Merge branch 'next' into add-zpm-method

.ci_fedora.sh

@@ -50,7 +50,7 @@ then
     cp -a /tmp/BOUT-dev /home/test/
     chown -R test /home/test
     chmod u+rwX /home/test -R
-    sudo -u test ${0/\/tmp/\/home\/test} $mpi
+    su - test -c "${0/\/tmp/\/home\/test} $mpi"
 ## If we are called as normal user, run test
 else
     . /etc/profile.d/modules.sh

.clang-tidy

@@ -2,7 +2,6 @@
 Checks:          'clang-diagnostic-*,clang-analyzer-*,performance-*,readability-*,bugprone-*,clang-analyzer-*,cppcoreguidelines-*,mpi-*,misc-*,-readability-magic-numbers,-cppcoreguidelines-avoid-magic-numbers,-misc-non-private-member-variables-in-classes,-clang-analyzer-optin.mpi*,-bugprone-exception-escape,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-readability-function-cognitive-complexity,-misc-no-recursion,-bugprone-easily-swappable-parameters'
 WarningsAsErrors: ''
 HeaderFilterRegex: ''
-AnalyzeTemporaryDtors: false
 FormatStyle:     file
 CheckOptions:
 

.github/workflows/tests.yml

@@ -39,7 +39,7 @@ jobs:
         is_cron:
           - ${{ github.event_name == 'cron' }}
         config:
-          - name: "CMake, PETSc unreleased, ADIOS"
+          - name: "CMake, PETSc unreleased, ADIOS2"
             os: ubuntu-20.04
             cmake_options: "-DBUILD_SHARED_LIBS=ON
                             -DBOUT_ENABLE_METRIC_3D=ON

.gitignore

@@ -85,3 +85,5 @@ coverage/
 /_version.txt
 /BOUT++-v*.tar.gz
 /BOUT++-v*.tar.xz
+/CMakeCache.txt
+/CMakeFiles/cmake.check_cache

.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]
+

CMakeLists.txt

@@ -935,7 +935,7 @@ message("
    SUNDIALS support         : ${BOUT_HAS_SUNDIALS}
    HYPRE support            : ${BOUT_HAS_HYPRE}
    NetCDF support           : ${BOUT_HAS_NETCDF}
-   ADIOS support            : ${BOUT_HAS_ADIOS}
+   ADIOS2 support           : ${BOUT_HAS_ADIOS2}
    FFTW support             : ${BOUT_HAS_FFTW}
    LAPACK support           : ${BOUT_HAS_LAPACK}
    OpenMP support           : ${BOUT_USE_OPENMP}

bin/bout-build-deps.sh

@@ -98,7 +98,7 @@ netcdf() {
 
 nccxx() {
     cd $BUILD
-    wget -c ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-cxx4-$NCCXXVER.tar.gz || :
+    wget -c https://downloads.unidata.ucar.edu/netcdf-cxx/$NCCXXVER/netcdf-cxx4-$NCCXXVER.tar.gz || :
     tar -xf netcdf-cxx4-$NCCXXVER.tar.gz
     cd netcdf-cxx4-$NCCXXVER
     CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib/" ./configure --prefix=$PREFIX $NCCXXFLAGS
@@ -286,17 +286,17 @@ set -x
 ## Setup folders and links
 setup
 ## Build and install hdf5
-hdf5
+test $NO_HDF5 || hdf5
 ## Build and install netcdf
-netcdf
+test $NO_NETCDF || netcdf
 ## Build and install C++ interface for netcdf
-nccxx
+test $NO_NCXX || nccxx
 ## Build and install FFTW
-fftw
+test $NO_FFTW || fftw
 ## Build and install Sundials
-sundials
+test $NO_SUNDIALS || sundials
 ## Build and install PETSc
-petsc
+test $NO_PETSC || petsc
 ## Download BOUT++ submodules
 submod
 # Install python packages