From 5a00e430e4754f0f70715b8986f409d1235db2ac Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Wed, 30 Jul 2025 11:07:23 -0400
Subject: [PATCH 01/27] Add aux_loc to q grid output

---
 src/2d/valout.f90 | 57 +++++++++++++++++++++++------------------------
 src/3d/valout.f90 |  1 +
 2 files changed, 29 insertions(+), 29 deletions(-)

diff --git a/src/2d/valout.f90 b/src/2d/valout.f90
index 4dc98215..0182e6a6 100644
--- a/src/2d/valout.f90
+++ b/src/2d/valout.f90
@@ -67,7 +67,7 @@ subroutine valout(level_begin, level_end, time, num_eqn, num_aux)
                                            "i6,'                 ndim'/,"   // &
                                            "i6,'                 nghost'/," // &
                                            "a10,'             format'/,/)"
-                                           
+
     character(len=*), parameter :: console_format = &
              "('AMRCLAW: Frame ',i4,' output files done at time t = ', d13.6,/)"
 
@@ -84,7 +84,7 @@ subroutine valout(level_begin, level_end, time, num_eqn, num_aux)
     ! Note:  Currently outputs all aux components if any are requested
     out_aux = ((output_aux_num > 0) .and.               &
               ((.not. output_aux_onlyonce) .or. (abs(time - t0) < 1d-90)))
-                
+
     ! Construct file names
     file_name(1) = 'fort.qxxxx'
     file_name(2) = 'fort.txxxx'
@@ -137,10 +137,11 @@ subroutine valout(level_begin, level_end, time, num_eqn, num_aux)
             num_cells(1) = node(ndihi, grid_ptr) - node(ndilo, grid_ptr) + 1
             num_cells(2) = node(ndjhi, grid_ptr) - node(ndjlo, grid_ptr) + 1
             q_loc = node(store1, grid_ptr)
+            aux_loc = node(storeaux, grid_ptr)
             lower_corner = [rnode(cornxlo, grid_ptr), rnode(cornylo, grid_ptr)]
 
-            ! Write out header data                 
-            
+            ! Write out header data
+
             write(out_unit, header_format_2d) grid_ptr, level,             &
                                               num_cells(1),                &
                                               num_cells(2),                &
@@ -149,8 +150,8 @@ subroutine valout(level_begin, level_end, time, num_eqn, num_aux)
                                               delta(1), delta(2)
 
             ! Output grids
-            
-            ! Round off if nearly zero 
+
+            ! Round off if nearly zero
             ! (Do this for all output_format's)
             forall (m = 1:num_eqn,                              &
                     i=num_ghost + 1:num_cells(1) + num_ghost,   &
@@ -162,7 +163,7 @@ subroutine valout(level_begin, level_end, time, num_eqn, num_aux)
 
             if (output_format == 1) then
                     ! ascii output
-                    
+
                     do j = num_ghost + 1, num_cells(2) + num_ghost
                         do i = num_ghost + 1, num_cells(1) + num_ghost
                             write(out_unit, "(50e26.16)")                      &
@@ -173,7 +174,7 @@ subroutine valout(level_begin, level_end, time, num_eqn, num_aux)
 
             else if (output_format==2 .or. output_format==3) then
                 ! binary32 or binary64
-                                
+
                 ! Note: We are writing out ghost cell data also,
                 ! so need to update this
                 call bound(time,num_eqn,num_ghost,alloc(q_loc),     &
@@ -183,7 +184,7 @@ subroutine valout(level_begin, level_end, time, num_eqn, num_aux)
 
                 i = (iadd(num_eqn, num_cells(1) + 2 * num_ghost, &
                                    num_cells(2) + 2 * num_ghost))
-                                   
+
                 if (output_format == 2) then
                     ! binary32 (shorten to 4-byte)
                     allocate(q4(num_eqn * (num_cells(1) + 2 * num_ghost)   &
@@ -196,11 +197,11 @@ subroutine valout(level_begin, level_end, time, num_eqn, num_aux)
                     ! binary64 (full 8-byte)
                     write(out_unit + 1) alloc(iadd(1, 1, 1):i)
                 endif
-                
-                
+
+
             else if (output_format == 4) then
 #ifdef HDF5
-                ! Create data space - handles dimensions of the corresponding 
+                ! Create data space - handles dimensions of the corresponding
                 ! data set - annoyingling need to stick grid size into other
                 ! data type
                 dims = (/ num_eqn, num_cells(1) + 2 * num_ghost,               &
@@ -221,7 +222,7 @@ subroutine valout(level_begin, level_end, time, num_eqn, num_aux)
 #endif
             else
                 print *, "Unsupported output format", output_format,"."
-                stop 
+                stop
             endif
 
             grid_ptr = node(levelptr, grid_ptr)
@@ -229,7 +230,7 @@ subroutine valout(level_begin, level_end, time, num_eqn, num_aux)
     end do
 
     close(out_unit)
-    
+
     if (output_format==2 .or. output_format==3) then
         close(unit=out_unit + 1)
     end if
@@ -253,7 +254,7 @@ subroutine valout(level_begin, level_end, time, num_eqn, num_aux)
 #ifdef HDF5
         ! Create group for aux
         call h5gcreate_f(hdf_file, "/aux", aux_group, hdf_error)
-#endif            
+#endif
         end if
 
         do level = level_begin, level_end
@@ -274,7 +275,7 @@ subroutine valout(level_begin, level_end, time, num_eqn, num_aux)
                     ! ASCII output
                     case(1)
 
-                        ! We only output header info for aux data if writing 
+                        ! We only output header info for aux data if writing
                         ! ASCII data
                         write(out_unit, header_format_2d) grid_ptr, level,    &
                                                           num_cells(1),       &
@@ -299,7 +300,7 @@ subroutine valout(level_begin, level_end, time, num_eqn, num_aux)
                             end do
                             write(out_unit, *) ' '
                         end do
-                        
+
                     case(2)
                         ! binary32
                         ! Note: We are writing out ghost cell data also
@@ -310,19 +311,19 @@ subroutine valout(level_begin, level_end, time, num_eqn, num_aux)
                         aux4 = real(alloc(iaddaux(1, 1, 1):i), kind=4)
                         write(out_unit) aux4
                         deallocate(aux4)
-                        
+
                     case(3)
                         ! binary64
                         ! Note: We are writing out ghost cell data also
                         i = (iaddaux(num_aux, num_cells(1) + 2 * num_ghost, &
                                               num_cells(2) + 2 * num_ghost))
                         write(out_unit) alloc(iaddaux(1, 1, 1):i)
-                        
+
 
                     ! HDF5 output
                     case(4)
 #ifdef HDF5
-                ! Create data space - handles dimensions of the corresponding 
+                ! Create data space - handles dimensions of the corresponding
                 ! data set - annoyingling need to stick grid size into other
                 ! data type
                 dims = (/ num_aux, num_cells(1) + 2 * num_ghost,               &
@@ -346,18 +347,18 @@ subroutine valout(level_begin, level_end, time, num_eqn, num_aux)
 #endif
                     case default
                         print *, "Unsupported output format", output_format,"."
-                        stop 
+                        stop
 
                 end select
                 grid_ptr = node(levelptr, grid_ptr)
             end do
         end do
-        
+
         if ((output_format == 1) .or. (output_format == 2) .or. &
             (output_format == 3)) then
             close(out_unit)
         end if
-        
+
     end if
 
 #ifdef HDF5
@@ -375,7 +376,7 @@ subroutine valout(level_begin, level_end, time, num_eqn, num_aux)
     ! Note:  We need to print out num_ghost too in order to strip ghost cells
     !        from q array when reading in pyclaw.io.binary
 
-    
+
     if (output_format == 1) then
         file_format = 'ascii'
     else if (output_format == 2) then
@@ -385,7 +386,7 @@ subroutine valout(level_begin, level_end, time, num_eqn, num_aux)
     else if (output_format == 4) then
         file_format = 'hdf'
     endif
-    
+
     write(out_unit, t_file_format) time, num_eqn, num_grids, num_aux, 2, &
                                    num_ghost, file_format
     close(out_unit)
@@ -395,7 +396,7 @@ subroutine valout(level_begin, level_end, time, num_eqn, num_aux)
     open(unit=out_unit, file=timing_file_name, form='formatted',         &
              status='unknown', action='write', position='append')
              !status='old', action='write', position='append')
-    
+
     timing_line = "(e16.6, ', ', e16.6, ', ', e16.6"
     do level=1, mxnest
         timing_substr = ", ', ', e16.6, ', ', e16.6, ', ', e16.6"
@@ -419,7 +420,7 @@ subroutine valout(level_begin, level_end, time, num_eqn, num_aux)
     write(out_unit, timing_line) time, timeTick_overall, t_CPU_overall, &
         (real(tvoll(i), kind=8) / real(clock_rate, kind=8), &
          tvollCPU(i), rvoll(i), i=1,mxnest)
-    
+
     close(out_unit)
 
     ! ==========================================================================
@@ -452,5 +453,3 @@ pure integer function iaddaux(m, i, j)
     end function iaddaux
 
 end subroutine valout
-
-
diff --git a/src/3d/valout.f90 b/src/3d/valout.f90
index 7e172a5a..56cf86de 100644
--- a/src/3d/valout.f90
+++ b/src/3d/valout.f90
@@ -127,6 +127,7 @@ subroutine valout(level_begin, level_end, time, num_eqn, num_aux)
             num_cells(2) = node(ndjhi, grid_ptr) - node(ndjlo, grid_ptr) + 1
             num_cells(3) = node(ndkhi, grid_ptr) - node(ndklo, grid_ptr) + 1
             q_loc = node(store1, grid_ptr)
+            aux_loc = node(storeaux, grid_ptr)
             lower_corner = [rnode(cornxlo, grid_ptr),       &
                             rnode(cornylo, grid_ptr),       &
                             rnode(cornzlo, grid_ptr)]

From 78768e1063d6362554c3b30c45c6631d5d64c53f Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 21 Aug 2025 10:30:35 -0400
Subject: [PATCH 02/27] Add flags to testing action to make testing more
 explicit

---
 .github/workflows/testing.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 20ea413f..97579a93 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -13,6 +13,8 @@ permissions:
 
 env:
   CLAW: ${{ github.workspace }}
+  FFLAGS: "-O1 -fopenmp"
+  OMP_NUM_THREADS: 2
 
 jobs:
   tests:
@@ -26,6 +28,7 @@ jobs:
       run: |
         sudo apt-get update
         sudo apt-get install gfortran
+        gfortran --version
         python -m pip install --upgrade pip
         pip install flake8 meson-python ninja pytest numpy
         # if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
@@ -39,7 +42,7 @@ jobs:
     - name: Checkout AMRClaw branch
       uses: actions/checkout@v4.1.5
       with:
-        path: amrclaw    
+        path: amrclaw
 
     - name: Install clawpack
       run: |

From ebd65ba9d7cf3983ca70a9bc227a3d3276fe9881 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 21 Aug 2025 10:58:32 -0400
Subject: [PATCH 03/27] Add matrix options for debug and optimization flags

---
 .github/workflows/testing.yml | 37 ++++++++++++++++++++++++++++++-----
 1 file changed, 32 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 97579a93..3d5edeef 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -13,17 +13,31 @@ permissions:
 
 env:
   CLAW: ${{ github.workspace }}
-  FFLAGS: "-O1 -fopenmp"
-  OMP_NUM_THREADS: 2
 
 jobs:
   tests:
-    runs-on: ubuntu-latest
+    name: >
+      Build and test a ${{ matrix.build }} version of AMRClaw on ${{ matrix.os }} with ${{ matrix.python-version }}.
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: [3.10]
+        build: [optimized, debug]
+        os: [ubuntu-latest, macos-latest]
+        include:
+          - os: ubuntu-latest
+            build: optimized
+          - os: ubuntu-latest
+            python-version: 3.10
+            build: debug
+          - os: macos-latest
+            python-version: 3.10
+            build: optimized
     steps:
-    - name: Set up Python 3.10
+    - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
+        python-version: ${{matrix.python-version}}
     - name: Install dependencies
       run: |
         sudo apt-get update
@@ -45,10 +59,13 @@ jobs:
         path: amrclaw
 
     - name: Install clawpack
+      env:
+
       run: |
         pip install --no-build-isolation --editable .
 
     - name: Lint with flake8
+      if: ${{ matrix.build == 'debug' }}
       run: |
         cd ${CLAW}/amrclaw
         # stop the build if there are Python syntax errors or undefined names
@@ -58,6 +75,16 @@ jobs:
 
     - name: Test with pytest
       run: |
+        if [ "${{ matrix.build }}" == "debug" ]; then
+          export FFLAGS="-O0 -W -Wall -fbounds-check -fcheck=all -pedantic-errors -Wunderflow -fbacktrace -ffpe-trap=invalid,zero,overflow -g"
+          export OMP_NUM_THREADS=1
+        elif [ "${{ matrix.build }}" == "optimized" ]; then
+          export FFLAGS="-O1 -fopenmp"
+          export OMP_NUM_THREADS=2
+        else
+          echo "Unknown build type: ${{ matrix.build }}"
+          exit 1
+        fi
         cd ${CLAW}/amrclaw
         pytest
 

From ac5b9ce47dbb784e4cbbd1094a212411d8851060 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 21 Aug 2025 11:00:11 -0400
Subject: [PATCH 04/27] Correct bug in testing script

---
 .github/workflows/testing.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 3d5edeef..d3a024d0 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -58,9 +58,7 @@ jobs:
       with:
         path: amrclaw
 
-    - name: Install clawpack
-      env:
-
+    - name: Install clawpack python
       run: |
         pip install --no-build-isolation --editable .
 

From 2f615c631800923b84b40d6a6b017de4e848f2b4 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 21 Aug 2025 11:04:13 -0400
Subject: [PATCH 05/27] Modify python versions for testing

---
 .github/workflows/testing.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index d3a024d0..0ce2c4ac 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -21,18 +21,18 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [3.10]
+        python-version: ["3.8", "3.10"]
         build: [optimized, debug]
         os: [ubuntu-latest, macos-latest]
         include:
           - os: ubuntu-latest
-            build: optimized
-          - os: ubuntu-latest
-            python-version: 3.10
             build: debug
-          - os: macos-latest
-            python-version: 3.10
+          - os: ubuntu-latest
+            python-version: "3.10"
             build: optimized
+          # - os: macos-latest
+          #   python-version: "3.10"
+          #   build: optimized
     steps:
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5

From a2faad305155ee982ad10f29ccb074b1fbb5aedf Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 21 Aug 2025 11:08:13 -0400
Subject: [PATCH 06/27] Add specific macos instructions

---
 .github/workflows/testing.yml | 22 +++++++++++++++-------
 1 file changed, 15 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 0ce2c4ac..a3e6ebc0 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -30,9 +30,9 @@ jobs:
           - os: ubuntu-latest
             python-version: "3.10"
             build: optimized
-          # - os: macos-latest
-          #   python-version: "3.10"
-          #   build: optimized
+          - os: macos-latest
+            python-version: "3.10"
+            build: optimized
     steps:
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
@@ -40,12 +40,20 @@ jobs:
         python-version: ${{matrix.python-version}}
     - name: Install dependencies
       run: |
-        sudo apt-get update
-        sudo apt-get install gfortran
-        gfortran --version
+        if [ "${{ matrix.os }}" == "macos-latest" ]; then
+          brew update
+          brew install gfortran
+          gfortran --version
+        elif [ "${{ matrix.os }}" == "ubuntu-latest" ]; then
+          sudo apt-get update
+          sudo apt-get install -y gfortran
+          gfortran --version
+        else
+          echo "Unsupported OS: ${{ matrix.os }}"
+          exit 1
+        fi
         python -m pip install --upgrade pip
         pip install flake8 meson-python ninja pytest numpy
-        # if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
 
     - name: Checkout Clawpack
       uses: actions/checkout@v4.1.5

From efb6a71124b69ece1825103e7997dfcd693a9cc3 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 21 Aug 2025 11:26:13 -0400
Subject: [PATCH 07/27] Use fort-lang's fortran compiler setup action

---
 .github/workflows/testing.yml | 34 +++++++++++++++++++++-------------
 1 file changed, 21 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index a3e6ebc0..f6a7f2a2 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -20,10 +20,17 @@ jobs:
       Build and test a ${{ matrix.build }} version of AMRClaw on ${{ matrix.os }} with ${{ matrix.python-version }}.
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false # Probably want to turn this off for a large matrix
       matrix:
         python-version: ["3.8", "3.10"]
         build: [optimized, debug]
         os: [ubuntu-latest, macos-latest]
+        toolchain:
+          - {compiler: gcc, version: 15}
+          - {compiler: intel, version: '2025.0'}
+          - {compiler: intel-classic, version: '2021.10'}
+          - {compiler: nvidia-hpc, version: '25.1'}
+          - {compiler: lfortran, version: '0.45.0'}
         include:
           - os: ubuntu-latest
             build: debug
@@ -33,25 +40,26 @@ jobs:
           - os: macos-latest
             python-version: "3.10"
             build: optimized
+        exclude:
+          - os: macos-latest
+            toolchain: {compiler: intel, version: '2023.2'}
+          - os: macos-latest
+            toolchain: {compiler: nvidia-hpc, version: '23.11'}
+
     steps:
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
         python-version: ${{matrix.python-version}}
-    - name: Install dependencies
+
+    - name: Set up compilers
+      uses: fortran-lang/setup-fortran
+      with:
+        compiler: ${{ matrix.toolchain.compiler }}
+        version: ${{ matrix.toolchain.version }}
+
+    - name: Install python dependencies
       run: |
-        if [ "${{ matrix.os }}" == "macos-latest" ]; then
-          brew update
-          brew install gfortran
-          gfortran --version
-        elif [ "${{ matrix.os }}" == "ubuntu-latest" ]; then
-          sudo apt-get update
-          sudo apt-get install -y gfortran
-          gfortran --version
-        else
-          echo "Unsupported OS: ${{ matrix.os }}"
-          exit 1
-        fi
         python -m pip install --upgrade pip
         pip install flake8 meson-python ninja pytest numpy
 

From ab9bebeed319521f42b8d32531f584ae77247f8a Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 21 Aug 2025 11:32:34 -0400
Subject: [PATCH 08/27] Fix fortran compiler action and added options for every
 compiler

---
 .github/workflows/testing.yml | 33 ++++++++++++++++++++++++++++++---
 1 file changed, 30 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index f6a7f2a2..437ec833 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -53,7 +53,8 @@ jobs:
         python-version: ${{matrix.python-version}}
 
     - name: Set up compilers
-      uses: fortran-lang/setup-fortran
+      uses: fortran-lang/setup-fortran@v1
+      id: setup-fortran
       with:
         compiler: ${{ matrix.toolchain.compiler }}
         version: ${{ matrix.toolchain.version }}
@@ -90,10 +91,36 @@ jobs:
     - name: Test with pytest
       run: |
         if [ "${{ matrix.build }}" == "debug" ]; then
-          export FFLAGS="-O0 -W -Wall -fbounds-check -fcheck=all -pedantic-errors -Wunderflow -fbacktrace -ffpe-trap=invalid,zero,overflow -g"
+          if [ "${{ matrix.toolchain.compiler}}" == "gcc" ]; then
+            export FFLAGS="-O0 -W -Wall -fbounds-check -fcheck=all -pedantic-errors -Wunderflow -fbacktrace -ffpe-trap=invalid,zero,overflow -g"
+          elif [ "${{ matrix.toolchain.compiler}}" == "intel" ]; then
+            export FFLAGS="-O0 -g -check all -warn all -traceback"
+          elif [ "${{ matrix.toolchain.compiler}}" == "intel-classic" ]; then
+            export FFLAGS="-O0 -g -check all -warn all -traceback"
+          elif [ "${{ matrix.toolchain.compiler}}" == "nvidia-hpc" ]; then
+            export FFLAGS="-O0 -g -check all -warn all -traceback"
+          elif [ "${{ matrix.toolchain.compiler}}" == "lfortran" ]; then
+            export FFLAGS="-O0 -g -fcheck=all -fbacktrace
+          else
+            echo "Unknown compiler: ${{ matrix.toolchain.compiler }}"
+            exit 1
+          fi
           export OMP_NUM_THREADS=1
         elif [ "${{ matrix.build }}" == "optimized" ]; then
-          export FFLAGS="-O1 -fopenmp"
+          if [ "${{ matrix.toolchain.compiler}}" == "gcc" ]; then
+            export FFLAGS="-O1 -march=native -mtune=native -fopenmp"
+          elif [ "${{ matrix.toolchain.compiler}}" == "intel" ]; then
+            export FFLAGS="-O1 -xHost -qopenmp"
+          elif [ "${{ matrix.toolchain.compiler}}" == "intel-classic" ]; then
+            export FFLAGS="-O1 -xHost -qopenmp"
+          elif [ "${{ matrix.toolchain.compiler}}" == "nvidia-hpc" ]; then
+            export FFLAGS="-O1 -xHost -qopenmp"
+          elif [ "${{ matrix.toolchain.compiler}}" == "lfortran" ]; then
+            export FFLAGS="-O1 -fopenmp"
+          else
+            echo "Unknown compiler: ${{ matrix.toolchain.compiler }}"
+            exit 1
+          fi
           export OMP_NUM_THREADS=2
         else
           echo "Unknown build type: ${{ matrix.build }}"

From 5f8ed40321e922659609db126494cb9b461fbfcd Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 21 Aug 2025 11:49:17 -0400
Subject: [PATCH 09/27] Simplify testing matrix

---
 .github/workflows/testing.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 437ec833..2fc2abcb 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -17,20 +17,20 @@ env:
 jobs:
   tests:
     name: >
-      Build and test a ${{ matrix.build }} version of AMRClaw on ${{ matrix.os }} with ${{ matrix.python-version }}.
+      Build ${{ matrix.build }} - ${{ matrix.os }} with ${{ matrix.python-version }}.
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false # Probably want to turn this off for a large matrix
       matrix:
         python-version: ["3.8", "3.10"]
         build: [optimized, debug]
-        os: [ubuntu-latest, macos-latest]
+        os: [ubuntu-latest] #, macos-latest]
         toolchain:
           - {compiler: gcc, version: 15}
-          - {compiler: intel, version: '2025.0'}
-          - {compiler: intel-classic, version: '2021.10'}
-          - {compiler: nvidia-hpc, version: '25.1'}
-          - {compiler: lfortran, version: '0.45.0'}
+          # - {compiler: intel, version: '2025.0'}
+          # - {compiler: intel-classic, version: '2021.10'}
+          # - {compiler: nvidia-hpc, version: '25.1'}
+          # - {compiler: lfortran, version: '0.45.0'} # Does not work with meson
         include:
           - os: ubuntu-latest
             build: debug

From 14f13325e4174e045f156882c89d375a6d096518 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 21 Aug 2025 12:03:59 -0400
Subject: [PATCH 10/27] Rework exclude/include lists

---
 .github/workflows/testing.yml | 20 +++++++-------------
 1 file changed, 7 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 2fc2abcb..c97df627 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -22,10 +22,11 @@ jobs:
     strategy:
       fail-fast: false # Probably want to turn this off for a large matrix
       matrix:
-        python-version: ["3.8", "3.10"]
-        build: [optimized, debug]
         os: [ubuntu-latest] #, macos-latest]
+        python-version: ["3.12"]
+        build: [optimized]
         toolchain:
+          - {compiler: gcc, version: 14}
           - {compiler: gcc, version: 15}
           # - {compiler: intel, version: '2025.0'}
           # - {compiler: intel-classic, version: '2021.10'}
@@ -33,18 +34,11 @@ jobs:
           # - {compiler: lfortran, version: '0.45.0'} # Does not work with meson
         include:
           - os: ubuntu-latest
-            build: debug
-          - os: ubuntu-latest
-            python-version: "3.10"
-            build: optimized
-          - os: macos-latest
-            python-version: "3.10"
-            build: optimized
+            build: [optimized, debug]
+            python-version: ["3.8", "3.12"]
         exclude:
-          - os: macos-latest
-            toolchain: {compiler: intel, version: '2023.2'}
-          - os: macos-latest
-            toolchain: {compiler: nvidia-hpc, version: '23.11'}
+          - os: ubuntu-latest
+            toolchain: {compiler: gcc, version: 15}
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

From 079f65c81e797abc44d8eaba24784020e076b565 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 21 Aug 2025 13:09:01 -0400
Subject: [PATCH 11/27] Fix bug in python version request

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

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index c97df627..4b740732 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -44,7 +44,7 @@ jobs:
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
-        python-version: ${{matrix.python-version}}
+        python-version: ${{ matrix.python-version }}
 
     - name: Set up compilers
       uses: fortran-lang/setup-fortran@v1

From e1a489722feee03f0413eda121cfc0979b92566d Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 21 Aug 2025 13:26:09 -0400
Subject: [PATCH 12/27] Try to correct the python version rule again

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

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 4b740732..8ab4d0aa 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -23,7 +23,7 @@ jobs:
       fail-fast: false # Probably want to turn this off for a large matrix
       matrix:
         os: [ubuntu-latest] #, macos-latest]
-        python-version: ["3.12"]
+        python-version: 3.12
         build: [optimized]
         toolchain:
           - {compiler: gcc, version: 14}

From a47420151e72ae40a4dce593cec0736df8c4b0e5 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 21 Aug 2025 13:28:35 -0400
Subject: [PATCH 13/27] Fix python version syntax

---
 .github/workflows/testing.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 8ab4d0aa..6dd2d322 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -23,7 +23,7 @@ jobs:
       fail-fast: false # Probably want to turn this off for a large matrix
       matrix:
         os: [ubuntu-latest] #, macos-latest]
-        python-version: 3.12
+        python-version: [3.12]
         build: [optimized]
         toolchain:
           - {compiler: gcc, version: 14}
@@ -35,7 +35,7 @@ jobs:
         include:
           - os: ubuntu-latest
             build: [optimized, debug]
-            python-version: ["3.8", "3.12"]
+            python-version: [3.8, 3.12]
         exclude:
           - os: ubuntu-latest
             toolchain: {compiler: gcc, version: 15}

From 520717091db782dc4c3399b947a8fc4003901696 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 21 Aug 2025 13:38:33 -0400
Subject: [PATCH 14/27] Modify settings of action script

---
 .github/workflows/testing.yml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 6dd2d322..7542c980 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false # Probably want to turn this off for a large matrix
       matrix:
-        os: [ubuntu-latest] #, macos-latest]
+        os: [ubuntu-latest, macos-latest]
         python-version: [3.12]
         build: [optimized]
         toolchain:
@@ -34,11 +34,13 @@ jobs:
           # - {compiler: lfortran, version: '0.45.0'} # Does not work with meson
         include:
           - os: ubuntu-latest
-            build: [optimized, debug]
-            python-version: [3.8, 3.12]
+            build: debug
+            python-version: 3.8
         exclude:
           - os: ubuntu-latest
             toolchain: {compiler: gcc, version: 15}
+          - os: macos-latest
+            toolchain: {compiler: gcc, version: 14}
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

From 129c7bc0a21b58bc6a0b09b80ac938bd93cbf97f Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 21 Aug 2025 14:07:27 -0400
Subject: [PATCH 15/27] Modify settings of action script

---
 .github/workflows/testing.yml | 70 +++++++++++++++++------------------
 1 file changed, 35 insertions(+), 35 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 7542c980..3ace3d86 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -86,42 +86,42 @@ jobs:
 
     - name: Test with pytest
       run: |
-        if [ "${{ matrix.build }}" == "debug" ]; then
-          if [ "${{ matrix.toolchain.compiler}}" == "gcc" ]; then
-            export FFLAGS="-O0 -W -Wall -fbounds-check -fcheck=all -pedantic-errors -Wunderflow -fbacktrace -ffpe-trap=invalid,zero,overflow -g"
-          elif [ "${{ matrix.toolchain.compiler}}" == "intel" ]; then
-            export FFLAGS="-O0 -g -check all -warn all -traceback"
-          elif [ "${{ matrix.toolchain.compiler}}" == "intel-classic" ]; then
-            export FFLAGS="-O0 -g -check all -warn all -traceback"
-          elif [ "${{ matrix.toolchain.compiler}}" == "nvidia-hpc" ]; then
-            export FFLAGS="-O0 -g -check all -warn all -traceback"
-          elif [ "${{ matrix.toolchain.compiler}}" == "lfortran" ]; then
-            export FFLAGS="-O0 -g -fcheck=all -fbacktrace
-          else
-            echo "Unknown compiler: ${{ matrix.toolchain.compiler }}"
+        case "${{ matrix.toolchain.compiler }}" in
+          gcc)
+            case "${{ matrix.build }}" in
+              debug)
+                export FFLAGS="-g -Wall -Wextra -Werror"
+                export OMP_NUM_THREADS=1
+                ;;
+              optimized)
+                export FFLAGS="-O1"
+                export OMP_NUM_THREADS=2
+                ;;
+              *)
+                echo "ERROR: Unknown build type: ${{ matrix.build }}"
+                exit 1
+                ;;
+            esac
+          intel)
+            case "${{ matrix.build }}" in
+              debug)
+                export FFLAGS="-g -Wall -Wextra -Werror"
+                export OMP_NUM_THREADS=1
+                ;;
+              optimized)
+                export FFLAGS="-O1 -xHost -qopenmp"
+                export OMP_NUM_THREADS=2
+                ;;
+              *)
+                echo "ERROR: Unknown build type: ${{ matrix.build }}"
+                exit 1
+                ;;
+            esac
+          *)
+            echo "ERROR: Unknown compiler: ${{ matrix.toolchain.compiler }}"
             exit 1
-          fi
-          export OMP_NUM_THREADS=1
-        elif [ "${{ matrix.build }}" == "optimized" ]; then
-          if [ "${{ matrix.toolchain.compiler}}" == "gcc" ]; then
-            export FFLAGS="-O1 -march=native -mtune=native -fopenmp"
-          elif [ "${{ matrix.toolchain.compiler}}" == "intel" ]; then
-            export FFLAGS="-O1 -xHost -qopenmp"
-          elif [ "${{ matrix.toolchain.compiler}}" == "intel-classic" ]; then
-            export FFLAGS="-O1 -xHost -qopenmp"
-          elif [ "${{ matrix.toolchain.compiler}}" == "nvidia-hpc" ]; then
-            export FFLAGS="-O1 -xHost -qopenmp"
-          elif [ "${{ matrix.toolchain.compiler}}" == "lfortran" ]; then
-            export FFLAGS="-O1 -fopenmp"
-          else
-            echo "Unknown compiler: ${{ matrix.toolchain.compiler }}"
-            exit 1
-          fi
-          export OMP_NUM_THREADS=2
-        else
-          echo "Unknown build type: ${{ matrix.build }}"
-          exit 1
-        fi
+            ;;
+        esac
         cd ${CLAW}/amrclaw
         pytest
 

From e26d46e0f1aa24f2f0dd9fb0308644e463a35acd Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Thu, 21 Aug 2025 15:19:04 -0400
Subject: [PATCH 16/27] Modify settings of action script

---
 .github/workflows/testing.yml | 29 ++++++++---------------------
 1 file changed, 8 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 3ace3d86..0d35fbc8 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -90,38 +90,25 @@ jobs:
           gcc)
             case "${{ matrix.build }}" in
               debug)
-                export FFLAGS="-g -Wall -Wextra -Werror"
+                export FFLAGS="-g -O0 -fcheck=all -fbacktrace"
                 export OMP_NUM_THREADS=1
                 ;;
               optimized)
-                export FFLAGS="-O1"
+                export FFLAGS="-O1 -fopenmp"
                 export OMP_NUM_THREADS=2
                 ;;
-              *)
-                echo "ERROR: Unknown build type: ${{ matrix.build }}"
-                exit 1
-                ;;
             esac
           intel)
-            case "${{ matrix.build }}" in
-              debug)
-                export FFLAGS="-g -Wall -Wextra -Werror"
-                export OMP_NUM_THREADS=1
-                ;;
-              optimized)
-                export FFLAGS="-O1 -xHost -qopenmp"
-                export OMP_NUM_THREADS=2
-                ;;
-              *)
-                echo "ERROR: Unknown build type: ${{ matrix.build }}"
-                exit 1
-                ;;
-            esac
+            echo "Using Intel compiler"
+            exit 1 # Temporarily disable Intel compiler testing
+            ;;
           *)
-            echo "ERROR: Unknown compiler: ${{ matrix.toolchain.compiler }}"
+            echo "Unknown compiler: ${{ matrix.toolchain.compiler }}"
             exit 1
             ;;
         esac
+        echo "FFLAGS: $FFLAGS"
+        echo "OMP_NUM_THREADS: $OMP_NUM_THREADS"
         cd ${CLAW}/amrclaw
         pytest
 

From 61c2b0a1ebb72cc2d748fa202e838d88934c43ec Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Fri, 22 Aug 2025 10:28:40 -0400
Subject: [PATCH 17/27] Modify settings of action script

---
 .github/workflows/testing.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 0d35fbc8..b2fd4a24 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -36,6 +36,7 @@ jobs:
           - os: ubuntu-latest
             build: debug
             python-version: 3.8
+            toolchain: {compiler: gcc, version: 14}
         exclude:
           - os: ubuntu-latest
             toolchain: {compiler: gcc, version: 15}
@@ -97,6 +98,10 @@ jobs:
                 export FFLAGS="-O1 -fopenmp"
                 export OMP_NUM_THREADS=2
                 ;;
+              *)
+                echo "Unknown build type: ${{ matrix.build }}"
+                exit 1
+                ;;
             esac
           intel)
             echo "Using Intel compiler"

From 7d6c75978dd585e4a43b0d33608d076fb9ecc8b1 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Fri, 22 Aug 2025 10:35:01 -0400
Subject: [PATCH 18/27] Switch back if-else

---
 .github/workflows/testing.yml | 49 ++++++++++++++++++-----------------
 1 file changed, 25 insertions(+), 24 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index b2fd4a24..405e70f6 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -87,31 +87,32 @@ jobs:
 
     - name: Test with pytest
       run: |
-        case "${{ matrix.toolchain.compiler }}" in
-          gcc)
-            case "${{ matrix.build }}" in
-              debug)
-                export FFLAGS="-g -O0 -fcheck=all -fbacktrace"
-                export OMP_NUM_THREADS=1
-                ;;
-              optimized)
-                export FFLAGS="-O1 -fopenmp"
-                export OMP_NUM_THREADS=2
-                ;;
-              *)
-                echo "Unknown build type: ${{ matrix.build }}"
-                exit 1
-                ;;
-            esac
-          intel)
-            echo "Using Intel compiler"
-            exit 1 # Temporarily disable Intel compiler testing
-            ;;
-          *)
-            echo "Unknown compiler: ${{ matrix.toolchain.compiler }}"
+        if [ "${{ matrix.toolchain.compiler }}" = "gcc" ]; then
+          if [ "${{ matrix.build }}" = "debug" ]; then
+            export FFLAGS="-g -O0 -fcheck=all -fbacktrace"
+            export OMP_NUM_THREADS=1
+          elif [ "${{ matrix.build }}" = "optimized" ]; then
+            export FFLAGS="-O1 -fopenmp"
+            export OMP_NUM_THREADS=2
+          else
+            echo "Unknown build type: ${{ matrix.build }}"
             exit 1
-            ;;
-        esac
+          fi
+        elif [ "${{ matrix.toolchain.compiler }}" = "intel" ]; then
+          if [ "${{ matrix.build }}" = "debug" ]; then
+            export FFLAGS="-g -O0 -check all -traceback"
+            export OMP_NUM_THREADS=1
+          elif [ "${{ matrix.build }}" = "optimized" ]; then
+            export FFLAGS="-O1 -qopenmp"
+            export OMP_NUM_THREADS=2
+          else
+            echo "Unknown build type: ${{ matrix.build }}"
+            exit 1
+          fi
+        else
+          echo "Unknown compiler: ${{ matrix.toolchain.compiler }}"
+          exit 1
+        fi
         echo "FFLAGS: $FFLAGS"
         echo "OMP_NUM_THREADS: $OMP_NUM_THREADS"
         cd ${CLAW}/amrclaw

From b0cdf4bd99037f15c8adf34d8eac9167df8669a7 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Fri, 22 Aug 2025 10:44:11 -0400
Subject: [PATCH 19/27] Add additional compiler options and remove python 3.8

---
 .github/workflows/testing.yml | 22 ++++++++++++++--------
 1 file changed, 14 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 405e70f6..bd7c6220 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -27,21 +27,20 @@ jobs:
         build: [optimized]
         toolchain:
           - {compiler: gcc, version: 14}
-          - {compiler: gcc, version: 15}
-          # - {compiler: intel, version: '2025.0'}
-          # - {compiler: intel-classic, version: '2021.10'}
+          - {compiler: intel, version: '2025.0'}
+          - {compiler: intel-classic, version: '2021.10'}
           # - {compiler: nvidia-hpc, version: '25.1'}
           # - {compiler: lfortran, version: '0.45.0'} # Does not work with meson
         include:
           - os: ubuntu-latest
             build: debug
-            python-version: 3.8
-            toolchain: {compiler: gcc, version: 14}
-        exclude:
-          - os: ubuntu-latest
+            # python-version: 3.8
+            # toolchain: {compiler: gcc, version: 14}
+          - os: macos-latest
             toolchain: {compiler: gcc, version: 15}
+        exclude:
           - os: macos-latest
-            toolchain: {compiler: gcc, version: 14}
+            toolchain: {compiler: intel, version: '2025.0'} # Intel not available on macOS runners
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -109,6 +108,13 @@ jobs:
             echo "Unknown build type: ${{ matrix.build }}"
             exit 1
           fi
+        elif [ "${{ matrix.toolchain.compiler }}" = "intel-classic" ]; then
+          if [ "${{ matrix.build }}" = "debug" ]; then
+            export FFLAGS="-g -O0 -check all -traceback"
+            export OMP_NUM_THREADS=1
+          elif [ "${{ matrix.build }}" = "optimized" ]; then
+            export FFLAGS="-O1 -openmp"
+            export OMP_NUM_THREADS=2
         else
           echo "Unknown compiler: ${{ matrix.toolchain.compiler }}"
           exit 1

From 9e88f160ed8339d6a370393220676f7c229897bd Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Fri, 22 Aug 2025 11:38:41 -0400
Subject: [PATCH 20/27] Add new flags and additional compilers

---
 .github/workflows/testing.yml | 41 ++++++++++++++++++++++++++++++-----
 1 file changed, 35 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index bd7c6220..35a1cce0 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -34,10 +34,12 @@ jobs:
         include:
           - os: ubuntu-latest
             build: debug
-            # python-version: 3.8
-            # toolchain: {compiler: gcc, version: 14}
+            toolchain: {compiler: intel, version: '2025.0'}
           - os: macos-latest
             toolchain: {compiler: gcc, version: 15}
+          - os: macos-latest
+            build: debug
+            toolchain: {compiler: gcc, version: 15}
         exclude:
           - os: macos-latest
             toolchain: {compiler: intel, version: '2025.0'} # Intel not available on macOS runners
@@ -88,15 +90,23 @@ jobs:
       run: |
         if [ "${{ matrix.toolchain.compiler }}" = "gcc" ]; then
           if [ "${{ matrix.build }}" = "debug" ]; then
-            export FFLAGS="-g -O0 -fcheck=all -fbacktrace"
+            export FFLAGS="-O0 -g -fcheck=all -fbacktrace -fbounds-check -ffpe-trap=invalid,zero,overflow -finit-real=nan -finit-integer=nan -Wall -Wunderflow -Wextra -Wconversion -Wuninitialized -Warray-bounds -Wshadow -Wno-unused-function -Wno-unused-variable -Wno-unused-parameter -Wno-unused-label -Wno-unused-but-set-variable"
             export OMP_NUM_THREADS=1
           elif [ "${{ matrix.build }}" = "optimized" ]; then
-            export FFLAGS="-O1 -fopenmp"
+            export FFLAGS="-O1 -fopenmp -funroll-loops -finline-functions -ftree-vectorize -fstack-protector-strong -flto -march=native"
             export OMP_NUM_THREADS=2
           else
             echo "Unknown build type: ${{ matrix.build }}"
             exit 1
           fi
+        elif [ "${{ matrix.toolchain.compiler }}" = "intel-classic" ]; then
+          if [ "${{ matrix.build }}" = "debug" ]; then
+            export FFLAGS="-O0 -debug all -check all -warn all,nodec,interfaces -gen_interfaces -traceback -fpe0 -ftrapuv -init=snan,arrays -check bounds"
+            export OMP_NUM_THREADS=1
+          elif [ "${{ matrix.build }}" = "optimized" ]; then
+            export FFLAGS="-O -qopenmp -unroll -finline-functions -inline-forceinline -ipo -ip "
+            export OMP_NUM_THREADS=2
+          fi
         elif [ "${{ matrix.toolchain.compiler }}" = "intel" ]; then
           if [ "${{ matrix.build }}" = "debug" ]; then
             export FFLAGS="-g -O0 -check all -traceback"
@@ -108,13 +118,32 @@ jobs:
             echo "Unknown build type: ${{ matrix.build }}"
             exit 1
           fi
-        elif [ "${{ matrix.toolchain.compiler }}" = "intel-classic" ]; then
+        elif [ "${{ matrix.toolchain.compiler }}" = "nvidia-hpc" ]; then
+          echo "nvidia-hpc compiler not yet supported"
+          exit 1
           if [ "${{ matrix.build }}" = "debug" ]; then
             export FFLAGS="-g -O0 -check all -traceback"
             export OMP_NUM_THREADS=1
           elif [ "${{ matrix.build }}" = "optimized" ]; then
-            export FFLAGS="-O1 -openmp"
+            export FFLAGS="-O1 -qopenmp"
             export OMP_NUM_THREADS=2
+          else
+            echo "Unknown build type: ${{ matrix.build }}"
+            exit 1
+          fi
+        elif [ "${{ matrix.toolchain.compiler }}" = "lfortran" ]; then
+          echo "lfortran compiler not yet supported"
+          exit 1
+          if [ "${{ matrix.build }}" = "debug" ]; then
+            export FFLAGS=""
+            export OMP_NUM_THREADS=1
+          elif [ "${{ matrix.build }}" = "optimized" ]; then
+            export FFLAGS=""
+            export OMP_NUM_THREADS=2
+          else
+            echo "Unknown build type: ${{ matrix.build }}"
+            exit 1
+          fi
         else
           echo "Unknown compiler: ${{ matrix.toolchain.compiler }}"
           exit 1

From db3a6ba571d090c5cb8948a036c06a6187e992e6 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Fri, 22 Aug 2025 11:57:22 -0400
Subject: [PATCH 21/27] Rework build matrix and fix bugs

---
 .github/workflows/testing.yml | 26 ++++++++++++++------------
 1 file changed, 14 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 35a1cce0..6e6ad9c4 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -17,32 +17,34 @@ env:
 jobs:
   tests:
     name: >
-      Build ${{ matrix.build }} - ${{ matrix.os }} with ${{ matrix.python-version }}.
+      Build ${{ matrix.os }} - ${{ matrix.toolchain.compiler }} ${{ matrix.build }}.
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false # Probably want to turn this off for a large matrix
       matrix:
         os: [ubuntu-latest, macos-latest]
         python-version: [3.12]
-        build: [optimized]
+        build: [opt]
         toolchain:
           - {compiler: gcc, version: 14}
           - {compiler: intel, version: '2025.0'}
           - {compiler: intel-classic, version: '2021.10'}
-          # - {compiler: nvidia-hpc, version: '25.1'}
-          # - {compiler: lfortran, version: '0.45.0'} # Does not work with meson
+          - {compiler: nvidia-hpc, version: '25.1'}
+          # - {compiler: lfortran, version: '0.45.0'} # lfortran not yet supported
+          # - {compiler: flang, version: '20.1.0'} # flang not yet supported
         include:
           - os: ubuntu-latest
             build: debug
             toolchain: {compiler: intel, version: '2025.0'}
-          - os: macos-latest
-            toolchain: {compiler: gcc, version: 15}
           - os: macos-latest
             build: debug
             toolchain: {compiler: gcc, version: 15}
         exclude:
+          # Remove compilers not available on macOS runners
+          - os: macos-latest
+            toolchain: {compiler: intel, version: '2025.0'}
           - os: macos-latest
-            toolchain: {compiler: intel, version: '2025.0'} # Intel not available on macOS runners
+            toolchain: {compiler: nvidia-hpc, version: '2021.10'}
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -92,7 +94,7 @@ jobs:
           if [ "${{ matrix.build }}" = "debug" ]; then
             export FFLAGS="-O0 -g -fcheck=all -fbacktrace -fbounds-check -ffpe-trap=invalid,zero,overflow -finit-real=nan -finit-integer=nan -Wall -Wunderflow -Wextra -Wconversion -Wuninitialized -Warray-bounds -Wshadow -Wno-unused-function -Wno-unused-variable -Wno-unused-parameter -Wno-unused-label -Wno-unused-but-set-variable"
             export OMP_NUM_THREADS=1
-          elif [ "${{ matrix.build }}" = "optimized" ]; then
+          elif [ "${{ matrix.build }}" = "opt" ]; then
             export FFLAGS="-O1 -fopenmp -funroll-loops -finline-functions -ftree-vectorize -fstack-protector-strong -flto -march=native"
             export OMP_NUM_THREADS=2
           else
@@ -103,7 +105,7 @@ jobs:
           if [ "${{ matrix.build }}" = "debug" ]; then
             export FFLAGS="-O0 -debug all -check all -warn all,nodec,interfaces -gen_interfaces -traceback -fpe0 -ftrapuv -init=snan,arrays -check bounds"
             export OMP_NUM_THREADS=1
-          elif [ "${{ matrix.build }}" = "optimized" ]; then
+          elif [ "${{ matrix.build }}" = "opt" ]; then
             export FFLAGS="-O -qopenmp -unroll -finline-functions -inline-forceinline -ipo -ip "
             export OMP_NUM_THREADS=2
           fi
@@ -111,7 +113,7 @@ jobs:
           if [ "${{ matrix.build }}" = "debug" ]; then
             export FFLAGS="-g -O0 -check all -traceback"
             export OMP_NUM_THREADS=1
-          elif [ "${{ matrix.build }}" = "optimized" ]; then
+          elif [ "${{ matrix.build }}" = "opt" ]; then
             export FFLAGS="-O1 -qopenmp"
             export OMP_NUM_THREADS=2
           else
@@ -124,7 +126,7 @@ jobs:
           if [ "${{ matrix.build }}" = "debug" ]; then
             export FFLAGS="-g -O0 -check all -traceback"
             export OMP_NUM_THREADS=1
-          elif [ "${{ matrix.build }}" = "optimized" ]; then
+          elif [ "${{ matrix.build }}" = "opt" ]; then
             export FFLAGS="-O1 -qopenmp"
             export OMP_NUM_THREADS=2
           else
@@ -137,7 +139,7 @@ jobs:
           if [ "${{ matrix.build }}" = "debug" ]; then
             export FFLAGS=""
             export OMP_NUM_THREADS=1
-          elif [ "${{ matrix.build }}" = "optimized" ]; then
+          elif [ "${{ matrix.build }}" = "opt" ]; then
             export FFLAGS=""
             export OMP_NUM_THREADS=2
           else

From 3533440a73fbb589414f3e0a0ea6f62603d8645b Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Fri, 22 Aug 2025 13:01:13 -0400
Subject: [PATCH 22/27] Again remove broken toolchains

---
 .github/workflows/testing.yml | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 6e6ad9c4..e79aa959 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -17,7 +17,7 @@ env:
 jobs:
   tests:
     name: >
-      Build ${{ matrix.os }} - ${{ matrix.toolchain.compiler }} ${{ matrix.build }}.
+      ${{ matrix.os }} - ${{ matrix.toolchain.compiler }} ${{ matrix.build }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false # Probably want to turn this off for a large matrix
@@ -29,7 +29,7 @@ jobs:
           - {compiler: gcc, version: 14}
           - {compiler: intel, version: '2025.0'}
           - {compiler: intel-classic, version: '2021.10'}
-          - {compiler: nvidia-hpc, version: '25.1'}
+          # - {compiler: nvidia-hpc, version: '25.1'} # does not build python
           # - {compiler: lfortran, version: '0.45.0'} # lfortran not yet supported
           # - {compiler: flang, version: '20.1.0'} # flang not yet supported
         include:
@@ -40,11 +40,8 @@ jobs:
             build: debug
             toolchain: {compiler: gcc, version: 15}
         exclude:
-          # Remove compilers not available on macOS runners
           - os: macos-latest
             toolchain: {compiler: intel, version: '2025.0'}
-          - os: macos-latest
-            toolchain: {compiler: nvidia-hpc, version: '2021.10'}
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -106,15 +103,15 @@ jobs:
             export FFLAGS="-O0 -debug all -check all -warn all,nodec,interfaces -gen_interfaces -traceback -fpe0 -ftrapuv -init=snan,arrays -check bounds"
             export OMP_NUM_THREADS=1
           elif [ "${{ matrix.build }}" = "opt" ]; then
-            export FFLAGS="-O -qopenmp -unroll -finline-functions -inline-forceinline -ipo -ip "
+            export FFLAGS="-O -qopenmp -unroll -finline-functions -inline-forceinline -ipo -ip"
             export OMP_NUM_THREADS=2
           fi
         elif [ "${{ matrix.toolchain.compiler }}" = "intel" ]; then
           if [ "${{ matrix.build }}" = "debug" ]; then
-            export FFLAGS="-g -O0 -check all -traceback"
+            export FFLAGS="-O0 -debug all -check all -warn all,nodec,interfaces -gen_interfaces -traceback -fpe0 -ftrapuv -init=snan,arrays -check bounds"
             export OMP_NUM_THREADS=1
           elif [ "${{ matrix.build }}" = "opt" ]; then
-            export FFLAGS="-O1 -qopenmp"
+            export FFLAGS="-O -qopenmp -unroll -finline-functions -inline-forceinline -ipo -ip"
             export OMP_NUM_THREADS=2
           else
             echo "Unknown build type: ${{ matrix.build }}"
@@ -133,8 +130,8 @@ jobs:
             echo "Unknown build type: ${{ matrix.build }}"
             exit 1
           fi
-        elif [ "${{ matrix.toolchain.compiler }}" = "lfortran" ]; then
-          echo "lfortran compiler not yet supported"
+        elif [ "${{ matrix.toolchain.compiler }}" = "flang" ]; then
+          echo "flang compiler not yet supported"
           exit 1
           if [ "${{ matrix.build }}" = "debug" ]; then
             export FFLAGS=""

From 47034e1bc5cad3ad8ea75db2903d8bfd42b21606 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Fri, 22 Aug 2025 15:21:43 -0400
Subject: [PATCH 23/27] Minor tweaks and removal of non-working toolchains

---
 .github/workflows/testing.yml | 28 ++++++++++++++++++++++------
 1 file changed, 22 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index e79aa959..8be82ce0 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -26,22 +26,23 @@ jobs:
         python-version: [3.12]
         build: [opt]
         toolchain:
-          - {compiler: gcc, version: 14}
-          - {compiler: intel, version: '2025.0'}
-          - {compiler: intel-classic, version: '2021.10'}
+          - {compiler: gcc, version: 10}
+          - {compiler: gcc, version: 15}
+          # - {compiler: intel, version: '2025.0'}
+          # - {compiler: intel-classic, version: '2021.10'}
           # - {compiler: nvidia-hpc, version: '25.1'} # does not build python
           # - {compiler: lfortran, version: '0.45.0'} # lfortran not yet supported
           # - {compiler: flang, version: '20.1.0'} # flang not yet supported
         include:
           - os: ubuntu-latest
             build: debug
-            toolchain: {compiler: intel, version: '2025.0'}
+            toolchain: {compiler: gcc, version: 14}
           - os: macos-latest
             build: debug
             toolchain: {compiler: gcc, version: 15}
         exclude:
-          - os: macos-latest
-            toolchain: {compiler: intel, version: '2025.0'}
+          - os: ubuntu-latest
+            toolchain: {compiler: gcc, version: 15}
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -143,6 +144,17 @@ jobs:
             echo "Unknown build type: ${{ matrix.build }}"
             exit 1
           fi
+        elif [ "${{ matrix.toolchain.compiler }}" = "lfortran" ]; then
+          if [ "${{ matrix.build }}" = "debug" ]; then
+            export FFLAGS=""
+            export OMP_NUM_THREADS=1
+          elif [ "${{ matrix.build }}" = "opt" ]; then
+            export FFLAGS="--fast --openmp"
+            export OMP_NUM_THREADS=2
+          else
+            echo "Unknown build type: ${{ matrix.build }}"
+            exit 1
+          fi
         else
           echo "Unknown compiler: ${{ matrix.toolchain.compiler }}"
           exit 1
@@ -159,3 +171,7 @@ jobs:
         name: test_results
         path: ${{ env.CLAW }}/amrclaw/*_output
         if-no-files-found: ignore
+
+
+# lfortran
+# optimized = --openmp

From 0bc8a878a5def8474c223f57b22295dac707d045 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Fri, 22 Aug 2025 16:54:44 -0400
Subject: [PATCH 24/27] Final tweak to compiler toolchain (hopefully)

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

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 8be82ce0..711f5100 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -26,7 +26,7 @@ jobs:
         python-version: [3.12]
         build: [opt]
         toolchain:
-          - {compiler: gcc, version: 10}
+          - {compiler: gcc, version: 12}
           - {compiler: gcc, version: 15}
           # - {compiler: intel, version: '2025.0'}
           # - {compiler: intel-classic, version: '2021.10'}

From 9824e54d4474846046fa5a09a7ad1598a5a139c6 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Fri, 22 Aug 2025 17:05:15 -0400
Subject: [PATCH 25/27] Remove GCC compiler version that is too old and add
 python versions

---
 .github/workflows/testing.yml | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 711f5100..24590afd 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -17,16 +17,16 @@ env:
 jobs:
   tests:
     name: >
-      ${{ matrix.os }} - ${{ matrix.toolchain.compiler }} ${{ matrix.build }}
+      ${{ matrix.os }} - ${{ matrix.toolchain.compiler }} ${{ matrix.build }} - py ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false # Probably want to turn this off for a large matrix
       matrix:
         os: [ubuntu-latest, macos-latest]
         python-version: [3.12]
-        build: [opt]
+        build: [debug, opt]
         toolchain:
-          - {compiler: gcc, version: 12}
+          - {compiler: gcc, version: 14}
           - {compiler: gcc, version: 15}
           # - {compiler: intel, version: '2025.0'}
           # - {compiler: intel-classic, version: '2021.10'}
@@ -35,14 +35,16 @@ jobs:
           # - {compiler: flang, version: '20.1.0'} # flang not yet supported
         include:
           - os: ubuntu-latest
-            build: debug
-            toolchain: {compiler: gcc, version: 14}
-          - os: macos-latest
-            build: debug
-            toolchain: {compiler: gcc, version: 15}
+            build: opt
+            python-version: 3.8
+        #   - os: macos-latest
+        #     build: debug
+        #     toolchain: {compiler: gcc, version: 15}
         exclude:
           - os: ubuntu-latest
             toolchain: {compiler: gcc, version: 15}
+          - os: macos-latest
+            toolchain: {compiler: gcc, version: 14}
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

From b97a6623a1363b5f9b80ac5a675361f180295b64 Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Fri, 22 Aug 2025 18:35:53 -0400
Subject: [PATCH 26/27] Fill out include and update matrix

---
 .github/workflows/testing.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 24590afd..2f8a2ba6 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -23,8 +23,8 @@ jobs:
       fail-fast: false # Probably want to turn this off for a large matrix
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: [3.12]
         build: [debug, opt]
+        python-version: [3.12]
         toolchain:
           - {compiler: gcc, version: 14}
           - {compiler: gcc, version: 15}
@@ -37,6 +37,7 @@ jobs:
           - os: ubuntu-latest
             build: opt
             python-version: 3.8
+            toolchain: {compiler: gcc, version: 14}
         #   - os: macos-latest
         #     build: debug
         #     toolchain: {compiler: gcc, version: 15}

From 250c6ee541da28427d61b4c9e94c0a3a705aae4e Mon Sep 17 00:00:00 2001
From: Kyle Mandli <kyle.mandli@gmail.com>
Date: Fri, 22 Aug 2025 18:43:27 -0400
Subject: [PATCH 27/27] Give up on more python versions

---
 .github/workflows/testing.yml | 18 ++++++------------
 1 file changed, 6 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 2f8a2ba6..3cd0bf43 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -33,14 +33,12 @@ jobs:
           # - {compiler: nvidia-hpc, version: '25.1'} # does not build python
           # - {compiler: lfortran, version: '0.45.0'} # lfortran not yet supported
           # - {compiler: flang, version: '20.1.0'} # flang not yet supported
-        include:
-          - os: ubuntu-latest
-            build: opt
-            python-version: 3.8
-            toolchain: {compiler: gcc, version: 14}
-        #   - os: macos-latest
-        #     build: debug
-        #     toolchain: {compiler: gcc, version: 15}
+        # include:
+        #   3.8 does not seem to work.
+        #   - os: ubuntu-latest
+        #     build: opt
+        #     python-version: 3.8
+        #     toolchain: {compiler: gcc, version: 14}
         exclude:
           - os: ubuntu-latest
             toolchain: {compiler: gcc, version: 15}
@@ -174,7 +172,3 @@ jobs:
         name: test_results
         path: ${{ env.CLAW }}/amrclaw/*_output
         if-no-files-found: ignore
-
-
-# lfortran
-# optimized = --openmp