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Add memory usage check to GitHub Actions workflow #75

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Merged
bqminh merged 16 commits into from
Sep 30, 2025
Merged

Add memory usage check to GitHub Actions workflow #75

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578eb82
add memory extract to the linux and mac
Hashara Jul 2, 2025
53473be
bug fix; modify ps1 for measure memory
Hashara Jul 2, 2025
7b5dc30
add memory checking for linux
Hashara Jul 2, 2025
ced2534
bug fix: memory checking for linux
Hashara Jul 2, 2025
8a2ac58
memory checking for linux and mac
Hashara Jul 3, 2025
c1c7f00
memory checking for windows
Hashara Jul 3, 2025
fd310c8
fix index in memory checking
Hashara Jul 3, 2025
5c1c5b8
fix index in memory checking, update values for failing checks
Hashara Jul 3, 2025
c9c09f4
update values for failing checks
Hashara Jul 3, 2025
e7115b8
resolve copilot suggestions
Hashara Jul 7, 2025
fea468f
replace column index to column name for verify memory
Hashara Jul 7, 2025
ee115db
add ps1 file to process with the column name
Hashara Jul 7, 2025
4ff421c
add verify_runtime.ps1 file to process with the column name
Hashara Jul 7, 2025
57e62c9
update values of failing checks
Hashara Jul 7, 2025
230ea88
add comment to clarify what are the expected inputs
Hashara Jul 7, 2025
5dcdf01
Update test_scripts/verify_memory.sh
Hashara Jul 7, 2025
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26 changes: 26 additions & 0 deletions .github/workflows/ci.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -25,11 +25,13 @@ jobs:
cmake-version: 3.14.7
upload: true
runtime-arg: 4
memory-arg: 3
# Latest supported gcc and cmake versions
- gcc-version: 12
cmake-version: latest
upload: false
runtime-arg: 5
memory-arg: 4

steps:
- name: Checkout
Expand Down Expand Up @@ -81,6 +83,11 @@ jobs:
chmod +x test_scripts/verify_runtime.sh
./test_scripts/verify_runtime.sh "${{ matrix.runtime-arg }}"

- name: Run verify_memory.sh
run: |
chmod +x test_scripts/verify_memory.sh
./test_scripts/verify_memory.sh "${{ matrix.memory-arg }}"

build-linux-aarch64:
name: Linux aarch64
runs-on: ubuntu-22.04-arm
Expand Down Expand Up @@ -127,6 +134,11 @@ jobs:
chmod +x test_scripts/verify_runtime.sh
./test_scripts/verify_runtime.sh 6

- name: Run verify_memory.sh
run: |
chmod +x test_scripts/verify_memory.sh
./test_scripts/verify_memory.sh 5

compile-linux-universal:
name: Linux Universal
runs-on: ubuntu-latest
Expand Down Expand Up @@ -212,6 +224,11 @@ jobs:
chmod +x test_scripts/verify_runtime.sh
./test_scripts/verify_runtime.sh 7

- name: Run verify_memory.sh
run: |
chmod +x test_scripts/verify_memory.sh
./test_scripts/verify_memory.sh 6

build-macos-arm:
name: Mac OS ARM64
runs-on: macos-14
Expand Down Expand Up @@ -260,6 +277,11 @@ jobs:
chmod +x test_scripts/verify_runtime.sh
./test_scripts/verify_runtime.sh 8

- name: Run verify_memory.sh
run: |
chmod +x test_scripts/verify_memory.sh
./test_scripts/verify_memory.sh 7

compile-mac-universal:
name: Mac OS Universal
runs-on: macos-14
Expand Down Expand Up @@ -371,3 +393,7 @@ jobs:
shell: pwsh
run: |
./test_scripts/verify_runtime.ps1

- name: Run verify_memory.sh
run: |
./test_scripts/verify_memory.ps1
26 changes: 26 additions & 0 deletions test_scripts/test_data/expected_memory.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,26 @@
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 3 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 3 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 3 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 3 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 3 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 3 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 3 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 3 25.57 25.66 24.47 21.26 15.77 22.72
build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -p test_scripts/test_data/turtle_aa.nex -B 1000 -T 1 -seed 73073 3 76.22 67.05 26.73 23.80 16.39 24.45
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 3 41.34 31.46 26.11 22.30 16.56 25.05
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 3 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 3 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 3 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 3 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 3 50.73 70.88 26.53 23.55 16.72 26.39
24 changes: 12 additions & 12 deletions test_scripts/test_data/expected_runtimes.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -2,21 +2,21 @@
turtle.fa.iqtree Total CPU time used 2 3.128169 3.299343 4.909145 4.93771 3.595236 3.21875
turtle.loci.iqtree Total CPU time used 2 3.376 3.6 4.561 5.737 2.786 3.359
turtle.merge.iqtree Total CPU time used 2 3.22134 3.336272 4.881305 4.074864 3.063053 3.34375
turtle.mix.iqtree Total CPU time used 1 2.288 2.437 3.653 2.043 2.607 2.391
turtle.mix.jc.link.iqtree Total CPU time used 1 0.678048 0.716485 1.05925 0.79052 0.798578 0.8125
turtle.mix.link.iqtree Total CPU time used 1 0.765474 0.829717 1.19517 0.856055 0.868658 0.90625
turtle.mixfinder.iqtree Total CPU time used 3 9.34105 9.95267 14.5544 9.57637 8.78048 8.40625
turtle.mix.iqtree Total CPU time used 1 2.288 2.437 3.653 4.416 2.607 2.391
turtle.mix.jc.link.iqtree Total CPU time used 1 0.678048 0.716485 1.05925 1.97384 0.798578 0.8125
turtle.mix.link.iqtree Total CPU time used 1 0.765474 0.829717 1.19517 2.31644 0.868658 0.90625
turtle.mixfinder.iqtree Total CPU time used 3 9.34105 9.95267 14.5544 13.1422 8.78048 8.40625
turtle.nex.constr.iqtree Total CPU time used 3 2.74033 2.88714 3.45122 4.30755 2.83421 2.85938
turtle.nex.constr2.iqtree Total CPU time used 3 3.172122 3.296328 3.914713 4.247386 3.261848 3.484375
turtle.nex.iqtree Total CPU time used 3 3.139167 3.257494 4.000374 4.824423 3.217744 3.578125
turtle.test.iqtree Total CPU time used 1 0.235 0.242 0.349 0.192 0.225 0.234
turtle.wpl.iqtree Total CPU time used 1 0.037859 0.036415 0.043837 0.041274 0.030318 0.015625
turtle_aa.fasta.iqtree Total CPU time used 12 61.60878 61.761949 100.241028 44.144877 44.523198 34.46875
turtle_aa.loci.iqtree Total CPU time used 12 55.21 56.31 89.16 32.3 45.828247 31.66
turtle_aa.merge.iqtree Total CPU time used 12 65.057715 65.34153 106.422985 48.539932 47.526024 36.890625
turtle_aa.nex.constr.iqtree Total CPU time used 12 60.3527 60.7689 98.7859 47.122 38.9924 34.4219
turtle_aa.nex.constr2.iqtree Total CPU time used 12 82.473306 82.646098 135.013106 54.514873 58.861398 47.40625
turtle_aa.nex.iqtree Total CPU time used 12 70.691887 71.079425 115.466386 54.95159 52.16108 40.890625
turtle_aa.test.iqtree Total CPU time used 1 1.69 1.81 2.72 0.862 0.979 0.922
turtle_aa.fasta.iqtree Total CPU time used 12 61.60878 61.761949 100.241028 56.571182 44.523198 34.46875
turtle_aa.loci.iqtree Total CPU time used 12 55.21 56.31 89.16 54.17 45.828247 31.66
turtle_aa.merge.iqtree Total CPU time used 12 65.057715 65.34153 106.422985 76.722846 47.526024 36.890625
turtle_aa.nex.constr.iqtree Total CPU time used 12 60.3527 60.7689 98.7859 59.6715 38.9924 34.4219
turtle_aa.nex.constr2.iqtree Total CPU time used 12 82.473306 82.646098 135.013106 85.280632 58.861398 47.40625
turtle_aa.nex.iqtree Total CPU time used 12 70.691887 71.079425 115.466386 71.812495 52.16108 40.890625
turtle_aa.test.iqtree Total CPU time used 1 1.69 1.81 2.72 2.24 0.979 0.922
turtle_aa.wpl.iqtree Total CPU time used 3 1.6987 1.701 2.7838 0.89948 1.0239 0.96875
turtle_aa.mix.iqtree Total CPU time used 3 12.8918 13.1371 21.3145 6.91331 9.35718 7.09375
turtle_aa.mix.iqtree Total CPU time used 3 12.8918 13.1371 21.3145 10.1353 9.35718 7.09375
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