Merge branch 'development' into front_tracker_fixes

.github/workflows/dependencies/dependencies_hip.sh

@@ -33,7 +33,9 @@ sudo apt-key add rocm.gpg.key
 
 source /etc/os-release # set UBUNTU_CODENAME: focal or jammy or ...
 
-echo "deb [arch=amd64] https://repo.radeon.com/rocm/apt/${1-latest} ${UBUNTU_CODENAME} main" \
+VERSION=${1-6.3.2}
+
+echo "deb [arch=amd64] https://repo.radeon.com/rocm/apt/${VERSION} ${UBUNTU_CODENAME} main" \
   | sudo tee /etc/apt/sources.list.d/rocm.list
 echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:$PATH' \
   | sudo tee -a /etc/profile.d/rocm.sh
@@ -53,16 +55,16 @@ sudo apt-get install -y --no-install-recommends \
     libnuma-dev     \
     libopenmpi-dev  \
     openmpi-bin     \
-    rocm-dev        \
-    roctracer-dev   \
-    rocprofiler-dev \
-    rocrand-dev     \
-    rocfft-dev      \
-    rocprim-dev     \
-    rocsparse-dev
+    rocm-dev${VERSION}        \
+    roctracer-dev${VERSION}   \
+    rocprofiler-dev${VERSION} \
+    rocrand-dev${VERSION}     \
+    rocfft-dev${VERSION}      \
+    rocprim-dev${VERSION}     \
+    rocsparse-dev${VERSION}
 
 # hiprand-dev is a new package that does not exist in old versions
-sudo apt-get install -y --no-install-recommends hiprand-dev || true
+sudo apt-get install -y --no-install-recommends hiprand-dev${VERSION} || true
 
 # activate
 #

.github/workflows/hip.yml

@@ -8,7 +8,7 @@ concurrency:
 
 jobs:
   hip-compile:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - uses: actions/checkout@v4
         with:
@@ -24,7 +24,7 @@ jobs:
           cd ../..
 
       - name: Dependencies
-        run: .github/workflows/dependencies/dependencies_hip.sh
+        run: .github/workflows/dependencies/dependencies_hip.sh 6.3.2
 
       - name: compile flame_wave
         run: |

Docs/source/build_system.rst

@@ -135,12 +135,8 @@ Microphysics Parameters
 
     .. index:: USE_REACT, general_null, GENERAL_NET_INPUTS, NETWORK_DIR, INTEGRATOR_DIR
 
-  * ``USE_REACT_SPARSE_JACOBIAN``
-
-  * ``USE_SPARSE_STOP_ON_OOB``
-
-  * ``EOS_DIR``: the equation of state to use.  This will be a subdirectory under the
-    Microphysics repo.
+    * ``EOS_DIR``: the equation of state to use.  This will be a subdirectory under the
+      Microphysics repo.
 
     .. index:: EOS_DIR
 
@@ -275,5 +271,3 @@ This is the current build system process.
 
 For all of this to work, we need the ``tmp_build_dir/s`` directory to
 be first in the vpath, so our modified sources are found and used.
-
-

Exec/Make.Castro

@@ -201,17 +201,6 @@ ifeq ($(USE_REACT), TRUE)
   DEFINES += -DREACTIONS
 endif
 
-ifeq ($(USE_REACT_SPARSE_JACOBIAN), TRUE)
-  DEFINES += -DREACT_SPARSE_JACOBIAN
-
-  # The following is sometimes useful to turn on for debugging sparse J indices
-  # (if a get/set/scale is called with (row, col) not in the sparse J, stop)
-  # Otherwise, set/scale do nothing, and get returns 0.
-  ifeq ($(USE_SPARSE_STOP_ON_OOB), TRUE)
-    DEFINES += -DSPARSE_STOP_ON_OOB
-  endif
-endif
-
 ifeq ($(USE_SIMPLIFIED_SDC), TRUE)
   DEFINES += -DSDC_EVOLVE_ENERGY
 endif

Exec/science/Detonation/GNUmakefile

@@ -18,7 +18,7 @@ EOS_DIR     := helmholtz
 
 # This sets the network directory in $(MICROPHYSICS_HOME)/networks
 ifeq ($(USE_NSE_NET), TRUE)
-	NETWORK_DIR := subch_base
+	NETWORK_DIR := he-burn/he-burn-18a
 	SCREEN_METHOD := chabrier1998
 else
 	NETWORK_DIR := aprox19

Exec/science/subch_planar/GNUmakefile

@@ -25,7 +25,7 @@ CASTRO_HOME ?= ../../..
 EOS_DIR     := helmholtz
 
 # This sets the network directory in $(MICROPHYSICS_HOME)/networks
-NETWORK_DIR := subch_simple
+NETWORK_DIR := he-burn/he-burn-22a
 
 PROBLEM_DIR ?= ./
 

Exec/science/subchandra/GNUmakefile

@@ -23,7 +23,7 @@ USE_SIMPLIFIED_SDC=TRUE
 EOS_DIR     := helmholtz
 
 # This sets the network directory in $(MICROPHYSICS_HOME)/networks
-NETWORK_DIR := subch_simple
+NETWORK_DIR := he-burn/he-burn-22a
 
 INTEGRATOR_DIR := VODE
 

Exec/science/subchandra/GNUmakefile.nse_net

@@ -23,7 +23,7 @@ USE_MODEL_PARSER = TRUE
 EOS_DIR     := helmholtz
 
 # This sets the network directory in $(MICROPHYSICS_HOME)/networks
-NETWORK_DIR := subch_base
+NETWORK_DIR := he-burn/he-burn-18a
 SCREEN_METHOD = chabrier1998
 
 INTEGRATOR_DIR := VODE

Exec/science/xrb_spherical/GNUmakefile

@@ -26,7 +26,7 @@ NUM_MODELS := 2
 EOS_DIR     := helmholtz
 
 # This sets the network directory in $(MICROPHYSICS_HOME)/networks
-NETWORK_DIR := subch_base
+NETWORK_DIR := he-burn/he-burn-18a
 
 INTEGRATOR_DIR := VODE
 

Source/driver/Castro.cpp

@@ -4490,7 +4490,7 @@ Castro::check_for_nan(const MultiFab& state_in, int check_ghost)
   }
 
   if (state_in.contains_nan(URHO,state_in.nComp(),ng,true)) {
-#ifdef AMREX_USE_GPU
+#if defined(AMREX_USE_GPU) && !defined(ALLOW_GPU_PRINTF)
       std::string abort_string = std::string("State has NaNs in check_for_nan()");
       amrex::Abort(abort_string.c_str());
 #else

Source/hydro/Castro_ctu.cpp

@@ -375,8 +375,8 @@ Castro::add_sdc_source_to_states(const Box& bx, const int idir, const Real dt,
 
             if (n >= QFS && n <= QFS-1+NumSpec) {
                 // mass fractions should be in [0, 1]
-                qleft(i,j,k,n) = std::clamp(qleft(i,j,k,n), 0.0_rt, 1.0_rt);
-                qright(i,j,k,n) = std::clamp(qright(i,j,k,n), 0.0_rt, 1.0_rt);
+                qleft(i,j,k,n) = amrex::Clamp(qleft(i,j,k,n), 0.0_rt, 1.0_rt);
+                qright(i,j,k,n) = amrex::Clamp(qright(i,j,k,n), 0.0_rt, 1.0_rt);
             }
         }
 

Source/hydro/HLL_solvers.H

@@ -488,7 +488,7 @@ namespace HLL {
         }
 
         Real frac = (1.0_rt + (spout + spin)/scr)*0.5_rt;
-        frac = std::clamp(frac, 0.0_rt, 1.0_rt);
+        frac = amrex::Clamp(frac, 0.0_rt, 1.0_rt);
 
         Real qint[NQ] = {0.0};
 

Source/hydro/flatten.H

@@ -24,7 +24,7 @@ Real flatten(int i, int j, int k,
 
     Real denom = std::max(small_pres, std::abs(q_arr(i+2,j,k,pres_comp) - q_arr(i-2,j,k,pres_comp)));
     Real zeta = std::abs(dp) / denom;
-    Real z = std::clamp(dzcut * (zeta - zcut1), 0.0_rt, 1.0_rt);
+    Real z = amrex::Clamp(dzcut * (zeta - zcut1), 0.0_rt, 1.0_rt);
 
     Real tst = 0.0_rt;
     if (q_arr(i-1,j,k,QU) - q_arr(i+1,j,k,QU) >= 0.0_rt) {
@@ -43,7 +43,7 @@ Real flatten(int i, int j, int k,
 
     denom = std::max(small_pres, std::abs(q_arr(i+2-ishft,j,k,pres_comp)-q_arr(i-2-ishft,j,k,pres_comp)));
     zeta = std::abs(dp) / denom;
-    Real z2 = std::clamp(dzcut * (zeta - zcut1), 0.0_rt, 1.0_rt);
+    Real z2 = amrex::Clamp(dzcut * (zeta - zcut1), 0.0_rt, 1.0_rt);
 
     tst = 0.0_rt;
     if (q_arr(i-1-ishft,j,k,QU) - q_arr(i+1-ishft,j,k,QU) >= 0.0_rt) {
@@ -69,7 +69,7 @@ Real flatten(int i, int j, int k,
 
     denom = std::max(small_pres, std::abs(q_arr(i,j+2,k,pres_comp) - q_arr(i,j-2,k,pres_comp)));
     zeta = std::abs(dp) / denom;
-    z = std::clamp(dzcut * (zeta - zcut1), 0.0_rt, 1.0_rt);
+    z = amrex::Clamp(dzcut * (zeta - zcut1), 0.0_rt, 1.0_rt);
 
     tst = 0.0_rt;
     if (q_arr(i,j-1,k,QV) - q_arr(i,j+1,k,QV) >= 0.0_rt) {
@@ -88,7 +88,7 @@ Real flatten(int i, int j, int k,
 
     denom = std::max(small_pres, std::abs(q_arr(i,j+2-ishft,k,pres_comp) - q_arr(i,j-2-ishft,k,pres_comp)));
     zeta = std::abs(dp) / denom;
-    z2 = std::clamp(dzcut * (zeta - zcut1), 0.0_rt, 1.0_rt);
+    z2 = amrex::Clamp(dzcut * (zeta - zcut1), 0.0_rt, 1.0_rt);
 
     tst = 0.0_rt;
     if (q_arr(i,j-1-ishft,k,QV) - q_arr(i,j+1-ishft,k,QV) >= 0.0_rt) {
@@ -115,7 +115,7 @@ Real flatten(int i, int j, int k,
 
     denom = std::max(small_pres, std::abs(q_arr(i,j,k+2,pres_comp) - q_arr(i,j,k-2,pres_comp)));
     zeta = std::abs(dp) / denom;
-    z = std::clamp(dzcut * (zeta - zcut1), 0.0_rt, 1.0_rt);
+    z = amrex::Clamp(dzcut * (zeta - zcut1), 0.0_rt, 1.0_rt);
 
     tst = 0.0_rt;
     if (q_arr(i,j,k-1,QW) - q_arr(i,j,k+1,QW) >= 0.0_rt) {
@@ -134,7 +134,7 @@ Real flatten(int i, int j, int k,
 
     denom = std::max(small_pres, std::abs(q_arr(i,j,k+2-ishft,pres_comp) - q_arr(i,j,k-2-ishft,pres_comp)));
     zeta = std::abs(dp) / denom;
-    z2 = std::clamp(dzcut * (zeta - zcut1), 0.0_rt, 1.0_rt);
+    z2 = amrex::Clamp(dzcut * (zeta - zcut1), 0.0_rt, 1.0_rt);
 
     tst = 0.0_rt;
     if (q_arr(i,j,k-1-ishft,QW) - q_arr(i,j,k+1-ishft,QW) >= 0.0_rt) {

Source/hydro/ppm.H

@@ -87,7 +87,7 @@ ppm_reconstruct(const amrex::Real* s,
 
         // Make sure sedge lies in between adjacent cell-centered values
 
-        sm = std::clamp(sm, std::min(s[i0], s[im1]), std::max(s[i0], s[im1]));
+        sm = amrex::Clamp(sm, std::min(s[i0], s[im1]), std::max(s[i0], s[im1]));
 
         // Compute van Leer slopes
 
@@ -115,7 +115,7 @@ ppm_reconstruct(const amrex::Real* s,
 
         // Make sure sedge lies in between adjacent cell-centered values
 
-        sp = std::clamp(sp, std::min(s[ip1], s[i0]), std::max(s[ip1], s[i0]));
+        sp = amrex::Clamp(sp, std::min(s[ip1], s[i0]), std::max(s[ip1], s[i0]));
 
 
         // Flatten the parabola

Source/hydro/riemann_2shock_solvers.H

@@ -29,7 +29,7 @@ namespace TwoShock {
 
       // CG Eq. 31
       gstar = (pstar-p)*gdot/(pstar+p) + gam;
-      gstar = std::clamp(gstar, gmin, gmax);
+      gstar = amrex::Clamp(gstar, gmin, gmax);
 
       // Now use that predicted value of game with the R-H jump conditions
       // to compute the wave speed.
@@ -666,7 +666,7 @@ namespace TwoShock {
 
       // interpolate for the case that we are in a rarefaction
       amrex::Real frac = (1.0_rt + (spout + spin)/scr)*0.5_rt;
-      frac = std::clamp(frac, 0.0_rt, 1.0_rt);
+      frac = amrex::Clamp(frac, 0.0_rt, 1.0_rt);
 
       qint.rho = frac*rstar + (1.0_rt - frac)*ro;
       qint.un = frac*ustar + (1.0_rt - frac)*uo;

Source/sdc/sdc_react_util.H

@@ -35,7 +35,7 @@ single_zone_react_source(burn_t& burn_state,
     eos(eos_input_re, burn_state);
 
     // eos_get_small_temp(&small_temp);
-    burn_state.T = std::clamp(burn_state.T, small_temp, integrator_rp::MAX_TEMP);
+    burn_state.T = amrex::Clamp(burn_state.T, small_temp, integrator_rp::MAX_TEMP);
 
     Array1D<Real, 1, neqs> ydot;
 

Util/exact_riemann/exact_riemann_shock.H

@@ -76,7 +76,7 @@ newton_shock(amrex::Real& W_s, const amrex::Real pstar,
             converged = true;
         }
 
-        W_s = std::clamp(W_s + dW, 0.5_rt * W_s, 2.0_rt * W_s);
+        W_s = amrex::Clamp(W_s + dW, 0.5_rt * W_s, 2.0_rt * W_s);
 
         // store some history
 

Util/exact_riemann/exact_riemann_star_state.H

@@ -149,7 +149,7 @@ riemann_star_state(const amrex::Real rho_l, const amrex::Real u_l, const amrex::
         }
 
         // get ready for the next iteration
-        pstar = std::clamp(pstar_new, 0.5 * pstar, 2.0 * pstar);
+        pstar = amrex::Clamp(pstar_new, 0.5 * pstar, 2.0 * pstar);
 
         iter++;
     }

Util/model_parser/model_parser.H

@@ -129,7 +129,7 @@ interpolate(const Real r, const int var_index, const int model_index=0) {
                                model::profile(model_index).state(id, var_index));
         Real maxvar = std::max(model::profile(model_index).state(id+1, var_index),
                                model::profile(model_index).state(id, var_index));
-        interp = std::clamp(interp, minvar, maxvar);
+        interp = amrex::Clamp(interp, minvar, maxvar);
     }
 
     return interp;

Util/model_parser/test/GNUmakefile

@@ -23,7 +23,7 @@ NUM_MODELS := 2
 EOS_DIR     := helmholtz
 
 # This sets the network directory in Castro/Networks
-NETWORK_DIR := subch_simple
+NETWORK_DIR := he-burn/he-burn-22a
 
 EXTERN_SEARCH += .