Merge branch 'development' into diffusion_doc

Author: zingale

.github/workflows/clang-tidy.yml

@@ -25,7 +25,7 @@ jobs:
 
       - name: Install dependencies
         run: |
-          .github/workflows/dependencies_clang-tidy-apt-llvm.sh 19
+          .github/workflows/dependencies/dependencies_clang-tidy-apt-llvm.sh 19
 
       - name: Compile flame_wave
         run: |

.github/workflows/dependencies_clang-tidy-apt-llvm.sh renamed to .github/workflows/dependencies/dependencies_clang-tidy-apt-llvm.sh

@@ -40,6 +40,7 @@ echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/r
 
 # we should not need to export HIP_PATH=/opt/rocm/hip with those installs
 
+sudo apt-get clean
 sudo apt-get update
 
 # Ref.: https://rocmdocs.amd.com/en/latest/Installation_Guide/Installation-Guide.html#installing-development-packages-for-cross-compilation
@@ -56,7 +57,9 @@ sudo apt-get install -y --no-install-recommends \
     roctracer-dev   \
     rocprofiler-dev \
     rocrand-dev     \
-    rocprim-dev
+    rocfft-dev      \
+    rocprim-dev     \
+    rocsparse-dev
 
 # hiprand-dev is a new package that does not exist in old versions
 sudo apt-get install -y --no-install-recommends hiprand-dev || true

.github/workflows/dependencies_hip.sh renamed to .github/workflows/dependencies/dependencies_hip.sh

@@ -0,0 +1,42 @@
+#!/usr/bin/env bash
+#
+# Copyright 2020-2022 Axel Huebl
+#
+# License: BSD-3-Clause-LBNL
+
+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
+
+sudo apt-get -qqq update
+sudo apt-get install -y \
+    build-essential     \
+    ca-certificates     \
+    cmake               \
+    g++                 \
+    gfortran            \
+    gnupg               \
+    libopenmpi-dev      \
+    openmpi-bin         \
+    pkg-config          \
+    wget
+
+VERSION_DOTTED=${1-12.0} && VERSION_DASHED=$(sed 's/\./-/' <<< $VERSION_DOTTED)
+curl -O https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-keyring_1.0-1_all.deb
+sudo dpkg -i cuda-keyring_1.0-1_all.deb
+sudo apt-get update
+sudo apt-get install -y \
+    cuda-command-line-tools-$VERSION_DASHED \
+    cuda-compiler-$VERSION_DASHED           \
+    cuda-cupti-dev-$VERSION_DASHED          \
+    cuda-minimal-build-$VERSION_DASHED      \
+    cuda-nvml-dev-$VERSION_DASHED           \
+    cuda-nvtx-$VERSION_DASHED               \
+    libcublas-dev-$VERSION_DASHED           \
+    libcufft-dev-$VERSION_DASHED            \
+    libcurand-dev-$VERSION_DASHED           \
+    libcusparse-dev-$VERSION_DASHED
+sudo ln -s cuda-$VERSION_DOTTED /usr/local/cuda

.github/workflows/dependencies/dependencies_nvcc.sh

@@ -29,14 +29,7 @@ jobs:
           sudo apt-get -qq -y install curl cmake jq clang g++>=9.3.0
 
       - name: Install CUDA
-        # from https://developer.nvidia.com/cuda-downloads?target_os=Linux&target_arch=x86_64&Distribution=Ubuntu&target_version=20.04&target_type=deb_network
-        run: |
-          wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-ubuntu2004.pin
-          sudo mv cuda-ubuntu2004.pin /etc/apt/preferences.d/cuda-repository-pin-600
-          sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/3bf863cc.pub
-          sudo add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/ /"
-          sudo apt-get update
-          sudo apt-get -y install cuda-toolkit-11-8
+        run: .github/workflows/dependencies/dependencies_nvcc.sh 11.8
 
       - name: Install hypre
         run: |

.github/workflows/gpu_action.yml

@@ -24,7 +24,7 @@ jobs:
           cd ../..
 
       - name: Dependencies
-        run: .github/workflows/dependencies_hip.sh
+        run: .github/workflows/dependencies/dependencies_hip.sh
 
       - name: compile flame_wave
         run: |

.github/workflows/hip.yml

@@ -126,7 +126,7 @@ frequency, and :math:`m`, :math:`n` and :math:`p` are constants. For the gray so
 
 ::
 
-    Opacity_dir := rad_power_law
+    OPACITY_DIR := rad_power_law
 
 in your GNUmakefile. See § \ `3.3.1 <#sec:opacpars>`__ for instructions on how
 to configure the parameters used for this opacity setup. If you would prefer a different

Docs/source/radiation.rst

@@ -17,7 +17,7 @@ EOS_DIR     := gamma_law
 NETWORK_DIR := general_null
 NETWORK_INPUTS := gammalaw.net
 
-Opacity_dir := rad_power_law
+OPACITY_DIR := rad_power_law
 
 PROBLEM_DIR ?= ./
 

Exec/radiation_tests/Rad2Tshock/GNUmakefile

@@ -15,7 +15,7 @@ EOS_DIR     := gamma_law
 NETWORK_DIR := general_null
 NETWORK_INPUTS := gammalaw.net
 
-Opacity_dir := rad_power_law
+OPACITY_DIR := rad_power_law
 
 PROBLEM_DIR ?= ./
 

Exec/radiation_tests/RadBlastWave/GNUmakefile

@@ -18,7 +18,7 @@ CASTRO_HOME ?= ../../..
 EOS_DIR     = breakout
 NETWORK_DIR := general_null
 NETWORK_INPUTS = breakout.net
-Opacity_dir = breakout
+OPACITY_DIR = breakout
 
 PROBLEM_DIR ?= ./
 

Exec/radiation_tests/RadBreakout/GNUmakefile

@@ -17,7 +17,7 @@ EOS_DIR     := gamma_law
 NETWORK_DIR := general_null
 NETWORK_INPUTS := gammalaw.net
 
-Opacity_dir := rad_power_law
+OPACITY_DIR := rad_power_law
 
 PROBLEM_DIR ?= ./
 

Exec/radiation_tests/RadFront/GNUmakefile

@@ -17,7 +17,7 @@ EOS_DIR     := rad_power_law
 NETWORK_DIR := general_null
 NETWORK_INPUTS := gammalaw.net
 
-Opacity_dir := rad_power_law
+OPACITY_DIR := rad_power_law
 
 # number of radiation groups -  this needs to correspond to radiation.nGroups in
 # the inputs file

Exec/radiation_tests/RadShestakovBolstad/GNUmakefile

@@ -20,7 +20,7 @@ EOS_DIR     := rad_power_law
 NETWORK_DIR := general_null
 NETWORK_INPUTS := gammalaw.net
 
-Opacity_dir := rad_power_law
+OPACITY_DIR := rad_power_law
 
 # use radiation interpbndry
 RAD_INTERP = TRUE

Exec/radiation_tests/RadSourceTest/GNUmakefile

@@ -17,7 +17,7 @@ EOS_DIR     := rad_power_law
 NETWORK_DIR := general_null
 NETWORK_INPUTS := gammalaw.net
 
-Opacity_dir := rad_power_law
+OPACITY_DIR := rad_power_law
 
 # number of radiation groups -  this needs to correspond to radiation.nGroups in
 # the inputs file

Exec/radiation_tests/RadSphere/GNUmakefile

@@ -16,7 +16,7 @@ EOS_DIR     := rad_power_law
 NETWORK_DIR := general_null
 NETWORK_INPUTS := gammalaw.net
 
-Opacity_dir := rad_power_law
+OPACITY_DIR := rad_power_law
 
 PROBLEM_DIR ?= ./
 

Exec/radiation_tests/RadSuOlson/GNUmakefile

@@ -17,7 +17,7 @@ EOS_DIR     := rad_power_law
 NETWORK_DIR := general_null
 NETWORK_INPUTS := gammalaw.net
 
-Opacity_dir := rad_power_law
+OPACITY_DIR := rad_power_law
 
 NGROUPS := 2
 

Exec/radiation_tests/RadSuOlsonMG/GNUmakefile

@@ -17,7 +17,7 @@ EOS_DIR     := gamma_law
 NETWORK_DIR := general_null
 NETWORK_INPUTS := gammalaw.net
 
-Opacity_dir := rad_power_law
+OPACITY_DIR := rad_power_law
 
 PROBLEM_DIR ?= ./
 

Exec/radiation_tests/RadThermalWave/GNUmakefile

@@ -29,7 +29,7 @@ NETWORK_DIR := general_null
 NETWORK_INPUTS := H_He.net
 
 # power-law opacity
-Opacity_dir := rad_power_law
+OPACITY_DIR := rad_power_law
 
 PROBLEM_DIR ?= ./
 

Exec/science/bwp-rad/GNUmakefile

@@ -33,7 +33,7 @@ NETWORK_DIR := general_null
 NETWORK_INPUTS := ./taeho.net
 
 # power-law opacity
-Opacity_dir := rad_power_law
+OPACITY_DIR := rad_power_law
 
 PROBLEM_DIR ?= ./