From a75ed433631980aedde053a58c673fae9b4f7664 Mon Sep 17 00:00:00 2001 From: Andrew Smith Date: Fri, 7 Jun 2024 17:33:39 -0700 Subject: [PATCH 01/14] Update abismal.cpp --- src/abismal.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/abismal.cpp b/src/abismal.cpp index 59e1479..5c9fef1 100644 --- a/src/abismal.cpp +++ b/src/abismal.cpp @@ -1002,8 +1002,10 @@ check_hits(const uint32_t offset, const PackedRead::const_iterator read_st, vector::const_iterator start_idx, result_type &res) { for (; start_idx != end_idx && !res.sure_ambig; ++start_idx) { // GS: adds the next candidate to L1d cache while current is compared +#ifdef __SSE__ _mm_prefetch(&(*(genome_st + ((*(start_idx + 10) - offset) >> 4))), _MM_HINT_T0); +#endif const uint32_t the_pos = *start_idx - offset; /* GS: the_pos & 15u tells if the position is a multiple of 16, in * which case it is aligned with the genome. Otherwise we need to From 56fb1034dbcd08162b1d445c64607a445703c3b7 Mon Sep 17 00:00:00 2001 From: Andrew Smith Date: Fri, 7 Jun 2024 17:36:36 -0700 Subject: [PATCH 02/14] Update macos-builds.yml --- .github/workflows/macos-builds.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/macos-builds.yml b/.github/workflows/macos-builds.yml index f45e6f3..9e3c0ba 100644 --- a/.github/workflows/macos-builds.yml +++ b/.github/workflows/macos-builds.yml @@ -11,13 +11,13 @@ jobs: build: runs-on: macos-12 steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: submodules: recursive - name: Update Homebrew run: brew update - name: Install autotools - run: brew install autoconf automake libtool + run: brew install automake - name: Install dependencies run: brew install htslib gsl - name: Generate configure script @@ -25,4 +25,4 @@ jobs: - name: configure with g++-13 run: ./configure CXX="g++-13" CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib" - name: make - run: make + run: make CXXFLAGS="-Wl,-ld_classic" From 7e8fb963e7c091d501002ede61fc4d3accb496f1 Mon Sep 17 00:00:00 2001 From: Andrew Smith Date: Fri, 7 Jun 2024 17:40:40 -0700 Subject: [PATCH 03/14] Update macos-builds.yml --- .github/workflows/macos-builds.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/macos-builds.yml b/.github/workflows/macos-builds.yml index 9e3c0ba..e37e1b1 100644 --- a/.github/workflows/macos-builds.yml +++ b/.github/workflows/macos-builds.yml @@ -17,7 +17,7 @@ jobs: - name: Update Homebrew run: brew update - name: Install autotools - run: brew install automake + run: brew install autoconf automake libtool - name: Install dependencies run: brew install htslib gsl - name: Generate configure script From 6c066478832f30603669273e462e23cca1563232 Mon Sep 17 00:00:00 2001 From: Andrew Smith Date: Fri, 7 Jun 2024 17:43:01 -0700 Subject: [PATCH 04/14] Update macos-builds.yml --- .github/workflows/macos-builds.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/macos-builds.yml b/.github/workflows/macos-builds.yml index e37e1b1..3bb4679 100644 --- a/.github/workflows/macos-builds.yml +++ b/.github/workflows/macos-builds.yml @@ -25,4 +25,4 @@ jobs: - name: configure with g++-13 run: ./configure CXX="g++-13" CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib" - name: make - run: make CXXFLAGS="-Wl,-ld_classic" + run: make From bf7e7b81c0a0c05ef479ef5567c15200a9c50828 Mon Sep 17 00:00:00 2001 From: Andrew Smith Date: Fri, 7 Jun 2024 17:46:41 -0700 Subject: [PATCH 05/14] Update macos-builds.yml --- .github/workflows/macos-builds.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/macos-builds.yml b/.github/workflows/macos-builds.yml index 3bb4679..b372225 100644 --- a/.github/workflows/macos-builds.yml +++ b/.github/workflows/macos-builds.yml @@ -9,15 +9,15 @@ on: jobs: build: - runs-on: macos-12 + runs-on: macos-13 steps: - uses: actions/checkout@v4 with: submodules: recursive - name: Update Homebrew run: brew update - - name: Install autotools - run: brew install autoconf automake libtool + - name: Install automake (autoconf and libtool assumed present) + run: brew install automake - name: Install dependencies run: brew install htslib gsl - name: Generate configure script From 08dbd31906e2bee2d2d50727a912812cca6d4fcd Mon Sep 17 00:00:00 2001 From: Andrew Smith Date: Fri, 7 Jun 2024 17:51:13 -0700 Subject: [PATCH 06/14] Update macos-builds.yml --- .github/workflows/macos-builds.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/macos-builds.yml b/.github/workflows/macos-builds.yml index b372225..4f483c6 100644 --- a/.github/workflows/macos-builds.yml +++ b/.github/workflows/macos-builds.yml @@ -25,4 +25,4 @@ jobs: - name: configure with g++-13 run: ./configure CXX="g++-13" CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib" - name: make - run: make + run: make CXXFLAGS="-O3 -DNDEBUG -Wl,-ld_classic" From 3c984ad466a914f3025cf0c78d88f1363730e420 Mon Sep 17 00:00:00 2001 From: Andrew Smith Date: Fri, 7 Jun 2024 17:58:44 -0700 Subject: [PATCH 07/14] Update macos-builds.yml --- .github/workflows/macos-builds.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/macos-builds.yml b/.github/workflows/macos-builds.yml index 4f483c6..76dccad 100644 --- a/.github/workflows/macos-builds.yml +++ b/.github/workflows/macos-builds.yml @@ -9,7 +9,7 @@ on: jobs: build: - runs-on: macos-13 + runs-on: macos-14 steps: - uses: actions/checkout@v4 with: From b984be879681c517ee6b483982d291f738854809 Mon Sep 17 00:00:00 2001 From: Andrew Smith Date: Fri, 7 Jun 2024 18:02:12 -0700 Subject: [PATCH 08/14] Update macos-builds.yml --- .github/workflows/macos-builds.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/macos-builds.yml b/.github/workflows/macos-builds.yml index 76dccad..8ab4037 100644 --- a/.github/workflows/macos-builds.yml +++ b/.github/workflows/macos-builds.yml @@ -26,3 +26,7 @@ jobs: run: ./configure CXX="g++-13" CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib" - name: make run: make CXXFLAGS="-O3 -DNDEBUG -Wl,-ld_classic" + - name: Run tests + run: make check + - name: Cleanup after build and test + run: make distclean From cfc00652c9349146868a9a0626c0425c06224bb7 Mon Sep 17 00:00:00 2001 From: Andrew Smith Date: Fri, 7 Jun 2024 18:10:22 -0700 Subject: [PATCH 09/14] Update ubuntu-builds.yml --- .github/workflows/ubuntu-builds.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/ubuntu-builds.yml b/.github/workflows/ubuntu-builds.yml index a993a91..b007120 100644 --- a/.github/workflows/ubuntu-builds.yml +++ b/.github/workflows/ubuntu-builds.yml @@ -26,6 +26,8 @@ jobs: run: ./configure CXX="g++" - name: make with g++ run: make + - name: test + run: make check - name: cleanup after GCC run: make distclean - name: install Clang dependencies From d2a587516d57cfd75f0b6610916fd64eddecf570 Mon Sep 17 00:00:00 2001 From: Andrew Smith Date: Fri, 7 Jun 2024 18:20:14 -0700 Subject: [PATCH 10/14] Update macos-builds.yml --- .github/workflows/macos-builds.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/macos-builds.yml b/.github/workflows/macos-builds.yml index 8ab4037..30bdf5f 100644 --- a/.github/workflows/macos-builds.yml +++ b/.github/workflows/macos-builds.yml @@ -25,7 +25,7 @@ jobs: - name: configure with g++-13 run: ./configure CXX="g++-13" CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib" - name: make - run: make CXXFLAGS="-O3 -DNDEBUG -Wl,-ld_classic" + run: make CXXFLAGS="-O2 -DNDEBUG -Wl,-ld_classic" - name: Run tests run: make check - name: Cleanup after build and test From 1ab55ae11c3cf48202814e08a9be95ef4f459c97 Mon Sep 17 00:00:00 2001 From: Andrew Smith Date: Fri, 7 Jun 2024 18:26:27 -0700 Subject: [PATCH 11/14] Update macos-builds.yml --- .github/workflows/macos-builds.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/macos-builds.yml b/.github/workflows/macos-builds.yml index 30bdf5f..67fb711 100644 --- a/.github/workflows/macos-builds.yml +++ b/.github/workflows/macos-builds.yml @@ -9,7 +9,7 @@ on: jobs: build: - runs-on: macos-14 + runs-on: macos-13 steps: - uses: actions/checkout@v4 with: From 3c03c77ba372904257b798161ab95c020b3e5bee Mon Sep 17 00:00:00 2001 From: Andrew Smith Date: Fri, 7 Jun 2024 18:40:49 -0700 Subject: [PATCH 12/14] Update macos-builds.yml --- .github/workflows/macos-builds.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/macos-builds.yml b/.github/workflows/macos-builds.yml index 67fb711..2f95b20 100644 --- a/.github/workflows/macos-builds.yml +++ b/.github/workflows/macos-builds.yml @@ -9,7 +9,7 @@ on: jobs: build: - runs-on: macos-13 + runs-on: macos-12 steps: - uses: actions/checkout@v4 with: @@ -19,13 +19,13 @@ jobs: - name: Install automake (autoconf and libtool assumed present) run: brew install automake - name: Install dependencies - run: brew install htslib gsl + run: brew install htslib - name: Generate configure script run: ./autogen.sh - - name: configure with g++-13 - run: ./configure CXX="g++-13" CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib" + - name: configure with g++-12 + run: ./configure CXX="g++-12" CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib" - name: make - run: make CXXFLAGS="-O2 -DNDEBUG -Wl,-ld_classic" + run: make CXXFLAGS="-O2 -DNDEBUG" - name: Run tests run: make check - name: Cleanup after build and test From 5de5e069a7b45ca9cf3a41361b6c7bba3c9853c6 Mon Sep 17 00:00:00 2001 From: Andrew Smith Date: Fri, 7 Jun 2024 18:52:05 -0700 Subject: [PATCH 13/14] Update macos-builds.yml --- .github/workflows/macos-builds.yml | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) diff --git a/.github/workflows/macos-builds.yml b/.github/workflows/macos-builds.yml index 2f95b20..eaac3e6 100644 --- a/.github/workflows/macos-builds.yml +++ b/.github/workflows/macos-builds.yml @@ -9,24 +9,20 @@ on: jobs: build: - runs-on: macos-12 + runs-on: macos-14 steps: - uses: actions/checkout@v4 with: submodules: recursive - name: Update Homebrew run: brew update - - name: Install automake (autoconf and libtool assumed present) + - name: Install automake run: brew install automake - name: Install dependencies run: brew install htslib - name: Generate configure script run: ./autogen.sh - - name: configure with g++-12 - run: ./configure CXX="g++-12" CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib" - - name: make - run: make CXXFLAGS="-O2 -DNDEBUG" - - name: Run tests - run: make check - - name: Cleanup after build and test - run: make distclean + - name: configure with g++-13 + run: ./configure CXX="g++-13" CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib" + - name: Build with g++ + run: make CXXFLAGS="-O3 -DNDEBUG -Wl,-ld_classic" From 9b33103c9d597ff43b4c3a06a8a1c392eec391e1 Mon Sep 17 00:00:00 2001 From: Andrew Smith Date: Fri, 7 Jun 2024 19:00:11 -0700 Subject: [PATCH 14/14] Update ubuntu-builds.yml --- .github/workflows/ubuntu-builds.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/ubuntu-builds.yml b/.github/workflows/ubuntu-builds.yml index b007120..a993a91 100644 --- a/.github/workflows/ubuntu-builds.yml +++ b/.github/workflows/ubuntu-builds.yml @@ -26,8 +26,6 @@ jobs: run: ./configure CXX="g++" - name: make with g++ run: make - - name: test - run: make check - name: cleanup after GCC run: make distclean - name: install Clang dependencies