diff --git a/ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/search-space_S1__intersection-method_I1/.astralx.lock b/ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/search-space_S1__intersection-method_I1/.astralx.lock new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/search-space_S1__intersection-method_I1/.astralx.success b/ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/search-space_S1__intersection-method_I1/.astralx.success new file mode 100644 index 0000000000000000000000000000000000000000..727839e971b24965babebfe3a69b28b128b5ba53 --- /dev/null +++ b/ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/search-space_S1__intersection-method_I1/.astralx.success @@ -0,0 +1,2 @@ +exit_code=0 +output=/root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre diff --git a/ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/search-space_S1__intersection-method_I1/.astralx_run.log b/ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/search-space_S1__intersection-method_I1/.astralx_run.log new file mode 100644 index 0000000000000000000000000000000000000000..f489ecdfdbe3e5e59c0cc723324b5352e4762ff0 --- /dev/null +++ b/ph/d/simulated/outputs/astralx_outputs/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/search-space_S1__intersection-method_I1/.astralx_run.log @@ -0,0 +1,153 @@ +=== ASTRAL-X Monitor Wrapper === +Input file: /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/all_gt.tre +Output file: /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre +ASTRAL-X root: /root/phylogeny/ASTRAL-X +ASTRAL-X opts: --search-space S1 --intersection-method I1 +Weight method: smaller-side-traversal +Time monitor: true +GPU monitor: true +Notifications: disabled + +=== Building ASTRAL-X === +Build OK -> /root/phylogeny/ASTRAL-X/build +Run: java -cp /root/phylogeny/ASTRAL-X/build astralx.Main -i -vv +=== ASTRAL-X === +Input: /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/all_gt.tre +Output: /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre +Build dir: /root/phylogeny/ASTRAL-X/build +Native dir: /root/phylogeny/ASTRAL-X/native +GPU ready: true +Java heap: -Xms4g -Xmx128g + + + ╔═══════════════════════════════════════════════════════════════╗ + ║  ASTRAL-X v1.0.0  ║ + ╚═══════════════════════════════════════════════════════════════╝ + + System ───────────────────────────────────────────────────────── + CPU 31 cores available → 31 threads configured + GPU NVIDIA GeForce RTX 4090 (CC 8.9) · 23.5 GB total · 23.1 GB free ✓ CUDA usable + + Run Configuration ────────────────────────────────────────────── + + Input file …/R1/all_gt.tre + Output file /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre + + Compute mode GPU (auto-selected CUDA device NVIDIA GeForce RTX 4090) + CPU threads 31 (31 available) + Tree treatment unrooted + Inference polytomies resolve (deterministic first-pair refinement) + Quartet-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] +[ 5207ms][INFO ] Read 1000 lines from /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R1/all_gt.tre +[17451ms][INFO ] Registered 75000 unique taxa + ▸ Parsing trees [░░░░░░░░░░░░░░░░░░░░░░░░░░░░] 0/1000 (0%) [00:00 1333675 unique clusters in 46422 ms [anchor-free X] + ✓ 46423 ms + peak RAM (this step): 42657 MiB │ peak RAM (so far): 42657 MiB + + ▶ Phase 4 Tripartition extraction [CPU] + ▸ Tripartition extraction [░░░░░░░░░░░░░░░░░░░░░░░░░░░░] 0/1000 (0%) [00:00 2638792 unique tripartitions in 35483 ms + ✓ 35483 ms + peak RAM (this step): 50704 MiB │ peak RAM (so far): 50704 MiB + + ▶ Phase 5 DP local transitions [CPU] + ▸ Local DP transitions [░░░░░░░░░░░░░░░░░░░░░░░░░░░░] 0/1000 (0%) [00:00 /root/phylogeny/ASTRAL-X/build +Run: java -cp /root/phylogeny/ASTRAL-X/build astralx.Main -i -vv +=== ASTRAL-X === +Input: /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R2/all_gt.tre +Output: /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R2/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre +Build dir: /root/phylogeny/ASTRAL-X/build +Native dir: /root/phylogeny/ASTRAL-X/native +GPU ready: true +Java heap: -Xms4g -Xmx128g + + + ╔═══════════════════════════════════════════════════════════════╗ + ║  ASTRAL-X v1.0.0  ║ + ╚═══════════════════════════════════════════════════════════════╝ + + System ───────────────────────────────────────────────────────── + CPU 31 cores available → 31 threads configured + GPU NVIDIA GeForce RTX 4090 (CC 8.9) · 23.5 GB total · 23.1 GB free ✓ CUDA usable + + Run Configuration ────────────────────────────────────────────── + + Input file …/R2/all_gt.tre + Output file /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R2/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre + + Compute mode GPU (auto-selected CUDA device NVIDIA GeForce RTX 4090) + CPU threads 31 (31 available) + Tree treatment unrooted + Inference polytomies resolve (deterministic first-pair refinement) + Quartet-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] +[ 5754ms][INFO ] Read 1000 lines from /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R2/all_gt.tre +[17549ms][INFO ] Registered 75000 unique taxa + ▸ Parsing trees [░░░░░░░░░░░░░░░░░░░░░░░░░░░░] 0/1000 (0%) [00:00 1131276 unique clusters in 46870 ms [anchor-free X] + ✓ 46871 ms + peak RAM (this step): 39832 MiB │ peak RAM (so far): 39832 MiB + + ▶ Phase 4 Tripartition extraction [CPU] + ▸ Tripartition extraction [░░░░░░░░░░░░░░░░░░░░░░░░░░░░] 0/1000 (0%) [00:00 2240833 unique tripartitions in 36006 ms + ✓ 36007 ms + peak RAM (this step): 48062 MiB │ peak RAM (so far): 48062 MiB + + ▶ Phase 5 DP local transitions [CPU] + ▸ Local DP transitions [░░░░░░░░░░░░░░░░░░░░░░░░░░░░] 0/1000 (0%) [00:00 /root/phylogeny/ASTRAL-X/build +Run: java -cp /root/phylogeny/ASTRAL-X/build astralx.Main -i -vv +=== ASTRAL-X === +Input: /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R3/all_gt.tre +Output: /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R3/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre +Build dir: /root/phylogeny/ASTRAL-X/build +Native dir: /root/phylogeny/ASTRAL-X/native +GPU ready: true +Java heap: -Xms4g -Xmx128g + + + ╔═══════════════════════════════════════════════════════════════╗ + ║  ASTRAL-X v1.0.0  ║ + ╚═══════════════════════════════════════════════════════════════╝ + + System ───────────────────────────────────────────────────────── + CPU 31 cores available → 31 threads configured + GPU NVIDIA GeForce RTX 4090 (CC 8.9) · 23.5 GB total · 23.1 GB free ✓ CUDA usable + + Run Configuration ────────────────────────────────────────────── + + Input file …/R3/all_gt.tre + Output file /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R3/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre + + Compute mode GPU (auto-selected CUDA device NVIDIA GeForce RTX 4090) + CPU threads 31 (31 available) + Tree treatment unrooted + Inference polytomies resolve (deterministic first-pair refinement) + Quartet-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] +[ 5845ms][INFO ] Read 1000 lines from /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R3/all_gt.tre +[16954ms][INFO ] Registered 75000 unique taxa + ▸ Parsing trees [░░░░░░░░░░░░░░░░░░░░░░░░░░░░] 0/1000 (0%) [00:00 1086909 unique clusters in 43006 ms [anchor-free X] + ✓ 43007 ms + peak RAM (this step): 41575 MiB │ peak RAM (so far): 41575 MiB + + ▶ Phase 4 Tripartition extraction [CPU] + ▸ Tripartition extraction [░░░░░░░░░░░░░░░░░░░░░░░░░░░░] 0/1000 (0%) [00:00 2154024 unique tripartitions in 33264 ms + ✓ 33264 ms + peak RAM (this step): 47741 MiB │ peak RAM (so far): 47741 MiB + + ▶ Phase 5 DP local transitions [CPU] + ▸ Local DP transitions [░░░░░░░░░░░░░░░░░░░░░░░░░░░░] 0/1000 (0%) [00:00 /root/phylogeny/ASTRAL-X/build +Run: java -cp /root/phylogeny/ASTRAL-X/build astralx.Main -i -vv +=== ASTRAL-X === +Input: /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R4/all_gt.tre +Output: /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R4/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre +Build dir: /root/phylogeny/ASTRAL-X/build +Native dir: /root/phylogeny/ASTRAL-X/native +GPU ready: true +Java heap: -Xms4g -Xmx128g + + + ╔═══════════════════════════════════════════════════════════════╗ + ║  ASTRAL-X v1.0.0  ║ + ╚═══════════════════════════════════════════════════════════════╝ + + System ───────────────────────────────────────────────────────── + CPU 31 cores available → 31 threads configured + GPU NVIDIA GeForce RTX 4090 (CC 8.9) · 23.5 GB total · 23.1 GB free ✓ CUDA usable + + Run Configuration ────────────────────────────────────────────── + + Input file …/R4/all_gt.tre + Output file /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R4/astralx_outputs/search-space_S1__intersection-method_I1/out-astralx.tre + + Compute mode GPU (auto-selected CUDA device NVIDIA GeForce RTX 4090) + CPU threads 31 (31 available) + Tree treatment unrooted + Inference polytomies resolve (deterministic first-pair refinement) + Quartet-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] +[ 5708ms][INFO ] Read 1000 lines from /root/phylogeny/data/simphy/data/t_75000_g_1000_sb_0.000001_spmin_100000_spmax_200000/R4/all_gt.tre +[18207ms][INFO ] Registered 75000 unique taxa + ▸ Parsing trees [░░░░░░░░░░░░░░░░░░░░░░░░░░░░] 0/1000 (0%) [00:00 688882 unique clusters in 46056 ms [anchor-free X] + ✓ 46057 ms + peak RAM (this step): 47059 MiB │ peak RAM (so far): 47059 MiB + + ▶ Phase 4 Tripartition extraction [CPU] + ▸ Tripartition extraction [░░░░░░░░░░░░░░░░░░░░░░░░░░░░] 0/1000 (0%) [00:00 1280531 unique tripartitions in 32426 ms + ✓ 32426 ms + peak RAM (this step): 53428 MiB │ peak RAM (so far): 53428 MiB + + ▶ Phase 5 DP local transitions [CPU] + ▸ Local DP transitions [░░░░░░░░░░░░░░░░░░░░░░░░░░░░] 0/1000 (0%) [00:00