Merge branch 'next' of github.com:boutproject/BOUT-dev into lazy-grid…

…-loading

.gitlab-ci.yml

@@ -0,0 +1,98 @@
+###############################################################################
+# Copyright (c) 2022-23, Lawrence Livermore National Security, LLC and RADIUSS
+# project contributors. See the COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (MIT)
+###############################################################################
+
+# DESCRIPTION:
+###############################################################################
+# General GitLab pipelines configurations for supercomputers and Linux clusters
+# at Lawrence Livermore National Laboratory (LLNL).
+# This entire pipeline is LLNL-specific
+#
+# Important note: This file is a template provided by llnl/radiuss-shared-ci.
+# Remains to set variable values, change the reference to the radiuss-shared-ci
+# repo, opt-in and out optional features. The project can then extend it with
+# additional stages.
+#
+# In addition, each project should copy over and complete:
+# - .gitlab/custom-jobs-and-variables.yml
+# - .gitlab/subscribed-pipelines.yml
+#
+# The jobs should be specified in a file local to the project,
+# - .gitlab/jobs/${CI_MACHINE}.yml
+# or generated (see LLNL/Umpire for an example).
+###############################################################################
+
+# We define the following GitLab pipeline variables:
+variables:
+##### LC GITLAB CONFIGURATION
+# Use an LLNL service user to run CI. This prevents from running pipelines as
+# an actual user.
+  LLNL_SERVICE_USER: ""
+# Use the service user workspace. Solves permission issues, stores everything
+# at the same location whoever triggers a pipeline.
+  CUSTOM_CI_BUILDS_DIR: "/usr/workspace/BOUT-GPU/gitlab-runner"
+# Tells Gitlab to recursively update the submodules when cloning the project.
+#  GIT_SUBMODULE_STRATEGY: recursive
+
+##### PROJECT VARIABLES
+# We build the projects in the CI clone directory.
+# Used in script/gitlab/build_and_test.sh script.
+# TODO: add a clean-up mechanism.
+  BUILD_ROOT: ${CI_PROJECT_DIR}
+
+##### SHARED_CI CONFIGURATION
+# Required information about GitHub repository
+  GITHUB_PROJECT_NAME: "boutproject"
+  GITHUB_PROJECT_ORG: "BOUT-dev"
+# Set the build-and-test command.
+# Nested variables are allowed and useful to customize the job command. We
+# prevent variable expansion so that you can define them at job level.
+  JOB_CMD:
+    value: "tests/gitlab/ci-tests.sh"
+    expand: false
+# Override the pattern describing branches that will skip the "draft PR filter
+# test".  Add protected branches here. See default value in
+# preliminary-ignore-draft-pr.yml.
+#  ALWAYS_RUN_PATTERN: ""
+
+# We organize the build-and-test stage with sub-pipelines. Each sub-pipeline
+# corresponds to a test batch on a given machine.
+
+# High level stages
+stages:
+  - prerequisites
+  - build-and-test
+
+# Template for jobs triggering a build-and-test sub-pipeline:
+.build-and-test:
+  stage: build-and-test
+  trigger:
+    include:
+      - local: '.gitlab/custom-jobs-and-variables.yml'
+      - project: 'radiuss/radiuss-shared-ci'
+        ref: 'v2024.07.0'
+        file: 'pipelines/${CI_MACHINE}.yml'
+      # Add your jobs
+      # you can use a local file
+      - local: '.gitlab/jobs/${CI_MACHINE}.yml'
+      # or a file generated in the previous steps
+      # - artifact: '${CI_MACHINE}-jobs.yml'
+      #   job: 'generate-job-file'
+      # (See Umpire CI setup for an example).
+    strategy: depend
+    forward:
+      pipeline_variables: true
+
+include:
+  # Sets ID tokens for every job using `default:`
+  - project: 'lc-templates/id_tokens'
+    file: 'id_tokens.yml'
+  # [Optional] checks preliminary to running the actual CI test
+  - project: 'radiuss/radiuss-shared-ci'
+    ref: 'v2024.07.0'
+    file: 'utilities/preliminary-ignore-draft-pr.yml'
+  # pipelines subscribed by the project
+  - local: '.gitlab/subscribed-pipelines.yml'

.gitlab/custom-jobs-and-variables.yml

@@ -0,0 +1,62 @@
+###############################################################################
+# Copyright (c) 2022-23, Lawrence Livermore National Security, LLC and RADIUSS
+# project contributors. See the COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (MIT)
+###############################################################################
+
+# We define the following GitLab pipeline variables:
+variables:
+# In some pipelines we create only one allocation shared among jobs in
+# order to save time and resources. This allocation has to be uniquely
+# named so that we are sure to retrieve it and avoid collisions.
+  ALLOC_NAME: ${CI_PROJECT_NAME}_ci_${CI_PIPELINE_ID}
+
+# Ruby
+# Arguments for top level allocation
+  RUBY_SHARED_ALLOC: "--mpi=none --exclusive --reservation=ci --time=20 --nodes=1"
+# Arguments for job level allocation
+  RUBY_JOB_ALLOC: "--mpi=none --reservation=ci --nodes=1"
+# Add variables that should apply to all the jobs on a machine:
+#  RUBY_MY_VAR: "..."
+
+# Poodle
+# Arguments for top level allocation
+  POODLE_SHARED_ALLOC: "--exclusive --partition=pdebug --time=10 --nodes=1"
+# Arguments for job level allocation
+  POODLE_JOB_ALLOC: "--nodes=1"
+# Add variables that should apply to all the jobs on a machine:
+#  POODLE_MY_VAR: "..."
+
+# Corona
+# Arguments for top level allocation
+# OPTIONAL: "-o per-resource.count=2" allows to get 2 jobs running on each node.
+  CORONA_SHARED_ALLOC: "--exclusive --time-limit=15m --nodes=1"
+# Arguments for job level allocation
+  CORONA_JOB_ALLOC: "--nodes=1 --begin-time=+5s"
+# Add variables that should apply to all the jobs on a machine:
+#  CORONA_MY_VAR: "..."
+
+# Tioga
+# Arguments for top level allocation
+# OPTIONAL: "-o per-resource.count=2" allows to get 2 jobs running on each node.
+  TIOGA_SHARED_ALLOC: "--queue=pci --exclusive --time-limit=15m --nodes=1"
+# Arguments for job level allocation
+  TIOGA_JOB_ALLOC: "--nodes=1 --begin-time=+5s"
+# Add variables that should apply to all the jobs on a machine:
+#  TIOGA_MY_VAR: "..."
+
+# Lassen uses a different job scheduler (spectrum lsf) that does not allow
+# pre-allocation the same way slurm does. Arguments for job level allocation
+  LASSEN_JOB_ALLOC: "1 -W 30 -q pci"
+# Add variables that should apply to all the jobs on a machine:
+#  LASSEN_MY_VAR: "..."
+
+
+# Configuration shared by build and test jobs specific to this project.
+# Not all configuration can be shared. Here projects can fine tune the
+# CI behavior.
+# See Umpire for an example (export junit test reports).
+.custom_job:
+  variables:
+    JOB_TEMPLATE_CANNOT_BE_EMPTY: "True"

.gitlab/jobs/lassen.yml

@@ -0,0 +1,59 @@
+###############################################################################
+# Copyright (c) 2022-23, Lawrence Livermore National Security, LLC and RADIUSS
+# project contributors. See the COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (MIT)
+###############################################################################
+
+# We require project to define their job command using a variable (JOB_CMD).
+# In customization/gitlab-ci.yml, we encourage to define this variable as
+# non-expandable, so that project can use nested variables to configure the job
+# command. The caveat is that the reproducer here cannot capture the
+# definition of these variables in a generic fashion. By overriding the
+# following section, projects can specify the variables to define in the
+# reproducer to exactly reproduce the CI build.
+.lassen_reproducer_vars:
+  script:
+    - echo -e "Running on Lassen\n"
+
+# With GitLab CI, included files cannot be empty.
+# TODO: remove when you have at least on job defined.
+variables:
+  INCLUDED_FILE_CANNOT_BE_EMPTY: "True"
+
+###############
+# Explanations:
+###############
+# RADIUSS Shared CI provides a pipeline for each machine, where a template job
+# is provided. Each of your jobs must extend this template to be added to the
+# list of jobs running on the associated machine.
+#
+# The job template then expects you to define the "JOB_CMD" variable with the
+# one line command used to trigger the build and test of your project.
+#
+# We suggest that you set your command in such a way that you can then
+# customize it per job with variables. E.g.:
+# "./path/to/my_ci_script ${A_VARIABLE}"
+
+## Adding jobs defined by the project.
+## Note: placing the extends section first allows you to override part of the
+## shared implementation if needed (and if you know what you are doing).
+#<job-name (typically build target description)>:
+#  extends: .job_on_lassen
+#  variables:
+#    <A_VARIABLE>: "<with job specific value>"
+
+.base-job:
+  extends: .job_on_lassen
+  before_script:
+    # Update BOUT-configs in the shared directory.
+    - pushd /usr/workspace/BOUT-GPU/BOUT-configs
+    - git pull
+    - popd
+    # Create the environment.
+    - source /usr/workspace/BOUT-GPU/BOUT-configs/lassen/setup-env.sh
+  after_script:
+    - rm -rf ${CI_BUILDS_DIR} ${CI_PROJECT_DIR}
+
+build-test-cuda-minimal:
+  extends: .base-job

.gitlab/subscribed-pipelines.yml

@@ -0,0 +1,91 @@
+###############################################################################
+# Copyright (c) 2022-23, Lawrence Livermore National Security, LLC and RADIUSS
+# project contributors. See the COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (MIT)
+###############################################################################
+
+# The template job to test whether a machine is up.
+# Expects CI_MACHINE defined to machine name.
+.machine-check:
+  stage: prerequisites
+  tags: [shell, oslic]
+  variables:
+    GIT_STRATEGY: none
+  script:
+    - |
+      if [[ $(jq '.[env.CI_MACHINE].total_nodes_up' /usr/global/tools/lorenz/data/loginnodeStatus) == 0 ]]
+      then
+        echo -e "\e[31mNo node available on ${CI_MACHINE}\e[0m"
+        curl --url "https://api.github.com/repos/${GITHUB_PROJECT_ORG}/${GITHUB_PROJECT_NAME}/statuses/${CI_COMMIT_SHA}" \
+             --header 'Content-Type: application/json' \
+             --header "authorization: Bearer ${GITHUB_TOKEN}" \
+             --data "{ \"state\": \"failure\", \"target_url\": \"${CI_PIPELINE_URL}\", \"description\": \"GitLab ${CI_MACHINE} down\", \"context\": \"ci/gitlab/${CI_MACHINE}\" }"
+        exit 1
+      fi
+
+###
+# Trigger a build-and-test pipeline for a machine.
+# Comment the jobs for machines you don’t need.
+###
+
+# RUBY
+#ruby-up-check:
+#  variables:
+#    CI_MACHINE: "ruby"
+#  extends: [.machine-check]
+#
+#ruby-build-and-test:
+#  variables:
+#    CI_MACHINE: "ruby"
+#  needs: [ruby-up-check]
+#  extends: [.build-and-test]
+
+## POODLE
+#poodle-up-check:
+#  variables:
+#    CI_MACHINE: "poodle"
+#  extends: [.machine-check]
+#
+#poodle-build-and-test:
+#  variables:
+#    CI_MACHINE: "poodle"
+#  needs: [poodle-up-check]
+#  extends: [.build-and-test]
+#
+## CORONA
+#corona-up-check:
+#  variables:
+#    CI_MACHINE: "corona"
+#  extends: [.machine-check]
+#
+#corona-build-and-test:
+#  variables:
+#    CI_MACHINE: "corona"
+#  needs: [corona-up-check]
+#  extends: [.build-and-test]
+#
+## TIOGA
+#tioga-up-check:
+#  variables:
+#    CI_MACHINE: "tioga"
+#  extends: [.machine-check]
+#
+#tioga-build-and-test:
+#  variables:
+#    CI_MACHINE: "tioga"
+#  needs: [tioga-up-check]
+#  extends: [.build-and-test]
+
+# LASSEN
+lassen-up-check:
+  variables:
+    CI_MACHINE: "lassen"
+  extends: [.machine-check]
+
+lassen-build-and-test:
+  variables:
+    CI_MACHINE: "lassen"
+  needs: [lassen-up-check]
+  extends: [.build-and-test]
+

cmake/FindPackageMultipass.cmake

@@ -108,7 +108,7 @@ macro (MULTIPASS_C_SOURCE_RUNS includes libraries source runs)
 endmacro (MULTIPASS_C_SOURCE_RUNS)
 
 macro (MULTIPASS_SOURCE_COMPILES includes libraries source runs language)
-  include (Check${language}SourceRuns)
+  include (Check${language}SourceCompiles)
   # This is a ridiculous hack.  CHECK_${language}_SOURCE_* thinks that if the
   # *name* of the return variable doesn't change, then the test does
   # not need to be re-run.  We keep an internal count which we

include/bout/bout_enum_class.hxx

@@ -86,7 +86,11 @@
         BOUT_ENUM_CLASS_MAP_ARGS(BOUT_STR_ENUM_CLASS, enumname, __VA_ARGS__)}; \
     auto found = fromString_map.find(s);                                       \
     if (found == fromString_map.end()) {                                       \
-      throw BoutException("Did not find enum {:s}", s);                        \
+      std::string valid_values {};                                             \
+      for (auto const& entry : fromString_map) {                               \
+        valid_values += std::string(" ") + entry.first;                        \
+      }                                                                        \
+      throw BoutException("Did not find enum {:s}. Valid values: {:s}", s, valid_values); \
     }                                                                          \
     return found->second;                                                      \
   }                                                                            \

include/bout/mask.hxx

@@ -66,6 +66,8 @@ public:
 
   inline bool& operator()(int jx, int jy, int jz) { return mask(jx, jy, jz); }
   inline const bool& operator()(int jx, int jy, int jz) const { return mask(jx, jy, jz); }
+
+  inline bool& operator[](const Ind3D& i) { return mask[i]; }
   inline const bool& operator[](const Ind3D& i) const { return mask[i]; }
 };
 

include/bout/options.hxx

@@ -1006,7 +1006,7 @@ namespace details {
 /// avoiding lengthy recompilation if we change it
 struct OptionsFormatterBase {
   auto parse(fmt::format_parse_context& ctx) -> fmt::format_parse_context::iterator;
-  auto format(const Options& options, fmt::format_context& ctx)
+  auto format(const Options& options, fmt::format_context& ctx) const
       -> fmt::format_context::iterator;
 
 private:

include/bout/output_bout_types.hxx

@@ -34,7 +34,7 @@ struct fmt::formatter<SpecificInd<N>> {
   // Formats the point p using the parsed format specification (presentation)
   // stored in this formatter.
   template <typename FormatContext>
-  auto format(const SpecificInd<N>& ind, FormatContext& ctx) {
+  auto format(const SpecificInd<N>& ind, FormatContext& ctx) const {
     // ctx.out() is an output iterator to write to.
     if (presentation == 'c') {
       switch (N) {

include/bout/parallel_boundary_region.hxx

@@ -95,11 +95,11 @@ public:
 
   /// Add a point to the boundary
   void add_point(Ind3D ind, BoutReal x, BoutReal y, BoutReal z, BoutReal length,
-                 char valid) {
+                 signed char valid) {
     bndry_points.push_back({ind, {x, y, z}, length, valid});
   }
   void add_point(int ix, int iy, int iz, BoutReal x, BoutReal y, BoutReal z,
-                 BoutReal length, char valid) {
+                 BoutReal length, signed char valid) {
     bndry_points.push_back({xyz2ind(ix, iy, iz, localmesh), {x, y, z}, length, valid});
   }
 
@@ -114,10 +114,10 @@ public:
   BoutReal s_y() const { return bndry_position->intersection.s_y; }
   BoutReal s_z() const { return bndry_position->intersection.s_z; }
   BoutReal length() const { return bndry_position->length; }
-  char valid() const { return bndry_position->valid; }
+  signed char valid() const { return bndry_position->valid; }
 
   // setter
-  void setValid(char val) { bndry_position->valid = val; }
+  void setValid(signed char val) { bndry_position->valid = val; }
 
   bool contains(const BoundaryRegionPar& bndry) const {
     return std::binary_search(