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Merged
bqminh merged 6 commits into from
Sep 8, 2026
Merged

Use different memory thresholds for different platforms in ci workflow #209

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17093d2
Clean up the incomplete message for ModelFinder
thomaskf Sep 8, 2026
6659a2d
Use different memory thresholds for different platforms in ci workflow
thomaskf Sep 8, 2026
022f73c
Merge branch 'master' into bugfix
thomaskf Sep 8, 2026
9cd237f
Fix the memory check format
thomaskf Sep 8, 2026
2d9665f
fixed the format for memory test in ci workflow
thomaskf Sep 8, 2026
d52aeab
finalize the thresholds for time and memory test for ic workflow
thomaskf Sep 8, 2026
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4 changes: 2 additions & 2 deletions .github/workflows/ci.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -94,12 +94,12 @@ jobs:
- name: Run verify_runtimes.sh
run: |
chmod +x test_scripts/verify_runtime.sh
./test_scripts/verify_runtime.sh time_log_iqtree2.tsv time_log_iqtree3.tsv Linux-clang-${{ matrix.clang-version }}
./test_scripts/verify_runtime.sh time_log_iqtree2.tsv time_log_iqtree3.tsv Linux-x86-64

- name: Run verify_memory.sh
run: |
chmod +x test_scripts/verify_memory.sh
./test_scripts/verify_memory.sh time_log_iqtree2.tsv time_log_iqtree3.tsv Linux-clang-${{ matrix.clang-version }}
./test_scripts/verify_memory.sh time_log_iqtree2.tsv time_log_iqtree3.tsv Linux-x86-64

build-linux-aarch64:
name: Linux aarch64
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2 changes: 1 addition & 1 deletion main/phylotesting.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -3192,7 +3192,7 @@ CandidateModel CandidateModelSet::test(Params &params, PhyloTree* in_tree, Model
else
cout << getSeqTypeName(in_tree->aln->seq_type);
cout << " models (sample size: " << ssize << " epsilon: " << params.modelfinder_eps << ") ..." << endl;
if (params.model_test_and_tree == 0)
if (params.model_test_and_tree == 0 && verbose_mode >= VB_MED)
cout << " No. Model -LnL df AIC AICc BIC" << endl;
}

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55 changes: 29 additions & 26 deletions test_scripts/test_data/expected_memory.tsv
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Original file line number Diff line number Diff line change
@@ -1,26 +1,29 @@
Command diff-threshold Linux-gcc-9 Linux-gcc-12 Linux-aarch64 mac-os-x86-64 mac-os-arm64 windows-x86
build/iqtree3 -s test_scripts/test_data/turtle.fa -B 1000 -T 1 -seed 73073 4 18.98 18.89 17.73 13.53 15.53 20.09
build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -B 1000 -T 1 -seed 73073 7 19.04 19.05 17.79 13.18 13.97 20.16
build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix test_scripts/test_data/turtle.merge -seed 73073 7 19.15 19.08 17.99 13.54 15.52 17.65
build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.merge.best_scheme.nex -z test_scripts/test_data/turtle.trees -zb 10000 -au -n 0 --prefix test_scripts/test_data/turtle.test -seed 73073 -T 1 3 27.80 27.77 26.76 22.50 23.45 28.15
build/iqtree3 -s test_scripts/test_data/turtle.fa -m GTR+F+I+R3+T -te test_scripts/test_data/turtle.trees -T 1 --prefix test_scripts/test_data/turtle.mix -seed 73073 3 9.79 10.05 8.92 4.39 5.44 9.45
build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex.best_scheme.nex -z test_scripts/test_data/turtle.trees -n 0 -wpl --prefix test_scripts/test_data/turtle.wpl -seed 73073 -T 1 3 9.27 9.30 8.18 3.61 4.75 9.43
build/iqtree3 -s test_scripts/test_data/turtle.fa -S test_scripts/test_data/turtle.nex --prefix test_scripts/test_data/turtle.loci -T 1 -seed 73073 7 10.43 10.55 8.79 5.66 6.59 10.3
build/iqtree3 -t test_scripts/test_data/turtle.nex.treefile --gcf test_scripts/test_data/turtle.loci.treefile -s test_scripts/test_data/turtle.fa --scf 100 -seed 73073 -T 1 3 6.30 6.55 5.92 2.29 2.75 6.57
build/iqtree3 -t test_scripts/test_data/turtle.fa.treefile --gcf test_scripts/test_data/turtle.loci.treefile -s test_scripts/test_data/turtle.fa --scf 100 -seed 73073 -T 1 3 6.30 6.55 5.92 2.27 3.00 6.59
build/iqtree3 -s test_scripts/test_data/turtle.fa -m MIX{GTR+FO,GTR+FO} --link-exchange-rates --prefix test_scripts/test_data/turtle.mix.link -seed 73073 -T 1 3 9.17 9.05 7.92 3.47 4.80 9.2
build/iqtree3 -s test_scripts/test_data/turtle.fa -m MIX{GTR{1,1,1,1,1,1}+FO,GTR{1,1,1,1,1,1}+FO} --link-exchange-rates --prefix test_scripts/test_data/turtle.mix.jc.link -seed 73073 -T 1 3 9.17 8.84 7.92 3.74 4.49 9.36
build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle.nex.constr -T 1 -seed 73073 7 10.57 10.45 8.80 5.86 6.78 10.43
build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle.nex.constr2 -T 1 -seed 73073 7 18.82 18.70 17.55 13.29 14.00 19.74
build/iqtree3 -s test_scripts/test_data/turtle.fa -m MIX+MF --prefix test_scripts/test_data/turtle.mixfinder -T 1 -seed 73073 7 14.55 15.50 11.68 9.21 9.28 20.19
build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -B 1000 -T 1 -seed 73073 5 25.57 25.66 24.47 21.26 15.77 26.65
build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -seed 73073 7 76.22 67.05 26.73 23.80 16.39 28.9
build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix test_scripts/test_data/turtle_aa.merge -seed 73073 12 41.34 31.46 26.11 22.30 16.56 28.35
build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.merge.best_scheme.nex -z test_scripts/test_data/turtle_aa.trees -zb 10000 -au -n 0 --prefix test_scripts/test_data/turtle_aa.test -seed 73073 -T 1 5 33.53 33.46 32.43 31.32 30.30 33.82
build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex.best_scheme.nex -z test_scripts/test_data/turtle_aa.trees -n 0 -wpl --prefix test_scripts/test_data/turtle_aa.wpl -seed 73073 -T 1 6 18.26 18.32 16.95 14.17 12.81 14.99
build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -S test_scripts/test_data/turtle_aa.nex --prefix test_scripts/test_data/turtle_aa.loci -T 1 -seed 73073 7 16.49 16.11 13.53 11.07 9.69 14.96
build/iqtree3 -t test_scripts/test_data/turtle_aa.nex.treefile --gcf test_scripts/test_data/turtle_aa.loci.treefile -s test_scripts/test_data/turtle_aa.fasta --scf 100 -seed 73073 -T 1 3 6.30 6.55 5.92 2.38 3.06 6.74
build/iqtree3 -t test_scripts/test_data/turtle_aa.fasta.treefile --gcf test_scripts/test_data/turtle_aa.loci.treefile -s test_scripts/test_data/turtle_aa.fasta --scf 100 -seed 73073 -T 1 3 6.29 6.55 5.93 2.29 3.09 6.64
build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -m MIX{LG+F,WAG+F} --prefix test_scripts/test_data/turtle_aa.mix -seed 73073 -T 1 3 11.79 11.80 10.67 6.39 6.78 11.94
build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle_aa.nex.constr -T 1 -seed 73073 20 59.79 60.66 18.28 18.67 10.61 16.95
build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle_aa.nex.constr2 -T 1 -seed 73073 7 63.79 70.88 26.53 23.55 16.72 26.39
Command diff-threshold Linux-x86-64 Linux-aarch64 mac-os-x86-64 mac-os-arm64 windows-x86 thr-Linux-x86-64 thr-Linux-aarch64 thr-mac-os-x86-64 thr-mac-os-arm64 thr-windows-x86
build/iqtree3 -s test_scripts/test_data/turtle.fa -B 1000 -T 1 -seed 73073 4 18.89 17.73 13.53 15.53 20.09 4 3 3 5 17
build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -B 1000 -T 1 -seed 73073 7 19.05 17.79 13.18 13.97 20.16 4 3 3 4 15
build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix test_scripts/test_data/turtle.merge -seed 73073 7 19.08 17.99 13.54 15.52 17.65 4 3 3 4 13
build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.merge.best_scheme.nex -z test_scripts/test_data/turtle.trees -zb 10000 -au -n 0 --prefix test_scripts/test_data/turtle.test -seed 73073 -T 1 3 27.77 26.76 22.50 23.45 28.15 5 3 3 4 3
build/iqtree3 -s test_scripts/test_data/turtle.fa -m GTR+F+I+R3+T -te test_scripts/test_data/turtle.trees -T 1 --prefix test_scripts/test_data/turtle.mix -seed 73073 3 10.05 8.92 4.39 5.44 9.45 4 3 3 4 3
build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex.best_scheme.nex -z test_scripts/test_data/turtle.trees -n 0 -wpl --prefix test_scripts/test_data/turtle.wpl -seed 73073 -T 1 3 9.30 8.18 3.61 4.75 9.43 5 3 3 4 4
build/iqtree3 -s test_scripts/test_data/turtle.fa -S test_scripts/test_data/turtle.nex --prefix test_scripts/test_data/turtle.loci -T 1 -seed 73073 7 10.55 8.79 5.66 6.59 10.3 5 3 3 4 3
build/iqtree3 -t test_scripts/test_data/turtle.nex.treefile --gcf test_scripts/test_data/turtle.loci.treefile -s test_scripts/test_data/turtle.fa --scf 100 -seed 73073 -T 1 3 6.55 5.92 2.29 2.75 6.57 4 3 3 3 8
build/iqtree3 -t test_scripts/test_data/turtle.fa.treefile --gcf test_scripts/test_data/turtle.loci.treefile -s test_scripts/test_data/turtle.fa --scf 100 -seed 73073 -T 1 3 6.55 5.92 2.27 3.00 6.59 4 3 3 3 9
build/iqtree3 -s test_scripts/test_data/turtle.fa -m MIX{GTR+FO,GTR+FO} --link-exchange-rates --prefix test_scripts/test_data/turtle.mix.link -seed 73073 -T 1 3 9.05 7.92 3.47 4.80 9.2 4 3 3 3 3
build/iqtree3 -s test_scripts/test_data/turtle.fa -m MIX{GTR{1,1,1,1,1,1}+FO,GTR{1,1,1,1,1,1}+FO} --link-exchange-rates --prefix test_scripts/test_data/turtle.mix.jc.link -seed 73073 -T 1 3 8.84 7.92 3.74 4.49 9.36 4 3 3 3 3
build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle.nex.constr -T 1 -seed 73073 7 10.45 8.80 5.86 6.78 10.43 5 3 3 4 3
build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle.nex.constr2 -T 1 -seed 73073 7 18.70 17.55 13.29 14.00 19.74 4 3 3 4 16
build/iqtree3 -s test_scripts/test_data/turtle.fa -m MIX+MF --prefix test_scripts/test_data/turtle.mixfinder -T 1 -seed 73073 7 15.50 11.68 9.21 9.28 20.19 9 3 3 5 3
build/iqtree3 -s test_scripts/test_data/turtle.fa -p test_scripts/test_data/turtle.nex -o phrynops -m GTR+G --prefix test_scripts/test_data/turtle.nex.outgroup -T 1 -seed 73073 5 12.38 10.25 4.89 5.85 12.87 5 4 3 3 3
build/iqtree3 -s test_scripts/test_data/turtle.fa -lmap 100 -o phrynops -m GTR+G --prefix test_scripts/test_data/turtle.lmap.outgroup -T 1 -seed 73073 5 12.12 9.75 4.75 5.60 12.50 5 3 3 3 3
build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -B 1000 -T 1 -seed 73073 5 25.66 24.47 21.26 15.77 26.65 4 3 3 6 21
build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -seed 73073 7 67.05 26.73 23.80 16.39 28.9 5 3 3 11 12
build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -m MFP+MERGE -rcluster 10 --prefix test_scripts/test_data/turtle_aa.merge -seed 73073 12 31.46 26.11 22.30 16.56 28.35 4 3 3 13 16
build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.merge.best_scheme.nex -z test_scripts/test_data/turtle_aa.trees -zb 10000 -au -n 0 --prefix test_scripts/test_data/turtle_aa.test -seed 73073 -T 1 5 33.46 32.43 31.32 30.30 33.82 5 3 6 4 3
build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex.best_scheme.nex -z test_scripts/test_data/turtle_aa.trees -n 0 -wpl --prefix test_scripts/test_data/turtle_aa.wpl -seed 73073 -T 1 6 18.32 16.95 14.17 12.81 14.99 8 7 8 8 4
build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -S test_scripts/test_data/turtle_aa.nex --prefix test_scripts/test_data/turtle_aa.loci -T 1 -seed 73073 7 16.11 13.53 11.07 9.69 14.96 7 3 3 4 4
build/iqtree3 -t test_scripts/test_data/turtle_aa.nex.treefile --gcf test_scripts/test_data/turtle_aa.loci.treefile -s test_scripts/test_data/turtle_aa.fasta --scf 100 -seed 73073 -T 1 3 6.55 5.92 2.38 3.06 6.74 4 3 3 3 9
build/iqtree3 -t test_scripts/test_data/turtle_aa.fasta.treefile --gcf test_scripts/test_data/turtle_aa.loci.treefile -s test_scripts/test_data/turtle_aa.fasta --scf 100 -seed 73073 -T 1 3 6.55 5.93 2.29 3.09 6.64 4 3 3 3 8
build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -m MIX{LG+F,WAG+F} --prefix test_scripts/test_data/turtle_aa.mix -seed 73073 -T 1 3 11.80 10.67 6.39 6.78 11.94 5 3 3 4 3
build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree --prefix test_scripts/test_data/turtle_aa.nex.constr -T 1 -seed 73073 20 60.66 18.28 18.67 10.61 16.95 35 7 8 4 4
build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -g test_scripts/test_data/turtle.constr.tree2 -B 1000 -alrt 1000 --prefix test_scripts/test_data/turtle_aa.nex.constr2 -T 1 -seed 73073 7 70.88 26.53 23.55 16.72 26.39 19 3 3 11 17
build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -m MUTSEL -ft AUTO --prefix test_scripts/test_data/turtle_aa.mutsel -T 1 -seed 73073 20 99.37 109.84 92.42 52.47 101.18 12 6 20 10 6
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