Update provenance after t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000

provenance/environment.txt

@@ -1,28 +1,28 @@
-recorded 2026-10-01T21:01:02Z
+recorded 2026-10-02T03:16:18Z
 $ uname -a
-Linux 0ff8fe63b433 6.8.0-124-generic #124~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue May 26 21:05:19 UTC  x86_64 x86_64 x86_64 GNU/Linux
+Linux ea348f22a9e9 6.17.0-19-generic #19~24.04.2-Ubuntu SMP PREEMPT_DYNAMIC Fri Mar  6 23:08:46 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
 $ sh -c 'head -4 /etc/os-release'
 PRETTY_NAME="Ubuntu 24.04.4 LTS"
 NAME="Ubuntu"
 VERSION_ID="24.04"
 VERSION="24.04.4 LTS (Noble Numbat)"
 $ sh -c 'lscpu | grep -E '"'"'Model name|^CPU\(s\)|Thread|Socket|MHz'"'"''
-CPU(s):                                  256
-Model name:                              AMD EPYC 7B13 64-Core Processor
+CPU(s):                                  32
+Model name:                              AMD Ryzen 9 9950X 16-Core Processor
 Thread(s) per core:                      2
-Socket(s):                               2
-CPU(s) scaling MHz:                      77%
-CPU max MHz:                             3541.3679
-CPU min MHz:                             1500.0000
+Socket(s):                               1
+CPU(s) scaling MHz:                      55%
+CPU max MHz:                             5756.4521
+CPU min MHz:                             624.1940
 $ nproc
-256
+32
 $ free -g
 total        used        free      shared  buff/cache   available
-Mem:             944         222         420          38         351         722
-Swap:              0           0           0
+Mem:             186           7          46           0         134         178
+Swap:              7           0           7
 $ df -h /workspace/phylogeny/data/simphy/data
 Filesystem      Size  Used Avail Use% Mounted on
-overlay         2.8T   83M  2.8T   1% /
+overlay         2.5T   54M  2.5T   1% /
 $ /workspace/phylo-bench/simphy/simphy-x -XV
 simphy-x 0.1.0 (SimPhy 1.0.2 compatible)
 $ sh -c 'zip -v | head -2'
@@ -30,7 +30,7 @@ Copyright (c) 1990-2008 Info-ZIP - Type 'zip "-L"' for software license.
 This is Zip 3.0 (July 5th 2008), by Info-ZIP.
 $ /usr/bin/python3 --version
 Python 3.12.3
-memory limit 453 GB
+memory limit 179 GB
 sha256 5c7d3cd390d658a51530e9147f79a57a3256ec097a17b4fe7fa958b6b41795c0  phylo-bench/simphy/simphy-x
 sha256 d7eb203ac3674927717024da453a3d6b8d2dc78ed8fd9b531394b58cb654a1a9  phylo-bench/simphy/run_simulator.sh
 sha256 322804a679cc8353f2e7c9d94fcd77b28a27c8227f7b591b2a5dc554bcfbfa5c  phylo-bench/simphy/concat_gene_trees.py

provenance/sha256-trees.txt

@@ -168,23 +168,73 @@ fe92fdb5a0753e93bf7fcc7047cb26d69c757340d59a8149b4f1fe07d270cddd  t_900000_g_100
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provenance/sha256-zips.txt

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provenance/sim-commands.log

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+{"start": "2026-10-02T04:10:47Z", "cwd": "/workspace/phylogeny/data/simphy/data", "argv": ["zip", "-r", "-q", "-6", "-X", "/workspace/sim1m/zips/t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000.R4-R5.zip", "t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000/t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000.db", "t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000/t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000.params", "t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000/t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000.command", "t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000/R4", "t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000/R5"], "command": "zip -r -q -6 -X /workspace/sim1m/zips/t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000.R4-R5.zip t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000/t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000.db t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000/t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000.params t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000/t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000.command t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000/R4 t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000/R5", "end": "2026-10-02T04:12:30Z", "seconds": 102.6, "exit": 0}
+{"start": "2026-10-02T04:10:47Z", "cwd": "/workspace/phylogeny/data/simphy/data", "argv": ["zip", "-r", "-q", "-6", "-X", "/workspace/sim1m/zips/t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000.R1-R3.zip", "t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000/t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000.db", "t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000/t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000.params", "t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000/t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000.command", "t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000/R1", "t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000/R2", "t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000/R3"], "command": "zip -r -q -6 -X /workspace/sim1m/zips/t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000.R1-R3.zip t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000/t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000.db t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000/t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000.params t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000/t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000.command t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000/R1 t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000/R2 t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000/R3", "end": "2026-10-02T04:13:17Z", "seconds": 149.7, "exit": 0}
+{"start": "2026-10-02T03:43:49Z", "cwd": "/workspace/phylo-bench", "env": {"PHYLOGENY_DATA_DIR": "/workspace/phylogeny/data"}, "argv": ["./scripts/sim.sh", "-rs", "5", "--simphy-data-dir", "/workspace/phylogeny/data/simphy/data", "--seed", "42", "--engine", "simphy-x-compat", "--sim-threads", "all", "-t", "1000", "-g", "400000", "--sb", "0.000001", "--spmin", "100000", "--spmax", "200000"], "command": "./scripts/sim.sh -rs 5 --simphy-data-dir /workspace/phylogeny/data/simphy/data --seed 42 --engine simphy-x-compat --sim-threads all -t 1000 -g 400000 --sb 0.000001 --spmin 100000 --spmax 200000", "end": "2026-10-02T04:14:19Z", "seconds": 1830.4, "exit": 0}
+{"start": "2026-10-02T04:14:47Z", "cwd": "/workspace/phylogeny/data/simphy/data", "argv": ["zip", "-q", "-X", "/workspace/sim1m/zips/t_1000_g_400000_sb_0.000001_spmin_100000_spmax_200000.zip", "t_1000_g_400000_sb_0.000001_spmin_100000_spmax_200000/"], "command": "zip -q -X /workspace/sim1m/zips/t_1000_g_400000_sb_0.000001_spmin_100000_spmax_200000.zip t_1000_g_400000_sb_0.000001_spmin_100000_spmax_200000/", "end": "2026-10-02T04:14:47Z", "seconds": 0.0, "exit": 0}

provenance/simphy-commands.txt

@@ -15,5 +15,10 @@ t_600000_g_1000_sb_0.000001_spmin_100000_spmax_200000: /workspace/phylo-bench/si
 t_1000_g_600000_sb_0.000001_spmin_100000_spmax_200000: /workspace/phylo-bench/simphy/simphy-x -XM compat -sb f:0.000001 -ld f:0 -lb f:0 -lt f:0 -rs 5 -rl f:600000 -rg 1 -o /workspace/phylogeny/data/simphy/data/t_1000_g_600000_sb_0.000001_spmin_100000_spmax_200000 -sp u:100000,200000 -su ln:-17.27461,0.6931472 -sg f:1 -sl f:1000 -st ln:16.2,1 -om 1 -v 2 -od 1 -op 1 -oc 1 -on 1 -cs 42
 t_900000_g_1000_sb_0.000001_spmin_100000_spmax_200000: /workspace/phylo-bench/simphy/simphy-x -XM compat -sb f:0.000001 -ld f:0 -lb f:0 -lt f:0 -rs 5 -rl f:1000 -rg 1 -o /workspace/phylogeny/data/simphy/data/t_900000_g_1000_sb_0.000001_spmin_100000_spmax_200000 -sp u:100000,200000 -su ln:-17.27461,0.6931472 -sg f:1 -sl f:900000 -st ln:16.2,1 -om 1 -v 2 -od 1 -op 1 -oc 1 -on 1 -cs 42
 t_800000_g_1000_sb_0.000001_spmin_100000_spmax_200000: /workspace/phylo-bench/simphy/simphy-x -XM compat -sb f:0.000001 -ld f:0 -lb f:0 -lt f:0 -rs 5 -rl f:1000 -rg 1 -o /workspace/phylogeny/data/simphy/data/t_800000_g_1000_sb_0.000001_spmin_100000_spmax_200000 -sp u:100000,200000 -su ln:-17.27461,0.6931472 -sg f:1 -sl f:800000 -st ln:16.2,1 -om 1 -v 2 -od 1 -op 1 -oc 1 -on 1 -cs 42
-t_1000_g_900000_sb_0.000001_spmin_100000_spmax_200000: /workspace/phylo-bench/simphy/simphy-x -XM compat -sb f:0.000001 -ld f:0 -lb f:0 -lt f:0 -rs 5 -rl f:900000 -rg 1 -o /workspace/phylogeny/data/simphy/data/t_1000_g_900000_sb_0.000001_spmin_100000_spmax_200000 -sp u:100000,200000 -su ln:-17.27461,0.6931472 -sg f:1 -sl f:1000 -st ln:16.2,1 -om 1 -v 2 -od 1 -op 1 -oc 1 -on 1 -cs 42
-t_1000_g_1000000_sb_0.000001_spmin_100000_spmax_200000: /workspace/phylo-bench/simphy/simphy-x -XM compat -sb f:0.000001 -ld f:0 -lb f:0 -lt f:0 -rs 5 -rl f:1000000 -rg 1 -o /workspace/phylogeny/data/simphy/data/t_1000_g_1000000_sb_0.000001_spmin_100000_spmax_200000 -sp u:100000,200000 -su ln:-17.27461,0.6931472 -sg f:1 -sl f:1000 -st ln:16.2,1 -om 1 -v 2 -od 1 -op 1 -oc 1 -on 1 -cs 42
+t_1000_g_300000_sb_0.000001_spmin_100000_spmax_200000: /workspace/phylo-bench/simphy/simphy-x -XM compat -sb f:0.000001 -ld f:0 -lb f:0 -lt f:0 -rs 5 -rl f:300000 -rg 1 -o /workspace/phylogeny/data/simphy/data/t_1000_g_300000_sb_0.000001_spmin_100000_spmax_200000 -sp u:100000,200000 -su ln:-17.27461,0.6931472 -sg f:1 -sl f:1000 -st ln:16.2,1 -om 1 -v 2 -od 1 -op 1 -oc 1 -on 1 -cs 42
+t_400000_g_1000_sb_0.000001_spmin_100000_spmax_200000: /workspace/phylo-bench/simphy/simphy-x -XM compat -sb f:0.000001 -ld f:0 -lb f:0 -lt f:0 -rs 5 -rl f:1000 -rg 1 -o /workspace/phylogeny/data/simphy/data/t_400000_g_1000_sb_0.000001_spmin_100000_spmax_200000 -sp u:100000,200000 -su ln:-17.27461,0.6931472 -sg f:1 -sl f:400000 -st ln:16.2,1 -om 1 -v 2 -od 1 -op 1 -oc 1 -on 1 -cs 42
+t_1000_g_200000_sb_0.000001_spmin_100000_spmax_200000: /workspace/phylo-bench/simphy/simphy-x -XM compat -sb f:0.000001 -ld f:0 -lb f:0 -lt f:0 -rs 5 -rl f:200000 -rg 1 -o /workspace/phylogeny/data/simphy/data/t_1000_g_200000_sb_0.000001_spmin_100000_spmax_200000 -sp u:100000,200000 -su ln:-17.27461,0.6931472 -sg f:1 -sl f:1000 -st ln:16.2,1 -om 1 -v 2 -od 1 -op 1 -oc 1 -on 1 -cs 42
+t_1000_g_500000_sb_0.000001_spmin_100000_spmax_200000: /workspace/phylo-bench/simphy/simphy-x -XM compat -sb f:0.000001 -ld f:0 -lb f:0 -lt f:0 -rs 5 -rl f:500000 -rg 1 -o /workspace/phylogeny/data/simphy/data/t_1000_g_500000_sb_0.000001_spmin_100000_spmax_200000 -sp u:100000,200000 -su ln:-17.27461,0.6931472 -sg f:1 -sl f:1000 -st ln:16.2,1 -om 1 -v 2 -od 1 -op 1 -oc 1 -on 1 -cs 42
+t_1000_g_600000_sb_0.000001_spmin_100000_spmax_200000: /workspace/phylo-bench/simphy/simphy-x -XM compat -sb f:0.000001 -ld f:0 -lb f:0 -lt f:0 -rs 5 -rl f:600000 -rg 1 -o /workspace/phylogeny/data/simphy/data/t_1000_g_600000_sb_0.000001_spmin_100000_spmax_200000 -sp u:100000,200000 -su ln:-17.27461,0.6931472 -sg f:1 -sl f:1000 -st ln:16.2,1 -om 1 -v 2 -od 1 -op 1 -oc 1 -on 1 -cs 42
+t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000: /workspace/phylo-bench/simphy/simphy-x -XM compat -sb f:0.000001 -ld f:0 -lb f:0 -lt f:0 -rs 5 -rl f:700000 -rg 1 -o /workspace/phylogeny/data/simphy/data/t_1000_g_700000_sb_0.000001_spmin_100000_spmax_200000 -sp u:100000,200000 -su ln:-17.27461,0.6931472 -sg f:1 -sl f:1000 -st ln:16.2,1 -om 1 -v 2 -od 1 -op 1 -oc 1 -on 1 -cs 42
+t_1000_g_400000_sb_0.000001_spmin_100000_spmax_200000: /workspace/phylo-bench/simphy/simphy-x -XM compat -sb f:0.000001 -ld f:0 -lb f:0 -lt f:0 -rs 5 -rl f:400000 -rg 1 -o /workspace/phylogeny/data/simphy/data/t_1000_g_400000_sb_0.000001_spmin_100000_spmax_200000 -sp u:100000,200000 -su ln:-17.27461,0.6931472 -sg f:1 -sl f:1000 -st ln:16.2,1 -om 1 -v 2 -od 1 -op 1 -oc 1 -on 1 -cs 42