From 01b4afc8279e181956be5b725a3144f6847bd50d Mon Sep 17 00:00:00 2001
From: Jordy Aaldering <33897257+JordyAaldering@users.noreply.github.com>
Date: Fri, 11 Sep 2026 15:16:48 +0200
Subject: [PATCH 01/13] build with cuda enabled on ubuntu runner

---
 .github/workflows/main.yml | 23 ++++++++++++++---------
 1 file changed, 14 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 7227a2f1..1941de4d 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -11,8 +11,8 @@ env:
   INTTEST_URL: https://github.com/SacBase/IntegrationTests.git
 
 jobs:
-  build-ubuntu24:
-    runs-on: ubuntu-24.04
+  build-ubuntu26:
+    runs-on: nvidia/cuda:13.3.1-devel-ubuntu26.04
     steps:
     - name: Get HEAD and submodules
       uses: actions/checkout@v6
@@ -27,17 +27,20 @@ jobs:
       run: |
         git clone --single-branch --recursive ${SAC2C_URL} sac2c
         cd sac2c
-        cmake -S . -B build -G Ninja -DCMAKE_BUILD_TYPE=RELEASE
-        cmake --build build -j4
+        cmake -S . -B build -G Ninja -DCMAKE_BUILD_TYPE=RELEASE -DCUDA=ON
+        cmake --build build --parallel
         ln -s $PWD/build/sac2c_p /usr/local/bin/sac2c
         sac2c -V
     - name: Configure build system
       run: |
-        cmake -S . -B build -G Ninja
+        cmake -S . -B build -G Ninja \
+          -DTARGETS="seq;seq_checks;mt_pth;cuda" \
+          -DBUILD_EXT=ON \
+          -DLINKSETSIZE=200
     - name: Build
       shell: bash
       run: |
-        cmake --build build -j4 2>&1 | tee build.log
+        cmake --build build --parallel 2>&1 | tee build.log
         if [ ${PIPESTATUS[0]} -ne 0 ]; then
           echo "!!! ERROR detected in build !!!";
           exit 1;
@@ -72,16 +75,18 @@ jobs:
         git clone --single-branch --recursive ${SAC2C_URL} sac2c
         cd sac2c
         cmake -S . -B build -G Ninja -DCMAKE_BUILD_TYPE=RELEASE
-        cmake --build build -j3
+        cmake --build build --parallel
         ln -s $PWD/build/sac2c_p /usr/local/bin/sac2c
         sac2c -V
     - name: Configure build system
       run: |
-        cmake -S . -B build -G Ninja
+        cmake -S . -B build -G Ninja \
+          -DTARGETS="seq;seq_checks;mt_pth" \
+          -DBUILD_EXT=ON
     - name: Build
       shell: bash
       run: |
-        cmake --build build -j3 2>&1 | tee build.log
+        cmake --build build --parallel 2>&1 | tee build.log
         if [ ${PIPESTATUS[0]} -ne 0 ]; then
           echo "!!! ERROR detected in build !!!";
           exit 1;

From d15d9559e92c33546801e0b5e6a54ac0437f19c4 Mon Sep 17 00:00:00 2001
From: Jordy Aaldering <33897257+JordyAaldering@users.noreply.github.com>
Date: Fri, 11 Sep 2026 15:55:12 +0200
Subject: [PATCH 02/13] see if this fixes the cuda error

---
 src/structures/src/String/Str.c | 4 ++++
 src/structures/src/String/Str.h | 8 ++++++++
 2 files changed, 12 insertions(+)

diff --git a/src/structures/src/String/Str.c b/src/structures/src/String/Str.c
index 9762b5d2..93f38376 100644
--- a/src/structures/src/String/Str.c
+++ b/src/structures/src/String/Str.c
@@ -14,7 +14,11 @@ string copy_string(string s)
     return s2;
 }
 
+#ifdef SAC_BACKEND_CUDA
+string free_string(void *s)
+#else
 string free_string(string s)
+#endif
 {
     free(s);
     return NULL;
diff --git a/src/structures/src/String/Str.h b/src/structures/src/String/Str.h
index 648a546a..2c718937 100644
--- a/src/structures/src/String/Str.h
+++ b/src/structures/src/String/Str.h
@@ -12,7 +12,15 @@
 typedef char *string;
 
 string copy_string(string s);
+
+#ifdef SAC_BACKEND_CUDA
+// CUDA compiles generated code as C++, where void* may not be implicitly
+// converted to char*, so we have to make the argument void* instead.
+string free_string(void *s);
+#else
 string free_string(string s);
+#endif
+
 
 string SACtostring(unsigned char *arr, sac_int length);
 string SACautotostring(SACarg *sarr);

From 73a12f909c25d27f04e89656908180a8760981cc Mon Sep 17 00:00:00 2001
From: Jordy Aaldering <33897257+JordyAaldering@users.noreply.github.com>
Date: Fri, 11 Sep 2026 16:02:20 +0200
Subject: [PATCH 03/13] fix github CICD

---
 .github/workflows/main.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 1941de4d..f039ed50 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -12,7 +12,9 @@ env:
 
 jobs:
   build-ubuntu26:
-    runs-on: nvidia/cuda:13.3.1-devel-ubuntu26.04
+    runs-on: ubuntu26.04
+    container:
+      image: nvidia/cuda:13.3.1-devel-ubuntu26.04
     steps:
     - name: Get HEAD and submodules
       uses: actions/checkout@v6

From 68dff81fb43292b03a0088cba2f02c4370689e6a Mon Sep 17 00:00:00 2001
From: Jordy Aaldering <33897257+JordyAaldering@users.noreply.github.com>
Date: Fri, 11 Sep 2026 16:03:35 +0200
Subject: [PATCH 04/13] fix github CICD

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index f039ed50..acd4f822 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -12,7 +12,7 @@ env:
 
 jobs:
   build-ubuntu26:
-    runs-on: ubuntu26.04
+    runs-on: ubuntu-26.04
     container:
       image: nvidia/cuda:13.3.1-devel-ubuntu26.04
     steps:

From ad89e5ed5f384e9fac5a9b784a52d49025b0adfc Mon Sep 17 00:00:00 2001
From: Jordy Aaldering <33897257+JordyAaldering@users.noreply.github.com>
Date: Fri, 11 Sep 2026 16:11:55 +0200
Subject: [PATCH 05/13] fix github CICD

---
 .github/workflows/main.yml | 27 ++++++++++++++++-----------
 1 file changed, 16 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index acd4f822..66408239 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -16,15 +16,20 @@ jobs:
     container:
       image: nvidia/cuda:13.3.1-devel-ubuntu26.04
     steps:
-    - name: Get HEAD and submodules
-      uses: actions/checkout@v6
-      with:
-        fetch-depth: 0
-        submodules: 'recursive'
     - name: Install dependencies
       run: |
-        sudo apt update
-        sudo apt install xsltproc -y
+        sudo apt-get update
+        sudo apt-get install -y \
+          ca-certificates cmake git ninja-build xsltproc
+    - name: Get HEAD and submodules
+      env:
+        GH_TOKEN: ${{ github.token }}
+      run: |
+        git clone --recursive \
+          "https://x-access-token:${GH_TOKEN}@github.com/${GITHUB_REPOSITORY}.git" \
+          "${GITHUB_WORKSPACE}"
+        cd "${GITHUB_WORKSPACE}"
+        git checkout "${GITHUB_SHA}"
     - name: Install sac2c
       run: |
         git clone --single-branch --recursive ${SAC2C_URL} sac2c
@@ -59,15 +64,15 @@ jobs:
   build-macos-arm:
     runs-on: macos-latest
     steps:
+    - name: Install dependencies
+      run: |
+        brew update
+        brew install libxslt
     - name: Get HEAD and submodules
       uses: actions/checkout@v6
       with:
         fetch-depth: 0
         submodules: 'recursive'
-    - name: Install dependencies
-      run: |
-        brew update
-        brew install libxslt
     - name: Set XCode version
       uses: maxim-lobanov/setup-xcode@v1
       with:

From b3921386c494691a809895e69e2091393edee77b Mon Sep 17 00:00:00 2001
From: Jordy Aaldering <33897257+JordyAaldering@users.noreply.github.com>
Date: Fri, 11 Sep 2026 16:15:21 +0200
Subject: [PATCH 06/13] fix github CICD

---
 .github/workflows/main.yml | 16 ++++++----------
 1 file changed, 6 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 66408239..7fa8c0d7 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -18,18 +18,14 @@ jobs:
     steps:
     - name: Install dependencies
       run: |
-        sudo apt-get update
-        sudo apt-get install -y \
+        apt-get update
+        apt-get install -y \
           ca-certificates cmake git ninja-build xsltproc
     - name: Get HEAD and submodules
-      env:
-        GH_TOKEN: ${{ github.token }}
-      run: |
-        git clone --recursive \
-          "https://x-access-token:${GH_TOKEN}@github.com/${GITHUB_REPOSITORY}.git" \
-          "${GITHUB_WORKSPACE}"
-        cd "${GITHUB_WORKSPACE}"
-        git checkout "${GITHUB_SHA}"
+      uses: actions/checkout@v6
+      with:
+        fetch-depth: 0
+        submodules: 'recursive'
     - name: Install sac2c
       run: |
         git clone --single-branch --recursive ${SAC2C_URL} sac2c

From 9d49cda9f5093e37cd8210dc69d1052d27cb6629 Mon Sep 17 00:00:00 2001
From: Jordy Aaldering <33897257+JordyAaldering@users.noreply.github.com>
Date: Fri, 11 Sep 2026 16:19:37 +0200
Subject: [PATCH 07/13] fix github CICD

---
 .github/workflows/main.yml | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 7fa8c0d7..9f952b75 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -20,7 +20,17 @@ jobs:
       run: |
         apt-get update
         apt-get install -y \
-          ca-certificates cmake git ninja-build xsltproc
+          git \
+          cmake \
+          ninja-build \
+          ca-certificates \
+          libhwloc-dev \
+          uuid-runtime \
+          uuid-dev \
+          xsltproc \
+          bison \
+          flex \
+          m4
     - name: Get HEAD and submodules
       uses: actions/checkout@v6
       with:

From 6825959e6211a45516778602e2c2aa4382a2ba95 Mon Sep 17 00:00:00 2001
From: Jordy Aaldering <33897257+JordyAaldering@users.noreply.github.com>
Date: Fri, 11 Sep 2026 16:33:09 +0200
Subject: [PATCH 08/13] fix github CICD

---
 .github/workflows/main.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 9f952b75..28fa8a11 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -22,6 +22,7 @@ jobs:
         apt-get install -y \
           git \
           cmake \
+          python3 \
           ninja-build \
           ca-certificates \
           libhwloc-dev \

From 8023fe41a0d834e7af2729f5509e796fdc39c991 Mon Sep 17 00:00:00 2001
From: Jordy Aaldering <33897257+JordyAaldering@users.noreply.github.com>
Date: Fri, 11 Sep 2026 16:44:51 +0200
Subject: [PATCH 09/13] fix github CICD

---
 .github/workflows/main.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 28fa8a11..3006cf44 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -19,7 +19,7 @@ jobs:
     - name: Install dependencies
       run: |
         apt-get update
-        apt-get install -y \
+        apt-get install --no-install-recommends -y \
           git \
           cmake \
           python3 \
@@ -45,6 +45,8 @@ jobs:
         cmake --build build --parallel
         ln -s $PWD/build/sac2c_p /usr/local/bin/sac2c
         sac2c -V
+    - name: Configure Git
+      run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
     - name: Configure build system
       run: |
         cmake -S . -B build -G Ninja \

From 03dd6a4b4f1263b194add4abfdf30fe44067cd04 Mon Sep 17 00:00:00 2001
From: Jordy Aaldering <33897257+JordyAaldering@users.noreply.github.com>
Date: Fri, 11 Sep 2026 16:55:06 +0200
Subject: [PATCH 10/13] that macro for the ifdef might not be passed into C

---
 src/structures/src/String/Str.c | 4 ----
 src/structures/src/String/Str.h | 5 -----
 2 files changed, 9 deletions(-)

diff --git a/src/structures/src/String/Str.c b/src/structures/src/String/Str.c
index 93f38376..125e6e9f 100644
--- a/src/structures/src/String/Str.c
+++ b/src/structures/src/String/Str.c
@@ -14,11 +14,7 @@ string copy_string(string s)
     return s2;
 }
 
-#ifdef SAC_BACKEND_CUDA
 string free_string(void *s)
-#else
-string free_string(string s)
-#endif
 {
     free(s);
     return NULL;
diff --git a/src/structures/src/String/Str.h b/src/structures/src/String/Str.h
index 2c718937..30e1c4e8 100644
--- a/src/structures/src/String/Str.h
+++ b/src/structures/src/String/Str.h
@@ -13,14 +13,9 @@ typedef char *string;
 
 string copy_string(string s);
 
-#ifdef SAC_BACKEND_CUDA
 // CUDA compiles generated code as C++, where void* may not be implicitly
 // converted to char*, so we have to make the argument void* instead.
 string free_string(void *s);
-#else
-string free_string(string s);
-#endif
-
 
 string SACtostring(unsigned char *arr, sac_int length);
 string SACautotostring(SACarg *sarr);

From 3f5b5a9dd6ffdeec4e065dbf151abd44e849f29b Mon Sep 17 00:00:00 2001
From: Jordy Aaldering <33897257+JordyAaldering@users.noreply.github.com>
Date: Fri, 11 Sep 2026 17:25:26 +0200
Subject: [PATCH 11/13] does disabling ctype pragma fix it?

---
 src/structures/String.sac       | 2 +-
 src/structures/src/String/Str.c | 2 +-
 src/structures/src/String/Str.h | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/structures/String.sac b/src/structures/String.sac
index 1f84cf4c..1a8f73f3 100644
--- a/src/structures/String.sac
+++ b/src/structures/String.sac
@@ -11,7 +11,7 @@ module String;
 export all except { indent };
 
 external typedef string;
-    #pragma ctype "char*"
+    // #pragma ctype "char*"
     #pragma copyfun "copy_string"
     #pragma freefun "free_string"
     #pragma linkobj "src/String/Str.o"
diff --git a/src/structures/src/String/Str.c b/src/structures/src/String/Str.c
index 125e6e9f..9762b5d2 100644
--- a/src/structures/src/String/Str.c
+++ b/src/structures/src/String/Str.c
@@ -14,7 +14,7 @@ string copy_string(string s)
     return s2;
 }
 
-string free_string(void *s)
+string free_string(string s)
 {
     free(s);
     return NULL;
diff --git a/src/structures/src/String/Str.h b/src/structures/src/String/Str.h
index 30e1c4e8..0e006343 100644
--- a/src/structures/src/String/Str.h
+++ b/src/structures/src/String/Str.h
@@ -15,7 +15,7 @@ string copy_string(string s);
 
 // CUDA compiles generated code as C++, where void* may not be implicitly
 // converted to char*, so we have to make the argument void* instead.
-string free_string(void *s);
+string free_string(string s);
 
 string SACtostring(unsigned char *arr, sac_int length);
 string SACautotostring(SACarg *sarr);

From b75b6526e83cf88bcb3740f52c7de74dafdaafd2 Mon Sep 17 00:00:00 2001
From: Jordy Aaldering <33897257+JordyAaldering@users.noreply.github.com>
Date: Fri, 11 Sep 2026 17:42:36 +0200
Subject: [PATCH 12/13] move cuda comment to right place

---
 src/structures/String.sac       | 3 +++
 src/structures/src/String/Str.h | 3 ---
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/structures/String.sac b/src/structures/String.sac
index 1a8f73f3..0e22d6ad 100644
--- a/src/structures/String.sac
+++ b/src/structures/String.sac
@@ -10,6 +10,9 @@ module String;
 
 export all except { indent };
 
+// Using `pragma ctype` leads to issues when compiling for CUDA. CUDA compiles
+// generated code as C++, where using `ctype` introduces an implicit cast from
+// void* to char*, which is not allowed in C++.
 external typedef string;
     // #pragma ctype "char*"
     #pragma copyfun "copy_string"
diff --git a/src/structures/src/String/Str.h b/src/structures/src/String/Str.h
index 0e006343..648a546a 100644
--- a/src/structures/src/String/Str.h
+++ b/src/structures/src/String/Str.h
@@ -12,9 +12,6 @@
 typedef char *string;
 
 string copy_string(string s);
-
-// CUDA compiles generated code as C++, where void* may not be implicitly
-// converted to char*, so we have to make the argument void* instead.
 string free_string(string s);
 
 string SACtostring(unsigned char *arr, sac_int length);

From efbe45d39059611baa65f3552f942fb2ce196884 Mon Sep 17 00:00:00 2001
From: Jordy Aaldering <33897257+JordyAaldering@users.noreply.github.com>
Date: Fri, 11 Sep 2026 18:47:39 +0200
Subject: [PATCH 13/13] --parallel causes OOM

---
 .github/workflows/main.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 3006cf44..eae05af6 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -42,7 +42,7 @@ jobs:
         git clone --single-branch --recursive ${SAC2C_URL} sac2c
         cd sac2c
         cmake -S . -B build -G Ninja -DCMAKE_BUILD_TYPE=RELEASE -DCUDA=ON
-        cmake --build build --parallel
+        cmake --build build -j4
         ln -s $PWD/build/sac2c_p /usr/local/bin/sac2c
         sac2c -V
     - name: Configure Git
@@ -56,7 +56,7 @@ jobs:
     - name: Build
       shell: bash
       run: |
-        cmake --build build --parallel 2>&1 | tee build.log
+        cmake --build build -j4 2>&1 | tee build.log
         if [ ${PIPESTATUS[0]} -ne 0 ]; then
           echo "!!! ERROR detected in build !!!";
           exit 1;
@@ -91,7 +91,7 @@ jobs:
         git clone --single-branch --recursive ${SAC2C_URL} sac2c
         cd sac2c
         cmake -S . -B build -G Ninja -DCMAKE_BUILD_TYPE=RELEASE
-        cmake --build build --parallel
+        cmake --build build -j3
         ln -s $PWD/build/sac2c_p /usr/local/bin/sac2c
         sac2c -V
     - name: Configure build system
@@ -102,7 +102,7 @@ jobs:
     - name: Build
       shell: bash
       run: |
-        cmake --build build --parallel 2>&1 | tee build.log
+        cmake --build build -j3 2>&1 | tee build.log
         if [ ${PIPESTATUS[0]} -ne 0 ]; then
           echo "!!! ERROR detected in build !!!";
           exit 1;