Merge branch 'development' of ssh://github.com/AMReX-Astro/Castro int…

…o development
AMReX-Astro · Dec 18, 2023 · de72a2a · de72a2a
2 parents 6f2aa14 + e65b3b9
commit de72a2a
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diff --git a/.github/workflows/dependencies_hip.sh b/.github/workflows/dependencies_hip.sh
@@ -1,17 +1,26 @@
 #!/usr/bin/env bash
 #
-# Copyright 2020-2022 The AMReX Community
+# Copyright 2020 The AMReX Community
 #
 # License: BSD-3-Clause-LBNL
 # Authors: Axel Huebl
 
+# search recursive inside a folder if a file contains tabs
+#
+# @result 0 if no files are found, else 1
+#
+
 set -eu -o pipefail
 
+# `man apt.conf`:
+#   Number of retries to perform. If this is non-zero APT will retry
+#   failed files the given number of times.
+echo 'Acquire::Retries "3";' | sudo tee /etc/apt/apt.conf.d/80-retries
 
 # Ref.: https://rocmdocs.amd.com/en/latest/Installation_Guide/Installation-Guide.html#ubuntu
 curl -O https://repo.radeon.com/rocm/rocm.gpg.key
 sudo apt-key add rocm.gpg.key
-echo 'deb [arch=amd64] https://repo.radeon.com/rocm/apt/debian/ ubuntu main' \
+echo "deb [arch=amd64] https://repo.radeon.com/rocm/apt/${1-debian}/ ubuntu main" \
   | sudo tee /etc/apt/sources.list.d/rocm.list
 echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:$PATH' \
   | sudo tee -a /etc/profile.d/rocm.sh
@@ -34,12 +43,14 @@ sudo apt-get install -y --no-install-recommends \
     roctracer-dev   \
     rocprofiler-dev \
     rocrand-dev     \
-    rocprim-dev
+    rocprim-dev     \
+    hiprand-dev
 
 # activate
 #
 source /etc/profile.d/rocm.sh
 hipcc --version
+hipconfig --full
 which clang
 which clang++
 which flang
diff --git a/Exec/Make.Castro b/Exec/Make.Castro
@@ -270,6 +270,10 @@ ifeq ($(USE_ROTATION), TRUE)
   DEFINES += -DROTATION
 endif
 
+ifeq ($(USE_SPECIES_SOURCES), TRUE)
+  DEFINES += -DCONS_SPECIES_HAVE_SOURCES
+endif
+
 ifeq ($(USE_PARTICLES), TRUE)
   Bdirs += Source/particles
 endif

diff --git a/Source/driver/Castro.cpp b/Source/driver/Castro.cpp
@@ -1260,8 +1260,7 @@ Castro::initData ()
              {
                const Box& box = mfi.validbox();
 
-               tmp.resize(box, 1);
-               Elixir elix_tmp = tmp.elixir();
+               tmp.resize(box, 1, The_Async_Arena());
                auto tmp_arr = tmp.array();
 
                make_fourth_in_place(box, Sborder.array(mfi), tmp_arr, domain_lo, domain_hi);
@@ -1287,8 +1286,7 @@ Castro::initData ()
            {
              const Box& box = mfi.growntilebox(2);
 
-             tmp.resize(box, 1);
-             Elixir elix_tmp = tmp.elixir();
+             tmp.resize(box, 1, The_Async_Arena());
              auto tmp_arr = tmp.array();
 
              make_cell_center_in_place(box, Sborder.array(mfi), tmp_arr, domain_lo, domain_hi);
@@ -1336,8 +1334,7 @@ Castro::initData ()
            {
              const Box& box = mfi.validbox();
 
-             tmp.resize(box, 1);
-             Elixir elix_tmp = tmp.elixir();
+             tmp.resize(box, 1, The_Async_Arena());
              auto tmp_arr = tmp.array();
 
              make_fourth_in_place(box, Sborder.array(mfi), tmp_arr, domain_lo, domain_hi);
@@ -3950,8 +3947,7 @@ Castro::computeTemp(
       compute_lap_term(bx0, Stemp.array(mfi), Eint_lap.array(mfi), UEINT,
                        domain_lo, domain_hi);
 
-      tmp.resize(bx, 1);
-      Elixir elix_tmp = tmp.elixir();
+      tmp.resize(bx, 1, The_Async_Arena());
       auto tmp_arr = tmp.array();
 
       make_cell_center_in_place(bx, Stemp.array(mfi), tmp_arr, domain_lo, domain_hi);
@@ -4067,8 +4063,7 @@ Castro::computeTemp(
 
       const Box& bx = mfi.tilebox();
 
-      tmp.resize(bx, 1);
-      Elixir elix_tmp = tmp.elixir();
+      tmp.resize(bx, 1, The_Async_Arena());
       auto tmp_arr = tmp.array();
 
       // only temperature

diff --git a/Source/driver/Castro_advance_sdc.cpp b/Source/driver/Castro_advance_sdc.cpp
@@ -122,8 +122,7 @@ Castro::do_advance_sdc (Real time,
           for (MFIter mfi(S_new); mfi.isValid(); ++mfi) {
             const Box& bx = mfi.tilebox();
 
-            tmp.resize(bx, 1);
-            Elixir elix_tmp = tmp.elixir();
+            tmp.resize(bx, 1, The_Async_Arena());
             auto tmp_arr = tmp.array();
 
             make_fourth_in_place(bx, old_source.array(mfi), tmp_arr, domain_lo, domain_hi);
@@ -305,8 +304,7 @@ Castro::do_advance_sdc (Real time,
       // pass in the reaction source at centers (Sburn_arr), including
       // one ghost cell and derive everything that is needed including
       // 1 ghost cell
-      R_center.resize(obx, R_new.nComp());
-      Elixir elix_r_center = R_center.elixir();
+      R_center.resize(obx, R_new.nComp(), The_Async_Arena());
       auto const R_center_arr = R_center.array();
 
       Array4<const Real> const Sburn_arr = Sburn.array(mfi);
@@ -315,8 +313,7 @@ Castro::do_advance_sdc (Real time,
       ca_store_reaction_state(obx, Sburn_arr, R_center_arr);
 
       // convert R_new from centers to averages in place
-      tmp.resize(bx, 1);
-      Elixir elix_tmp = tmp.elixir();
+      tmp.resize(bx, 1, The_Async_Arena());
       auto const tmp_arr = tmp.array();
 
       make_fourth_in_place(bx, R_center_arr, tmp_arr, domain_lo, domain_hi);

diff --git a/Source/driver/Derive.cpp b/Source/driver/Derive.cpp
@@ -352,8 +352,7 @@ extern "C"
       const Box& obx = amrex::grow(bx, 1);
 
       FArrayBox coeff_cc;
-      coeff_cc.resize(obx, 1);
-      Elixir elix_coeff_cc = coeff_cc.elixir();
+      coeff_cc.resize(obx, 1, The_Async_Arena());
       Array4<Real> const coeff_arr = coeff_cc.array();
 
       auto const dat = datfab.array();

diff --git a/Source/driver/_cpp_parameters b/Source/driver/_cpp_parameters
@@ -84,9 +84,11 @@ hybrid_hydro                 int           0
 # reconstruction type:
 # 0: piecewise linear;
 # 1: classic Colella \& Woodward ppm;
-# 2: extrema-preserving ppm
 ppm_type                     int           1
 
+# do we limit the ppm parabola?
+ppm_do_limiting              int           1
+
 # For MHD + PLM, do we limit on characteristic or primitive variables
 mhd_limit_characteristic     int           1
 

diff --git a/Source/driver/_variables b/Source/driver/_variables
@@ -16,9 +16,9 @@
    energy-density         UEDEN     NSRC                                  1                 None
    internal-energy        UEINT     NSRC                                  1                 None
    temperature            UTEMP     NSRC                                  1                 None
-   advected               UFA       None                                  NumAdv            None
-   species                UFS       None                                  NumSpec           None
-   auxiliary              UFX       None                                  NumAux            None
+   advected               UFA       [(NSRC, CONS_SPECIES_HAVE_SOURCES)]   NumAdv            None
+   species                UFS       [(NSRC, CONS_SPECIES_HAVE_SOURCES)]   NumSpec           None
+   auxiliary              UFX       [(NSRC, CONS_SPECIES_HAVE_SOURCES)]   NumAux            None
    shock                  USHK      None                                  1                 SHOCK_VAR
    mu_p                   UMUP      None                                  1                 NSE_NET
    mu_n                   UMUN      None                                  1                 NSE_NET