Merge branch 'development' into ROCK4

AMReX-Astro · Jul 30, 2024 · 518f806 · 518f806
2 parents ba5a8fc + 727afa9
commit 518f806
Show file tree

Hide file tree

Showing 460 changed files with 58,590 additions and 22,517 deletions.
diff --git a/.codespellrc b/.codespellrc
@@ -1,5 +1,5 @@
 [codespell]
-skip = .git,*.ipynb,*.bib,*.ps,*~
+skip = .git,*.ipynb,*.bib,*.ps,*~,./util/autodiff
 ignore-words = .codespell-ignore-words
 
 
diff --git a/.editorconfig b/.editorconfig
@@ -53,8 +53,8 @@ indent_style = tab
 indent_size = unset
 
 
-[util/gcem/**]
-# don't mess with the gcem subtree
+[util/{autodiff,gcem}/**]
+# don't mess with the autodiff or gcem subtrees
 indent_style = unset
 indent_size = unset
 trim_trailing_whitespace = unset

diff --git a/.github/workflows/burn_cell.yml b/.github/workflows/burn_cell.yml
@@ -26,21 +26,21 @@ jobs:
           sudo apt-get update -y -qq
           sudo apt-get -qq -y install curl cmake jq clang g++>=9.3.0
 
-      - name: Compile, burn_cell (VODE, subch_approx)
+      - name: Compile, burn_cell (VODE, subch_simple)
         run: |
           cd unit_test/burn_cell
           make realclean
-          make NETWORK_DIR=subch_approx -j 4
+          make NETWORK_DIR=subch_simple -j 4
 
-      - name: Run burn_cell (VODE, subch_approx)
+      - name: Run burn_cell (VODE, subch_simple)
         run: |
           cd unit_test/burn_cell
-          ./main3d.gnu.ex inputs_subch_approx > test.out
+          ./main3d.gnu.ex inputs_subch_simple amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out
 
-      - name: Compare to stored output (VODE, subch_approx)
+      - name: Compare to stored output (VODE, subch_simple)
         run: |
           cd unit_test/burn_cell
-          diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/subch_approx_unit_test.out
+          diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/subch_simple_unit_test.out
 
       - name: Compile, burn_cell (VODE, ECSN)
         run: |
@@ -51,7 +51,9 @@ jobs:
       - name: Run burn_cell (VODE, ECSN)
         run: |
           cd unit_test/burn_cell
-          ./main3d.gnu.ex inputs_ecsn > test.out
+          # disable fpe_trap_overflow, as there's a spurious exception when
+          # calculating DEL in vode_dvnlsd.H.
+          ./main3d.gnu.ex inputs_ecsn amrex.fpe_trap_{invalid,zero}=1 > test.out
 
       - name: Compare to stored output (VODE, ECSN)
         run: |
@@ -67,7 +69,7 @@ jobs:
       - name: Run burn_cell (VODE, ignition_chamulak)
         run: |
           cd unit_test/burn_cell
-          ./main3d.gnu.ex inputs_ignition_chamulak > test.out
+          ./main3d.gnu.ex inputs_ignition_chamulak amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out
 
       - name: Compare to stored output (VODE, ignition_chamulak)
         run: |
@@ -83,28 +85,28 @@ jobs:
       - name: Run burn_cell (ForwardEuler, triple_alpha_plus_cago)
         run: |
           cd unit_test/burn_cell
-          ./main3d.gnu.ex inputs_triple > test.out
+          ./main3d.gnu.ex inputs_triple amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out
 
       - name: Compare to stored output (ForwardEuler, triple_alpha_plus_cago)
         run: |
           cd unit_test/burn_cell
           diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/triple_alpha_plus_cago_FE_unit_test.out
 
-      - name: Compile, burn_cell (BackwardEuler, subch_approx)
+      - name: Compile, burn_cell (BackwardEuler, subch_simple)
         run: |
           cd unit_test/burn_cell
           make realclean
-          make NETWORK_DIR=subch_approx INTEGRATOR_DIR=BackwardEuler -j 4
+          make NETWORK_DIR=subch_simple INTEGRATOR_DIR=BackwardEuler -j 4
 
-      - name: Run burn_cell (BackwardEuler, subch_approx)
+      - name: Run burn_cell (BackwardEuler, subch_simple)
         run: |
           cd unit_test/burn_cell
-          ./main3d.gnu.ex inputs_subch_approx > test.out
+          ./main3d.gnu.ex inputs_subch_simple amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out
 
-      - name: Compare to stored output (BackwardEuler, subch_approx)
+      - name: Compare to stored output (BackwardEuler, subch_simple)
         run: |
           cd unit_test/burn_cell
-          diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/subch_approx_BE_unit_test.out
+          diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/subch_simple_BE_unit_test.out
 
       - name: Compile, burn_cell (QSS, aprox13)
         run: |
@@ -115,7 +117,7 @@ jobs:
       - name: Run burn_cell (QSS, aprox13)
         run: |
           cd unit_test/burn_cell
-          ./main3d.gnu.ex inputs_aprox13 > test.out
+          ./main3d.gnu.ex inputs_aprox13 amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out
 
       - name: Compare to stored output (QSS, aprox13)
         run: |
@@ -131,9 +133,13 @@ jobs:
       - name: Run burn_cell (RKC, aprox13)
         run: |
           cd unit_test/burn_cell
-          ./main3d.gnu.ex inputs_aprox13 unit_test.temperature=1.e9 > test.out
+          ./main3d.gnu.ex inputs_aprox13 unit_test.temperature=1.e9 amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out
 
       - name: Compare to stored output (RKC, aprox13)
         run: |
           cd unit_test/burn_cell
           diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/aprox13_RKC_unit_test.out
+
+      - name: Print backtrace
+        if: ${{ failure() && hashFiles('unit_test/burn_cell/Backtrace.0') != '' }}
+        run: cat unit_test/burn_cell/Backtrace.0
diff --git a/.github/workflows/burn_cell_primordial_chem.yml b/.github/workflows/burn_cell_primordial_chem.yml
@@ -32,7 +32,11 @@ jobs:
         run: |
           cd unit_test/burn_cell_primordial_chem
           make -j 2
-          ./main1d.gnu.DEBUG.ex inputs_primordial_chem > test.out
+          ./main1d.gnu.DEBUG.ex inputs_primordial_chem amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out
+
+      - name: Print backtrace
+        if: ${{ failure() && hashFiles('unit_test/burn_cell_primordial_chem/Backtrace.0') != '' }}
+        run: cat unit_test/burn_cell_primordial_chem/Backtrace.0
 
       - name: Compare to stored output
         run: |

diff --git a/.github/workflows/burn_cell_sdc.yml b/.github/workflows/burn_cell_sdc.yml
@@ -35,7 +35,7 @@ jobs:
       - name: Run burn_cell_sdc (aprox19)
         run: |
           cd unit_test/burn_cell_sdc
-          ./main3d.gnu.ex inputs_aprox19.ci
+          ./main3d.gnu.ex inputs_aprox19.ci amrex.fpe_trap_{invalid,zero,overflow}=1
 
       - name: Compare to stored output (aprox19)
         run: |
@@ -51,7 +51,7 @@ jobs:
       - name: Run burn_cell_sdc (BackwardEuler, aprox19)
         run: |
           cd unit_test/burn_cell_sdc
-          ./main3d.gnu.ex inputs_aprox19.ci
+          ./main3d.gnu.ex inputs_aprox19.ci amrex.fpe_trap_{invalid,zero,overflow}=1
 
       - name: Compare to stored output (BackwardEuler, aprox19)
         run: |
@@ -67,10 +67,13 @@ jobs:
       - name: Run burn_cell_sdc (RKC, aprox19)
         run: |
           cd unit_test/burn_cell_sdc
-          ./main3d.gnu.ex inputs_aprox19.ci
+          ./main3d.gnu.ex inputs_aprox19.ci amrex.fpe_trap_{invalid,zero,overflow}=1
 
       - name: Compare to stored output (RKC, aprox19)
         run: |
           cd unit_test/burn_cell_sdc
           diff state_over_time.txt ci-benchmarks/aprox19_RKC_state_over_time.txt
 
+      - name: Print backtrace
+        if: ${{ failure() && hashFiles('unit_test/burn_cell_sdc/Backtrace.0') != '' }}
+        run: cat unit_test/burn_cell_sdc/Backtrace.0
diff --git a/.github/workflows/check_ifdefs.py b/.github/workflows/check_ifdefs.py
@@ -78,6 +78,9 @@ def check_file(filename):
         if "tmp_build_dir" in f.parts:
             # skip generated files
             continue
+        if f.parts[:2] == ("util", "autodiff"):
+            # skip third-party autodiff files
+            continue
         ierr, defines = check_file(f)
         all_defines += defines
         total_errors += ierr

diff --git a/.github/workflows/check_powi.py b/.github/workflows/check_powi.py
@@ -5,18 +5,21 @@
 
 
 def pow_to_powi(text):
-    # Finds all possible std::pow(x, n) or gcem::pow(x, n)
+    # Finds all possible std::pow(x, n), gcem::pow(x, n), or admath::pow(x, n)
     # where n is a potential integer to amrex::Math::powi<n>(x)
 
-    # Check for all positive and negative integer, whole float numbers
+    # Match all positive and negative integers, whole float numbers
     # with and without _rt
-    match_pattern = r"([^,]+),\s*(-?(?:\d+\.0*_rt?|\d))"
+    integer_pattern = r"-?(?:\d+\.0*(?:e0)?(?:_rt)?|\d)"
+
+    # Check for an integer in the second argument
+    match_pattern = rf"([^,]+),\s*({integer_pattern})"
 
     # Match fails when there is a nested pow, so only inner most pow is matched
-    negate_pattern = r"(?![\s\S]*(?:std|gcem)::pow\((?:[^,]+),\s*(?:-?(?:\d+\.0*_rt?|\d))\))"
+    negate_pattern = rf"(?![\s\S]*(?:std|gcem|admath)::pow\((?:[^,]+),\s*(?:{integer_pattern})\))"
 
     # Final pattern
-    pattern = rf"(?:std|gcem)::pow\({negate_pattern}{match_pattern}\)"
+    pattern = rf"(?:std|gcem|admath)::pow\({negate_pattern}{match_pattern}\)"
     # pattern = rf"(?:std|gcem)::pow\((?![\s\S]*(?:std|gcem)::pow\((?:[^,]+),\s*(?:-?(?:\d+\.0*_rt?|\d))\))([^,]+),\s*(-?(?:\d+\.0*_rt?|\d))\)"
 
     def replacement(match):
@@ -33,6 +36,8 @@ def replacement(match):
 def process_content(dir_path):
     # This function processes all text in the given directory
     for root, dirs, filenames in os.walk(dir_path):
+        if "util/autodiff/" in root:
+            continue
         for filename in filenames:
             if filename.endswith(".H") or filename.endswith(".cpp"):
                 filepath = os.path.join(root, filename)
@@ -58,9 +63,9 @@ def git_diff():
 
     # Print out suggested change and raise error after detecting modification
     if git_diff_output.stdout:
-        print("Detected potential usage to replace std::pow" +
-              "with integer powers via amrex::Math::powi\n")
-        print("Below are the suggested change:\n")
+        print("Detected potential usage to replace std::pow"
+              " with integer powers via amrex::Math::powi\n")
+        print("Below are the suggested changes:\n")
         print(git_diff_output.stdout)
 
         raise RuntimeError("Changes detected after modification")

diff --git a/.github/workflows/cuda.yml b/.github/workflows/cuda.yml
@@ -41,8 +41,8 @@ jobs:
           make realclean
           make NETWORK_DIR=ignition_reaclib/URCA-simple USE_CUDA=TRUE COMP=gnu USE_MPI=FALSE -j 2
 
-      - name: compile test_ase (ase)
+      - name: compile test_nse_net (ase)
         run: |
           export PATH=/usr/local/nvidia/bin:/usr/local/cuda/bin:${PATH}
-          cd unit_test/test_ase
+          cd unit_test/test_nse_net
           make USE_CUDA=TRUE COMP=gnu USE_MPI=FALSE -j 2
diff --git a/.github/workflows/eos_cell.yml b/.github/workflows/eos_cell.yml
@@ -35,7 +35,7 @@ jobs:
       - name: Run eos_cell (helmholtz)
         run: |
           cd unit_test/eos_cell
-          ./main3d.gnu.ex inputs_eos > test.out
+          ./main3d.gnu.ex inputs_eos amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out
 
       - name: Compare to stored output (helmholtz)
         run: |
@@ -51,11 +51,13 @@ jobs:
       - name: Run eos_cell (gamma_law)
         run: |
           cd unit_test/eos_cell
-          ./main3d.gnu.ex inputs_eos > test.out
+          ./main3d.gnu.ex inputs_eos amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out
 
       - name: Compare to stored output (gamma_law)
         run: |
           cd unit_test/eos_cell
           diff -I "^Initializing AMReX" -I "^AMReX" test.out ci-benchmarks/eos_gamma_law.out
 
-
+      - name: Print backtrace
+        if: ${{ failure() && hashFiles('unit_test/eos_cell/Backtrace.0') != '' }}
+        run: cat unit_test/eos_cell/Backtrace.0
diff --git a/.github/workflows/find_changed_files.py b/.github/workflows/find_changed_files.py
@@ -97,7 +97,7 @@ def run(SHAs=None, make_options=''):
 
     parser = argparse.ArgumentParser(description='')
     parser.add_argument('-make-options',
-                        default='-j 2',
+                        default='-j 4',
                         help='make options')
     parser.add_argument('SHAs', nargs='*', default=None,
                         help='SHAs to be compared')

diff --git a/.github/workflows/good_defines.txt b/.github/workflows/good_defines.txt
@@ -1,3 +1,4 @@
+ALLOW_GPU_PRINTF
 ALLOW_JACOBIAN_CACHING
 AMREX_USE_CUDA
 AMREX_USE_GPU

diff --git a/.github/workflows/nse_test.yml → .github/workflows/jac_cell.yml b/.github/workflows/nse_test.yml → .github/workflows/jac_cell.yml
@@ -1,8 +1,8 @@
-name: nse_test
+name: jac_cell
 
 on: [pull_request]
 jobs:
-  nse_test:
+  nse_table:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -26,19 +26,20 @@ jobs:
           sudo apt-get update -y -qq
           sudo apt-get -qq -y install curl cmake jq clang g++>=9.3.0
 
-      - name: Compile, test_nse (aprox21)
+      - name: Compile jac_cell
         run: |
-          cd unit_test/test_nse
-          make realclean
-          make NETWORK_DIR=aprox21 -j 4
+          cd unit_test/jac_cell
+          make -j 4
 
-      - name: Run test_nse (aprox21)
+      - name: Run jac_cell
         run: |
-          cd unit_test/test_nse
-          ./main3d.gnu.ex inputs_aprox21 > test.out
+          cd unit_test/jac_cell
+          ./main3d.gnu.ex inputs_aprox13 > test.out
 
-      - name: Compare to stored output (aprox21)
+      - name: Compare to stored output
         run: |
-          cd unit_test/test_nse
-          diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" -I "^0x" test.out ci-benchmarks/aprox21_ci.out
+          cd unit_test/jac_cell
+          diff -I "^Initializing AMReX" -I "^AMReX"  test.out ci-benchmarks/jac_cell_aprox13.out
+
+
 
diff --git a/.github/workflows/nse_net.yml b/.github/workflows/nse_net.yml
@@ -26,34 +26,42 @@ jobs:
           sudo apt-get update -y -qq
           sudo apt-get -qq -y install curl cmake jq clang g++>=9.3.0
 
-      - name: Compile, test_ase (NSE_NET, ase)
+      - name: Compile, test_nse_net (NSE_NET, ase)
         run: |
-          cd unit_test/test_ase
+          cd unit_test/test_nse_net
           make realclean
           make -j 4
 
-      - name: Run test_ase (NSE_NET, ase)
+      - name: Run test_nse_net (NSE_NET, ase)
         run: |
-          cd unit_test/test_ase
-          ./main3d.gnu.ex inputs_ase > test.out
+          cd unit_test/test_nse_net
+          ./main3d.gnu.ex inputs_ase amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out
+
+      - name: Print backtrace
+        if: ${{ failure() && hashFiles('unit_test/test_nse_net/Backtrace.0') != '' }}
+        run: cat unit_test/test_nse_net/Backtrace.0
 
       - name: Compare to stored output (NSE_NET, ase)
         run: |
-          cd unit_test/test_ase
-          diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/ase_nse_net_unit_test.out
+          cd unit_test/test_nse_net
+          diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/nse_net_unit_test.out
 
-      - name: Compile, test_ase/make_table (NSE_NET, ase, make_table)
+      - name: Compile, test_nse_net/make_table (NSE_NET, ase, make_table)
         run: |
-          cd unit_test/test_ase/make_table
+          cd unit_test/test_nse_net/make_table
           make realclean
           make -j 4
 
-      - name: Run, test_ase/make_table (NSE_NET, ase, make_table)
+      - name: Run, test_nse_net/make_table (NSE_NET, ase, make_table)
         run: |
-          cd unit_test/test_ase/make_table
-          ./main3d.gnu.ex > test.out
+          cd unit_test/test_nse_net/make_table
+          ./main3d.gnu.ex amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out
+
+      - name: Print backtrace
+        if: ${{ failure() && hashFiles('unit_test/test_nse_net/make_table/Backtrace.0') != '' }}
+        run: cat unit_test/test_nse_net/make_table/Backtrace.0
 
       - name: Compare to stored output (NSE_NET, ase, make_table)
         run: |
-          cd unit_test/test_ase/make_table
-          diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/ase_nse_net_make_table_unit_test.out
+          cd unit_test/test_nse_net/make_table
+          diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/nse_net_make_table_unit_test.out