DP transitions  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 3230.5it/s]
     ▸  Local DP transitions  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 2833.2it/s]
+[  386ms][INFO ] DP table: 29 clusters with splits, 41 unique splits (90 emitted) in 4 ms
+     ✓  6 ms
+        peak RAM (this step): 147 MiB  │  peak RAM (so far): 147 MiB
+
+  ▶  Phase 6  Weight calculation  [GPU]
+[  445ms][INFO ] Weight accumulation: LONG (exact 64-bit integer)  [taxa=10, genes=10, est. max 2·score ≈ 2.40e+03 within long-safe 1.15e+18].
+[  445ms][INFO ] DP reachability prune: clusters 29/29 reachable (100.0%), splits 41/41 need to be scored (100.0%) — 0 unreachable splits skipped
+[  446ms][INFO ] Weight table: GPU path (smaller-side traversal)  splits=41  uniqueParts=32  trees=10  batching=auto (free-VRAM adaptive, occupancy=75%)
+[STELAR-X GPU] weight accumulator: LONG (exact 64-bit integer)
+[STELAR-X GPU] weight static data uploaded (smaller-side traversal, no prefix sums):
+  orderings :    0.0 MB
+  invIndex  :    0.0 MB
+  parts     :    0.0 MB  (32 unique child partitions × 8 ints)
+  ─────────────────────
+  static total :    0.0 MB   (VRAM free after: 5974.8 MB / 6086.3 MB)
+[STELAR-X GPU] adaptive batch: freeVRAM=5.97 GB, occupancy=75%, usable=4.48 GB, perSplit=48 B → batchSize=41  (numSplits=41, numBatches=1)
+[  550ms][INFO ]   GPU kernel returned in 103 ms
+[  551ms][INFO ] Weight table: 41 splits scored [LONG], maxScore=669, totalScore=4480 in 106 ms
+     ✓  108 ms
+        peak RAM (this step): 157 MiB  │  peak RAM (so far): 157 MiB
+        peak VRAM (this step): 106 MiB  │  peak VRAM (so far): 106 MiB
+
+  ▶  Phase 7  Inference  [CPU]
+[  648ms][INFO ] Inference DP: optimization-objective triplet score = 987  [long]  (0 ms)
+     ✓  4 ms
+        peak RAM (this step): 155 MiB  │  peak RAM (so far): 157 MiB
+[  699ms][INFO ] Species tree written to /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+[  699ms][INFO ] Final triplet score = 987  [reused inference DP score; no unresolved input polytomies detected]
+[  702ms][INFO ] Total time: 544 ms
+
+  Run Summary  ──────────────────────────────────────────────────
+
+    Triplet score      987
+    Running time       0.544 s
+    Max CPU RAM        157 MiB
+    Max GPU VRAM       106 MiB
+
+	Command being timed: "./run.sh --input /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/all_gt.tre --output /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre --search-space S1 --intersection-method I1"
+	User time (seconds): 7.63
+	System time (seconds): 0.50
+	Percent of CPU this job got: 366%
+	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.22
+	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): 261004
+	Average resident set size (kbytes): 0
+	Major (requiring I/O) page faults: 0
+	Minor (reclaiming a frame) page faults: 90610
+	Voluntary context switches: 25405
+	Involuntary context switches: 516
+	Swaps: 0
+	File system inputs: 0
+	File system outputs: 1808
+	Socket messages sent: 0
+	Socket messages received: 0
+	Signals delivered: 0
+	Page size (bytes): 4096
+	Exit status: 0
+
+=== STELAR-X Execution Summary ===
+Status:         SUCCESS
+Running time:   2.228s
+Max CPU RAM:    254.887 MB
+Max GPU VRAM:   107.520 MB
+Triplet score:  987
+Output exists:  Yes
+Stats saved to: /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx_stats.csv
+Command saved to: /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.command

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/search-space_S1__intersection-method_I1/out-stelarx.command

@@ -0,0 +1,20 @@
+# STELAR-X run command (written by run-stelarx-with-monitor.sh)
+# date:         2026-09-11T14:06:28+0600
+# host:         LOQ
+# stelarx_root: /home/aaniksahaa/research/STELAR-X-2
+# git_commit:   6a20c4d (with uncommitted changes)
+# input:        /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/all_gt.tre
+# output:       /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+# wrapper:      /home/aaniksahaa/research/STELAR-X-2/run-stelarx-with-monitor.sh -i /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/all_gt.tre -o /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre --stelarx-root /home/aaniksahaa/research/STELAR-X-2 --no-notify --opts --search-space\ S1\ --intersection-method\ I1
+# exact STELAR-X invocation (run from stelarx_root):
+cd /home/aaniksahaa/research/STELAR-X-2 && ./run.sh --input /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/all_gt.tre --output /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre --search-space S1 --intersection-method I1
+# exit_code:    0
+# running_time: 2.228s
+# --- simulated-run context (test-stelarx-simulated.sh) ---
+# dataset:      t_10_g_10_sb_0.000001_spmin_100000_spmax_200000
+# replicate:    R3
+# setting:      search-space_S1__intersection-method_I1
+# true tree:    /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/s_tree.trees
+# rf_rate:      0.2857
+# invoked as:   /home/aaniksahaa/research/STELAR-X-2/test-stelarx-simulated.sh -r R3 --simphy-data-dir /home/aaniksahaa/phylogeny/data/simphy/data --no-notify -t 10 -g 10 --sb 0.000001 --spmin 100000 --spmax 200000 --opts --search-space\ S1\ --intersection-method\ I1
+# wrapper cmd:  /home/aaniksahaa/research/STELAR-X-2/run-stelarx-with-monitor.sh -i /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/all_gt.tre -o /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre --stelarx-root /home/aaniksahaa/research/STELAR-X-2 --no-notify --opts --search-space\ S1\ --intersection-method\ I1

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/search-space_S1__intersection-method_I1/out-stelarx.tre

@@ -0,0 +1 @@
+(10,((((2,((3,4),9)),1),((7,5),6)),8));

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/search-space_S1__intersection-method_I1/out-stelarx_stats.csv

@@ -0,0 +1,2 @@
+algorithm,input_file,output_file,running_time_s,max_cpu_mb,max_gpu_mb,optimal_triplet_score,rf_rate,exit_code
+stelar-x,all_gt.tre,out-stelarx.tre,2.228,254.887,107.520,987,NA,0

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R3/search-space_S1__intersection-method_I1/stat-stelarx.csv

@@ -0,0 +1,2 @@
+alg,setting,num-taxa,gene-trees,replicate,sb,spmin,spmax,rf-rate,optimal-triplet-score,running-time-s,max-cpu-mb,max-gpu-mb
+stelarx,search-space_S1__intersection-method_I1,10,10,R3,0.000001,100000,200000,0.2857,987,2.228,254.887,107.520

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/search-space_S1__intersection-method_I1/.stelarx.success

@@ -0,0 +1,2 @@
+exit_code=0
+output=/home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/search-space_S1__intersection-method_I1/.stelarx_run.log

@@ -0,0 +1,151 @@
+=== STELAR-X Monitor Wrapper ===
+Input file:     /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/all_gt.tre
+Output file:    /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+STELAR-X root:  /home/aaniksahaa/research/STELAR-X-2
+STELAR-X opts:  --search-space S1 --intersection-method I1
+Weight method:  smaller-side-traversal
+Time monitor:   true
+GPU monitor:    true
+Notifications:  disabled
+
+=== Building STELAR-X ===
+Build OK -> /home/aaniksahaa/research/STELAR-X-2/build
+Run: ./stelarx -i <rooted-input.tre> -vv --no-build
+=== STELAR-X ===
+Input:       /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/all_gt.tre
+Output:      /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+Build dir:   /home/aaniksahaa/research/STELAR-X-2/build
+Native dir:  /home/aaniksahaa/research/STELAR-X-2/native
+GPU ready:   true
+Java heap:   -Xms256m -Xmx128g
+
+
+  ╔═══════════════════════════════════════════════════════════════╗
+  ║                       STELAR-X  v1.0.0                        ║
+  ╚═══════════════════════════════════════════════════════════════╝
+
+  System  ─────────────────────────────────────────────────────────
+    CPU      16 cores available  →  16 threads configured
+    GPU      NVIDIA GeForce RTX 3050 6GB Laptop GPU  (CC 8.6)  ·  5.7 GB total  ·  5.6 GB free  ✓ CUDA usable
+
+  Run Configuration  ──────────────────────────────────────────────
+
+    Input file                             …/R4/all_gt.tre
+    Output file                            /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+
+    Compute mode                           GPU  (auto-selected CUDA device NVIDIA GeForce RTX 3050 6GB Laptop GPU)
+    CPU threads                            16  (16 available)
+    Tree treatment                         rooted
+    Inference polytomies                   resolve  (deterministic first-pair refinement)
+    Triplet-score polytomies               keep  (always; native input topology)
+
+    Search mode                            local
+    Hash seeds                             2
+    Verbosity                              info
+
+    Weight batching                        auto  (method-specific)
+      VRAM occupancy factor                0.75  →  batch = freeVRAM × factor
+      Tree-walk scratch cap                512 MiB  (automatic simple-tree-walk batches)
+    DP state-space construction memory cap (GPU) (n/a)
+
+  ───────────────────────────────────────────────────────────────
+
+
+  ▶  Phase 1  Parse gene trees  [CPU]
+[  159ms][INFO ] Read 10 lines from /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/all_gt.tre
+[  160ms][INFO ] Registered 10 unique taxa
+     ▸  Parsing trees  [░░░░░░░░░░░░░░░░░░░░░░░░░░░░]  0/10 (0%)  [00:00<?, ?it/s]
     ▸  Parsing trees  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 2749.1it/s]
     ▸  Parsing trees  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 2540.1it/s]
+[  165ms][INFO ] Parsed 10 gene trees in 6 ms
+[  165ms][INFO ] Input binary refinement: no multifurcations detected
+     ✓  7 ms
+        peak RAM (this step): 144 MiB  │  peak RAM (so far): 144 MiB
+
+  ▶  Phase 2  Taxon hashing  [CPU]
+[  217ms][INFO ] Built prefix hash arrays: k=10 trees, m=2 seeds in 0 ms
+     ✓  0 ms
+        peak RAM (this step): 147 MiB  │  peak RAM (so far): 147 MiB
+
+  ▶  Phase 3  Cluster extraction  [CPU]
+     ▸  Cluster extraction  [░░░░░░░░░░░░░░░░░░░░░░░░░░░░]  0/10 (0%)  [00:00<?, ?it/s]
     ▸  Cluster extraction  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 2793.2it/s]
     ▸  Cluster extraction  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 2272.3it/s]
+[  275ms][INFO ] Cluster extraction: 180 candidates -> 20 unique clusters in 5 ms
+     ✓  7 ms
+        peak RAM (this step): 147 MiB  │  peak RAM (so far): 147 MiB
+
+  ▶  Phase 4  Rooted child-partition extraction  [CPU]
+     ▸  Child-partition extraction  [░░░░░░░░░░░░░░░░░░░░░░░░░░░░]  0/10 (0%)  [00:00<?, ?it/s]
     ▸  Child-partition extraction  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 3325.7it/s]
     ▸  Child-partition extraction  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 2614.3it/s]
+[  327ms][INFO ] Rooted partition extraction: 90 internal nodes -> 58 contributing occurrences (32 identically zero skipped) -> 9 unique child partitions in 4 ms
+     ✓  6 ms
+        peak RAM (this step): 147 MiB  │  peak RAM (so far): 147 MiB
+
+  ▶  Phase 5  DP local transitions  [CPU]
+     ▸  Local DP transitions  [░░░░░░░░░░░░░░░░░░░░░░░░░░░░]  0/10 (0%)  [00:00<?, ?it/s]
     ▸  Local DP transitions  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 3004.2it/s]
     ▸  Local DP transitions  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 2472.1it/s]
+[  381ms][INFO ] DP table: 11 clusters with splits, 13 unique splits (90 emitted) in 5 ms
+     ✓  7 ms
+        peak RAM (this step): 147 MiB  │  peak RAM (so far): 147 MiB
+
+  ▶  Phase 6  Weight calculation  [GPU]
+[  443ms][INFO ] Weight accumulation: LONG (exact 64-bit integer)  [taxa=10, genes=10, est. max 2·score ≈ 2.40e+03 within long-safe 1.15e+18].
+[  443ms][INFO ] DP reachability prune: clusters 11/11 reachable (100.0%), splits 13/13 need to be scored (100.0%) — 0 unreachable splits skipped
+[  444ms][INFO ] Weight table: GPU path (smaller-side traversal)  splits=13  uniqueParts=9  trees=10  batching=auto (free-VRAM adaptive, occupancy=75%)
+[STELAR-X GPU] weight accumulator: LONG (exact 64-bit integer)
+[STELAR-X GPU] weight static data uploaded (smaller-side traversal, no prefix sums):
+  orderings :    0.0 MB
+  invIndex  :    0.0 MB
+  parts     :    0.0 MB  (9 unique child partitions × 8 ints)
+  ─────────────────────
+  static total :    0.0 MB   (VRAM free after: 5974.8 MB / 6086.3 MB)
+[STELAR-X GPU] adaptive batch: freeVRAM=5.97 GB, occupancy=75%, usable=4.48 GB, perSplit=48 B → batchSize=13  (numSplits=13, numBatches=1)
+[  549ms][INFO ]   GPU kernel returned in 105 ms
+[  550ms][INFO ] Weight table: 13 splits scored [LONG], maxScore=840, totalScore=1320 in 107 ms
+     ✓  110 ms
+        peak RAM (this step): 158 MiB  │  peak RAM (so far): 158 MiB
+        peak VRAM (this step): 106 MiB  │  peak VRAM (so far): 106 MiB
+
+  ▶  Phase 7  Inference  [CPU]
+[  644ms][INFO ] Inference DP: optimization-objective triplet score = 1191  [long]  (0 ms)
+     ✓  2 ms
+        peak RAM (this step): 156 MiB  │  peak RAM (so far): 158 MiB
+[  695ms][INFO ] Species tree written to /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+[  696ms][INFO ] Final triplet score = 1191  [reused inference DP score; no unresolved input polytomies detected]
+[  698ms][INFO ] Total time: 541 ms
+
+  Run Summary  ──────────────────────────────────────────────────
+
+    Triplet score      1191
+    Running time       0.541 s
+    Max CPU RAM        158 MiB
+    Max GPU VRAM       106 MiB
+
+	Command being timed: "./run.sh --input /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/all_gt.tre --output /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre --search-space S1 --intersection-method I1"
+	User time (seconds): 7.39
+	System time (seconds): 0.46
+	Percent of CPU this job got: 360%
+	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.17
+	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): 231236
+	Average resident set size (kbytes): 0
+	Major (requiring I/O) page faults: 0
+	Minor (reclaiming a frame) page faults: 87286
+	Voluntary context switches: 23855
+	Involuntary context switches: 569
+	Swaps: 0
+	File system inputs: 0
+	File system outputs: 1776
+	Socket messages sent: 0
+	Socket messages received: 0
+	Signals delivered: 0
+	Page size (bytes): 4096
+	Exit status: 0
+
+=== STELAR-X Execution Summary ===
+Status:         SUCCESS
+Running time:   2.184s
+Max CPU RAM:    225.816 MB
+Max GPU VRAM:   107.520 MB
+Triplet score:  1191
+Output exists:  Yes
+Stats saved to: /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx_stats.csv
+Command saved to: /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.command

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/search-space_S1__intersection-method_I1/out-stelarx.command

@@ -0,0 +1,20 @@
+# STELAR-X run command (written by run-stelarx-with-monitor.sh)
+# date:         2026-09-11T14:06:30+0600
+# host:         LOQ
+# stelarx_root: /home/aaniksahaa/research/STELAR-X-2
+# git_commit:   6a20c4d (with uncommitted changes)
+# input:        /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/all_gt.tre
+# output:       /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+# wrapper:      /home/aaniksahaa/research/STELAR-X-2/run-stelarx-with-monitor.sh -i /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/all_gt.tre -o /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre --stelarx-root /home/aaniksahaa/research/STELAR-X-2 --no-notify --opts --search-space\ S1\ --intersection-method\ I1
+# exact STELAR-X invocation (run from stelarx_root):
+cd /home/aaniksahaa/research/STELAR-X-2 && ./run.sh --input /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/all_gt.tre --output /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre --search-space S1 --intersection-method I1
+# exit_code:    0
+# running_time: 2.184s
+# --- simulated-run context (test-stelarx-simulated.sh) ---
+# dataset:      t_10_g_10_sb_0.000001_spmin_100000_spmax_200000
+# replicate:    R4
+# setting:      search-space_S1__intersection-method_I1
+# true tree:    /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/s_tree.trees
+# rf_rate:      0.0000
+# invoked as:   /home/aaniksahaa/research/STELAR-X-2/test-stelarx-simulated.sh -r R4 --simphy-data-dir /home/aaniksahaa/phylogeny/data/simphy/data --no-notify -t 10 -g 10 --sb 0.000001 --spmin 100000 --spmax 200000 --opts --search-space\ S1\ --intersection-method\ I1
+# wrapper cmd:  /home/aaniksahaa/research/STELAR-X-2/run-stelarx-with-monitor.sh -i /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/all_gt.tre -o /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre --stelarx-root /home/aaniksahaa/research/STELAR-X-2 --no-notify --opts --search-space\ S1\ --intersection-method\ I1

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/search-space_S1__intersection-method_I1/out-stelarx.tre

@@ -0,0 +1 @@
+(((1,(((3,5),2),6)),(7,4)),((10,9),8));

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/search-space_S1__intersection-method_I1/out-stelarx_stats.csv

@@ -0,0 +1,2 @@
+algorithm,input_file,output_file,running_time_s,max_cpu_mb,max_gpu_mb,optimal_triplet_score,rf_rate,exit_code
+stelar-x,all_gt.tre,out-stelarx.tre,2.184,225.816,107.520,1191,NA,0

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R4/search-space_S1__intersection-method_I1/stat-stelarx.csv

@@ -0,0 +1,2 @@
+alg,setting,num-taxa,gene-trees,replicate,sb,spmin,spmax,rf-rate,optimal-triplet-score,running-time-s,max-cpu-mb,max-gpu-mb
+stelarx,search-space_S1__intersection-method_I1,10,10,R4,0.000001,100000,200000,0.0000,1191,2.184,225.816,107.520

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/search-space_S1__intersection-method_I1/.stelarx.success

@@ -0,0 +1,2 @@
+exit_code=0
+output=/home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/search-space_S1__intersection-method_I1/.stelarx_run.log

@@ -0,0 +1,151 @@
+=== STELAR-X Monitor Wrapper ===
+Input file:     /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/all_gt.tre
+Output file:    /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+STELAR-X root:  /home/aaniksahaa/research/STELAR-X-2
+STELAR-X opts:  --search-space S1 --intersection-method I1
+Weight method:  smaller-side-traversal
+Time monitor:   true
+GPU monitor:    true
+Notifications:  disabled
+
+=== Building STELAR-X ===
+Build OK -> /home/aaniksahaa/research/STELAR-X-2/build
+Run: ./stelarx -i <rooted-input.tre> -vv --no-build
+=== STELAR-X ===
+Input:       /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/all_gt.tre
+Output:      /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+Build dir:   /home/aaniksahaa/research/STELAR-X-2/build
+Native dir:  /home/aaniksahaa/research/STELAR-X-2/native
+GPU ready:   true
+Java heap:   -Xms256m -Xmx128g
+
+
+  ╔═══════════════════════════════════════════════════════════════╗
+  ║                       STELAR-X  v1.0.0                        ║
+  ╚═══════════════════════════════════════════════════════════════╝
+
+  System  ─────────────────────────────────────────────────────────
+    CPU      16 cores available  →  16 threads configured
+    GPU      NVIDIA GeForce RTX 3050 6GB Laptop GPU  (CC 8.6)  ·  5.7 GB total  ·  5.6 GB free  ✓ CUDA usable
+
+  Run Configuration  ──────────────────────────────────────────────
+
+    Input file                             …/R5/all_gt.tre
+    Output file                            /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+
+    Compute mode                           GPU  (auto-selected CUDA device NVIDIA GeForce RTX 3050 6GB Laptop GPU)
+    CPU threads                            16  (16 available)
+    Tree treatment                         rooted
+    Inference polytomies                   resolve  (deterministic first-pair refinement)
+    Triplet-score polytomies               keep  (always; native input topology)
+
+    Search mode                            local
+    Hash seeds                             2
+    Verbosity                              info
+
+    Weight batching                        auto  (method-specific)
+      VRAM occupancy factor                0.75  →  batch = freeVRAM × factor
+      Tree-walk scratch cap                512 MiB  (automatic simple-tree-walk batches)
+    DP state-space construction memory cap (GPU) (n/a)
+
+  ───────────────────────────────────────────────────────────────
+
+
+  ▶  Phase 1  Parse gene trees  [CPU]
+[  222ms][INFO ] Read 10 lines from /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/all_gt.tre
+[  223ms][INFO ] Registered 10 unique taxa
+     ▸  Parsing trees  [░░░░░░░░░░░░░░░░░░░░░░░░░░░░]  0/10 (0%)  [00:00<?, ?it/s]
     ▸  Parsing trees  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 2289.2it/s]
     ▸  Parsing trees  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 2021.7it/s]
+[  229ms][INFO ] Parsed 10 gene trees in 7 ms
+[  229ms][INFO ] Input binary refinement: no multifurcations detected
+     ✓  8 ms
+        peak RAM (this step): 143 MiB  │  peak RAM (so far): 143 MiB
+
+  ▶  Phase 2  Taxon hashing  [CPU]
+[  280ms][INFO ] Built prefix hash arrays: k=10 trees, m=2 seeds in 0 ms
+     ✓  0 ms
+        peak RAM (this step): 146 MiB  │  peak RAM (so far): 146 MiB
+
+  ▶  Phase 3  Cluster extraction  [CPU]
+     ▸  Cluster extraction  [░░░░░░░░░░░░░░░░░░░░░░░░░░░░]  0/10 (0%)  [00:00<?, ?it/s]
     ▸  Cluster extraction  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 2735.0it/s]
     ▸  Cluster extraction  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 2262.5it/s]
+[  338ms][INFO ] Cluster extraction: 180 candidates -> 21 unique clusters in 5 ms
+     ✓  7 ms
+        peak RAM (this step): 146 MiB  │  peak RAM (so far): 146 MiB
+
+  ▶  Phase 4  Rooted child-partition extraction  [CPU]
+     ▸  Child-partition extraction  [░░░░░░░░░░░░░░░░░░░░░░░░░░░░]  0/10 (0%)  [00:00<?, ?it/s]
     ▸  Child-partition extraction  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 3161.0it/s]
     ▸  Child-partition extraction  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 2561.1it/s]
+[  389ms][INFO ] Rooted partition extraction: 90 internal nodes -> 69 contributing occurrences (21 identically zero skipped) -> 12 unique child partitions in 4 ms
+     ✓  6 ms
+        peak RAM (this step): 146 MiB  │  peak RAM (so far): 146 MiB
+
+  ▶  Phase 5  DP local transitions  [CPU]
+     ▸  Local DP transitions  [░░░░░░░░░░░░░░░░░░░░░░░░░░░░]  0/10 (0%)  [00:00<?, ?it/s]
     ▸  Local DP transitions  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 8437.2it/s]
     ▸  Local DP transitions  [████████████████████████████]  10/10 (100%)  [00:00<00:00, 7276.2it/s]
+[  437ms][INFO ] DP table: 12 clusters with splits, 15 unique splits (90 emitted) in 1 ms
+     ✓  2 ms
+        peak RAM (this step): 147 MiB  │  peak RAM (so far): 147 MiB
+
+  ▶  Phase 6  Weight calculation  [GPU]
+[  512ms][INFO ] Weight accumulation: LONG (exact 64-bit integer)  [taxa=10, genes=10, est. max 2·score ≈ 2.40e+03 within long-safe 1.15e+18].
+[  514ms][INFO ] DP reachability prune: clusters 12/12 reachable (100.0%), splits 15/15 need to be scored (100.0%) — 0 unreachable splits skipped
+[  515ms][INFO ] Weight table: GPU path (smaller-side traversal)  splits=15  uniqueParts=12  trees=10  batching=auto (free-VRAM adaptive, occupancy=75%)
+[STELAR-X GPU] weight accumulator: LONG (exact 64-bit integer)
+[STELAR-X GPU] weight static data uploaded (smaller-side traversal, no prefix sums):
+  orderings :    0.0 MB
+  invIndex  :    0.0 MB
+  parts     :    0.0 MB  (12 unique child partitions × 8 ints)
+  ─────────────────────
+  static total :    0.0 MB   (VRAM free after: 5974.8 MB / 6086.3 MB)
+[STELAR-X GPU] adaptive batch: freeVRAM=5.97 GB, occupancy=75%, usable=4.48 GB, perSplit=48 B → batchSize=15  (numSplits=15, numBatches=1)
+[  619ms][INFO ]   GPU kernel returned in 103 ms
+[  619ms][INFO ] Weight table: 15 splits scored [LONG], maxScore=652, totalScore=2420 in 107 ms
+     ✓  110 ms
+        peak RAM (this step): 157 MiB  │  peak RAM (so far): 157 MiB
+        peak VRAM (this step): 106 MiB  │  peak VRAM (so far): 106 MiB
+
+  ▶  Phase 7  Inference  [CPU]
+[  714ms][INFO ] Inference DP: optimization-objective triplet score = 1150  [long]  (0 ms)
+     ✓  4 ms
+        peak RAM (this step): 155 MiB  │  peak RAM (so far): 157 MiB
+[  764ms][INFO ] Species tree written to /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+[  764ms][INFO ] Final triplet score = 1150  [reused inference DP score; no unresolved input polytomies detected]
+[  765ms][INFO ] Total time: 545 ms
+
+  Run Summary  ──────────────────────────────────────────────────
+
+    Triplet score      1150
+    Running time       0.545 s
+    Max CPU RAM        157 MiB
+    Max GPU VRAM       106 MiB
+
+	Command being timed: "./run.sh --input /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/all_gt.tre --output /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre --search-space S1 --intersection-method I1"
+	User time (seconds): 8.32
+	System time (seconds): 0.63
+	Percent of CPU this job got: 370%
+	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.41
+	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): 260016
+	Average resident set size (kbytes): 0
+	Major (requiring I/O) page faults: 0
+	Minor (reclaiming a frame) page faults: 96657
+	Voluntary context switches: 31585
+	Involuntary context switches: 755
+	Swaps: 0
+	File system inputs: 0
+	File system outputs: 1808
+	Socket messages sent: 0
+	Socket messages received: 0
+	Signals delivered: 0
+	Page size (bytes): 4096
+	Exit status: 0
+
+=== STELAR-X Execution Summary ===
+Status:         SUCCESS
+Running time:   2.423s
+Max CPU RAM:    253.922 MB
+Max GPU VRAM:   107.520 MB
+Triplet score:  1150
+Output exists:  Yes
+Stats saved to: /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx_stats.csv
+Command saved to: /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.command

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/search-space_S1__intersection-method_I1/out-stelarx.command

@@ -0,0 +1,20 @@
+# STELAR-X run command (written by run-stelarx-with-monitor.sh)
+# date:         2026-09-11T14:06:33+0600
+# host:         LOQ
+# stelarx_root: /home/aaniksahaa/research/STELAR-X-2
+# git_commit:   6a20c4d (with uncommitted changes)
+# input:        /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/all_gt.tre
+# output:       /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre
+# wrapper:      /home/aaniksahaa/research/STELAR-X-2/run-stelarx-with-monitor.sh -i /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/all_gt.tre -o /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre --stelarx-root /home/aaniksahaa/research/STELAR-X-2 --no-notify --opts --search-space\ S1\ --intersection-method\ I1
+# exact STELAR-X invocation (run from stelarx_root):
+cd /home/aaniksahaa/research/STELAR-X-2 && ./run.sh --input /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/all_gt.tre --output /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre --search-space S1 --intersection-method I1
+# exit_code:    0
+# running_time: 2.423s
+# --- simulated-run context (test-stelarx-simulated.sh) ---
+# dataset:      t_10_g_10_sb_0.000001_spmin_100000_spmax_200000
+# replicate:    R5
+# setting:      search-space_S1__intersection-method_I1
+# true tree:    /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/s_tree.trees
+# rf_rate:      0.0000
+# invoked as:   /home/aaniksahaa/research/STELAR-X-2/test-stelarx-simulated.sh -r R5 --simphy-data-dir /home/aaniksahaa/phylogeny/data/simphy/data --no-notify -t 10 -g 10 --sb 0.000001 --spmin 100000 --spmax 200000 --opts --search-space\ S1\ --intersection-method\ I1
+# wrapper cmd:  /home/aaniksahaa/research/STELAR-X-2/run-stelarx-with-monitor.sh -i /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/all_gt.tre -o /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/stelarx_outputs/search-space_S1__intersection-method_I1/out-stelarx.tre --stelarx-root /home/aaniksahaa/research/STELAR-X-2 --no-notify --opts --search-space\ S1\ --intersection-method\ I1

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/search-space_S1__intersection-method_I1/out-stelarx.tre

@@ -0,0 +1 @@
+((((2,((7,1),6)),3),(5,((4,9),8))),10);

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/search-space_S1__intersection-method_I1/out-stelarx_stats.csv

@@ -0,0 +1,2 @@
+algorithm,input_file,output_file,running_time_s,max_cpu_mb,max_gpu_mb,optimal_triplet_score,rf_rate,exit_code
+stelar-x,all_gt.tre,out-stelarx.tre,2.423,253.922,107.520,1150,NA,0

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/R5/search-space_S1__intersection-method_I1/stat-stelarx.csv

@@ -0,0 +1,2 @@
+alg,setting,num-taxa,gene-trees,replicate,sb,spmin,spmax,rf-rate,optimal-triplet-score,running-time-s,max-cpu-mb,max-gpu-mb
+stelarx,search-space_S1__intersection-method_I1,10,10,R5,0.000001,100000,200000,0.0000,1150,2.423,253.922,107.520

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000.command

@@ -0,0 +1 @@
+/home/aaniksahaa/research/STELAR-X-2/simphy/simphy_lnx64 -sb f:0.000001 -ld f:0 -lb f:0 -lt f:0 -rs 5 -rl f:10 -rg 1 -o /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000 -sp u:100000,200000 -su ln:-17.27461,0.6931472 -sg f:1 -sl f:10 -st ln:16.2,1 -om 1 -v 2 -od 1 -op 1 -oc 1 -on 1 -cs 42 

ph/d/simulated/outputs/stelarx_outputs/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000.params

@@ -0,0 +1,40 @@
+
+Global settings:
+--------------------
+
+Trees:
+	-Species trees: 5 Birth-death simulations
+		-Speciation rate: Fixed 1.000000e-06,
+		-Extinction rate: Fixed 0.000000e+00,
+		-Outgroup addition: No addition
+		-Stopping rules:
+			-Number of leaves: Fixed 10,
+			-Generations: LogN(1.620000e+01,1)
+	-Locus trees: Fixed 10, directly obtained from each species tree (no birth-death process)
+
+	-Gene trees: 1 multilocus coalescent simulations
+
+Parameters:
+	-Haploid efective population size: Uniform[100000,200000]
+	-Generation time: Fixed 1,
+	-Global substitution rate: LogN(-1.727461e+01,6.931472e-01)
+	-Substitution rate heterogeneities
+		-Lineage (species) specific rate heterogeneity gamma shape: No heterogeneity
+		-Gene family (locus tree) specific rate heterogeneity gamma shape: No heterogeneity
+		-Gene tree branch specific rate heterogeneity gamma shape: Genome-wide parameter (hyperhyperparameter) No heterogeneity, locus-tree related parameter No heterogeneity, Gamma parameter(gene-tree related) No heterogeneity
+	-Individuals per species: Fixed 1,
+
+Misc parameters:
+	-Rooting method epsilon: 0.000001
+	-Seed: 42
+
+I/O options:
+	-Output files prefix: /home/aaniksahaa/phylogeny/data/simphy/data/t_10_g_10_sb_0.000001_spmin_100000_spmax_200000
+	-Verbosity: 2
+	-Stats file: OFF
+	-Mapping: ON
+	-Database: ON
+	-Parameterization: ON 
+	-Command-line arguments: ON
+	-Bounded locus subtrees: ON
+	-Output trees with internal node labels: OFF