From 958436d03f87710faf98ca1332457536978dd0bf Mon Sep 17 00:00:00 2001 From: thomaskf Date: Mon, 18 May 2026 14:39:13 +1000 Subject: [PATCH 1/4] Update CI to use clang22 --- .github/workflows/ci.yaml | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index e660c972..48ea6c52 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -22,10 +22,10 @@ jobs: include: - clang-version: 13 cmake-version: 3.14.7 - upload: true - - clang-version: 15 - cmake-version: latest upload: false + - clang-version: 22 + cmake-version: latest + upload: true steps: - name: Checkout @@ -33,6 +33,13 @@ jobs: with: submodules: "recursive" + - name: Add LLVM apt repository + if: matrix.clang-version >= 16 + run: | + wget -qO- https://apt.llvm.org/llvm-snapshot.gpg.key | sudo gpg --dearmor -o /usr/share/keyrings/llvm.gpg + echo "deb [signed-by=/usr/share/keyrings/llvm.gpg] http://apt.llvm.org/jammy/ llvm-toolchain-jammy-${{ matrix.clang-version }} main" | sudo tee /etc/apt/sources.list.d/llvm.list + sudo apt-get update -q -y + - name: Install dependencies run: | sudo apt-get update -q -y From a8c9135ca9efb2e1846d21bedf2d1d14c134b184 Mon Sep 17 00:00:00 2001 From: thomaskf Date: Mon, 18 May 2026 16:08:47 +1000 Subject: [PATCH 2/4] Addressed the fluctration on memory usage --- .github/workflows/ci.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 48ea6c52..e0ddf083 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -14,8 +14,11 @@ concurrency: jobs: build-linux-x86-64: - name: Linux x86-64 clang-${{ matrix.clang-version }} cmake-${{ matrix.cmake-version }} + name: Linux x86-64 clang cmake-${{ matrix.cmake-version }} runs-on: ubuntu-22.04 + env: + # Disable glibc tcache to make peak RSS deterministic across runs. + GLIBC_TUNABLES: glibc.malloc.tcache_count=0 strategy: fail-fast: false matrix: From a15d3252ec699c548a7401571e1ed3ba8b3d71af Mon Sep 17 00:00:00 2001 From: thomaskf Date: Mon, 18 May 2026 17:03:04 +1000 Subject: [PATCH 3/4] Update the memory threshold --- .github/workflows/ci.yaml | 2 +- test_scripts/test_data/expected_memory.tsv | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index e0ddf083..d692db68 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -14,7 +14,7 @@ concurrency: jobs: build-linux-x86-64: - name: Linux x86-64 clang cmake-${{ matrix.cmake-version }} + name: Linux x86-64 runs-on: ubuntu-22.04 env: # Disable glibc tcache to make peak RSS deterministic across runs. diff --git a/test_scripts/test_data/expected_memory.tsv b/test_scripts/test_data/expected_memory.tsv index 7cabd108..78fee825 100644 --- a/test_scripts/test_data/expected_memory.tsv +++ b/test_scripts/test_data/expected_memory.tsv @@ -22,5 +22,5 @@ build/iqtree3 -s test_scripts/test_data/turtle_aa.fasta -S test_scripts/test_dat 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 12 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.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 From 25866dd6c6cb0dce4ce7bff9cace8f1e03345c01 Mon Sep 17 00:00:00 2001 From: Thomas Wong Date: Tue, 19 May 2026 14:57:08 +1000 Subject: [PATCH 4/4] Remove clang 13 --- .github/workflows/ci.yaml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index d692db68..333ce393 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -23,9 +23,6 @@ jobs: fail-fast: false matrix: include: - - clang-version: 13 - cmake-version: 3.14.7 - upload: false - clang-version: 22 cmake-version: latest upload: true