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Author SHA1 Message Date
camierjs f2a424720b Merge branch 'main' into hpcftools/flowSolver-gpu 2025-06-30 11:17:56 -07:00
camierjs e5fad8067c Merge branch 'master' into hpcftools/flowSolver-gpu 2025-06-30 11:17:45 -07:00
camierjs 0b5bb52996 miniapps/navier/incompressible_navier_dfem 2025-06-30 11:17:11 -07:00
camierjs 563bfe9514 Merge branch 'master' 2025-06-30 08:43:14 -07:00
camierjs 9afef578d5 Merge branch 'master' into hpcftools/flowSolver-gpu 2025-05-02 09:59:44 -07:00
camierjs 9ecc414c62 dot reduced tests 2024-12-04 18:25:05 -08:00
camierjs 263b9d32c1 Merge branch 'hpcftools/flowSolver' 2024-12-04 11:59:05 -08:00
Mathias Rainer Schmidt 74e4ad3e2c - updated flow solver
- added comments to Blf and Lf contributions
- split setup and step into vel, auxiliary and pressure part
2024-11-25 11:04:30 -08:00
camierjs 79039e0f6f Switched to PA 2024-11-21 10:52:39 -08:00
Mathias Rainer Schmidt cf9fcd8dde Merge remote-tracking branch 'origin/master' into hpcftools/flowSolver 2024-11-14 13:52:27 -08:00
camierjs c857fde13b Merge branch 'hpcftools/flowSolver' 2024-11-01 15:59:50 -07:00
Mathias Rainer Schmidt fa8617ada3 - added partial assembly option 2024-11-01 13:20:29 -07:00
camierjs c06cbb69d5 Setup and cleanup 2024-10-30 11:37:00 -07:00
Mathias Rainer Schmidt f7e5db2cea - added ortho solver to phi field 2024-10-24 16:06:37 -07:00
Mathias Rainer Schmidt 60c11776b6 - added executable 2024-10-21 15:57:23 -07:00
Mathias Rainer Schmidt 6238f8ca76 - update solution 2024-10-16 16:00:08 -07:00
Mathias Rainer Schmidt 6a256db9aa - added linear solvers to step 2024-10-16 15:56:46 -07:00
Mathias Rainer Schmidt e0fb9658ca - added linear form integrators 2024-10-15 17:30:09 -07:00
Mathias Rainer Schmidt a1089efac3 - added BilinearForms 2024-10-15 13:46:36 -07:00
Mathias Rainer Schmidt 83f7f769dc - inital flow solver commit 2024-10-15 12:44:25 -07:00
162 changed files with 3881 additions and 5818 deletions
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@@ -1,154 +0,0 @@
# Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
# LICENSE and NOTICE for details. LLNL-CODE-806117.
#
# This file is part of the MFEM library. For more information and source code
# availability visit https://mfem.org.
#
# MFEM is free software; you can redistribute it and/or modify it under the
# terms of the BSD-3 license. We welcome feedback and contributions, see file
# CONTRIBUTING.md for details.
---
name: Sanitizer Config
description: Sets up environment variables for MFEM sanitizer workflow
inputs:
DEBUG:
description: If true, use intermediate caches to speed up the workflow
by reusing previous builds.
default: false
REPOSITORY:
description: Repository to checkout
default: mfem/mfem
BRANCH:
description: Branch to checkout
default: ubsan
CLANG_VER:
description: CLANG version to use
default: 18
# https://github.com/llvm/llvm-project/releases
LLVM_VER:
description: LLVM version to use
default: 19.1.7
# https://github.com/hypre-space/hypre/releases
HYPRE_VER:
description: HYPRE version to use
default: 2.19.0
METIS_VER:
description: METIS version to use
default: 4.0.3
CTEST:
description: CTest command to use
default: ctest -j --test-load $(nproc)
--schedule-random
--stop-on-failure --output-on-failure
--test-dir
# https://clang.llvm.org/docs/AddressSanitizer.html
ASAN_OPTIONS:
default: detect_leaks=1,
strict_init_order=1,
strict_string_checks=1,
check_initialization_order=1,
detect_stack_use_after_return=1
ASAN_CXXFLAGS:
default: -fsanitize=address
-fsanitize-address-use-after-scope
ASAN_LDFLAGS:
default: -fsanitize=address
# https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html
UBSAN_OPTIONS:
default: halt_on_error=1, print_stacktrace=1
UBSAN_CXXFLAGS:
default: -fsanitize=undefined
UBSAN_LDFLAGS:
default: -fsanitize=undefined
# https://clang.llvm.org/docs/MemorySanitizer.html
MSAN_OPTIONS:
default: "poison_in_dtor=1"
MSAN_CXXFLAGS:
default: -fsanitize=memory
-fsanitize-memory-track-origins
-fsanitize-memory-use-after-dtor
MSAN_LDFLAGS:
default: -fsanitize=memory
LSAN_DIR:
description: LSAN suppression directory
default: lsan
LSAN_FILE:
description: LSAN suppression file
default: lsan.supp
NO_FLAGS:
description: If true, do not set any CXXFLAGS or LDFLAGS.
default: false
runs:
using: 'composite'
steps:
- name: Env (Inputs)
run: |
echo DEBUG=${{inputs.DEBUG}} >> $GITHUB_ENV
echo REPOSITORY=${{inputs.REPOSITORY}} >> $GITHUB_ENV
echo BRANCH=${{inputs.BRANCH}} >> $GITHUB_ENV
echo CLANG_VER=${{inputs.CLANG_VER}} >> $GITHUB_ENV
echo LLVM_VER=${{inputs.LLVM_VER}} >> $GITHUB_ENV
echo HYPRE_VER=${{inputs.HYPRE_VER}} >> $GITHUB_ENV
echo METIS_VER=${{inputs.METIS_VER}} >> $GITHUB_ENV
echo CTEST=${{inputs.CTEST}} >> $GITHUB_ENV
echo ASAN_OPTIONS=${{inputs.ASAN_OPTIONS}} >> $GITHUB_ENV
echo UBSAN_OPTIONS=${{inputs.UBSAN_OPTIONS}} >> $GITHUB_ENV
echo MSAN_OPTIONS=${{inputs.MSAN_OPTIONS}} >> $GITHUB_ENV
echo LSAN_DIR=${{inputs.LSAN_DIR}} >> $GITHUB_ENV
echo LSAN_FILE=${{inputs.LSAN_FILE}} >> $GITHUB_ENV
echo ASAN_CXXFLAGS=${{inputs.ASAN_CXXFLAGS}} >> $GITHUB_ENV
echo ASAN_LDFLAGS=${{inputs.ASAN_LDFLAGS}} >> $GITHUB_ENV
echo UBSAN_CXXFLAGS=${{inputs.UBSAN_CXXFLAGS}} >> $GITHUB_ENV
echo UBSAN_LDFLAGS=${{inputs.UBSAN_LDFLAGS}} >> $GITHUB_ENV
echo MSAN_CXXFLAGS=${{inputs.MSAN_CXXFLAGS}} >> $GITHUB_ENV
echo MSAN_LDFLAGS=${{inputs.MSAN_LDFLAGS}} >> $GITHUB_ENV
shell: bash
- name: Env (dir)
run: |
echo LLVM_DIR=${{github.workspace}}/llvm >> $GITHUB_ENV
echo HYPRE_DIR=hypre-${{inputs.HYPRE_VER}} >> $GITHUB_ENV
echo METIS_DIR=metis-${{inputs.METIS_VER}} >> $GITHUB_ENV
shell: bash
- name: Env (bis)
run: |
echo CC=clang-${{inputs.CLANG_VER}} >> $GITHUB_ENV
echo CXX=clang++-${{inputs.CLANG_VER}} >> $GITHUB_ENV
echo LLVM_INC=${{env.LLVM_DIR}}/include/c++/v1 >> $GITHUB_ENV
echo LLVM_LIB=${{env.LLVM_DIR}}/lib >> $GITHUB_ENV
echo HYPRE_TGZ=v${{inputs.HYPRE_VER}}.tar.gz >> $GITHUB_ENV
echo METIS_TGZ=metis-${{inputs.METIS_VER}}.tar.gz >> $GITHUB_ENV
LSAN_SUPPRESSIONS="${{github.workspace}}/${{inputs.LSAN_DIR}}/${{inputs.LSAN_FILE}}"
echo "LSAN_OPTIONS=suppressions=$LSAN_SUPPRESSIONS" >> $GITHUB_ENV
shell: bash
- name: Env (ter)
if: ${{ inputs.NO_FLAGS != 'true' }}
run: |
echo LLVM_CXXFLAGS=-stdlib=libc++ -I${{env.LLVM_INC}} -Isystem${{env.LLVM_INC}} >> $GITHUB_ENV
echo LLVM_LDFLAGS=-L${{env.LLVM_LIB}} -lc++abi -Wl,-rpath,${{env.LLVM_LIB}} >> $GITHUB_ENV
shell: bash
- name: Env (quater)
if: ${{ inputs.NO_FLAGS != 'true' }}
run: |
echo CXXFLAGS=${{env.LLVM_CXXFLAGS}} >> $GITHUB_ENV
echo LDFLAGS=${{env.LLVM_LDFLAGS}} >> $GITHUB_ENV
shell: bash
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@@ -1,91 +0,0 @@
# Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
# LICENSE and NOTICE for details. LLNL-CODE-806117.
#
# This file is part of the MFEM library. For more information and source code
# availability visit https://mfem.org.
#
# MFEM is free software; you can redistribute it and/or modify it under the
# terms of the BSD-3 license. We welcome feedback and contributions, see file
# CONTRIBUTING.md for details.
---
name: 'MFEM Compilation'
description: 'MFEM Compilation'
inputs:
par:
description: 'Whether to build for parallel (true/false)'
default: false
sanitizer:
description: 'Sanitizer to use (asan, msan, ubsan)'
default: asan
runs:
using: 'composite'
steps:
- uses: ./.github/actions/sanitize/config
- uses: actions/cache@v4
if: ${{env.DEBUG == 'true'}}
id: debug
with:
path: mfem/build
key: build-${{inputs.par}}-${{inputs.sanitizer}}
- uses: ./.github/actions/sanitize/setup
if: ${{steps.debug.outputs.cache-hit != 'true'}}
with:
par: ${{inputs.par}}
sanitizer: ${{inputs.sanitizer}}
- name: Build with ASAN
if: inputs.sanitizer == 'asan'
run: echo CXXFLAGS=${{env.CXXFLAGS}} ${{env.ASAN_CXXFLAGS}} >> $GITHUB_ENV
shell: bash
- name: Build with MSAN
if: inputs.sanitizer == 'msan'
run: echo CXXFLAGS=${{env.CXXFLAGS}} ${{env.MSAN_CXXFLAGS}} >> $GITHUB_ENV
shell: bash
- name: Build with UBSAN
if: inputs.sanitizer == 'ubsan'
run: echo CXXFLAGS=${{env.CXXFLAGS}} ${{env.UBSAN_CXXFLAGS}} >> $GITHUB_ENV
shell: bash
- uses: mfem/github-actions/build-mfem@v2.5
if: ${{steps.debug.outputs.cache-hit != 'true'}}
env:
CXXFLAGS: ${{env.CXXFLAGS}}
LDFLAGS: ${{env.LDFLAGS}}
with:
mpi: ${{inputs.par == 'false' && 'seq' || 'par'}}
mfem-dir: mfem
os: ${{runner.os}}
library-only: true
build-system: cmake
hypre-dir: ${{env.HYPRE_DIR}}
metis-dir: ${{env.METIS_DIR}}
config-options: >-
-GNinja
-DMPICXX=${{env.CXX}}
-DCMAKE_CXX_STANDARD=17
-DMFEM_USE_MEMALLOC=OFF
-DCMAKE_BUILD_TYPE=Release
-DCMAKE_VERBOSE_MAKEFILE=ON
-DCMAKE_CXX_COMPILER=${{env.CXX}}
-DCMAKE_CXX_FLAGS_RELEASE='-g -O1 -fno-omit-frame-pointer'
- name: Delete object files
if: ${{steps.debug.outputs.cache-hit != 'true'}}
working-directory: mfem/build
run: find . -type f -name '*.o' -delete
shell: bash
- uses: actions/upload-artifact@v4
with:
name: build-${{inputs.par}}-${{inputs.sanitizer}}
path: mfem/build
if-no-files-found: error
retention-days: 1
overwrite: false
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@@ -1,33 +0,0 @@
# Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
# LICENSE and NOTICE for details. LLNL-CODE-806117.
#
# This file is part of the MFEM library. For more information and source code
# availability visit https://mfem.org.
#
# MFEM is free software; you can redistribute it and/or modify it under the
# terms of the BSD-3 license. We welcome feedback and contributions, see file
# CONTRIBUTING.md for details.
---
name: 'Install MPI'
description: 'Installs MPI and set up its environment variables'
runs:
using: 'composite'
steps:
- name: Install
run: sudo apt-get install openmpi-bin libopenmpi-dev
shell: bash
- name: Env
run: |
echo PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe >> $GITHUB_ENV
echo MPI_INC=$(mpicxx --showme:compile) >> $GITHUB_ENV
echo MPI_LIB=$(mpicxx --showme:link) >> $GITHUB_ENV
shell: bash
- name: Env (bis)
run: |
echo CXXFLAGS=${{env.CXXFLAGS}} ${{env.MPI_INC}} >> $GITHUB_ENV
echo LDFLAGS=${{env.LDFLAGS}} ${{env.MPI_LIB}} >> $GITHUB_ENV
shell: bash
@@ -1,71 +0,0 @@
# Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
# LICENSE and NOTICE for details. LLNL-CODE-806117.
#
# This file is part of the MFEM library. For more information and source code
# availability visit https://mfem.org.
#
# MFEM is free software; you can redistribute it and/or modify it under the
# terms of the BSD-3 license. We welcome feedback and contributions, see file
# CONTRIBUTING.md for details.
---
name: 'Restore state'
description: 'Restore state to be able to run checks, tests'
inputs:
par:
description: 'Whether to build for parallel (true/false)'
default: false
sanitizer:
description: 'Sanitizer to use (asan, msan, ubsan)'
default: asan
cache-path:
description: 'path to what needs to be restored'
default: none
cache-skip:
description: 'Skip cache restoration'
default: false
outputs:
cache-hit:
description: 'Output from a specific step'
value: ${{steps.debug.outputs.cache-hit}}
runs:
using: 'composite'
steps:
- uses: ./.github/actions/sanitize/config
- uses: actions/cache@v4
if: ${{env.DEBUG == 'true' && inputs.cache-skip != 'true'}}
id: debug
with:
path: ${{inputs.cache-path}}
key: ${{github.job}}-${{inputs.par}}-${{inputs.sanitizer}}
- uses: ./.github/actions/sanitize/setup
if: ${{steps.debug.outputs.cache-hit != 'true'}}
with:
par: ${{inputs.par}}
sanitizer: ${{inputs.sanitizer}}
- uses: actions/download-artifact@v4
with:
name: build-${{inputs.par}}-${{inputs.sanitizer}}
path: mfem/build
- name: Ninja Patch
working-directory: mfem/build
run: |
sed -i -e 's/CXX_STATIC_LIBRARY_LINKER__mfem_Release.*/CUSTOM_COMMAND/' build.ninja
sed -i -e '/build tests\/unit\/all:/ s/tests\/unit\/[^ ]*unit_tests[^ ]*//g' build.ninja
sed -i -e '/^add_test(\[=\[\(unit_tests\|punit_tests\)\]=\]/ s/)/ "--input-file .\/list-test-names-${{matrix.tag}}" "--min-duration 1")/' tests/unit/CTestTestfile.cmake
shell: bash
- name: Copy Data
if: ${{steps.debug.outputs.cache-hit != 'true'}}
working-directory: mfem/build
run: |
ninja cmake_object_order_depends_target_unit_tests
cp -pR ../tests/unit/data tests/unit
shell: bash
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@@ -1,64 +0,0 @@
# Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
# LICENSE and NOTICE for details. LLNL-CODE-806117.
#
# This file is part of the MFEM library. For more information and source code
# availability visit https://mfem.org.
#
# MFEM is free software; you can redistribute it and/or modify it under the
# terms of the BSD-3 license. We welcome feedback and contributions, see file
# CONTRIBUTING.md for details.
---
name: 'Setup state'
description: 'Sets up the state to be able to run build & run'
inputs:
par:
description: 'Whether to build for parallel (true/false)'
default: false
sanitizer:
description: 'Sanitizer to use (asan, msan, ubsan)'
default: asan
runs:
using: 'composite'
steps:
- uses: actions/cache/restore@v4 # Cache for LLVM libcxx
with:
path: ${{env.LLVM_DIR}}
fail-on-cache-miss: true
key: build-libcxx-${{env.LLVM_VER}}-${{inputs.sanitizer}}
- uses: ./.github/actions/sanitize/mpi
if: ${{inputs.par == 'true'}}
- uses: actions/cache/restore@v4 # Cache for Hypre
if: ${{inputs.par == 'true'}}
with:
path: ${{env.HYPRE_DIR}}
fail-on-cache-miss: true
key: ${{runner.os}}-ompi-build-${{env.HYPRE_DIR}}-int32-fp64-v2.5
- uses: actions/cache/restore@v4 # Cache for Metis
if: ${{inputs.par == 'true'}}
with:
path: ${{env.METIS_DIR}}
fail-on-cache-miss: true
key: ${{runner.os}}-build-${{env.METIS_DIR}}-v2.5
- name: Hypre/Metis links
if: ${{inputs.par == 'true'}}
run: ln -s -f ${{env.HYPRE_DIR}} hypre && ln -s -f ${{env.METIS_DIR}} metis-4.0
shell: bash
- uses: actions/cache/restore@v4 # Cache for LSAN suppression file
with:
path: ${{env.LSAN_DIR}}
fail-on-cache-miss: true
key: build-lsan-suppression-file
- uses: actions/checkout@v4 # Checkout the repository
with:
path: mfem
# ref: ${{env.BRANCH}}
# repository: ${{env.REPOSITORY}}
+7 -26
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@@ -7,17 +7,18 @@
https://mfem.org
This directory contains the GitHub CI scripts for MFEM.
Note that some of these scripts use the shared MFEM GitHub Actions from the external mfem/github-actions repository:
<https://github.com/mfem/github-actions>
https://github.com/mfem/github-actions
For a particular action, e.g. `mfem/github-actions/build-mfem@v2.5`, the `v2.5` suffix denotes the branch in the above from which the action is taken.
For a particular action, e.g. `mfem/github-actions/build-mfem@v2.1`, the `v2.1` suffix denotes the branch in the above from which the action is taken.
The current CI workflows are:
## `repo-check.yml`
### `repo-check.yml`
Runs a number of static repository-level sanity checks.
@@ -29,39 +30,19 @@ Runs a number of static repository-level sanity checks.
- `branch-history` guards against accidental commits of large files using the `--history` option of the `config/githooks/pre-push` script.
## `mfem-analysis.yml` (`build-analysis`)
### `mfem-analysis.yml` (`build-analysis`)
Checks if the code builds and satisfies minimal requirements.
- `gitignore` builds hypre, METIS, and MFEM using `mfem/github-actions/build-hypre`, `mfem/github-actions/build-metis`, and `mfem/github-actions/build-mfem` and checks for correct `.gitignore` settings by running the `tests/scripts/gitignore` script.
## `builds-and-tests.yml`
### `builds-and-tests.yml`
Runs a matrix of builds and tests runs with different compilers, OS, mfem/hypre settings, etc. Also processes and upload Codecov reports.
Uses the following GitHub Actions from <https://github.com/mfem/github-actions>:
Uses the following GitHub Actions from https://github.com/mfem/github-actions:
- `mfem/github-actions/build-hypre`
- `mfem/github-actions/build-metis`
- `mfem/github-actions/build-mfem`
- `mfem/github-actions/upload-coverage`
## Sanitizer Workflow for MFEM Verification
This workflow validates MFEM unit tests, examples, and miniapps using sanitizer tools.
- `sanitizers.yml` orchestrates:
- Building and caching dependencies: HYPRE, METIS, LSAN suppression file, and LLVM libcxx.
- Launching fine-grained jobs for serial (ASAN, MSAN, UBSAN) and parallel (ASAN, UBSAN) sanitizers.
- `sanitize-tests.yml` is a reusable workflow accepting `par` mode (`true` for parallel) and `sanitizer` (ASAN, MSAN, or UBSAN) as inputs. It executes the following jobs:
- **Build**: Compiles the MFEM library with specified parallel and sanitizer settings.
- **Check**: Runs verification checks.
- Parallel jobs to test the following: **Examples**, **Miniapps** and **Unit tests**
The workflow leverages composite actions in `.github/actions/sanitize/`:
- `config`: Centralizes settings for the sanitizer workflow.
- `mfem`: Manages the MFEM library build process.
- `mpi`: Installs MPI and applies additional compilation flags.
- `restore`: Restores the testing environment state.
- `setup`: Builds or restores cached dependencies.
+5 -8
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@@ -168,13 +168,10 @@ jobs:
env
shell: bash
# For info on Xcode see:
# - https://github.com/actions/runner-images/issues/12541
# - https://github.com/actions/runner-images/blob/releases/macos-15-arm64/20250811/images/macos/macos-15-arm64-Readme.md#xcode
- name: Xcode version setup (MacOS)
if: matrix.os == 'macos-latest'
run: |
XCODE_PATH="/Applications/Xcode_16.4.app"
XCODE_PATH="/Applications/Xcode_15.3.app"
echo "> sudo xcode-select -s ${XCODE_PATH}"
sudo xcode-select -s ${XCODE_PATH}
echo "> g++ -v"
@@ -292,10 +289,10 @@ jobs:
run: |
export HOMEBREW_NO_INSTALL_CLEANUP=1
brew update
brew install llvm@20 enzyme
echo "LLVM_PREFIX=$(brew --prefix llvm@20)" >> $GITHUB_ENV
echo "OMPI_CC=$(brew --prefix llvm@20)/bin/clang" >> $GITHUB_ENV
echo "OMPI_CXX=$(brew --prefix llvm@20)/bin/clang++" >> $GITHUB_ENV
brew install llvm@19 enzyme
echo "LLVM_PREFIX=$(brew --prefix llvm@19)" >> $GITHUB_ENV
echo "OMPI_CC=$(brew --prefix llvm@19)/bin/clang" >> $GITHUB_ENV
echo "OMPI_CXX=$(brew --prefix llvm@19)/bin/clang++" >> $GITHUB_ENV
# MFEM build and test
- name: build
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@@ -0,0 +1,69 @@
# Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
# LICENSE and NOTICE for details. LLNL-CODE-806117.
#
# This file is part of the MFEM library. For more information and source code
# availability visit https://mfem.org.
#
# MFEM is free software; you can redistribute it and/or modify it under the
# terms of the BSD-3 license. We welcome feedback and contributions, see file
# CONTRIBUTING.md for details.
name: "Sanitizer"
permissions:
actions: write
on:
push:
branches:
- master
- next
pull_request:
workflow_dispatch:
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
jobs:
Serial:
runs-on: ubuntu-24.04
steps:
- name: MFEM Checkout
uses: actions/checkout@v4
with:
path: mfem
- name: MFEM Build
uses: mfem/github-actions/build-mfem@v2.5
with:
os: ${{ runner.os }}
target: opt
mpi: seq
hypre-dir: unused-hypre-dir
metis-dir: unused-metis-dir
mfem-dir: mfem
build-system: make
library-only: false
config-options:
CXX="clang++-18"
CXXFLAGS="-g -O1 -std=c++17
-fsanitize=address
-fno-omit-frame-pointer
-fsanitize-address-use-after-scope"
- name: MFEM Info
working-directory: mfem
run: make info
- name: MFEM Sanitize
working-directory: mfem
run:
ASAN_OPTIONS="detect_leaks=1,
strict_init_order=1,
strict_string_checks=1,
check_initialization_order=1,
detect_stack_use_after_return=1"
make test
@@ -1,39 +0,0 @@
# Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
# LICENSE and NOTICE for details. LLNL-CODE-806117.
#
# This file is part of the MFEM library. For more information and source code
# availability visit https://mfem.org.
#
# MFEM is free software; you can redistribute it and/or modify it under the
# terms of the BSD-3 license. We welcome feedback and contributions, see file
# CONTRIBUTING.md for details.
---
name: build-hypre
on:
workflow_call:
jobs:
build-hypre:
runs-on: ubuntu-latest
name: 2.19.0
steps:
- uses: actions/checkout@v4
- uses: ./.github/actions/sanitize/config
- name: Cache
id: cache
uses: actions/cache@v4
with:
path: ${{env.HYPRE_DIR}}
key: ${{runner.os}}-ompi-build-${{env.HYPRE_DIR}}-int32-fp64-v2.5
- name: Setup
if: steps.cache.outputs.cache-hit != 'true'
uses: ./.github/actions/sanitize/mpi
- name: Build
if: steps.cache.outputs.cache-hit != 'true'
uses: mfem/github-actions/build-hypre@v2.5
with:
archive: ${{env.HYPRE_TGZ}}
dir: ${{env.HYPRE_DIR}}
target: int32
precision: fp64
build-system: make
@@ -1,76 +0,0 @@
# Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
# LICENSE and NOTICE for details. LLNL-CODE-806117.
#
# This file is part of the MFEM library. For more information and source code
# availability visit https://mfem.org.
#
# MFEM is free software; you can redistribute it and/or modify it under the
# terms of the BSD-3 license. We welcome feedback and contributions, see file
# CONTRIBUTING.md for details.
---
name: build-libcxx
on:
workflow_call:
jobs:
build-llvm-libcxx:
runs-on: ubuntu-latest
strategy:
matrix:
sanitizer: [asan, msan, ubsan]
include:
- sanitizer: asan
llvm_use_sanitizer: "Address"
- sanitizer: msan
llvm_use_sanitizer: "MemoryWithOrigins"
- sanitizer: ubsan
llvm_use_sanitizer: "Undefined"
name: ${{matrix.sanitizer}}
steps:
- uses: actions/checkout@v4
- uses: ./.github/actions/sanitize/config
with:
NO_FLAGS: true
- name: Cache
id: cache
uses: actions/cache@v4
with:
path: ${{env.LLVM_DIR}}
key: build-libcxx-${{env.LLVM_VER}}-${{matrix.sanitizer}}
- name: Clone
if: ${{ steps.cache.outputs.cache-hit != 'true' }}
run: >
git clone --filter=blob:none --depth=1
--branch llvmorg-${{env.LLVM_VER}}
--no-checkout https://github.com/llvm/llvm-project.git llvm-project
- name: Checkout
if: ${{ steps.cache.outputs.cache-hit != 'true' }}
working-directory: llvm-project
run: |
git sparse-checkout set --cone
git checkout llvmorg-${{env.LLVM_VER}}
git sparse-checkout set cmake llvm/cmake runtimes libcxx libcxxabi
- name: Mkdir
if: ${{ steps.cache.outputs.cache-hit != 'true' }}
run: mkdir ${{env.LLVM_DIR}}
- name: CMake
if: ${{ steps.cache.outputs.cache-hit != 'true' }}
working-directory: ${{env.LLVM_DIR}}
run: >
VERBOSE=1
cmake -GNinja ../llvm-project/runtimes/
-DCMAKE_C_COMPILER=${{env.CC}}
-DCMAKE_CXX_COMPILER=${{env.CXX}}
-DCMAKE_BUILD_TYPE=RelWithDebInfo
-DCMAKE_INSTALL_PREFIX=/usr
-DLLVM_USE_SANITIZER=${{matrix.llvm_use_sanitizer}}
-DLLVM_BUILD_32_BITS=OFF
-DLIBCXXABI_USE_LLVM_UNWINDER=OFF
-DLLVM_INCLUDE_TESTS=OFF
-DLIBCXX_INCLUDE_TESTS=OFF
-DLIBCXX_INCLUDE_BENCHMARKS=OFF
-DLLVM_ENABLE_RUNTIMES='libcxx;libcxxabi'
- name: Build
if: ${{ steps.cache.outputs.cache-hit != 'true' }}
working-directory: ${{env.LLVM_DIR}}
run: cmake --build . -- cxx cxxabi
-38
View File
@@ -1,38 +0,0 @@
# Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
# LICENSE and NOTICE for details. LLNL-CODE-806117.
#
# This file is part of the MFEM library. For more information and source code
# availability visit https://mfem.org.
#
# MFEM is free software; you can redistribute it and/or modify it under the
# terms of the BSD-3 license. We welcome feedback and contributions, see file
# CONTRIBUTING.md for details.
---
name: build-file-lsan
on:
workflow_call:
jobs:
build-file-lsan:
runs-on: ubuntu-latest
name: lsan.supp
steps:
- uses: actions/checkout@v4
- uses: ./.github/actions/sanitize/config
- name: Cache
id: cache
uses: actions/cache@v4
with:
path: ${{env.LSAN_DIR}}
key: build-lsan-suppression-file
- name: Setup
if: steps.cache.outputs.cache-hit != 'true'
run: |
mkdir -p ${{env.LSAN_DIR}}
cat << EOF > ${{env.LSAN_DIR}}/${{env.LSAN_FILE}}
leak:libevent_core-2.1.so
leak:ompi_mpi_finalize
leak:ompi_mpi_init
leak:PMPI_Init
leak:strdup
EOF
@@ -1,36 +0,0 @@
# Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
# LICENSE and NOTICE for details. LLNL-CODE-806117.
#
# This file is part of the MFEM library. For more information and source code
# availability visit https://mfem.org.
#
# MFEM is free software; you can redistribute it and/or modify it under the
# terms of the BSD-3 license. We welcome feedback and contributions, see file
# CONTRIBUTING.md for details.
---
name: build-metis
on:
workflow_call:
jobs:
build-metis:
runs-on: ubuntu-latest
name: 4.0.3
steps:
- uses: actions/checkout@v4
- uses: ./.github/actions/sanitize/config
- name: Cache
id: cache
uses: actions/cache@v4
with:
path: ${{env.METIS_DIR}}
key: ${{runner.os}}-build-${{env.METIS_DIR}}-v2.5
- name: Setup
if: steps.cache.outputs.cache-hit != 'true'
uses: ./.github/actions/sanitize/mpi
- name: Build
if: steps.cache.outputs.cache-hit != 'true'
uses: mfem/github-actions/build-metis@v2.5
with:
archive: ${{env.METIS_TGZ}}
dir: ${{env.METIS_DIR}}
-197
View File
@@ -1,197 +0,0 @@
# Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
# LICENSE and NOTICE for details. LLNL-CODE-806117.
#
# This file is part of the MFEM library. For more information and source code
# availability visit https://mfem.org.
#
# MFEM is free software; you can redistribute it and/or modify it under the
# terms of the BSD-3 license. We welcome feedback and contributions, see file
# CONTRIBUTING.md for details.
---
name: Sanitize
on:
workflow_call:
inputs:
par:
description: 'Whether to build for parallel (true/false)'
required: false
default: false
type: boolean
sanitizer:
description: 'Sanitizer to use (asan, msan, ubsan)'
required: true
default: asan
type: string
jobs:
build:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: ./.github/actions/sanitize/mfem
with:
par: ${{inputs.par}}
sanitizer: ${{inputs.sanitizer}}
check:
needs: [build]
runs-on: ubuntu-latest
env:
ex: ${{inputs.par && 'ex1p' || 'ex1'}}
steps:
- uses: actions/checkout@v4
- uses: ./.github/actions/sanitize/restore
id: restore
with:
par: ${{inputs.par}}
sanitizer: ${{inputs.sanitizer}}
cache-path: mfem/build/examples/${{env.ex}}
- name: MFEM Check
if: ${{steps.restore.outputs.cache-hit != 'true'}}
working-directory: mfem/build
run: ninja -v check
examples:
needs: [check]
runs-on: ubuntu-latest
env:
exclude: ${{inputs.par && '-E "_ser"' || ''}}
steps:
- uses: actions/checkout@v4
- uses: ./.github/actions/sanitize/restore
id: restore
with:
par: ${{inputs.par}}
sanitizer: ${{inputs.sanitizer}}
cache-path: mfem/build/examples/ex1
- name: Build Examples
if: ${{steps.restore.outputs.cache-hit != 'true'}}
working-directory: mfem/build
run: ninja -v examples
- name: Test Examples
if: ${{steps.restore.outputs.cache-hit != 'true'}}
working-directory: mfem/build
run: |
${{env.CTEST}} examples ${{env.exclude}} --show-only
${{env.CTEST}} examples ${{env.exclude}}
miniapps:
needs: [check]
runs-on: ubuntu-latest
env:
exclude: ${{inputs.par && '-E "_ser"' || ''}}
steps:
- uses: actions/checkout@v4
- uses: ./.github/actions/sanitize/restore
id: restore
with:
par: ${{inputs.par}}
sanitizer: ${{inputs.sanitizer}}
cache-path: mfem/build/miniapps/meshing/minimal-surface
- name: Build Miniapps
if: ${{steps.restore.outputs.cache-hit != 'true'}}
working-directory: mfem/build
run: ninja -v miniapps
- name: Test Miniapps
if: ${{steps.restore.outputs.cache-hit != 'true'}}
working-directory: mfem/build
run: |
${{env.CTEST}} miniapps ${{env.exclude}} --show-only
${{env.CTEST}} miniapps ${{env.exclude}}
tests-miniapps:
needs: [check]
runs-on: ubuntu-latest
env:
run: ${{inputs.par && '-R "_cpu_np"' || ''}}
exclude: ${{inputs.par && '"unit_tests|debug"' || '"^unit_tests$|debug"'}}
steps:
- uses: actions/checkout@v4
- uses: ./.github/actions/sanitize/restore
id: restore
with:
par: ${{inputs.par}}
sanitizer: ${{inputs.sanitizer}}
cache-path: mfem/build/tests/unit/sedov_tests_cpu
- name: Build Tests Unit Miniapps
if: ${{steps.restore.outputs.cache-hit != 'true'}}
working-directory: mfem/build
run: ninja -v tests/unit/all
- name: Run Tests Unit Miniapps
if: ${{steps.restore.outputs.cache-hit != 'true'}}
working-directory: mfem/build
run: |
${{env.CTEST}} tests/unit -E ${{env.exclude}} ${{env.run}} --show-only
${{env.CTEST}} tests/unit -E ${{env.exclude}} ${{env.run}}
tests-unit-build:
needs: [check]
runs-on: ubuntu-latest
env:
unit_tests: ${{inputs.par && 'punit_tests' || 'unit_tests'}}
steps:
- uses: actions/checkout@v4
- uses: ./.github/actions/sanitize/restore
id: restore
with:
par: ${{inputs.par}}
sanitizer: ${{inputs.sanitizer}}
cache-path: mfem/build/tests/unit/${{env.unit_tests}}
- name: Build Unit Tests
if: ${{steps.restore.outputs.cache-hit != 'true'}}
working-directory: mfem/build
run: ninja -v ${{env.unit_tests}}
- name: Delete object files
if: ${{steps.restore.outputs.cache-hit != 'true'}}
working-directory: mfem/build/tests/unit
run: find . -type f -name '*.o' -delete
- uses: actions/upload-artifact@v4
with:
name: tests-${{inputs.par}}-${{inputs.sanitizer}}
path: mfem/build/tests/unit/${{env.unit_tests}}
if-no-files-found: error
retention-days: 1
overwrite: false
tests-unit-run:
needs: [tests-unit-build]
runs-on: ubuntu-latest
strategy:
matrix:
tag: [0, 1, 2, 3]
name: tests-unit-run-${{matrix.tag}}
env:
unit_tests: ${{inputs.par && 'punit_tests' || 'unit_tests'}}
np: ${{inputs.par && '_np=2' || ''}}
steps:
- uses: actions/checkout@v4
- uses: ./.github/actions/sanitize/restore
id: restore
with:
par: ${{inputs.par}}
sanitizer: ${{inputs.sanitizer}}
cache-path: mfem/build/tests/unit/${{env.unit_tests}}
- uses: actions/download-artifact@v4
if: ${{steps.restore.outputs.cache-hit != 'true'}}
with:
name: tests-${{inputs.par}}-${{inputs.sanitizer}}
path: mfem/build/tests/unit
- name: Split Unit Tests
if: ${{steps.restore.outputs.cache-hit != 'true'}}
working-directory: mfem/build/tests/unit
run: |
chmod 755 ${{env.unit_tests}}
./${{env.unit_tests}} --list-test-names-only | tail -n +2 > list-test-names
shuf list-test-names -o list-test-names
split --verbose -n l/4 -d -a 1 list-test-names list-test-names-
- name: Cat Unit Tests ${{matrix.tag}}
if: ${{steps.restore.outputs.cache-hit != 'true'}}
working-directory: mfem/build/tests/unit
run: cat list-test-names-${{matrix.tag}}
- name: Run Unit Tests ${{matrix.tag}}
if: ${{steps.restore.outputs.cache-hit != 'true'}}
working-directory: mfem/build
run: |
${{env.CTEST}} tests/unit -R "${{env.unit_tests}}${{env.np}}" --show-only
${{env.CTEST}} tests/unit -R "${{env.unit_tests}}${{env.np}}"
-73
View File
@@ -1,73 +0,0 @@
# Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
# LICENSE and NOTICE for details. LLNL-CODE-806117.
#
# This file is part of the MFEM library. For more information and source code
# availability visit https://mfem.org.
#
# MFEM is free software; you can redistribute it and/or modify it under the
# terms of the BSD-3 license. We welcome feedback and contributions, see file
# CONTRIBUTING.md for details.
---
name: Sanitizers
permissions:
actions: write
on:
push:
branches: ["master", "next"]
pull_request:
workflow_dispatch:
concurrency:
group: ${{github.workflow}}-${{github.ref}}
cancel-in-progress: true
jobs:
# Build steps for dependencies
build-hypre:
uses: ./.github/workflows/sanitize-build-hypre.yml
build-metis:
uses: ./.github/workflows/sanitize-build-metis.yml
build-lsan:
uses: ./.github/workflows/sanitize-build-lsan.yml
build-libcxx:
uses: ./.github/workflows/sanitize-build-libcxx.yml
# Serial sanitizers: asan, msan, ubsan
seq-asan:
needs: [build-libcxx]
uses: ./.github/workflows/sanitize-tests.yml
with:
sanitizer: asan
seq-msan:
needs: [build-libcxx]
uses: ./.github/workflows/sanitize-tests.yml
with:
sanitizer: msan
seq-ubsan:
needs: [build-libcxx]
uses: ./.github/workflows/sanitize-tests.yml
with:
sanitizer: ubsan
# Parallel sanitizers: asan, ubsan
par-asan:
needs: [build-libcxx, build-hypre, build-metis]
uses: ./.github/workflows/sanitize-tests.yml
with:
par: true
sanitizer: asan
par-ubsan:
needs: [build-libcxx, build-hypre, build-metis]
uses: ./.github/workflows/sanitize-tests.yml
with:
par: true
sanitizer: ubsan
+9 -8
View File
@@ -19,6 +19,9 @@ CMakeFiles/
# Clangd server cache
*.cache*
# VSCode configuration
/.vscode/
# Backup files
*~
@@ -211,7 +214,7 @@ miniapps/electromagnetics/joule
miniapps/electromagnetics/Volta-AMR*
miniapps/electromagnetics/Tesla-AMR*
miniapps/electromagnetics/Maxwell-Parallel*
miniapps/electromagnetics/Joule_[0-9]*
miniapps/electromagnetics/Joule_*
miniapps/gslib/field-diff
miniapps/gslib/field-interp
@@ -267,9 +270,9 @@ miniapps/meshing/bounding-box*
miniapps/meshing/jacobian-determinant*
miniapps/mtop/parheat
miniapps/mtop/ParHeat/*
miniapps/mtop/ParHeat*
miniapps/mtop/seqheat
miniapps/mtop/SeqHeat/*
miniapps/mtop/SeqHeat*
miniapps/autodiff/paradiff
miniapps/autodiff/seqadiff
@@ -277,7 +280,7 @@ miniapps/autodiff/seqtest
miniapps/autodiff/par_example
miniapps/autodiff/seq_example
miniapps/autodiff/seq_test
miniapps/autodiff/Example/*
miniapps/autodiff/Exampl*
miniapps/navier/navier_mms
miniapps/navier/navier_kovasznay
@@ -300,7 +303,6 @@ miniapps/nurbs/nurbs_solenoidal
miniapps/nurbs/nurbs_printfunc
miniapps/nurbs/nurbs_patch_ex1
miniapps/nurbs/nurbs_curveint
miniapps/nurbs/nurbs_surface
miniapps/nurbs/refined.mesh
miniapps/nurbs/mesh.*
miniapps/nurbs/sol_?.gf
@@ -319,7 +321,6 @@ miniapps/nurbs/nurbs_naca_cmesh
miniapps/nurbs/naca-cmesh.mesh
miniapps/nurbs/glvis_naca-cmesh.mesh
miniapps/nurbs/Naca_cmesh
miniapps/nurbs/*-Surface.mesh
miniapps/performance/ex1
miniapps/performance/ex1p
@@ -415,8 +416,8 @@ miniapps/diag-smoothers/mg-abs-l1-jacobi
tests/unit/output_meshes
tests/unit/unit_tests
tests/unit/punit_tests
tests/unit/gpu_unit_tests
tests/unit/pgpu_unit_tests
tests/unit/cunit_tests
tests/unit/pcunit_tests
tests/unit/sedov_tests_*
tests/unit/psedov_tests_*
tests/unit/tmop_pa_tests_*
+5 -5
View File
@@ -22,7 +22,7 @@ include:
# the "needs" keyword and express the DAG of jobs for more efficiency.
# - We use setup and setup_baseline phases to download content outside of mfem
# directory.
# - Allocate/Release is where Dane resource are allocated/released once for all.
# - Allocate/Release is where ruby resource are allocated/released once for all.
# - Build and Test is where we build and MFEM for multiple toolchains.
# - Baseline_checks gathers baseline-type test suites execution
# - Baseline_publish, only available on master, allows to update baseline
@@ -53,7 +53,7 @@ variables:
AUTOTEST_COMMIT: "YES"
# Trigger subpipelines:
dane-build-and-test:
ruby-build-and-test:
stage: sub-pipelines
variables:
# Explicitly pass down values that we want to be able to set when triggering
@@ -61,10 +61,10 @@ dane-build-and-test:
AUTOTEST: "${AUTOTEST}"
AUTOTEST_COMMIT: "${AUTOTEST_COMMIT}"
trigger:
include: .gitlab/dane-build-and-test.yml
include: .gitlab/ruby-build-and-test.yml
strategy: depend
dane-baseline:
ruby-baseline:
stage: sub-pipelines
variables:
# Explicitly pass down values that we want to be able to set when triggering
@@ -73,7 +73,7 @@ dane-baseline:
AUTOTEST: "${AUTOTEST}"
AUTOTEST_COMMIT: "${AUTOTEST_COMMIT}"
trigger:
include: .gitlab/dane-baseline.yml
include: .gitlab/ruby-baseline.yml
strategy: depend
lassen-build-and-test:
+3 -3
View File
@@ -24,7 +24,7 @@ and `test type`.
Machines typically include:
* Dane: Intel Sapphire Rapids
* Ruby: 2nd Gen Intel Xeon (Cascade Lake)
* Lassen: Power9 + Nvidia GPU
* Corona: AMD GPU
@@ -76,13 +76,13 @@ with a spack spec of MFEM, within the limits permitted by the MFEM spack
package.
In any build-and-test sub-pipeline a job basically consists in defining the
spack spec to use. Adding a job on Dane for example resumes to:
spack spec to use. Adding a job on ruby for example resumes to:
```yaml
<job_name>:
variables:
SPEC: "<spack_spec>"
extends: .build_and_test_on_dane
extends: .build_and_test_on_ruby
```
The remaining and non trivial work is to make sure this spec is working. To
+1 -1
View File
@@ -24,7 +24,7 @@ variables:
# TODO: add a clean-up mechanism
BUILD_ROOT: ${USER_CI_TOP_DIR}/${CI_PROJECT_NAME}-${MACHINE_NAME}-pipeline-${CI_PIPELINE_ID}
# On LLNL's Dane, there is only one allocation shared among jobs in order to
# On LLNL's ruby, there is only one allocation shared among jobs in order to
# save time and resource. This allocation has to be uniquely named so that we
# are sure to retrieve it.
ALLOC_NAME: ${CI_PROJECT_NAME}_ci_${CI_PIPELINE_ID}
@@ -9,17 +9,17 @@
# terms of the BSD-3 license. We welcome feedback and contributions, see file
# CONTRIBUTING.md for details.
# GitLab pipelines configurations for the Dane machine at LLNL
# GitLab pipelines configurations for the Ruby machine at LLNL
variables:
MACHINE_NAME: dane
MACHINE_NAME: ruby
.on_dane:
.on_ruby:
tags:
- shell
- dane
- ruby
rules:
# Don't run dane jobs if...
- if: '$CI_COMMIT_BRANCH =~ /_qnone/ || $ON_DANE == "OFF"'
# Don't run ruby jobs if...
- if: '$CI_COMMIT_BRANCH =~ /_qnone/ || $ON_RUBY == "OFF"'
when: never
# Don't run autotest update if...
- if: '$CI_JOB_NAME =~ /report/ && $AUTOTEST != "YES"'
@@ -40,17 +40,16 @@ variables:
- when: on_success
# Spack helped builds
# Generic dane build job, extending build script
.build_and_test_on_dane:
extends: [.on_dane]
# Generic ruby build job, extending build script
.build_and_test_on_ruby:
extends: [.on_ruby]
stage: build_and_test
script:
# THREADS is used by 'tests/gitlab/build_and_test', run below
# Dane has 224 threads/node and we run 7 separate jobs: 224=7*32
- export THREADS=28
- export THREADS=16
- echo ${ALLOC_NAME}
- export JOBID=$(squeue -h --name=${ALLOC_NAME} --format=%A)
- echo ${JOBID}
- echo ${MFEM_DATA_DIR}
- echo ${SPEC}
- srun $( [[ -n "${JOBID}" ]] && echo "--jobid=${JOBID}" ) --reservation=ci -t 60 -N 1 tests/gitlab/build_and_test --spec "${SPEC}" --data-dir "${MFEM_DATA_DIR}" --data
- srun $( [[ -n "${JOBID}" ]] && echo "--jobid=${JOBID}" ) --reservation=ci -t 45 -N 1 tests/gitlab/build_and_test --spec "${SPEC}" --data-dir "${MFEM_DATA_DIR}" --data
+1 -1
View File
@@ -18,7 +18,7 @@
setup_baseline:
tags:
- shell
- dane
- ruby
stage: setup
variables:
GIT_STRATEGY: none
+1 -1
View File
@@ -16,7 +16,7 @@
setup:
tags:
- shell
- dane
- ruby
stage: setup
variables:
GIT_STRATEGY: none
@@ -19,8 +19,8 @@ stages:
- cleanup
- baseline_publish
baselinecheck_mfem_intel_dane:
extends: [.on_dane]
baselinecheck_mfem_intel_ruby:
extends: [.on_ruby]
stage: baseline_check
variables:
# TPLS_DIR is used in .gitlab/scripts/baseline to provide the tpls location
@@ -31,8 +31,8 @@ baselinecheck_mfem_intel_dane:
script:
- echo ${BUILD_ROOT}
- echo ${TPLS_DIR}
# Used by the tests in MFEM/tests, dane has 224 threads/node:
- export MFEM_TEST_NP=192
# Used by the tests in MFEM/tests:
- export MFEM_TEST_NP=48
# The next script uses the following environment variables:
# * BASELINE_TEST, SYS_TYPE, CI_PROJECT_DIR, ARTIFACTS_DIR,
# * BUILD_ROOT, TPLS_DIR, MACHINE_NAME
@@ -44,7 +44,7 @@ baselinecheck_mfem_intel_dane:
allow_failure: true
cleanup:
extends: .on_dane
extends: .on_ruby
stage: cleanup
variables:
GIT_STRATEGY: none
@@ -53,7 +53,7 @@ cleanup:
- rm -rf "${BUILD_ROOT}" || true
report_baseline:
extends: [.on_dane]
extends: [.on_ruby]
stage: baseline_report
script:
- echo ${MACHINE_NAME}
@@ -113,8 +113,8 @@ report_baseline:
exit $err
) 9> autotest.lock
baselinepublish_mfem_dane:
extends: [.on_dane]
baselinepublish_mfem_ruby:
extends: [.on_ruby]
stage: baseline_publish
rules:
# - if: '$CI_COMMIT_BRANCH == "master" || $REBASELINE == "YES"'
@@ -129,5 +129,5 @@ baselinepublish_mfem_dane:
include:
- local: .gitlab/configs/common.yml
- local: .gitlab/configs/dane-config.yml
- local: .gitlab/configs/ruby-config.yml
- local: .gitlab/configs/setup-baseline.yml
@@ -19,54 +19,54 @@ stages:
allocate_resource:
variables:
GIT_STRATEGY: none
extends: .on_dane
extends: .on_ruby
stage: allocate_resource
script:
- echo ${ALLOC_NAME}
- salloc --exclusive --nodes=1 --reservation=ci --time=60 --no-shell --job-name=${ALLOC_NAME}
timeout: 6h
# GitLab jobs for the Dane machine at LLNL
# GitLab jobs for the Ruby machine at LLNL
debug_ser_gcc_10:
variables:
SPEC: "%gcc@10.3.1 +debug~mpi"
extends: .build_and_test_on_dane
extends: .build_and_test_on_ruby
debug_par_gcc_10:
variables:
SPEC: "%gcc@10.3.1 +debug+mpi"
extends: .build_and_test_on_dane
extends: .build_and_test_on_ruby
opt_ser_gcc_10:
variables:
SPEC: "%gcc@10.3.1 ~mpi"
extends: .build_and_test_on_dane
extends: .build_and_test_on_ruby
opt_par_gcc_10:
variables:
SPEC: "%gcc@10.3.1"
extends: .build_and_test_on_dane
extends: .build_and_test_on_ruby
opt_par_gcc_10_sundials:
variables:
SPEC: "%gcc@10.3.1 +sundials"
extends: .build_and_test_on_dane
extends: .build_and_test_on_ruby
opt_par_gcc_10_petsc:
variables:
SPEC: "%gcc@10.3.1 +petsc ^petsc+mumps~superlu-dist"
extends: .build_and_test_on_dane
extends: .build_and_test_on_ruby
opt_par_gcc_10_pumi:
variables:
SPEC: "%gcc@10.3.1 +pumi"
extends: .build_and_test_on_dane
extends: .build_and_test_on_ruby
# Release
release_resource:
variables:
GIT_STRATEGY: none
extends: .on_dane
extends: .on_ruby
stage: release_resource_and_report
script:
- echo ${ALLOC_NAME}
@@ -78,17 +78,17 @@ release_resource:
report_job_success:
stage: release_resource_and_report
extends:
- .on_dane
- .on_ruby
- .report_job_success
report_job_failure:
stage: release_resource_and_report
extends:
- .on_dane
- .on_ruby
- .report_job_failure
include:
- local: .gitlab/configs/common.yml
- local: .gitlab/configs/dane-config.yml
- local: .gitlab/configs/ruby-config.yml
- local: .gitlab/configs/setup-build-and-test.yml
- local: .gitlab/configs/report-build-and-test.yml
+2 -2
View File
@@ -14,7 +14,7 @@
# locals
glob_err=${BASELINE_TEST}.err
base=${BASELINE_TEST}-${SYS_TYPE}
if [[ "${MACHINE_NAME}" == "dane" ]]; then
if [[ "${MACHINE_NAME}" == "ruby" ]]; then
base="${BASELINE_TEST}-${MACHINE_NAME}"
fi
base_diff=${base}.diff
@@ -31,7 +31,7 @@ cd tests
mkdir _${BASELINE_TEST} && cd _${BASELINE_TEST}
# run
if [[ "${MACHINE_NAME}" == "dane" ]]; then
if [[ "${MACHINE_NAME}" == "ruby" ]]; then
salloc --nodes=1 --exclusive --reservation=ci ../runtest ../../mfem "${BASELINE_TEST} ${TPLS_DIR}"
elif [[ ${MACHINE_NAME} == "corona" ]]; then
salloc --nodes=1 -t 60 -p pbatch ../runtest ../../mfem "${BASELINE_TEST} ${TPLS_DIR}"
+2 -2
View File
@@ -11,7 +11,7 @@
# terms of the BSD-3 license. We welcome feedback and contributions, see file
# CONTRIBUTING.md for details.
# There will be collision between corona and dane baselines.
# There will be collision between corona and ruby baselines.
# Once the corresponding files have been generated, we can switch to machine
# specific ref.
ARTIFACT_PATH=${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/baseline-${SYS_TYPE}
@@ -21,7 +21,7 @@ PATCH_FILE=${ARTIFACT_PATH}.patch
FULL_FILE=${ARTIFACT_PATH}.out
DIFF_FILE=${ARTIFACT_PATH}.diff
# There will be collision between corona and dane baselines.
# There will be collision between corona and ruby baselines.
# Once the corresponding files have been generated, we can switch to machine
# specific ref.
SAVED_NAME=baseline-${SYS_TYPE}.saved
+1 -26
View File
@@ -29,14 +29,9 @@ Discretization improvements
Meshing improvements
--------------------
- Added support for higher order meshes in Mesh::MakeSimplicial and
ParMesh::MakeSimplicial.
- Added a new miniapp for interpolating a surface grid of points in 3D using a
smooth NURBS surface, that can then be sampled at arbitrary resolution while
staying close to the original geometry. See miniapps/nurbs/nurbs_surface.
GPU computing
-------------
- The function Vector::SetSubVector(const Array<int> &, const real_t) now
@@ -44,13 +39,6 @@ GPU computing
set. This is most often used for setting constant essential boundary
conditions. A new function Vector::SetSubVectorHost has been added in cases
where host execution is always needed (e.g. when the DOFs array is small).
- Introduced MFEM_FOREACH_THREAD_DIRECT, which directly maps loop tasks to GPU
threads, assigning one task per thread.
- Implemented a GPU-accelerated matrix-free AMR derefinement `GridFunction`
update operator. This supports mixed geometry meshes and variable order
spaces, and is the default derefinement operator constructed by
`FiniteElementSpace::Update` and `ParFiniteElementSpace::Update`.
The operator requires `FiniteElementSpace::Nonconforming() == true`.
New and updated examples and miniapps
-------------------------------------
@@ -60,26 +48,13 @@ New and updated examples and miniapps
operators as smoothers.
These miniapps can be found in `miniapps/diag-smoothers`.
API changes
API changes:
-----------
- mfem::internal::tensor and mfem::internal::dual have been moved to
mfem::future::tensor and mfem::future::dual.
- API addition: in class `Operator`, added virtual functions: `AbsMult`, and
`AbsMultTranspose`; in class `Vector`, added `Abs` and `Pow`.
Miscellaneous
-------------
- Added the "gpu", "raja-gpu", and "ceed-gpu" backend aliases/shortcuts which
automatically select between CUDA or HIP.
- The CUDA-specific names used by some of the unit tests like 'cunit_tests' and
'pcunit_tests' were replaced by names using 'gpu' instead of 'c' (short for
CUDA) or 'cuda'. These tests automatically run the CUDA/HIP tests based on the
MFEM build configuration.
- Added the option to enable GPU-aware MPI in MFEM using the environment
variable 'MFEM_GPU_AWARE_MPI' set to any value. Setting this environment
variable is an alternative to calling 'Device::SetGPUAwareMPI(true)'.
- Added parallel Address Sanitizer, serial and parallel Undefined Behavior
Sanitizer and serial Memory Sanitizer GitHub actions tests on Ubuntu.
Version 4.8, released on Apr 9, 2025
====================================
+5 -14
View File
@@ -598,20 +598,14 @@ set(MFEM_TPLS OPENMP HYPRE LAPACK BLAS SuperLUDist STRUMPACK METIS SuiteSparse
BENCHMARK PARELAG TRIBOL MPI_CXX HIP HIPBLAS HIPSPARSE MOONOLITH BLITZ
ALGOIM ENZYME)
# Add all created targets and *_FOUND libraries in the variables TPL_TARGETS and
# TPL_LIBRARIES, respectively.
set(TPL_TARGETS)
# Add all *_FOUND libraries in the variable TPL_LIBRARIES.
set(TPL_LIBRARIES "")
set(TPL_INCLUDE_DIRS "")
foreach(TPL IN LISTS MFEM_TPLS)
if (${TPL}_FOUND OR TARGET ${TPL})
if (${TPL}_FOUND)
message(STATUS "MFEM: using package ${TPL}")
if (TARGET ${TPL})
list(APPEND TPL_TARGETS ${TPL})
else()
list(APPEND TPL_LIBRARIES ${${TPL}_LIBRARIES})
list(APPEND TPL_INCLUDE_DIRS ${${TPL}_INCLUDE_DIRS})
endif()
list(APPEND TPL_LIBRARIES ${${TPL}_LIBRARIES})
list(APPEND TPL_INCLUDE_DIRS ${${TPL}_INCLUDE_DIRS})
endif()
endforeach(TPL)
list(REVERSE TPL_LIBRARIES)
@@ -686,10 +680,7 @@ set(MFEM_INSTALL_DIR ${CMAKE_INSTALL_PREFIX})
# Declaring the library
mfem_add_library(mfem ${SOURCES} ${HEADERS} ${MASTER_HEADERS})
# message(STATUS "TPL_LIBRARIES = ${TPL_LIBRARIES}")
target_link_libraries(mfem PUBLIC ${TPL_LIBRARIES} ${TPL_TARGETS})
if (TPL_TARGETS)
add_dependencies(mfem ${TPL_TARGETS})
endif()
target_link_libraries(mfem PUBLIC ${TPL_LIBRARIES})
if (MINGW)
target_link_libraries(mfem PRIVATE ws2_32)
endif()
-16
View File
@@ -121,11 +121,6 @@ Parallel build:
make -j 4
(For METIS 5, see https://mfem.org/building/#parallel-build-using-metis-5)
Parallel build with fetching of hypre and METIS:
mkdir <mfem-buil-dir> ; cd <mfem-build-dir>
cmake <mfem-source-dir> -DMFEM_USE_MPI=YES -DFETCH_TPLS=YES
make -j 4
CUDA build:
(this build requires CMake 3.17 or newer)
mkdir <mfem-build-dir> ; cd <mfem-build-dir>
@@ -668,7 +663,6 @@ The specific libraries and their options are:
- OpenMP (optional), usually part of compiler, used when either MFEM_USE_OPENMP
or MFEM_USE_LEGACY_OPENMP is set to YES.
Options: OPENMP_OPT, OPENMP_LIB.
Versions: OpenMP >= 3.1 when MFEM_USE_OPENMP=YES.
- High-resolution POSIX clocks: when using MFEM_TIMER_TYPE = 2, it may be
necessary to link with a system library (e.g. librt.so).
@@ -848,7 +842,6 @@ The specific libraries and their options are:
- HIP (optional), used when MFEM_USE_HIP = YES.
URL: https://rocmdocs.amd.com
Options: HIP_CXX, HIP_ARCH, HIP_OPT, HIP_LIB.
Versions: ROCm >= 5.6.1.
- OCCA (optional), used when MFEM_USE_OCCA = YES.
URL: https://libocca.org
@@ -1081,9 +1074,6 @@ The following options are CMake specific:
MFEM_ENABLE_TESTING - Enable the ctest framework for testing.
MFEM_ENABLE_EXAMPLES - Build all of the examples by default.
MFEM_ENABLE_MINIAPPS - Build all of the miniapps by default.
FETCH_TPLS - Enable fetching of all supported third-party libraries.
HYPRE_FETCH - Enable fetching of hypre.
METIS_FETCH - Enable fetching of metis.
External libraries (CMake):
---------------------------
@@ -1145,12 +1135,6 @@ The following built-in CMake packages are also used:
set the <LIBNAME>_LIBRARIES option directly; the configuration option
<LIBNAME>_DIR is not supported.
The MFEM CMake build system also provides fetching (automated building) for the
packages/libraries listed below. Note that when fetching is enabled, any related
auto-detection functionality is disabled.
- HYPRE
- METIS
Building without GNU make or CMake
==================================
+2 -54
View File
@@ -9,18 +9,15 @@
# terms of the BSD-3 license. We welcome feedback and contributions, see file
# CONTRIBUTING.md for details.
# Defines the following variables if fetching of TPLs is disabled (default):
# Defines the following variables:
# - HYPRE_FOUND
# - HYPRE_LIBRARIES
# - HYPRE_INCLUDE_DIRS
# - HYPRE_VERSION
# - HYPRE_USING_CUDA (internal)
# - HYPRE_USING_HIP (internal)
# otherwise, the following are defined:
# - HYPRE (imported library target)
# - HYPRE_VERSION (cache variable)
if (HYPRE_FOUND OR TARGET HYPRE)
if (HYPRE_FOUND)
if (HYPRE_USING_CUDA)
find_package(CUDAToolkit REQUIRED)
endif()
@@ -36,55 +33,6 @@ if (HYPRE_FOUND OR TARGET HYPRE)
endif()
endif()
if (HYPRE_FETCH OR FETCH_TPLS)
set(HYPRE_FETCH_VERSION 2.33.0)
add_library(HYPRE STATIC IMPORTED)
# set options and associated dependencies
set(CMAKE_OPTIONS)
list(APPEND CMAKE_OPTIONS -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE})
if (MFEM_USE_CUDA)
list(APPEND CMAKE_OPTIONS -DHYPRE_WITH_CUDA:BOOL=ON)
find_package(CUDAToolkit REQUIRED)
target_link_libraries(HYPRE INTERFACE CUDA::cusparse CUDA::curand CUDA::cublas)
elseif (MFEM_USE_HIP)
list(APPEND CMAKE_OPTIONS -DHYPRE_WITH_HIP:BOOL=ON)
find_package(rocsparse REQUIRED)
find_package(rocrand REQUIRED)
target_link_libraries(HYPRE INTERFACE rocsparse rocrand)
endif()
if (MFEM_USE_SINGLE)
list(APPEND CMAKE_OPTIONS -DHYPRE_ENABLE_SINGLE:BOOL=ON)
endif()
# define external project and create future include directory so it is present
# to pass CMake checks at end of MFEM configuration step
message(STATUS "Will fetch HYPRE ${HYPRE_FETCH_VERSION} to be built with ${CMAKE_OPTIONS}")
set(PREFIX ${CMAKE_BINARY_DIR}/fetch/hypre)
include(ExternalProject)
ExternalProject_Add(hypre
GIT_REPOSITORY https://github.com/hypre-space/hypre.git
GIT_TAG v${HYPRE_FETCH_VERSION}
GIT_SHALLOW TRUE
UPDATE_DISCONNECTED TRUE
SOURCE_SUBDIR src
PREFIX ${PREFIX}
CMAKE_CACHE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${PREFIX} -DCMAKE_INSTALL_LIBDIR:PATH=lib ${CMAKE_OPTIONS})
file(MAKE_DIRECTORY ${PREFIX}/include)
# set imported library target properties
add_dependencies(HYPRE hypre)
set_target_properties(HYPRE PROPERTIES
IMPORTED_LOCATION ${PREFIX}/lib/libHYPRE.a
INTERFACE_INCLUDE_DIRECTORIES ${PREFIX}/include)
# convert HYPRE version to integer
string(REGEX MATCHALL "[0-9]+" HYPRE_SPLIT_VERSION ${HYPRE_FETCH_VERSION})
list(GET HYPRE_SPLIT_VERSION 0 HYPRE_MAJOR_VERSION)
list(GET HYPRE_SPLIT_VERSION 1 HYPRE_MINOR_VERSION)
list(GET HYPRE_SPLIT_VERSION 2 HYPRE_PATCH_VERSION)
math(EXPR HYPRE_VERSION "10000*${HYPRE_MAJOR_VERSION} + 100*${HYPRE_MINOR_VERSION} + ${HYPRE_PATCH_VERSION}")
# set cache variables that would otherwise be set after mfem_find_package call
set(HYPRE_VERSION ${HYPRE_VERSION} CACHE STRING "HYPRE version." FORCE)
return()
endif()
include(MfemCmakeUtilities)
mfem_find_package(HYPRE HYPRE HYPRE_DIR "include" "HYPRE.h" "lib" "HYPRE"
"Paths to headers required by HYPRE." "Libraries required by HYPRE."
+1 -29
View File
@@ -9,38 +9,10 @@
# terms of the BSD-3 license. We welcome feedback and contributions, see file
# CONTRIBUTING.md for details.
# Defines the following variables if fetching of TPLs is disabled (default):
# Defines the following variables:
# - METIS_FOUND
# - METIS_LIBRARIES
# - METIS_INCLUDE_DIRS
# - METIS_VERSION_5
# otherwise, the following are defined:
# - METIS (imported library target)
# - METIS_VERSION_5 (cache variable)
if (METIS_FETCH OR FETCH_TPLS)
set(METIS_FETCH_VERSION 4.0.3)
add_library(METIS STATIC IMPORTED)
# define external project
message(STATUS "Will fetch METIS ${METIS_FETCH_VERSION} to be built with default options")
set(PREFIX ${CMAKE_BINARY_DIR}/fetch/metis)
include(ExternalProject)
ExternalProject_Add(metis
GIT_REPOSITORY https://github.com/mfem/tpls
GIT_TAG b60352fbe9675d374b00828055e55be4584c7995 # tag from 1/16/25
GIT_SHALLOW TRUE
UPDATE_DISCONNECTED TRUE
PREFIX ${PREFIX}
CONFIGURE_COMMAND tar -xzf ../metis/metis-${METIS_FETCH_VERSION}-mac.tgz --strip=1
INSTALL_COMMAND mkdir -p ${PREFIX}/lib && cp libmetis.a ${PREFIX}/lib/)
# set imported library target properties
add_dependencies(METIS metis)
set_target_properties(METIS PROPERTIES
IMPORTED_LOCATION ${PREFIX}/lib/libmetis.a)
# set cache variables that would otherwise be set after mfem_find_package call
set(METIS_VERSION_5 FALSE CACHE BOOL "Is METIS version 5?")
return()
endif()
include(MfemCmakeUtilities)
mfem_find_package(METIS METIS METIS_DIR "include;Lib" "metis.h"
+1 -4
View File
@@ -23,14 +23,11 @@
#include "_config.hpp"
#endif
#include <cstdint>
#include <climits>
namespace mfem
{
#if (defined(MFEM_USE_CUDA) && defined(__CUDACC__)) || \
(defined(MFEM_USE_HIP) && defined(__HIP__))
(defined(MFEM_USE_HIP) && defined(__HIPCC__))
#define MFEM_HOST_DEVICE __host__ __device__
#else
#define MFEM_HOST_DEVICE
-6
View File
@@ -89,12 +89,6 @@ option(MFEM_ENABLE_EXAMPLES "Build all of the examples" OFF)
option(MFEM_ENABLE_MINIAPPS "Build all of the miniapps" OFF)
option(MFEM_ENABLE_BENCHMARKS "Build all of the benchmarks" OFF)
# Allow a user to specify fetching of certain third-party libraries instead of
# searching for existing installations.
option(FETCH_TPLS "Enable fetching of all supported third-party libraries" OFF)
option(HYPRE_FETCH "Enable fetching of hypre" OFF)
option(METIS_FETCH "Enable fetching of METIS" OFF)
# Setting CXX/MPICXX on the command line or in user.cmake will overwrite the
# autodetected C++ compiler.
# set(CXX g++)
-3
View File
@@ -82,8 +82,6 @@ set(SRCS
fe/fe_ser.cpp
fe_coll.cpp
fespace.cpp
derefmat_op.cpp
pderefmat_op.cpp
geom.cpp
gridfunc.cpp
hybridization.cpp
@@ -249,7 +247,6 @@ set(HDRS
nonlinearform_ext.hpp
nonlininteg.hpp
qfunction.hpp
qinterp/det.hpp
qinterp/eval.hpp
qinterp/eval_hdiv.hpp
qinterp/grad.hpp
-1
View File
@@ -515,7 +515,6 @@ struct InvTNewtonSolver<Geometry::SEGMENT, SDim, SType, max_team_x>
phys_tol += pptr[idx + d * npts] * pptr[idx + d * npts];
}
phys_tol = fmax(phys_rtol * phys_rtol, phys_tol * phys_rtol * phys_rtol);
hit_bdr[0] = prev_hit_bdr[0] = false;
}
// for each iteration
while (true)
-41
View File
@@ -1275,22 +1275,6 @@ void BilinearForm::Update(FiniteElementSpace *nfes)
height = width = fes->GetVSize();
if (ext) { ext->Update(); }
for (int k = 0; k < domain_integs.Size(); ++k)
{
domain_integs[k]->Update();
}
for (int k = 0; k < boundary_integs.Size(); ++k)
{
boundary_integs[k]->Update();
}
for (int k = 0; k < interior_face_integs.Size(); ++k)
{
interior_face_integs[k]->Update();
}
for (int k = 0; k < boundary_integs.Size(); ++k)
{
boundary_face_integs[k]->Update();
}
}
void BilinearForm::SetDiagonalPolicy(DiagonalPolicy policy)
@@ -2353,31 +2337,6 @@ void MixedBilinearForm::Update()
height = test_fes->GetVSize();
width = trial_fes->GetVSize();
if (ext) { ext->Update(); }
for (int k = 0; k < domain_integs.Size(); ++k)
{
domain_integs[k]->Update();
}
for (int k = 0; k < boundary_integs.Size(); ++k)
{
boundary_integs[k]->Update();
}
for (int k = 0; k < interior_face_integs.Size(); ++k)
{
interior_face_integs[k]->Update();
}
for (int k = 0; k < boundary_integs.Size(); ++k)
{
boundary_face_integs[k]->Update();
}
for (int k = 0; k < trace_face_integs.Size(); ++k)
{
trace_face_integs[k]->Update();
}
for (int k = 0; k < boundary_trace_face_integs.Size(); ++k)
{
boundary_trace_face_integs[k]->Update();
}
}
MixedBilinearForm::~MixedBilinearForm()
+64 -26
View File
@@ -266,7 +266,11 @@ void PABilinearFormExtension::SetupRestrictionOperators(const L2FaceValues m)
// Gather the attributes on the host from all the elements
const Mesh &mesh = *trial_fes->GetMesh();
elem_attributes = &mesh.GetElementAttributes();
elem_attributes.SetSize(mesh.GetNE());
for (int i = 0; i < mesh.GetNE(); ++i)
{
elem_attributes[i] = mesh.GetAttribute(i);
}
}
// Construct face restriction operators only if the bilinear form has
@@ -325,7 +329,45 @@ void PABilinearFormExtension::SetupRestrictionOperators(const L2FaceValues m)
bdr_face_dYdn.SetSize(bdr_face_restrict_lex->Height());
}
bdr_face_attributes = &trial_fes->GetMesh()->GetBdrFaceAttributes();
const Mesh &mesh = *trial_fes->GetMesh();
// See LinearFormExtension::Update for explanation of f_to_be logic.
std::unordered_map<int,int> f_to_be;
for (int i = 0; i < mesh.GetNBE(); ++i)
{
const int f = mesh.GetBdrElementFaceIndex(i);
f_to_be[f] = i;
}
const int nf_bdr = trial_fes->GetNFbyType(FaceType::Boundary);
bdr_attributes.SetSize(nf_bdr);
int f_ind = 0;
int missing_bdr_elems = 0;
for (int f = 0; f < mesh.GetNumFaces(); ++f)
{
if (!mesh.GetFaceInformation(f).IsOfFaceType(FaceType::Boundary))
{
continue;
}
int attribute = 1; // default value
if (f_to_be.find(f) != f_to_be.end())
{
const int be = f_to_be[f];
attribute = mesh.GetBdrAttribute(be);
}
else
{
// If a boundary face does not correspond to the a boundary element,
// we assign it the default attribute of 1. We also generate a
// warning at runtime with the number of such missing elements.
++missing_bdr_elems;
}
bdr_attributes[f_ind] = attribute;
++f_ind;
}
if (missing_bdr_elems)
{
MFEM_WARNING("Missing " << missing_bdr_elems << " boundary elements "
"for boundary faces.");
}
}
}
@@ -387,7 +429,7 @@ void PABilinearFormExtension::AssembleDiagonal(Vector &y) const
mfem::forall(ne, [=] MFEM_HOST_DEVICE (int e)
{
const int attr = d_attr[e];
if (attr <= 0 || d_m[attr - 1] == 0)
if (d_m[attr - 1] == 0)
{
for (int i = 0; i < nd; ++i)
{
@@ -408,7 +450,7 @@ void PABilinearFormExtension::AssembleDiagonal(Vector &y) const
for (int i = 0; i < iSz; ++i)
{
assemble_diagonal_with_markers(*integrators[i], elem_markers[i],
*elem_attributes, localY);
elem_attributes, localY);
}
const ElementRestriction* H1elem_restrict =
dynamic_cast<const ElementRestriction*>(elem_restrict);
@@ -434,7 +476,7 @@ void PABilinearFormExtension::AssembleDiagonal(Vector &y) const
for (int i = 0; i < iSz; ++i)
{
assemble_diagonal_with_markers(*integrators[i], elem_markers[i],
*elem_attributes, y);
elem_attributes, y);
}
}
@@ -447,7 +489,7 @@ void PABilinearFormExtension::AssembleDiagonal(Vector &y) const
for (int i = 0; i < n_bdr_integs; ++i)
{
assemble_diagonal_with_markers(*bdr_integs[i], bdr_markers[i],
*bdr_face_attributes, bdr_face_Y);
bdr_attributes, bdr_face_Y);
}
bdr_face_restrict_lex->AddAbsMultTranspose(bdr_face_Y, y);
}
@@ -546,7 +588,7 @@ void PABilinearFormExtension::MultInternal(const Vector &x, Vector &y,
for (int i = 0; i < iSz; ++i)
{
AddMultWithMarkers(*integrators[i], localX, elem_markers[i],
*elem_attributes, false, localY, useAbs);
elem_attributes, false, localY, useAbs);
}
if (H1elem_restrict && useAbs)
{
@@ -648,8 +690,8 @@ void PABilinearFormExtension::MultInternal(const Vector &x, Vector &y,
}
for (int i = 0; i < n_bdr_integs; ++i)
{
AddMultWithMarkers(*bdr_integs[i], bdr_face_X, bdr_markers[i],
*bdr_face_attributes, false, bdr_face_Y);
AddMultWithMarkers(*bdr_integs[i], bdr_face_X, bdr_markers[i], bdr_attributes,
false, bdr_face_Y);
}
for (int i = 0; i < n_bdr_face_integs; ++i)
{
@@ -657,14 +699,12 @@ void PABilinearFormExtension::MultInternal(const Vector &x, Vector &y,
{
AddMultNormalDerivativesWithMarkers(
*bdr_face_integs[i], bdr_face_X, bdr_face_dXdn,
bdr_face_markers[i], *bdr_face_attributes, bdr_face_Y,
bdr_face_dYdn);
bdr_face_markers[i], bdr_attributes, bdr_face_Y, bdr_face_dYdn);
}
else
{
AddMultWithMarkers(*bdr_face_integs[i], bdr_face_X,
bdr_face_markers[i], *bdr_face_attributes, false,
bdr_face_Y);
AddMultWithMarkers(*bdr_face_integs[i], bdr_face_X, bdr_face_markers[i],
bdr_attributes, false, bdr_face_Y);
}
}
bdr_face_restrict_lex->AddMultTransposeInPlace(bdr_face_Y, y);
@@ -687,7 +727,7 @@ void PABilinearFormExtension::MultTranspose(const Vector &x, Vector &y) const
localY = 0.0;
for (int i = 0; i < iSz; ++i)
{
AddMultWithMarkers(*integrators[i], localX, elem_markers[i], *elem_attributes,
AddMultWithMarkers(*integrators[i], localX, elem_markers[i], elem_attributes,
true, localY);
}
elem_restrict->MultTranspose(localY, y);
@@ -734,14 +774,13 @@ void PABilinearFormExtension::MultTranspose(const Vector &x, Vector &y) const
bdr_face_Y = 0.0;
for (int i = 0; i < n_bdr_integs; ++i)
{
AddMultWithMarkers(*bdr_integs[i], bdr_face_X, bdr_markers[i],
*bdr_face_attributes, true, bdr_face_Y);
AddMultWithMarkers(*bdr_integs[i], bdr_face_X, bdr_markers[i], bdr_attributes,
true, bdr_face_Y);
}
for (int i = 0; i < n_bdr_face_integs; ++i)
{
AddMultWithMarkers(*bdr_face_integs[i], bdr_face_X,
bdr_face_markers[i], *bdr_face_attributes, true,
bdr_face_Y);
AddMultWithMarkers(*bdr_face_integs[i], bdr_face_X, bdr_face_markers[i],
bdr_attributes, true, bdr_face_Y);
}
bdr_face_restrict_lex->AddMultTransposeInPlace(bdr_face_Y, y);
}
@@ -765,7 +804,7 @@ static void AddWithMarkers_(
mfem::forall(ne, [=] MFEM_HOST_DEVICE (int e)
{
const int attr = d_attr[e];
if (attr <= 0 || d_m[attr - 1] == 0) { return; }
if (d_m[attr - 1] == 0) { return; }
for (int i = 0; i < nd; ++i)
{
d_y(i, e) += d_x(i, e);
@@ -881,8 +920,7 @@ void EABilinearFormExtension::Assemble()
{
const int i = idx % sz;
const int e = idx / sz;
const real_t val =
d_a[e] > 0 ? (d_m[d_a[e] - 1] ? d_ea_1(i, e) : 0) : 0;
const real_t val = d_m[d_a[e] - 1] ? d_ea_1(i, e) : 0.0;
if (add)
{
d_ea_2(i, e) += val;
@@ -915,7 +953,7 @@ void EABilinearFormExtension::Assemble()
ea_data_tmp.SetSize(ea_data.Size());
integrators[i]->AssembleEA(*a->FESpace(), ea_data_tmp, false);
add_with_markers(ea_data_tmp, ea_data, ne, *markers,
*elem_attributes, add);
elem_attributes, add);
}
}
}
@@ -944,7 +982,7 @@ void EABilinearFormExtension::Assemble()
ea_data_tmp.SetSize(ea_data_bdr.Size());
bdr_integs[i]->AssembleEABoundary(*a->FESpace(), ea_data_tmp, add);
add_with_markers(ea_data_tmp, ea_data_bdr, nf_bdr, *markers,
*bdr_face_attributes, add);
bdr_attributes, add);
}
}
}
@@ -993,7 +1031,7 @@ void EABilinearFormExtension::Assemble()
ea_data_tmp,
add);
add_with_markers(ea_data_tmp, ea_data_bdr, nf_bdr, *markers,
*bdr_face_attributes, add);
bdr_attributes, add);
}
}
}
+1 -2
View File
@@ -69,8 +69,7 @@ class PABilinearFormExtension : public BilinearFormExtension
protected:
const FiniteElementSpace *trial_fes, *test_fes; // Not owned
/// Attributes of all mesh elements.
const Array<int> *elem_attributes; // Not owned
const Array<int> *bdr_face_attributes; // Not owned
Array<int> elem_attributes, bdr_attributes;
mutable Vector tmp_evec; // Work array
mutable Vector localX, localY;
mutable Vector int_face_X, int_face_Y;
-11
View File
@@ -21,11 +21,6 @@ using namespace std;
namespace mfem
{
void BilinearFormIntegrator::Update()
{
// default no-op
}
void BilinearFormIntegrator::AssemblePA(const FiniteElementSpace&)
{
MFEM_ABORT("BilinearFormIntegrator::AssemblePA(fes)\n"
@@ -3465,12 +3460,6 @@ real_t ElasticityIntegrator::ComputeFluxEnergy(const FiniteElement &fluxelem,
return energy;
}
void DGTraceIntegrator::Update()
{
qspace[0].reset();
qspace[1].reset();
}
void DGTraceIntegrator::AssembleFaceMatrix(const FiniteElement &el1,
const FiniteElement &el2,
FaceElementTransformations &Trans,
+10 -19
View File
@@ -23,8 +23,6 @@
namespace mfem
{
class QuadratureSpace;
class FaceQuadratureSpace;
/// Abstract base class BilinearFormIntegrator
class BilinearFormIntegrator : public NonlinearFormIntegrator
@@ -46,10 +44,6 @@ public:
// make sense for the action of the nonlinear operator (but they all make
// sense for its Jacobian).
/// Signal this integrator that something about either the trial or test space has changed.
virtual void Update();
/// Method defining partial assembly.
/** The result of the partial assembly is stored internally so that it can be
used later in the methods AddMultPA() and AddMultTransposePA(). */
@@ -818,7 +812,7 @@ protected:
const FiniteElement & test_fe) const
{
return (trial_fe.GetDim() == 1 && test_fe.GetDim() == 1 &&
trial_fe.GetDerivType() == mfem::FiniteElement::GRAD &&
trial_fe.GetDerivType() == mfem::FiniteElement::GRAD &&
test_fe.GetRangeType() == mfem::FiniteElement::SCALAR );
}
@@ -890,7 +884,7 @@ protected:
const FiniteElement & trial_fe,
const FiniteElement & test_fe) const
{
return (trial_fe.GetDerivType() == mfem::FiniteElement::DIV &&
return (trial_fe.GetDerivType() == mfem::FiniteElement::DIV &&
test_fe.GetRangeType() == mfem::FiniteElement::SCALAR );
}
@@ -925,7 +919,7 @@ protected:
const FiniteElement & trial_fe,
const FiniteElement & test_fe) const
{
return (trial_fe.GetDerivType() == mfem::FiniteElement::DIV &&
return (trial_fe.GetDerivType() == mfem::FiniteElement::DIV &&
test_fe.GetRangeType() == mfem::FiniteElement::VECTOR );
}
@@ -1606,7 +1600,7 @@ public:
{
return (trial_fe.GetCurlDim() == 3 && test_fe.GetRangeDim() == 3 &&
trial_fe.GetRangeType() == mfem::FiniteElement::VECTOR &&
trial_fe.GetDerivType() == mfem::FiniteElement::CURL &&
trial_fe.GetDerivType() == mfem::FiniteElement::CURL &&
test_fe.GetRangeType() == mfem::FiniteElement::VECTOR );
}
@@ -1641,7 +1635,7 @@ public:
{
return (trial_fe.GetDim() == 2 && test_fe.GetDim() == 2 &&
trial_fe.GetRangeType() == mfem::FiniteElement::VECTOR &&
trial_fe.GetDerivType() == mfem::FiniteElement::CURL &&
trial_fe.GetDerivType() == mfem::FiniteElement::CURL &&
test_fe.GetRangeType() == mfem::FiniteElement::VECTOR );
}
@@ -1675,7 +1669,7 @@ public:
{
return (trial_fe.GetDim() == 2 && test_fe.GetDim() == 2 &&
trial_fe.GetRangeType() == mfem::FiniteElement::SCALAR &&
trial_fe.GetDerivType() == mfem::FiniteElement::GRAD &&
trial_fe.GetDerivType() == mfem::FiniteElement::GRAD &&
test_fe.GetRangeType() == mfem::FiniteElement::SCALAR );
}
@@ -1766,7 +1760,7 @@ public:
const FiniteElement & test_fe) const
{
return (trial_fe.GetRangeType() == mfem::FiniteElement::SCALAR &&
trial_fe.GetDerivType() == mfem::FiniteElement::GRAD &&
trial_fe.GetDerivType() == mfem::FiniteElement::GRAD &&
test_fe.GetRangeType() == mfem::FiniteElement::SCALAR );
}
@@ -1799,7 +1793,7 @@ public:
const FiniteElement & test_fe) const
{
return (trial_fe.GetRangeType() == mfem::FiniteElement::SCALAR &&
trial_fe.GetDerivType() == mfem::FiniteElement::GRAD &&
trial_fe.GetDerivType() == mfem::FiniteElement::GRAD &&
test_fe.GetRangeType() == mfem::FiniteElement::VECTOR &&
test_fe.GetDerivType() == mfem::FiniteElement::DIV );
}
@@ -1838,7 +1832,7 @@ public:
const FiniteElement & test_fe) const
{
return (trial_fe.GetRangeType() == mfem::FiniteElement::VECTOR &&
trial_fe.GetDerivType() == mfem::FiniteElement::DIV &&
trial_fe.GetDerivType() == mfem::FiniteElement::DIV &&
test_fe.GetRangeType() == mfem::FiniteElement::SCALAR &&
test_fe.GetDerivType() == mfem::FiniteElement::GRAD
);
@@ -1979,7 +1973,7 @@ protected:
const FiniteElement & test_fe) const override
{
return (trial_fe.GetCurlDim() == 3 && test_fe.GetRangeDim() == 3 &&
trial_fe.GetDerivType() == mfem::FiniteElement::CURL &&
trial_fe.GetDerivType() == mfem::FiniteElement::CURL &&
test_fe.GetRangeType() == mfem::FiniteElement::VECTOR );
}
@@ -3317,7 +3311,6 @@ protected:
VectorCoefficient *u;
real_t alpha, beta;
// PA extension
std::unique_ptr<FaceQuadratureSpace> qspace[2];
Vector pa_data;
const DofToQuad *maps; ///< Not owned
const FaceGeometricFactors *geom; ///< Not owned
@@ -3340,8 +3333,6 @@ public:
real_t a, real_t b)
{ rho = &rho_; u = &u_; alpha = a; beta = b; }
void Update() override;
using BilinearFormIntegrator::AssembleFaceMatrix;
void AssembleFaceMatrix(const FiniteElement &el1,
const FiniteElement &el2,
+4 -4
View File
@@ -912,7 +912,7 @@ ConduitDataCollection::GridFunctionToBlueprintField(mfem::GridFunction *gf,
if (vdim == 1) // scalar case
{
n_field["values"].set_external(const_cast<real_t *>(gf->HostRead()),
n_field["values"].set_external(gf->GetData(),
ndofs);
}
else // vector case
@@ -925,18 +925,18 @@ ConduitDataCollection::GridFunctionToBlueprintField(mfem::GridFunction *gf,
int vdim_stride = (ordering == Ordering::byNODES ? ndofs : 1);
index_t offset = 0;
index_t stride = sizeof(real_t) * entry_stride;
index_t stride = sizeof(double) * entry_stride;
for (int d = 0; d < vdim; d++)
{
std::ostringstream oss;
oss << "v" << d;
std::string comp_name = oss.str();
n_field["values"][comp_name].set_external(const_cast<real_t *>(gf->HostRead()),
n_field["values"][comp_name].set_external(gf->GetData(),
ndofs,
offset,
stride);
offset += sizeof(real_t) * vdim_stride;
offset += sizeof(double) * vdim_stride;
}
}
+10 -12
View File
@@ -764,9 +764,9 @@ ParaViewDataCollectionBase::ParaViewDataCollectionBase(
{
cycle = 0;
#ifdef MFEM_USE_ZLIB
// If we have zlib, enable compression. Otherwise, compression is disabled in
// the DataCollection base class constructor.
compression = true;
compression = true; // if we have zlib, enable compression
#else
compression = false; // otherwise, disable compression
#endif
}
@@ -784,8 +784,13 @@ void ParaViewDataCollectionBase::SetCompressionLevel(int compression_level_)
{
MFEM_ASSERT(compression_level_ >= -1 && compression_level_ <= 9,
"Compression level must be between -1 and 9 (inclusive).");
if (compression_level_ != 0) { SetCompression(true);}
compression_level = compression_level_;
compression = compression_level_ != 0;
}
void ParaViewDataCollectionBase::SetCompression(bool compression_)
{
compression = compression_;
}
int ParaViewDataCollectionBase::GetCompressionLevel() const
@@ -1169,14 +1174,7 @@ const char *ParaViewDataCollection::GetDataTypeString() const
ParaViewHDFDataCollection::ParaViewHDFDataCollection(
const std::string &collection_name, Mesh *mesh)
: ParaViewDataCollectionBase(collection_name, mesh)
{
compression = true;
}
void ParaViewHDFDataCollection::SetCompression(bool compression_)
{
compression = compression_;
}
{ }
void ParaViewHDFDataCollection::EnsureVTKHDF()
{
+7 -6
View File
@@ -537,6 +537,13 @@ public:
/// Any nonzero compression level will enable compression.
void SetCompressionLevel(int compression_level_);
/// @brief Enable or disable zlib compression.
///
/// If the input is true, use the default zlib compression level (unless the
/// compression level has previously been set by calling
/// SetCompressionLevel()).
void SetCompression(bool compression_) override;
/// @brief Sets whether or not to output the data as high-order elements
/// (false by default).
///
@@ -626,12 +633,6 @@ public:
ParaViewHDFDataCollection(const std::string& collection_name,
Mesh *mesh_ = nullptr);
/// @brief Enable or disable compression.
///
/// The compression level can be set with SetCompressionLevel()). VTKHDF
/// compression does not require MFEM to be compiled with zlib support.
void SetCompression(bool compression_) override;
/// Save the collection.
void Save() override;
-266
View File
@@ -1,266 +0,0 @@
// Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
// LICENSE and NOTICE for details. LLNL-CODE-806117.
//
// This file is part of the MFEM library. For more information and source code
// availability visit https://mfem.org.
//
// MFEM is free software; you can redistribute it and/or modify it under the
// terms of the BSD-3 license. We welcome feedback and contributions, see file
// CONTRIBUTING.md for details.
#include "derefmat_op.hpp"
#include "fes_kernels.hpp"
/// \cond DO_NOT_DOCUMENT
namespace mfem
{
namespace internal
{
template <Ordering::Type Order, bool Atomic>
static void DerefMultKernelImpl(const DerefineMatrixOp &op, const Vector &x,
Vector &y)
{
DerefineMatrixOpMultFunctor<Order, Atomic> func;
func.xptr = x.Read();
y.UseDevice();
y = 0.;
func.yptr = y.ReadWrite();
func.bsptr = op.block_storage.Read();
func.boptr = op.block_offsets.Read();
func.brptr = op.block_row_idcs_offsets.Read();
func.bcptr = op.block_col_idcs_offsets.Read();
func.rptr = op.row_idcs.Read();
func.cptr = op.col_idcs.Read();
func.vdims = op.fespace->GetVDim();
func.nblocks = op.block_offsets.Size();
func.width = op.Width() / func.vdims;
func.height = op.Height() / func.vdims;
func.Run(op.max_rows);
}
} // namespace internal
DerefineMatrixOp::DerefineMatrixOp(FiniteElementSpace &fespace_, int old_ndofs,
const Table *old_elem_dof,
const Table *old_elem_fos)
: Operator(fespace_.GetVSize(), old_ndofs * fespace_.GetVDim()),
fespace(&fespace_)
{
static Kernels kernels;
constexpr int max_team_size = 256;
/// TODO: Implement DofTransformation support
MFEM_VERIFY(fespace->Nonconforming(),
"Not implemented for conforming meshes.");
MFEM_VERIFY(old_ndofs, "Missing previous (finer) space.");
MFEM_VERIFY(fespace->GetNDofs() <= old_ndofs,
"Previous space is not finer.");
const CoarseFineTransformations &dtrans =
fespace->GetMesh()->ncmesh->GetDerefinementTransforms();
MFEM_ASSERT(dtrans.embeddings.Size() == old_elem_dof->Size(), "");
const bool is_dg = fespace->FEColl()->GetContType()
== FiniteElementCollection::DISCONTINUOUS;
DenseMatrix localRVO; // for variable-order only
DenseTensor localR[Geometry::NumGeom];
int total_rows = 0;
int total_cols = 0;
block_offsets.SetSize(dtrans.embeddings.Size());
block_offsets.HostWrite();
if (fespace->IsVariableOrder())
{
// TODO: any potential for some compression here?
// determine storage size and offsets
block_offsets[0] = 0;
int total_size = 0;
for (int k = 0; k < dtrans.embeddings.Size(); ++k)
{
const Embedding &emb = dtrans.embeddings[k];
const FiniteElement *fe = fespace->GetFE(emb.parent);
const int ldof = fe->GetDof();
if (k + 1 < dtrans.embeddings.Size())
{
block_offsets[k + 1] = block_offsets[k] + ldof * ldof;
}
total_rows += ldof;
total_cols += ldof;
total_size += ldof * ldof;
}
block_storage.SetSize(total_size);
}
else
{
// compression scheme:
// block_offsets is the start of each block, potentially repeated
// only need to store localR for used shapes
Mesh::GeometryList elem_geoms(*fespace->GetMesh());
int geom_offsets[Geometry::NumGeom];
{
int size = 0;
for (int i = 0; i < elem_geoms.Size(); ++i)
{
fespace->GetLocalDerefinementMatrices(elem_geoms[i],
localR[elem_geoms[i]]);
geom_offsets[elem_geoms[i]] = size;
size += localR[elem_geoms[i]].TotalSize();
}
block_storage.SetSize(size);
// copy blocks into block_storage
auto bs_ptr = block_storage.HostWrite();
for (int i = 0; i < elem_geoms.Size(); ++i)
{
std::copy(localR[elem_geoms[i]].Data(),
localR[elem_geoms[i]].Data()
+ localR[elem_geoms[i]].TotalSize(),
bs_ptr);
bs_ptr += localR[elem_geoms[i]].TotalSize();
}
}
for (int k = 0; k < dtrans.embeddings.Size(); ++k)
{
const Embedding &emb = dtrans.embeddings[k];
Geometry::Type geom =
fespace->GetMesh()->GetElementBaseGeometry(emb.parent);
auto size = localR[geom].SizeI() * localR[geom].SizeJ();
total_rows += localR[geom].SizeI();
total_cols += localR[geom].SizeJ();
// set block offsets and sizes
block_offsets[k] = geom_offsets[geom] + size * emb.matrix;
}
}
row_idcs.SetSize(total_rows);
row_idcs.HostWrite();
col_idcs.SetSize(total_cols);
col_idcs.HostWrite();
block_row_idcs_offsets.SetSize(dtrans.embeddings.Size() + 1);
block_row_idcs_offsets.HostWrite();
block_col_idcs_offsets.SetSize(dtrans.embeddings.Size() + 1);
block_col_idcs_offsets.HostWrite();
block_row_idcs_offsets[0] = 0;
block_col_idcs_offsets[0] = 0;
// compute index information
Array<int> dofs, old_dofs;
max_rows = 1;
{
Array<int> mark(fespace->GetNDofs());
mark = 0;
auto bs_ptr = block_storage.HostWrite();
int ridx = 0;
int cidx = 0;
int num_marked = 0;
for (int k = 0; k < dtrans.embeddings.Size(); k++)
{
const Embedding &emb = dtrans.embeddings[k];
Geometry::Type geom =
fespace->GetMesh()->GetElementBaseGeometry(emb.parent);
if (fespace->IsVariableOrder())
{
const FiniteElement *fe = fespace->GetFE(emb.parent);
const DenseTensor &pmats = dtrans.point_matrices[geom];
const int ldof = fe->GetDof();
IsoparametricTransformation isotr;
isotr.SetIdentityTransformation(geom);
localRVO.SetSize(ldof, ldof);
isotr.SetPointMat(pmats(emb.matrix));
// Local restriction is size ldofxldof assuming that the parent
// and child are of same polynomial order.
fe->GetLocalRestriction(isotr, localRVO);
// copy block
auto size = localRVO.Height() * localRVO.Width();
std::copy(localRVO.Data(), localRVO.Data() + size, bs_ptr);
bs_ptr += size;
}
DenseMatrix &lR =
fespace->IsVariableOrder() ? localRVO : localR[geom](emb.matrix);
block_row_idcs_offsets[k + 1] =
block_row_idcs_offsets[k] + lR.Height();
block_col_idcs_offsets[k + 1] = block_col_idcs_offsets[k] + lR.Width();
max_rows = std::max(lR.Height(), max_rows);
// index information
fespace->elem_dof->GetRow(emb.parent, dofs);
old_elem_dof->GetRow(k, old_dofs);
MFEM_VERIFY(old_dofs.Size() == dofs.Size(),
"Parent and child must have same #dofs.");
for (int i = 0; i < lR.Height(); ++i, ++ridx)
{
if (!std::isfinite(lR(i, 0)))
{
row_idcs[ridx] = INT_MAX;
continue;
}
int r = dofs[i];
int m = (r >= 0) ? r : (-1 - r);
if (is_dg || !mark[m])
{
row_idcs[ridx] = r;
mark[m] = 1;
++num_marked;
}
else
{
row_idcs[ridx] = INT_MAX;
}
}
for (int i = 0; i < lR.Width(); ++i, ++cidx)
{
col_idcs[cidx] = old_dofs[i];
}
}
if (!is_dg && !fespace->IsVariableOrder())
{
MFEM_VERIFY(num_marked * fespace->GetVDim() == Height(),
"internal error: not all rows were set.");
}
}
// if not using GPU, set max_rows/max_cols to zero
if (Device::Allows(Backend::DEVICE_MASK))
{
max_rows = std::min(max_rows, max_team_size);
}
else
{
max_rows = 1;
}
}
void DerefineMatrixOp::Mult(const Vector &x, Vector &y) const
{
const bool is_dg = fespace->FEColl()->GetContType()
== FiniteElementCollection::DISCONTINUOUS;
// DG needs atomic summation
MultKernel::Run(fespace->GetOrdering(), is_dg, *this, x, y);
}
DerefineMatrixOp::Kernels::Kernels()
{
MultKernel::Specialization<Ordering::byNODES, false>::Add();
MultKernel::Specialization<Ordering::byVDIM, false>::Add();
MultKernel::Specialization<Ordering::byNODES, true>::Add();
MultKernel::Specialization<Ordering::byVDIM, true>::Add();
}
template <Ordering::Type Order, bool Atomic>
DerefineMatrixOp::MultKernelType DerefineMatrixOp::MultKernel::Kernel()
{
return internal::DerefMultKernelImpl<Order, Atomic>;
}
DerefineMatrixOp::MultKernelType
DerefineMatrixOp::MultKernel::Fallback(Ordering::Type, bool)
{
MFEM_ABORT("invalid MultKernel parameters");
}
} // namespace mfem
/// \endcond DO_NOT_DOCUMENT
-65
View File
@@ -1,65 +0,0 @@
// Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
// LICENSE and NOTICE for details. LLNL-CODE-806117.
//
// This file is part of the MFEM library. For more information and source code
// availability visit https://mfem.org.
//
// MFEM is free software; you can redistribute it and/or modify it under the
// terms of the BSD-3 license. We welcome feedback and contributions, see file
// CONTRIBUTING.md for details.
#ifndef MFEM_DEREFMAT_OP
#define MFEM_DEREFMAT_OP
#include "fespace.hpp"
#include "kernel_dispatch.hpp"
namespace mfem
{
/// \cond DO_NOT_DOCUMENT
struct DerefineMatrixOp : public Operator
{
FiniteElementSpace *fespace;
/// offsets into block_storage
Array<int> block_offsets;
/// offsets into row_idcs
Array<int> block_row_idcs_offsets;
/// offsets into col_idcs
Array<int> block_col_idcs_offsets;
/// mapping for row dofs, INT_MAX indicates the block row should be ignored.
/// negative means the row data should be negated.
Array<int> row_idcs;
/// mapping for col dofs, negative means the col data should be negated.
Array<int> col_idcs;
/// dense block matrices which can be reused to construct the full matrix
/// operation. These are stored contiguously and blocks have no restrictions
/// on shape (can be rectangle and differ from block to block).
Vector block_storage;
/// maximum height of any block in block_storage for GPU
/// parallelization, or 1 for CPU runs.
int max_rows;
using MultKernelType = void (*)(const DerefineMatrixOp &, const Vector &,
Vector &);
/// template args: ordering, atomic
MFEM_REGISTER_KERNELS(MultKernel, MultKernelType, (Ordering::Type, bool));
struct Kernels
{
Kernels();
};
void Mult(const Vector &x, Vector &y) const;
DerefineMatrixOp(FiniteElementSpace &fespace_, int old_ndofs,
const Table *old_elem_dof, const Table *old_elem_fos);
};
/// \endcond DO_NOT_DOCUMENT
} // namespace mfem
#endif
-1
View File
@@ -241,7 +241,6 @@ public:
{
MFEM_ASSERT(!action_callbacks.empty(), "no integrators have been set");
prolongation(solutions, solutions_t, solutions_l);
residual_l = 0.0;
for (auto &action : action_callbacks)
{
action(solutions_l, parameters_l, residual_l);
+8 -9
View File
@@ -327,8 +327,8 @@ void print_mpi_sync(const std::string& msg)
// First gather string lengths
size_t msg_len = msg.length();
std::vector<size_t> lengths(nranks);
MPI_Gather(&msg_len, 1, MPITypeMap<size_t>::mpi_type,
lengths.data(), 1, MPITypeMap<size_t>::mpi_type,
MPI_Gather(&msg_len, 1, MPI_INT,
lengths.data(), 1, MPI_INT,
0, MPI_COMM_WORLD);
if (myrank == 0)
@@ -568,7 +568,7 @@ struct ThreadBlocks
int z = 1;
};
#if defined(MFEM_USE_CUDA_OR_HIP)
#if (defined(MFEM_USE_CUDA) || defined(MFEM_USE_HIP))
template <typename func_t>
__global__ void forall_kernel_shmem(func_t f, int n)
{
@@ -591,7 +591,7 @@ void forall(func_t f,
if (Device::Allows(Backend::CUDA_MASK) ||
Device::Allows(Backend::HIP_MASK))
{
#if defined(MFEM_USE_CUDA_OR_HIP)
#if (defined(MFEM_USE_CUDA) || defined(MFEM_USE_HIP))
// int gridsize = (N + Z - 1) / Z;
int num_bytes = num_shmem * sizeof(decltype(shmem));
dim3 block_size(blocks.x, blocks.y, blocks.z);
@@ -987,7 +987,7 @@ get_restriction_transpose(
{
auto RT = [=](const Vector &v_e, Vector &v_l)
{
v_l += v_e;
v_l = v_e;
};
return std::make_tuple(RT, 1);
}
@@ -996,7 +996,7 @@ get_restriction_transpose(
const Operator *R = get_restriction<entity_t>(f, o);
std::function<void(const Vector&, Vector&)> RT = [=](const Vector &x, Vector &y)
{
R->AddMultTranspose(x, y);
R->MultTranspose(x, y);
};
return std::make_tuple(RT, R->Height());
}
@@ -1708,7 +1708,6 @@ std::array<DofToQuadMap, N> load_dtq_mem(
const auto B = Reshape(&dtq[i].B[0], nqp_b, dim_b, ndof_b);
auto mem_Bi = Reshape(reinterpret_cast<real_t *>(mem) + offset, nqp_b, dim_b,
ndof_b);
MFEM_FOREACH_THREAD(q, x, nqp_b)
{
MFEM_FOREACH_THREAD(d, y, ndof_b)
@@ -2159,7 +2158,7 @@ template <
std::size_t... Is>
std::array<DofToQuadMap, N> create_dtq_maps_impl(
field_operator_ts &fops,
std::vector<const DofToQuad*> &dtqs,
std::vector<const DofToQuad*> dtqs,
const std::array<int, N> &field_map,
std::index_sequence<Is...>)
{
@@ -2244,7 +2243,7 @@ template <
std::size_t num_fields>
std::array<DofToQuadMap, num_fields> create_dtq_maps(
field_operator_ts &fops,
std::vector<const DofToQuad*> &dtqmaps,
std::vector<const DofToQuad*> dtqmaps,
const std::array<int, num_fields> &to_field_map)
{
return create_dtq_maps_impl<entity_t>(
-249
View File
@@ -1,249 +0,0 @@
// Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
// LICENSE and NOTICE for details. LLNL-CODE-806117.
//
// This file is part of the MFEM library. For more information and source code
// availability visit https://mfem.org.
//
// MFEM is free software; you can redistribute it and/or modify it under the
// terms of the BSD-3 license. We welcome feedback and contributions, see file
// CONTRIBUTING.md for details.
#ifndef MFEM_FES_KERNELS_HPP
#define MFEM_FES_KERNELS_HPP
#include "../general/forall.hpp"
#include <climits>
namespace mfem
{
/// \cond DO_NOT_DOCUMENT
namespace internal
{
///
/// Implements matrix-vector multiply $y = A x$ for a sparse matrix composed of
/// a sum of smaller dense blocks. There is additional permutation/sign
/// information associated with each block. The base class only implements
/// helper routines such as computing block widths, index into x, index into y,
/// and column in A given sub-block information.
/// @sa DerefineMatrixOpMultFunctor
///
/// @tparam Order vdim ordering for x and y. Note that for Diag = false this is
/// ignored for x as x has a special interleaved order.
/// @tparam Base used for the curious recurring template pattern (CRTP) so the
/// base class can access child class fields without virtual functions
/// @tparam Diag true if this corresponds to the diagonal block (coarse element
/// and fine element are on our rank), false otherwise (coarse element is on our
/// rank, fine element is on a different rank).
///
template <Ordering::Type Order, class Base, bool Diag = true>
struct DerefineMatrixOpFunctorBase;
template <class Base>
struct DerefineMatrixOpFunctorBase<Ordering::byNODES, Base, true>
{
/// block column indices offsets
const int *bcptr;
/// column indices
const int *cptr;
int MFEM_HOST_DEVICE BlockWidth(int k) const
{
return bcptr[k + 1] - bcptr[k];
}
void MFEM_HOST_DEVICE Col(int j, int k, int &col, int &sign) const
{
col = cptr[bcptr[k] + j];
if (col < 0)
{
col = -1 - col;
sign = -sign;
}
}
int MFEM_HOST_DEVICE IndexX(int col, int vdim, int) const
{
return col + vdim * static_cast<const Base *>(this)->width;
}
int MFEM_HOST_DEVICE IndexY(int row, int vdim) const
{
return row + vdim * static_cast<const Base *>(this)->height;
}
};
template <class Base>
struct DerefineMatrixOpFunctorBase<Ordering::byVDIM, Base, true>
{
/// block column indices offsets
const int *bcptr;
/// column indices
const int *cptr;
int MFEM_HOST_DEVICE BlockWidth(int k) const
{
return bcptr[k + 1] - bcptr[k];
}
void MFEM_HOST_DEVICE Col(int j, int k, int &col, int &sign) const
{
col = cptr[bcptr[k] + j];
if (col < 0)
{
col = -1 - col;
sign = -sign;
}
}
int MFEM_HOST_DEVICE IndexX(int col, int vdim, int) const
{
return vdim + col * static_cast<const Base *>(this)->vdims;
}
int MFEM_HOST_DEVICE IndexY(int row, int vdim) const
{
return vdim + row * static_cast<const Base *>(this)->vdims;
}
};
template <class Base>
struct DerefineMatrixOpFunctorBase<Ordering::byNODES, Base, false>
{
/// receive segment offsets
const int *segptr;
/// receive segment index
const int *rsptr;
/// off-diagonal block column offsets
const int *coptr;
/// off-diagonal block widths
const int *bwptr;
int MFEM_HOST_DEVICE BlockWidth(int k) const { return bwptr[k]; }
void MFEM_HOST_DEVICE Col(int j, int k, int &col, int &sign) const
{
col = coptr[k] + j;
}
int MFEM_HOST_DEVICE IndexX(int col, int vdim, int k) const
{
int tmp = rsptr[k];
int segwidth = segptr[tmp + 1] - segptr[tmp];
return segptr[tmp] * static_cast<const Base *>(this)->vdims + col +
vdim * segwidth;
}
int MFEM_HOST_DEVICE IndexY(int row, int vdim) const
{
return row + vdim * static_cast<const Base *>(this)->height;
}
};
template <class Base>
struct DerefineMatrixOpFunctorBase<Ordering::byVDIM, Base, false>
{
/// receive segment offsets
const int *segptr;
/// receive segment index
const int *rsptr;
/// off-diagonal block column offsets
const int *coptr;
/// off-diagonal block widths
const int *bwptr;
int MFEM_HOST_DEVICE BlockWidth(int k) const { return bwptr[k]; }
void MFEM_HOST_DEVICE Col(int j, int k, int &col, int &sign) const
{
col = coptr[k] + j;
}
int MFEM_HOST_DEVICE IndexX(int col, int vdim, int k) const
{
int tmp = rsptr[k];
int segwidth = segptr[tmp + 1] - segptr[tmp];
return segptr[tmp] * static_cast<const Base *>(this)->vdims + col +
vdim * segwidth;
}
int MFEM_HOST_DEVICE IndexY(int row, int vdim) const
{
return vdim + row * static_cast<const Base *>(this)->vdims;
}
};
/// internally used to implement the derefinement operator Mult diagonal
/// block
template <Ordering::Type Order, bool Atomic, bool Diag = true>
struct DerefineMatrixOpMultFunctor
: public DerefineMatrixOpFunctorBase<
Order, DerefineMatrixOpMultFunctor<Order, Atomic, Diag>, Diag>
{
const real_t *xptr;
real_t *yptr;
/// block storage
const real_t *bsptr;
/// block offsets
const int *boptr;
/// block row index offsets
const int *brptr;
/// row indices
const int *rptr;
// number of blocks
int nblocks;
// number of components
int vdims;
/// overall operator height (for vdim = 1)
int height;
/// overall operator width (for vdim = 1)
int width;
void MFEM_HOST_DEVICE operator()(int kidx) const
{
int k = kidx % nblocks;
int vdim = kidx / nblocks;
int block_height = brptr[k + 1] - brptr[k];
int block_width = this->BlockWidth(k);
MFEM_FOREACH_THREAD(i, x, block_height)
{
int row = rptr[brptr[k] + i];
int rsign = 1;
if (row < 0)
{
row = -1 - row;
rsign = -1;
}
if (row < INT_MAX)
{
// row not marked as unused
real_t sum = 0;
for (int j = 0; j < block_width; ++j)
{
int col, sign = rsign;
this->Col(j, k, col, sign);
sum += sign * bsptr[boptr[k] + i + j * block_height] *
xptr[this->IndexX(col, vdim, k)];
}
#if defined(__CUDA_ARCH__) or defined(__HIP_DEVICE_COMPILE__)
if (Atomic)
{
atomicAdd(yptr + this->IndexY(row, vdim), sum);
}
else
#endif
{
yptr[this->IndexY(row, vdim)] += sum;
}
}
}
}
/// N is the max block row size (doesn't have to be a power of 2)
void Run(int N) const { forall_2D(nblocks * vdims, N, 1, *this); }
};
} // namespace internal
/// \endcond DO_NOT_DOCUMENT
} // namespace mfem
#endif
+6 -13
View File
@@ -17,9 +17,6 @@
#include "fem.hpp"
#include "ceed/interface/util.hpp"
#include "derefmat_op.hpp"
#include <algorithm>
#include <cmath>
#include <cstdarg>
@@ -27,9 +24,9 @@ using namespace std;
namespace mfem
{
template <>
void Ordering::DofsToVDofs<Ordering::byNODES>(int ndofs, int vdim,
Array<int> &dofs)
template <> void Ordering::
DofsToVDofs<Ordering::byNODES>(int ndofs, int vdim, Array<int> &dofs)
{
// static method
int size = dofs.Size();
@@ -43,9 +40,8 @@ void Ordering::DofsToVDofs<Ordering::byNODES>(int ndofs, int vdim,
}
}
template <>
void Ordering::DofsToVDofs<Ordering::byVDIM>(int ndofs, int vdim,
Array<int> &dofs)
template <> void Ordering::
DofsToVDofs<Ordering::byVDIM>(int ndofs, int vdim, Array<int> &dofs)
{
// static method
int size = dofs.Size();
@@ -59,6 +55,7 @@ void Ordering::DofsToVDofs<Ordering::byVDIM>(int ndofs, int vdim,
}
}
FiniteElementSpace::FiniteElementSpace()
: mesh(NULL), fec(NULL), vdim(0), ordering(Ordering::byNODES),
ndofs(0), nvdofs(0), nedofs(0), nfdofs(0), nbdofs(0),
@@ -4247,11 +4244,7 @@ void FiniteElementSpace::Update(bool want_transform)
case Mesh::DEREFINE:
{
BuildConformingInterpolation();
#if 0
Th.Reset(DerefinementMatrix(old_ndofs, old_elem_dof, old_elem_fos));
#else
Th.Reset(new DerefineMatrixOp(*this, old_ndofs, old_elem_dof, old_elem_fos));
#endif
if (IsVariableOrder())
{
if (cP && cR_hp)
+1 -2
View File
@@ -113,7 +113,7 @@ class QuadratureSpace;
class QuadratureInterpolator;
class FaceQuadratureInterpolator;
class PRefinementTransferOperator;
struct DerefineMatrixOp;
/** @brief Class FiniteElementSpace - responsible for providing FEM view of the
mesh, mainly managing the set of degrees of freedom.
@@ -246,7 +246,6 @@ class FiniteElementSpace
friend class PRefinementTransferOperator;
friend void Mesh::Swap(Mesh &, bool);
friend class LORBase;
friend struct DerefineMatrixOp;
protected:
/// The mesh that FE space lives on (not owned).
+1 -1
View File
@@ -4334,7 +4334,7 @@ real_t LSZZErrorEstimator(BilinearFormIntegrator &blfi, // input
u.GetSubVector(udofs, ul);
utrans.InvTransformPrimal(ul);
Transf = ufes->GetElementTransformation(ielem);
const auto *dummy = ufes->GetFE(ielem);
FiniteElement *dummy = nullptr;
blfi.ComputeElementFlux(*ufes->GetFE(ielem), *Transf, ul,
*dummy, fl, with_coeff, ir);
+4 -11
View File
@@ -139,6 +139,8 @@ void DGTraceIntegrator::SetupPA(const FiniteElementSpace &fes, FaceType type)
const MemoryType mt = (pa_mt == MemoryType::DEFAULT) ?
Device::GetDeviceMemoryType() : pa_mt;
nf = fes.GetNFbyType(type);
if (nf==0) { return; }
// Assumes tensor-product elements
Mesh *mesh = fes.GetMesh();
const FiniteElement &el = *fes.GetTypicalTraceElement();
@@ -146,17 +148,6 @@ void DGTraceIntegrator::SetupPA(const FiniteElementSpace &fes, FaceType type)
IntRule:
&GetRule(el.GetGeomType(), el.GetOrder(),
*mesh->GetTypicalElementTransformation());
if (!qspace[static_cast<int>(type)])
{
qspace[static_cast<int>(type)].reset(
new FaceQuadratureSpace(*mesh, *ir, type));
}
FaceQuadratureSpace& qs = *qspace[static_cast<int>(type)];
nf = qs.GetNumFaces();
if (nf==0) { return; }
const int symmDims = 4;
nq = ir->GetNPoints();
dim = mesh->Dimension();
@@ -168,6 +159,8 @@ void DGTraceIntegrator::SetupPA(const FiniteElementSpace &fes, FaceType type)
dofs1D = maps->ndof;
quad1D = maps->nqpt;
pa_data.SetSize(symmDims * nq * nf, Device::GetMemoryType());
FaceQuadratureSpace qs(*mesh, *ir, type);
CoefficientVector vel(*u, qs, CoefficientStorage::COMPRESSED);
CoefficientVector r(qs, CoefficientStorage::COMPRESSED);
+25 -26
View File
@@ -1009,7 +1009,6 @@ inline void SmemPADiffusionApply3D(const int NE,
auto d = Reshape(d_.Read(), Q1D, Q1D, Q1D, symmetric ? 6 : 9, NE);
auto x = Reshape(x_.Read(), D1D, D1D, D1D, NE);
auto y = Reshape(y_.ReadWrite(), D1D, D1D, D1D, NE);
MFEM_VERIFY(D1D <= Q1D, "THREAD_DIRECT requires D1D <= Q1D");
mfem::forall_3D(NE, Q1D, Q1D, Q1D, [=] MFEM_HOST_DEVICE (int e)
{
const int D1D = T_D1D ? T_D1D : d1d;
@@ -1039,11 +1038,11 @@ inline void SmemPADiffusionApply3D(const int NE,
real_t (*QDD0)[MD1][MD1] = (real_t (*)[MD1][MD1]) (sm0+0);
real_t (*QDD1)[MD1][MD1] = (real_t (*)[MD1][MD1]) (sm0+1);
real_t (*QDD2)[MD1][MD1] = (real_t (*)[MD1][MD1]) (sm0+2);
MFEM_FOREACH_THREAD_DIRECT(dz,z,D1D)
MFEM_FOREACH_THREAD(dz,z,D1D)
{
MFEM_FOREACH_THREAD_DIRECT(dy,y,D1D)
MFEM_FOREACH_THREAD(dy,y,D1D)
{
MFEM_FOREACH_THREAD_DIRECT(dx,x,D1D)
MFEM_FOREACH_THREAD(dx,x,D1D)
{
X[dz][dy][dx] = x(dx,dy,dz,e);
}
@@ -1051,9 +1050,9 @@ inline void SmemPADiffusionApply3D(const int NE,
}
if (MFEM_THREAD_ID(z) == 0)
{
MFEM_FOREACH_THREAD_DIRECT(dy,y,D1D)
MFEM_FOREACH_THREAD(dy,y,D1D)
{
MFEM_FOREACH_THREAD_DIRECT(qx,x,Q1D)
MFEM_FOREACH_THREAD(qx,x,Q1D)
{
B[qx][dy] = b(qx,dy);
G[qx][dy] = g(qx,dy);
@@ -1061,11 +1060,11 @@ inline void SmemPADiffusionApply3D(const int NE,
}
}
MFEM_SYNC_THREAD;
MFEM_FOREACH_THREAD_DIRECT(dz,z,D1D)
MFEM_FOREACH_THREAD(dz,z,D1D)
{
MFEM_FOREACH_THREAD_DIRECT(dy,y,D1D)
MFEM_FOREACH_THREAD(dy,y,D1D)
{
MFEM_FOREACH_THREAD_DIRECT(qx,x,Q1D)
MFEM_FOREACH_THREAD(qx,x,Q1D)
{
real_t u = 0.0, v = 0.0;
MFEM_UNROLL(MD1)
@@ -1081,11 +1080,11 @@ inline void SmemPADiffusionApply3D(const int NE,
}
}
MFEM_SYNC_THREAD;
MFEM_FOREACH_THREAD_DIRECT(dz,z,D1D)
MFEM_FOREACH_THREAD(dz,z,D1D)
{
MFEM_FOREACH_THREAD_DIRECT(qy,y,Q1D)
MFEM_FOREACH_THREAD(qy,y,Q1D)
{
MFEM_FOREACH_THREAD_DIRECT(qx,x,Q1D)
MFEM_FOREACH_THREAD(qx,x,Q1D)
{
real_t u = 0.0, v = 0.0, w = 0.0;
MFEM_UNROLL(MD1)
@@ -1102,11 +1101,11 @@ inline void SmemPADiffusionApply3D(const int NE,
}
}
MFEM_SYNC_THREAD;
MFEM_FOREACH_THREAD_DIRECT(qz,z,Q1D)
MFEM_FOREACH_THREAD(qz,z,Q1D)
{
MFEM_FOREACH_THREAD_DIRECT(qy,y,Q1D)
MFEM_FOREACH_THREAD(qy,y,Q1D)
{
MFEM_FOREACH_THREAD_DIRECT(qx,x,Q1D)
MFEM_FOREACH_THREAD(qx,x,Q1D)
{
real_t u = 0.0, v = 0.0, w = 0.0;
MFEM_UNROLL(MD1)
@@ -1137,9 +1136,9 @@ inline void SmemPADiffusionApply3D(const int NE,
MFEM_SYNC_THREAD;
if (MFEM_THREAD_ID(z) == 0)
{
MFEM_FOREACH_THREAD_DIRECT(dy,y,D1D)
MFEM_FOREACH_THREAD(dy,y,D1D)
{
MFEM_FOREACH_THREAD_DIRECT(qx,x,Q1D)
MFEM_FOREACH_THREAD(qx,x,Q1D)
{
Bt[dy][qx] = b(qx,dy);
Gt[dy][qx] = g(qx,dy);
@@ -1147,11 +1146,11 @@ inline void SmemPADiffusionApply3D(const int NE,
}
}
MFEM_SYNC_THREAD;
MFEM_FOREACH_THREAD_DIRECT(qz,z,Q1D)
MFEM_FOREACH_THREAD(qz,z,Q1D)
{
MFEM_FOREACH_THREAD_DIRECT(qy,y,Q1D)
MFEM_FOREACH_THREAD(qy,y,Q1D)
{
MFEM_FOREACH_THREAD_DIRECT(dx,x,D1D)
MFEM_FOREACH_THREAD(dx,x,D1D)
{
real_t u = 0.0, v = 0.0, w = 0.0;
MFEM_UNROLL(MQ1)
@@ -1168,11 +1167,11 @@ inline void SmemPADiffusionApply3D(const int NE,
}
}
MFEM_SYNC_THREAD;
MFEM_FOREACH_THREAD_DIRECT(qz,z,Q1D)
MFEM_FOREACH_THREAD(qz,z,Q1D)
{
MFEM_FOREACH_THREAD_DIRECT(dy,y,D1D)
MFEM_FOREACH_THREAD(dy,y,D1D)
{
MFEM_FOREACH_THREAD_DIRECT(dx,x,D1D)
MFEM_FOREACH_THREAD(dx,x,D1D)
{
real_t u = 0.0, v = 0.0, w = 0.0;
MFEM_UNROLL(Q1D)
@@ -1189,11 +1188,11 @@ inline void SmemPADiffusionApply3D(const int NE,
}
}
MFEM_SYNC_THREAD;
MFEM_FOREACH_THREAD_DIRECT(dz,z,D1D)
MFEM_FOREACH_THREAD(dz,z,D1D)
{
MFEM_FOREACH_THREAD_DIRECT(dy,y,D1D)
MFEM_FOREACH_THREAD(dy,y,D1D)
{
MFEM_FOREACH_THREAD_DIRECT(dx,x,D1D)
MFEM_FOREACH_THREAD(dx,x,D1D)
{
real_t u = 0.0, v = 0.0, w = 0.0;
MFEM_UNROLL(MQ1)
+56 -25
View File
@@ -59,23 +59,26 @@ void MassIntegrator::AssemblePA(const FiniteElementSpace &fes)
QuadratureSpace qs(*mesh, *ir);
CoefficientVector coeff(Q, qs, CoefficientStorage::COMPRESSED);
const int NE = ne;
const int Q1D = quad1D;
const int NQ = pow(Q1D, dim);
const bool const_c = coeff.Size() == 1;
const bool by_val = map_type == FiniteElement::VALUE;
const auto W = Reshape(ir->GetWeights().Read(), NQ);
const auto J = Reshape(geom->detJ.Read(), NQ, NE);
const auto C = const_c ? Reshape(coeff.Read(), 1, 1) :
Reshape(coeff.Read(), NQ,NE);
auto v = Reshape(pa_data.Write(), NQ, NE);
mfem::forall_2D(NE, NQ, 1, [=] MFEM_HOST_DEVICE (int e)
{
const int NE = ne;
const int NQ = nq;
const bool const_c = coeff.Size() == 1;
const bool by_val = map_type == FiniteElement::VALUE;
const auto W = Reshape(ir->GetWeights().Read(), NQ);
const auto J = Reshape(geom->detJ.Read(), NQ, NE);
const auto C =
const_c ? Reshape(coeff.Read(), 1, 1) : Reshape(coeff.Read(), NQ, NE);
auto v = Reshape(pa_data.Write(), NQ, NE);
mfem::forall(NQ, NE, [=] MFEM_HOST_DEVICE(int q, int e)
MFEM_FOREACH_THREAD(i, x, NQ)
{
const real_t detJ = J(q, e);
const real_t coeff = const_c ? C(0, 0) : C(q, e);
v(q, e) = W(q) * coeff * (by_val ? detJ : 1.0 / detJ);
});
}
const real_t detJ = J(i,e);
const real_t coeff = const_c ? C(0,0) : C(i,e);
v(i,e) = W(i) * coeff * (by_val ? detJ : 1.0/detJ);
}
});
}
void MassIntegrator::AssemblePABoundary(const FiniteElementSpace &fes)
@@ -106,22 +109,50 @@ void MassIntegrator::AssemblePABoundary(const FiniteElementSpace &fes)
CoefficientVector coeff(Q, qs, CoefficientStorage::COMPRESSED);
const int NE = ne;
const int NQ = nq;
const int Q1D = quad1D;
const bool const_c = coeff.Size() == 1;
const bool by_val = map_type == FiniteElement::VALUE;
if (dim==1)
{
const auto W = Reshape(ir->GetWeights().Read(), NQ);
const auto J = Reshape(face_geom->detJ.Read(), NQ, NE);
const auto C = const_c ? Reshape(coeff.Read(), 1, 1)
: Reshape(coeff.Read(), NQ, NE);
auto v = Reshape(pa_data.Write(), NQ, NE);
mfem::forall(NQ, NE, [=] MFEM_HOST_DEVICE(int q, int e)
const auto W = Reshape(ir->GetWeights().Read(), Q1D);
const auto J = Reshape(face_geom->detJ.Read(), Q1D, NE);
const auto C = const_c ? Reshape(coeff.Read(), 1, 1) :
Reshape(coeff.Read(), Q1D, NE);
auto v = Reshape(pa_data.Write(), Q1D, NE);
mfem::forall_2D(NE, Q1D, 1, [=] MFEM_HOST_DEVICE (int e)
{
const real_t detJ = J(q, e);
const real_t coeff = const_c ? C(0, 0) : C(q, e);
v(q, e) = W(q) * coeff * (by_val ? detJ : 1.0 / detJ);
MFEM_FOREACH_THREAD(qx,x,Q1D)
{
const real_t detJ = J(qx,e);
const real_t coeff = const_c ? C(0,0) : C(qx,e);
v(qx,e) = W(qx) * coeff * (by_val ? detJ : 1.0/detJ);
}
});
}
else if (dim==2)
{
const auto W = Reshape(ir->GetWeights().Read(), Q1D,Q1D);
const auto J = Reshape(face_geom->detJ.Read(), Q1D,Q1D,NE);
const auto C = const_c ? Reshape(coeff.Read(), 1,1,1) :
Reshape(coeff.Read(), Q1D,Q1D,NE);
auto v = Reshape(pa_data.Write(), Q1D,Q1D, NE);
mfem::forall_2D(NE, Q1D, Q1D, [=] MFEM_HOST_DEVICE (int e)
{
MFEM_FOREACH_THREAD(qx,x,Q1D)
{
MFEM_FOREACH_THREAD(qy,y,Q1D)
{
const real_t detJ = J(qx,qy,e);
const real_t coeff = const_c ? C(0,0,0) : C(qx,qy,e);
v(qx,qy,e) = W(qx,qy) * coeff * (by_val ? detJ : 1.0/detJ);
}
}
});
}
else
{
MFEM_ABORT("Not supported.");
}
}
void MassIntegrator::AssembleDiagonalPA(Vector &diag)
+29 -29
View File
@@ -346,13 +346,13 @@ private:
template<typename T>
T operator() (const blitz::TinyVector<T,3>& x) const
{
const int el_order = el->GetOrder();
std::vector<T> u1(el_order+1);
std::vector<T> u2(el_order+1);
std::vector<T> u3(el_order+1);
TmplPoly_1D::CalcBernstein(el_order, x[0], u1.data());
TmplPoly_1D::CalcBernstein(el_order, x[1], u2.data());
TmplPoly_1D::CalcBernstein(el_order, x[2], u3.data());
int el_order=el->GetOrder();
T u1[el_order+1];
T u2[el_order+1];
T u3[el_order+1];
TmplPoly_1D::CalcBernstein(el_order, x[0], u1);
TmplPoly_1D::CalcBernstein(el_order, x[1], u2);
TmplPoly_1D::CalcBernstein(el_order, x[2], u3);
const Array<int>& dof_map=el->GetDofMap();
@@ -370,17 +370,17 @@ private:
template<typename T>
blitz::TinyVector<T,3> grad(const blitz::TinyVector<T,3>& x) const
{
const int el_order = el->GetOrder();
std::vector<T> u1(el_order+1);
std::vector<T> u2(el_order+1);
std::vector<T> u3(el_order+1);
std::vector<T> d1(el_order+1);
std::vector<T> d2(el_order+1);
std::vector<T> d3(el_order+1);
int el_order=el->GetOrder();
T u1[el_order+1];
T u2[el_order+1];
T u3[el_order+1];
T d1[el_order+1];
T d2[el_order+1];
T d3[el_order+1];
TmplPoly_1D::CalcBernstein(el_order,x[0], u1.data(), d1.data());
TmplPoly_1D::CalcBernstein(el_order,x[1], u2.data(), d2.data());
TmplPoly_1D::CalcBernstein(el_order,x[2], u3.data(), d3.data());
TmplPoly_1D::CalcBernstein(el_order,x[0], u1, d1);
TmplPoly_1D::CalcBernstein(el_order,x[1], u2, d2);
TmplPoly_1D::CalcBernstein(el_order,x[2], u3, d3);
blitz::TinyVector<T,3> res(T(0.0),T(0.0),T(0.0));
@@ -415,11 +415,11 @@ private:
template<typename T>
T operator() (const blitz::TinyVector<T,2>& x) const
{
const int el_order = el->GetOrder();
std::vector<T> u1(el_order+1);
std::vector<T> u2(el_order+1);
TmplPoly_1D::CalcBernstein(el_order, x[0], u1.data());
TmplPoly_1D::CalcBernstein(el_order, x[1], u2.data());
int el_order=el->GetOrder();
T u1[el_order+1];
T u2[el_order+1];
TmplPoly_1D::CalcBernstein(el_order, x[0], u1);
TmplPoly_1D::CalcBernstein(el_order, x[1], u2);
const Array<int>& dof_map=el->GetDofMap();
@@ -437,14 +437,14 @@ private:
template<typename T>
blitz::TinyVector<T,2> grad(const blitz::TinyVector<T,2>& x) const
{
const int el_order = el->GetOrder();
std::vector<T> u1(el_order+1);
std::vector<T> u2(el_order+1);
std::vector<T> d1(el_order+1);
std::vector<T> d2(el_order+1);
int el_order=el->GetOrder();
T u1[el_order+1];
T u2[el_order+1];
T d1[el_order+1];
T d2[el_order+1];
TmplPoly_1D::CalcBernstein(el_order,x[0], u1.data(), d1.data());
TmplPoly_1D::CalcBernstein(el_order,x[1], u2.data(), d2.data());
TmplPoly_1D::CalcBernstein(el_order,x[0], u1, d1);
TmplPoly_1D::CalcBernstein(el_order,x[1], u2, d2);
blitz::TinyVector<T,2> res(T(0.0),T(0.0));
+32 -10
View File
@@ -51,7 +51,7 @@ void LinearFormExtension::Assemble()
{
// scan the attributes to set the markers to 0 or 1
const int NE = fes.GetNE();
const auto attr = attributes->Read();
const auto attr = attributes.Read();
const auto dimk = domain_integs_marker_k->Read();
auto markers_w = markers.Write();
mfem::forall(NE, [=] MFEM_HOST_DEVICE (int e)
@@ -93,14 +93,13 @@ void LinearFormExtension::Assemble()
else
{
// scan the attributes to set the markers to 0 or 1
const int NBE = bdr_face_attributes->Size();
const auto attr = bdr_face_attributes->Read();
const int NBE = bdr_attributes.Size();
const auto attr = bdr_attributes.Read();
const auto attr_markers = boundary_integs_marker_k->Read();
auto markers_w = bdr_markers.Write();
mfem::forall(NBE, [=] MFEM_HOST_DEVICE(int e)
mfem::forall(NBE, [=] MFEM_HOST_DEVICE (int e)
{
markers_w[e] =
attr[e] > 0 ? (attr_markers[attr[e] - 1] == 1) : false;
markers_w[e] = attr_markers[attr[e]-1] == 1;
});
}
@@ -126,7 +125,8 @@ void LinearFormExtension::Update()
//markers.UseDevice(true);
// Gather the attributes on the host from all the elements
attributes = &mesh.GetElementAttributes();
attributes.SetSize(NE);
for (int i = 0; i < NE; ++i) { attributes[i] = mesh.GetAttribute(i); }
elem_restrict_lex = fes.GetElementRestriction(ordering);
MFEM_VERIFY(elem_restrict_lex, "Element restriction not available");
@@ -136,12 +136,34 @@ void LinearFormExtension::Update()
if (lf->boundary_integs.Size() > 0)
{
bdr_face_attributes = &mesh.GetBdrFaceAttributes();
const int nf_bdr = bdr_face_attributes->Size();
const int nf_bdr = fes.GetNFbyType(FaceType::Boundary);
bdr_markers.SetSize(nf_bdr);
// bdr_markers.UseDevice(true);
// The face restriction will give us "face E-vectors" on the boundary that
// are numbered in the order of the faces of mesh. This numbering will be
// different than the numbering of the boundary elements. We compute
// mappings so that the array `bdr_attributes[i]` gives the boundary
// attribute of the `i`th boundary face in the mesh face order.
std::unordered_map<int,int> f_to_be;
for (int i = 0; i < mesh.GetNBE(); ++i)
{
const int f = mesh.GetBdrElementFaceIndex(i);
f_to_be[f] = i;
}
MFEM_VERIFY(size_t(nf_bdr) == f_to_be.size(), "Incompatible sizes");
bdr_attributes.SetSize(nf_bdr);
int f_ind = 0;
for (int f = 0; f < mesh.GetNumFaces(); ++f)
{
if (f_to_be.find(f) != f_to_be.end())
{
const int be = f_to_be[f];
bdr_attributes[f_ind] = mesh.GetBdrAttribute(be);
++f_ind;
}
}
bdr_restrict_lex =
dynamic_cast<const FaceRestriction*>(
fes.GetFaceRestriction(ordering, FaceType::Boundary,
+1 -2
View File
@@ -25,8 +25,7 @@ class LinearForm;
class LinearFormExtension
{
/// Attributes of all mesh elements.
const Array<int> *attributes; // Not owned
const Array<int> *bdr_face_attributes; // Not owned
Array<int> attributes, bdr_attributes;
/// Temporary markers for device kernels.
Array<int> markers, bdr_markers;
+1 -1
View File
@@ -673,7 +673,7 @@ public:
int myid;
MPI_Comm_rank(comm, &myid);
int seed = (seed_ > 0) ? seed_ + myid : time(nullptr) + myid;
int seed = (seed_ > 0) ? seed_ + myid : (int)time(0) + myid;
SetSeed(seed);
}
#else
-591
View File
@@ -1,591 +0,0 @@
// Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
// LICENSE and NOTICE for details. LLNL-CODE-806117.
//
// This file is part of the MFEM library. For more information and source code
// availability visit https://mfem.org.
//
// MFEM is free software; you can redistribute it and/or modify it under the
// terms of the BSD-3 license. We welcome feedback and contributions, see file
// CONTRIBUTING.md for details.
#include "pderefmat_op.hpp"
#ifdef MFEM_USE_MPI
#include "fes_kernels.hpp"
/// \cond DO_NOT_DOCUMENT
namespace mfem
{
namespace internal
{
template <Ordering::Type Order, bool Atomic>
static void ParDerefMultKernelImpl(const ParDerefineMatrixOp &op,
const Vector &x, Vector &y)
{
// pack sends
if (op.xghost_send.Size())
{
auto src = x.Read();
auto idcs = op.send_permutations.Read();
auto dst = Device::GetGPUAwareMPI() ? op.xghost_send.Write()
: op.xghost_send.HostWrite();
auto vdims = op.fespace->GetVDim();
auto sptr = op.send_segment_idcs.Read();
auto lptr = op.send_segments.Read();
auto old_ndofs = x.Size() / vdims;
forall(op.send_permutations.Size(), [=] MFEM_HOST_DEVICE(int i)
{
int seg = sptr[i];
int width = lptr[seg + 1] - lptr[seg];
auto tdst = dst + i + lptr[seg] * vdims;
int sign = 1;
int col = idcs[i];
if (col < 0)
{
sign = -1;
col = -1 - col;
}
for (int vdim = 0; vdim < vdims; ++vdim)
{
tdst[vdim * width] =
sign
* src[Order == Ordering::byNODES ? (col + vdim * old_ndofs)
: (col * vdims + vdim)];
}
});
// TODO: is this needed so we can send the packed data correctly?
// unclear for GPU-aware MPI, definitely required otherwise
MFEM_DEVICE_SYNC;
}
// initialize off-diagonal receive and send
op.requests.clear();
if (op.xghost_recv.Size())
{
auto vdims = op.fespace->GetVDim();
auto rcv = Device::GetGPUAwareMPI() ? op.xghost_recv.Write()
: op.xghost_recv.HostWrite();
for (int i = 0; i < op.recv_ranks.Size(); ++i)
{
op.requests.emplace_back();
MPI_Irecv(rcv + op.recv_segments[i] * vdims,
(op.recv_segments[i + 1] - op.recv_segments[i]) * vdims,
MPITypeMap<real_t>::mpi_type, op.recv_ranks[i],
MessageTag::DEREFINEMENT_MATRIX_CONSTRUCTION_DATA,
op.fespace->GetComm(), &op.requests.back());
}
}
if (op.xghost_send.Size())
{
auto vdims = op.fespace->GetVDim();
// only is a GPU mem ptr if GPU-aware MPI is enabled
auto dst = Device::GetGPUAwareMPI() ? op.xghost_send.Write()
: op.xghost_send.HostWrite();
for (int i = 0; i < op.send_ranks.Size(); ++i)
{
op.requests.emplace_back();
MPI_Isend(dst + op.send_segments[i] * vdims,
(op.send_segments[i + 1] - op.send_segments[i]) * vdims,
MPITypeMap<real_t>::mpi_type, op.send_ranks[i],
MessageTag::DEREFINEMENT_MATRIX_CONSTRUCTION_DATA,
op.fespace->GetComm(), &op.requests.back());
}
}
{
// diagonal
DerefineMatrixOpMultFunctor<Order, Atomic, true> func;
func.xptr = x.Read();
y.UseDevice();
y = 0.;
func.yptr = y.ReadWrite();
func.bsptr = op.block_storage.Read();
func.boptr = op.block_offsets.Read();
func.brptr = op.block_row_idcs_offsets.Read();
func.bcptr = op.block_col_idcs_offsets.Read();
func.rptr = op.row_idcs.Read();
func.cptr = op.col_idcs.Read();
func.vdims = op.fespace->GetVDim();
func.nblocks = op.block_offsets.Size();
func.width = op.Width() / func.vdims;
func.height = op.Height() / func.vdims;
func.Run(op.max_rows);
}
// wait for comm to finish, if any
if (op.requests.size())
{
MPI_Waitall(op.requests.size(), op.requests.data(), MPI_STATUSES_IGNORE);
if (op.xghost_recv.Size())
{
// off-diagonal kernel
DerefineMatrixOpMultFunctor<Order, Atomic, false> func;
// directly read from host-pinned memory if not using GPU-aware MPI
func.xptr = Device::GetGPUAwareMPI() ? op.xghost_recv.Read()
: op.xghost_recv.HostRead();
func.yptr = y.ReadWrite();
func.bsptr = op.block_storage.Read();
func.boptr = op.off_diag_block_offsets.Read();
func.brptr = op.block_off_diag_row_idcs_offsets.Read();
func.rsptr = op.recv_segment_idcs.Read();
func.segptr = op.recv_segments.Read();
func.coptr = op.block_off_diag_col_offsets.Read();
func.bwptr = op.block_off_diag_widths.Read();
func.rptr = op.row_off_diag_idcs.Read();
func.vdims = op.fespace->GetVDim();
func.nblocks = op.off_diag_block_offsets.Size();
func.width = op.xghost_recv.Size() / func.vdims;
func.height = op.Height() / func.vdims;
func.Run(op.max_rows);
}
}
}
} // namespace internal
template <Ordering::Type Order, bool Atomic>
ParDerefineMatrixOp::MultKernelType ParDerefineMatrixOp::MultKernel::Kernel()
{
return internal::ParDerefMultKernelImpl<Order, Atomic>;
}
ParDerefineMatrixOp::MultKernelType
ParDerefineMatrixOp::MultKernel::Fallback(Ordering::Type, bool)
{
MFEM_ABORT("invalid MultKernel parameters");
}
ParDerefineMatrixOp::Kernels::Kernels()
{
MultKernel::Specialization<Ordering::byNODES, false>::Add();
MultKernel::Specialization<Ordering::byVDIM, false>::Add();
MultKernel::Specialization<Ordering::byNODES, true>::Add();
MultKernel::Specialization<Ordering::byVDIM, true>::Add();
}
void ParDerefineMatrixOp::Mult(const Vector &x, Vector &y) const
{
const bool is_dg = fespace->FEColl()->GetContType()
== FiniteElementCollection::DISCONTINUOUS;
// DG needs atomic summation
MultKernel::Run(fespace->GetOrdering(), is_dg, *this, x, y);
// use this to prevent xghost* from being re-purposed for subsequent Mult
// calls
MFEM_DEVICE_SYNC;
}
ParDerefineMatrixOp::ParDerefineMatrixOp(ParFiniteElementSpace &fespace_,
int old_ndofs,
const Table *old_elem_dof,
const Table *old_elem_fos)
: Operator(fespace_.GetVSize(), old_ndofs * fespace_.GetVDim()),
fespace(&fespace_)
{
static Kernels kernels;
constexpr int max_team_size = 256;
const int NRanks = fespace->GetNRanks();
const int nrk = HYPRE_AssumedPartitionCheck() ? 2 : NRanks;
MFEM_VERIFY(fespace->Nonconforming(),
"Not implemented for conforming meshes.");
MFEM_VERIFY(fespace->old_dof_offsets[nrk],
"Missing previous (finer) space.");
const int MyRank = fespace->GetMyRank();
ParNCMesh *old_pncmesh = fespace->GetParMesh()->pncmesh;
const CoarseFineTransformations &dtrans =
old_pncmesh->GetDerefinementTransforms();
const Array<int> &old_ranks = old_pncmesh->GetDerefineOldRanks();
const bool is_dg = fespace->FEColl()->GetContType()
== FiniteElementCollection::DISCONTINUOUS;
DenseMatrix localRVO; // for variable-order only
DenseTensor localR[Geometry::NumGeom];
int diag_rows = 0;
int off_diag_rows = 0;
int diag_cols = 0;
auto get_ldofs = [&](int k) -> int
{
const Embedding &emb = dtrans.embeddings[k];
if (fespace->IsVariableOrder())
{
const FiniteElement *fe = fespace->GetFE(emb.parent);
return fe->GetDof();
}
else
{
Geometry::Type geom =
fespace->GetParMesh()->GetElementBaseGeometry(emb.parent);
return fespace->FEColl()->FiniteElementForGeometry(geom)->GetDof();
}
};
Array<int> dofs, old_dofs;
max_rows = 1;
// first pass:
// - determine memory block lengths
// - identify dofs in x we need to send/receive
// don't need to send the indices, fine rank will re-arrange and sign
// change x before transmitting the ghost data
// key: coarse rank to send to
// value: old dofs to send (with sign)
std::map<int, std::vector<int>> to_send;
// key: fine rank
// value: indices into dtrans.embeddings
std::map<int, std::vector<int>> od_ks;
// key: fine rank
// value: recv segment length
std::map<int, int> od_seg_lens;
int send_len = 0;
int recv_len = 0;
// size of block_storage, if fespace->IsVariableOrder()
// otherwise unused
int total_size = 0;
int num_diagonal_blocks = 0;
int num_offdiagonal_blocks = 0;
for (int k = 0; k < dtrans.embeddings.Size(); ++k)
{
const Embedding &emb = dtrans.embeddings[k];
int fine_rank = old_ranks[k];
int coarse_rank = (emb.parent < 0) ? (-1 - emb.parent)
: old_pncmesh->ElementRank(emb.parent);
if (coarse_rank != MyRank && fine_rank == MyRank)
{
// this rank needs to send data in x to course_rank
old_elem_dof->GetRow(k, old_dofs);
auto &tmp = to_send[coarse_rank];
send_len += old_dofs.Size();
for (int i = 0; i < old_dofs.Size(); ++i)
{
tmp.emplace_back(old_dofs[i]);
}
}
else if (coarse_rank == MyRank && fine_rank != MyRank)
{
// this rank needs to receive data in x from fine_rank
MFEM_ASSERT(emb.parent >= 0, "");
auto ldofs = get_ldofs(k);
off_diag_rows += ldofs;
recv_len += ldofs;
od_ks[fine_rank].emplace_back(k);
od_seg_lens[fine_rank] += ldofs;
++num_offdiagonal_blocks;
if (fespace->IsVariableOrder())
{
total_size += ldofs * ldofs;
}
}
else if (coarse_rank == MyRank && fine_rank == MyRank)
{
MFEM_ASSERT(emb.parent >= 0, "");
// diagonal
++num_diagonal_blocks;
auto ldofs = get_ldofs(k);
diag_rows += ldofs;
diag_cols += ldofs;
if (fespace->IsVariableOrder())
{
total_size += ldofs * ldofs;
}
}
}
send_segments.SetSize(to_send.size() + 1);
send_segments.HostWrite();
send_ranks.SetSize(to_send.size());
send_ranks.HostWrite();
{
int idx = 0;
send_segments[0] = 0;
for (auto &tmp : to_send)
{
send_ranks[idx] = tmp.first;
send_segments[idx + 1] = send_segments[idx] + tmp.second.size();
++idx;
}
}
recv_segment_idcs.SetSize(off_diag_rows);
recv_segment_idcs.HostWrite();
recv_segments.SetSize(od_ks.size() + 1);
recv_segments.HostWrite();
recv_ranks.SetSize(od_ks.size());
recv_ranks.HostWrite();
// set sizes
row_idcs.SetSize(diag_rows);
row_idcs.HostWrite();
row_off_diag_idcs.SetSize(off_diag_rows);
row_off_diag_idcs.HostWrite();
col_idcs.SetSize(diag_cols);
col_idcs.HostWrite();
block_row_idcs_offsets.SetSize(num_diagonal_blocks + 1);
block_row_idcs_offsets.HostWrite();
block_col_idcs_offsets.SetSize(num_diagonal_blocks + 1);
block_col_idcs_offsets.HostWrite();
block_off_diag_row_idcs_offsets.SetSize(num_offdiagonal_blocks + 1);
block_off_diag_row_idcs_offsets.HostWrite();
block_off_diag_col_offsets.SetSize(num_offdiagonal_blocks);
block_off_diag_col_offsets.HostWrite();
block_off_diag_widths.SetSize(num_offdiagonal_blocks);
block_off_diag_widths.HostWrite();
pack_col_idcs.SetSize(send_len);
// memory manager doesn't appear to have a graceful fallback for
// HOST_PINNED if not built with CUDA or HIP
#if defined(MFEM_USE_CUDA) or defined(MFEM_USE_HIP)
xghost_send.SetSize(send_len * fespace->GetVDim(),
Device::GetGPUAwareMPI() ? MemoryType::DEFAULT
: MemoryType::HOST_PINNED);
xghost_recv.SetSize(recv_len * fespace->GetVDim(),
Device::GetGPUAwareMPI() ? MemoryType::DEFAULT
: MemoryType::HOST_PINNED);
#else
xghost_send.SetSize(send_len * fespace->GetVDim());
xghost_recv.SetSize(recv_len * fespace->GetVDim());
#endif
send_permutations.SetSize(send_len);
send_segment_idcs.SetSize(send_len);
block_offsets.SetSize(num_diagonal_blocks);
block_offsets.HostWrite();
off_diag_block_offsets.SetSize(num_offdiagonal_blocks);
off_diag_block_offsets.HostWrite();
int geom_offsets[Geometry::NumGeom];
real_t *bs_ptr;
if (fespace->IsVariableOrder())
{
block_storage.SetSize(total_size);
bs_ptr = block_storage.HostWrite();
// compute block data later
}
else
{
// compression scheme:
// block_offsets is the start of each block, potentially repeated
// only need to store localR for used shapes
Mesh::GeometryList elem_geoms(*fespace->GetMesh());
int size = 0;
for (int i = 0; i < elem_geoms.Size(); ++i)
{
fespace->GetLocalDerefinementMatrices(elem_geoms[i],
localR[elem_geoms[i]]);
geom_offsets[elem_geoms[i]] = size;
size += localR[elem_geoms[i]].TotalSize();
}
block_storage.SetSize(size);
bs_ptr = block_storage.HostWrite();
// copy blocks into block_storage
for (int i = 0; i < elem_geoms.Size(); ++i)
{
std::copy(localR[elem_geoms[i]].Data(),
localR[elem_geoms[i]].Data()
+ localR[elem_geoms[i]].TotalSize(),
bs_ptr);
bs_ptr += localR[elem_geoms[i]].TotalSize();
}
}
// second pass:
// - initialize buffers
{
auto ptr = send_permutations.HostWrite();
auto ptr2 = send_segment_idcs.HostWrite();
int i = 0;
for (auto &v : to_send)
{
ptr = std::copy(v.second.begin(), v.second.end(), ptr);
for (size_t idx = 0; idx < v.second.size(); ++idx)
{
*ptr2 = i;
++ptr2;
}
++i;
}
}
block_row_idcs_offsets[0] = 0;
block_col_idcs_offsets[0] = 0;
block_off_diag_row_idcs_offsets[0] = 0;
Array<int> mark(fespace->GetNDofs());
mark = 0;
{
int idx = 0;
recv_segments[0] = 0;
for (auto &v : od_seg_lens)
{
recv_ranks[idx] = v.first;
recv_segments[idx + 1] = recv_segments[idx] + v.second;
++idx;
}
}
// key: index into dtrans.embeddings
// value: off-diagonal block offset, od_ridx, seg id
std::unordered_map<int, std::array<int, 3>> ks_map;
{
int od_ridx = 0;
int seg_id = 0;
for (auto &v1 : od_ks)
{
for (auto k : v1.second)
{
auto &tmp = ks_map[k];
tmp[0] = ks_map.size() - 1;
tmp[1] = od_ridx;
tmp[2] = seg_id;
od_ridx += get_ldofs(k);
}
++seg_id;
}
}
int diag_idx = 0;
int var_offset = 0;
int ridx = 0;
int cidx = 0;
// can't break this up into separate diagonals/off-diagonals loops because
// of mark
for (int k = 0; k < dtrans.embeddings.Size(); ++k)
{
const Embedding &emb = dtrans.embeddings[k];
if (emb.parent < 0)
{
continue;
}
int fine_rank = old_ranks[k];
int coarse_rank = (emb.parent < 0) ? (-1 - emb.parent)
: old_pncmesh->ElementRank(emb.parent);
if (coarse_rank == MyRank)
{
// either diagonal or off-diagonal
Geometry::Type geom =
fespace->GetMesh()->GetElementBaseGeometry(emb.parent);
if (fespace->IsVariableOrder())
{
const FiniteElement *fe = fespace->GetFE(emb.parent);
const DenseTensor &pmats = dtrans.point_matrices[geom];
const int ldof = fe->GetDof();
IsoparametricTransformation isotr;
isotr.SetIdentityTransformation(geom);
localRVO.SetSize(ldof, ldof);
isotr.SetPointMat(pmats(emb.matrix));
// Local restriction is size ldofxldof assuming that the parent
// and child are of same polynomial order.
fe->GetLocalRestriction(isotr, localRVO);
// copy block
auto s = localRVO.Height() * localRVO.Width();
std::copy(localRVO.Data(), localRVO.Data() + s, bs_ptr);
bs_ptr += s;
}
DenseMatrix &lR =
fespace->IsVariableOrder() ? localRVO : localR[geom](emb.matrix);
max_rows = std::max(lR.Height(), max_rows);
auto size = lR.Height() * lR.Width();
fespace->elem_dof->GetRow(emb.parent, dofs);
if (fine_rank == MyRank)
{
// diagonal
old_elem_dof->GetRow(k, old_dofs);
MFEM_VERIFY(old_dofs.Size() == dofs.Size(),
"Parent and child must have same #dofs.");
block_row_idcs_offsets[diag_idx + 1] =
block_row_idcs_offsets[diag_idx] + lR.Height();
block_col_idcs_offsets[diag_idx + 1] =
block_col_idcs_offsets[diag_idx] + lR.Width();
if (fespace->IsVariableOrder())
{
block_offsets[diag_idx] = var_offset;
var_offset += size;
}
else
{
block_offsets[diag_idx] = geom_offsets[geom] + size * emb.matrix;
}
for (int i = 0; i < lR.Height(); ++i, ++ridx)
{
if (!std::isfinite(lR(i, 0)))
{
row_idcs[ridx] = INT_MAX;
continue;
}
int r = dofs[i];
int m = (r >= 0) ? r : (-1 - r);
if (is_dg || !mark[m])
{
row_idcs[ridx] = r;
mark[m] = 1;
}
else
{
row_idcs[ridx] = INT_MAX;
}
}
for (int i = 0; i < lR.Width(); ++i, ++cidx)
{
col_idcs[cidx] = old_dofs[i];
}
++diag_idx;
}
else
{
// off-diagonal
auto &tmp = ks_map.at(k);
auto od_idx = tmp[0];
auto od_ridx = tmp[1];
block_off_diag_row_idcs_offsets[od_idx + 1] =
block_off_diag_row_idcs_offsets[od_idx] + lR.Height();
block_off_diag_col_offsets[od_idx] = od_ridx;
block_off_diag_widths[od_idx] = lR.Width();
recv_segment_idcs[od_idx] = tmp[2];
if (fespace->IsVariableOrder())
{
off_diag_block_offsets[od_idx] = var_offset;
var_offset += size;
}
else
{
off_diag_block_offsets[od_idx] =
geom_offsets[geom] + size * emb.matrix;
}
for (int i = 0; i < lR.Height(); ++i, ++od_ridx)
{
if (!std::isfinite(lR(i, 0)))
{
row_off_diag_idcs[od_ridx] = INT_MAX;
continue;
}
int r = dofs[i];
int m = (r >= 0) ? r : (-1 - r);
if (is_dg || !mark[m])
{
row_off_diag_idcs[od_ridx] = r;
mark[m] = 1;
}
else
{
row_off_diag_idcs[od_ridx] = INT_MAX;
}
}
++od_idx;
}
}
}
// if not using GPU, set max_rows/max_cols to zero
if (Device::Allows(Backend::DEVICE_MASK))
{
max_rows = std::min(max_rows, max_team_size);
}
else
{
max_rows = 1;
}
requests.reserve(recv_ranks.Size() + send_ranks.Size());
}
} // namespace mfem
/// \endcond DO_NOT_DOCUMENT
#endif
-111
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@@ -1,111 +0,0 @@
// Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
// LICENSE and NOTICE for details. LLNL-CODE-806117.
//
// This file is part of the MFEM library. For more information and source code
// availability visit https://mfem.org.
//
// MFEM is free software; you can redistribute it and/or modify it under the
// terms of the BSD-3 license. We welcome feedback and contributions, see file
// CONTRIBUTING.md for details.
#ifndef MFEM_PDEREFMAT_OP
#define MFEM_PDEREFMAT_OP
#include "../config/config.hpp"
#ifdef MFEM_USE_MPI
#include "pfespace.hpp"
#include "kernel_dispatch.hpp"
#include <vector>
namespace mfem
{
/// \cond DO_NOT_DOCUMENT
struct ParDerefineMatrixOp : public Operator
{
ParFiniteElementSpace *fespace;
/// offsets into block_storage for diagonal
Array<int> block_offsets;
/// offsets into row_idcs for diagonal
Array<int> block_row_idcs_offsets;
/// offsets into col_idcs for diagonal
Array<int> block_col_idcs_offsets;
/// offsets into block_storage for off-diagonal
Array<int> off_diag_block_offsets;
/// offsets into row_idcs for off-diagonal
Array<int> block_off_diag_row_idcs_offsets;
Array<int> block_off_diag_col_offsets;
Array<int> block_off_diag_widths;
/// mapping for row dofs, INT_MAX indicates the block row should be ignored.
/// negative means the row data should be negated.
/// only for diagonal blocks
Array<int> row_idcs;
/// mapping for col dofs, negative means the col data should be negated.
/// only for diagonal blocks
Array<int> col_idcs;
Array<int> pack_col_idcs;
/// mapping for row dofs, INT_MAX indicates the block row should be ignored.
/// negative means the row data should be negated.
/// only for off-diagonal blocks
Array<int> row_off_diag_idcs;
/// dense block matrices which can be reused to construct the full matrix
/// operation. These are stored contiguously and blocks have no restrictions
/// on shape (can be rectangle and differ from block to block).
/// This is only for the diagonal block.
Vector block_storage;
/// maximum height of any block in block_storage for GPU
/// parallelization, or 1 for CPU runs.
int max_rows;
/// quasi Ordering::byNODES, broken into sections by ranks we need to send
/// the data to
mutable Vector xghost_send;
/// quasi Ordering::byNODES, broken into sections by ranks we received
/// the data from
mutable Vector xghost_recv;
/// maps off-diagonal k to segment
Array<int> recv_segment_idcs;
/// cumulative count of dofs which will be received from other ranks
Array<int> recv_segments;
/// Source rank of each recv segment
Array<int> recv_ranks;
/// What send segment each entry in send_permutations corresponds to
Array<int> send_segment_idcs;
/// cumulative count of dofs which will be sent to other ranks
Array<int> send_segments;
/// Destination rank of each send segment
Array<int> send_ranks;
/// how to permute/sign change values from our local x to send to other ranks
Array<int> send_permutations;
/// internal buffer for MPI requests
mutable std::vector<MPI_Request> requests;
using MultKernelType = void (*)(const ParDerefineMatrixOp &, const Vector &,
Vector &);
/// template args: ordering, atomic
MFEM_REGISTER_KERNELS(MultKernel, MultKernelType, (Ordering::Type, bool));
struct Kernels
{
Kernels();
};
void Mult(const Vector &x, Vector &y) const;
ParDerefineMatrixOp(ParFiniteElementSpace &fespace_, int old_ndofs,
const Table *old_elem_dof, const Table *old_elem_fos);
};
/// \endcond DO_NOT_DOCUMENT
} // namespace mfem
#endif
#endif
+33 -51
View File
@@ -22,13 +22,12 @@
#include "../mesh/mesh_headers.hpp"
#include "../general/binaryio.hpp"
#include "pderefmat_op.hpp"
#include <limits>
#include <list>
namespace mfem
{
ParFiniteElementSpace::ParFiniteElementSpace(
const ParFiniteElementSpace &orig, ParMesh *pmesh,
const FiniteElementCollection *fec)
@@ -4488,6 +4487,13 @@ ParFiniteElementSpace::RebalanceMatrix(int old_ndofs,
return M;
}
struct DerefDofMessage
{
std::vector<HYPRE_BigInt> dofs;
MPI_Request request;
};
HypreParMatrix*
ParFiniteElementSpace::ParallelDerefinementMatrix(int old_ndofs,
const Table* old_elem_dof,
@@ -4530,13 +4536,7 @@ ParFiniteElementSpace::ParallelDerefinementMatrix(int old_ndofs,
old_pncmesh->GetDerefinementTransforms();
const Array<int> &old_ranks = old_pncmesh->GetDerefineOldRanks();
// key: other rank
// value: send or recieve buffer
std::map<int, std::vector<HYPRE_BigInt>> to_send;
std::map<int, std::vector<HYPRE_BigInt>> to_recv;
// key: index into dtrans.embeddings
// value: [start, stop]
std::unordered_map<int, std::array<size_t, 2>> recv_messages;
std::map<int, DerefDofMessage> messages;
HYPRE_BigInt old_offset = HYPRE_AssumedPartitionCheck()
? old_dof_offsets[0] : old_dof_offsets[MyRank];
@@ -4556,46 +4556,30 @@ ParFiniteElementSpace::ParallelDerefinementMatrix(int old_ndofs,
old_elem_dof->GetRow(k, dofs);
DofsToVDofs(dofs, old_ndofs);
std::vector<HYPRE_BigInt>& send_buf = to_send[coarse_rank];
auto pos = send_buf.size();
send_buf.resize(pos + dofs.Size());
DerefDofMessage &msg = messages[k];
msg.dofs.resize(dofs.Size());
for (int i = 0; i < dofs.Size(); i++)
{
send_buf[pos + i] = old_offset + dofs[i];
msg.dofs[i] = old_offset + dofs[i];
}
MPI_Isend(&msg.dofs[0], static_cast<int>(msg.dofs.size()), HYPRE_MPI_BIG_INT,
coarse_rank, 291, MyComm, &msg.request);
}
else if (coarse_rank == MyRank && fine_rank != MyRank)
{
MFEM_ASSERT(emb.parent >= 0, "");
Geometry::Type geom = mesh->GetElementBaseGeometry(emb.parent);
std::vector<HYPRE_BigInt>& recv_buf = to_recv[fine_rank];
auto& msg = recv_messages[k];
msg[0] = recv_buf.size();
recv_buf.resize(recv_buf.size() + ldof[geom] * vdim);
msg[1] = recv_buf.size();
}
}
DerefDofMessage &msg = messages[k];
msg.dofs.resize(ldof[geom]*vdim);
// assume embedding orders are consistent (i.e. what we expect to receive
// first from a given rank is sent first, etc.)
std::vector<MPI_Request> requests;
requests.reserve(to_send.size() + to_recv.size());
// enqueue recvs
for (auto &v : to_recv)
{
requests.emplace_back();
MPI_Irecv(v.second.data(), v.second.size(), HYPRE_MPI_BIG_INT, v.first,
MessageTag::DEREFINEMENT_MATRIX_CONSTRUCTION_DATA, MyComm,
&requests.back());
}
// enqueue sends
for (auto &v : to_send)
{
requests.emplace_back();
MPI_Isend(v.second.data(), v.second.size(), HYPRE_MPI_BIG_INT, v.first,
MessageTag::DEREFINEMENT_MATRIX_CONSTRUCTION_DATA, MyComm,
&requests.back());
MPI_Irecv(&msg.dofs[0], ldof[geom]*vdim, HYPRE_MPI_BIG_INT,
fine_rank, 291, MyComm, &msg.request);
}
// TODO: coalesce Isends/Irecvs to the same rank. Typically, on uniform
// derefinement, there should be just one send to MyRank-1 and one recv
// from MyRank+1
}
DenseTensor localR[Geometry::NumGeom];
@@ -4653,7 +4637,10 @@ ParFiniteElementSpace::ParallelDerefinementMatrix(int old_ndofs,
diag->Finalize();
// wait for all sends/receives to complete
MPI_Waitall(requests.size(), requests.data(), MPI_STATUSES_IGNORE);
for (auto it = messages.begin(); it != messages.end(); ++it)
{
MPI_Wait(&it->second.request, MPI_STATUS_IGNORE);
}
// create the off-diagonal part of the derefinement matrix
SparseMatrix *offd = new SparseMatrix(ndofs*vdim, 1);
@@ -4674,14 +4661,13 @@ ParFiniteElementSpace::ParallelDerefinementMatrix(int old_ndofs,
elem_dof->GetRow(emb.parent, dofs);
auto& odofs = to_recv.at(fine_rank);
auto &msg = recv_messages[k];
MFEM_ASSERT(msg[1] > msg[0], "");
DerefDofMessage &msg = messages[k];
MFEM_ASSERT(msg.dofs.size(), "");
for (int vd = 0; vd < vdim; vd++)
{
MFEM_ASSERT(ldof[geom], "");
HYPRE_BigInt *remote_dofs = odofs.data() + msg[0] + vd * ldof[geom];
HYPRE_BigInt* remote_dofs = &msg.dofs[vd*ldof[geom]];
for (int i = 0; i < lR.Height(); i++)
{
@@ -4708,6 +4694,7 @@ ParFiniteElementSpace::ParallelDerefinementMatrix(int old_ndofs,
}
}
messages.clear();
offd->Finalize(0);
offd->SetWidth(static_cast<int>(col_map.size()));
@@ -4959,13 +4946,8 @@ void ParFiniteElementSpace::Update(bool want_transform)
case Mesh::DEREFINE:
{
#if 0
Th.Reset(ParallelDerefinementMatrix(old_ndofs, old_elem_dof,
old_elem_fos));
#else
Th.Reset(new ParDerefineMatrixOp(*this, old_ndofs, old_elem_dof,
old_elem_fos));
#endif
if (Nonconforming())
{
Th.SetOperatorOwner(false);
@@ -5277,7 +5259,7 @@ DeviceConformingProlongationOperator::DeviceConformingProlongationOperator(
gc.GetNeighborLTDofTable(nbr_ltdof);
const int nb_connections = nbr_ltdof.Size_of_connections();
shr_ltdof.SetSize(nb_connections);
if (nb_connections > 0) { shr_ltdof.CopyFrom(nbr_ltdof.GetJ()); }
shr_ltdof.CopyFrom(nbr_ltdof.GetJ());
shr_buf.SetSize(nb_connections);
shr_buf.UseDevice(true);
shr_buf_offsets = nbr_ltdof.GetIMemory();
@@ -5306,7 +5288,7 @@ DeviceConformingProlongationOperator::DeviceConformingProlongationOperator(
gc.GetNeighborLDofTable(nbr_ldof);
const int nb_connections = nbr_ldof.Size_of_connections();
ext_ldof.SetSize(nb_connections);
if (nb_connections > 0) { ext_ldof.CopyFrom(nbr_ldof.GetJ()); }
ext_ldof.CopyFrom(nbr_ldof.GetJ());
ext_ldof.GetMemory().UseDevice(true);
ext_buf.SetSize(nb_connections);
ext_buf.UseDevice(true);
-3
View File
@@ -24,12 +24,9 @@
namespace mfem
{
struct ParDerefineMatrixOp;
/// Abstract parallel finite element space.
class ParFiniteElementSpace : public FiniteElementSpace
{
friend struct ParDerefineMatrixOp;
private:
/// MPI data.
MPI_Comm MyComm;
+10 -10
View File
@@ -214,16 +214,16 @@ public:
inline void QuadratureFunction::GetValues(
int idx, Vector &values)
{
const int s_offset = qspace->Offset(idx);
const int sl_size = qspace->Offset(idx + 1) - s_offset;
const int s_offset = qspace->offsets[idx];
const int sl_size = qspace->offsets[idx+1] - s_offset;
values.MakeRef(*this, vdim*s_offset, vdim*sl_size);
}
inline void QuadratureFunction::GetValues(
int idx, Vector &values) const
{
const int s_offset = qspace->Offset(idx);
const int sl_size = qspace->Offset(idx + 1) - s_offset;
const int s_offset = qspace->offsets[idx];
const int sl_size = qspace->offsets[idx+1] - s_offset;
values.SetSize(vdim*sl_size);
values.HostWrite();
const real_t *q = HostRead() + vdim*s_offset;
@@ -236,14 +236,14 @@ inline void QuadratureFunction::GetValues(
inline void QuadratureFunction::GetValues(
int idx, const int ip_num, Vector &values)
{
const int s_offset = qspace->Offset(idx) * vdim + ip_num * vdim;
const int s_offset = qspace->offsets[idx] * vdim + ip_num * vdim;
values.MakeRef(*this, s_offset, vdim);
}
inline void QuadratureFunction::GetValues(
int idx, const int ip_num, Vector &values) const
{
const int s_offset = qspace->Offset(idx) * vdim + ip_num * vdim;
const int s_offset = qspace->offsets[idx] * vdim + ip_num * vdim;
values.SetSize(vdim);
values.HostWrite();
const real_t *q = HostRead() + s_offset;
@@ -256,8 +256,8 @@ inline void QuadratureFunction::GetValues(
inline void QuadratureFunction::GetValues(
int idx, DenseMatrix &values)
{
const int s_offset = qspace->Offset(idx);
const int sl_size = qspace->Offset(idx + 1) - s_offset;
const int s_offset = qspace->offsets[idx];
const int sl_size = qspace->offsets[idx+1] - s_offset;
// Make the values matrix memory an alias of the quadrature function memory
Memory<real_t> &values_mem = values.GetMemory();
values_mem.Delete();
@@ -268,8 +268,8 @@ inline void QuadratureFunction::GetValues(
inline void QuadratureFunction::GetValues(
int idx, DenseMatrix &values) const
{
const int s_offset = qspace->Offset(idx);
const int sl_size = qspace->Offset(idx + 1) - s_offset;
const int s_offset = qspace->offsets[idx];
const int sl_size = qspace->offsets[idx+1] - s_offset;
values.SetSize(vdim, sl_size);
values.HostWrite();
const real_t *q = HostRead() + vdim*s_offset;
+280 -3
View File
@@ -9,16 +9,278 @@
// terms of the BSD-3 license. We welcome feedback and contributions, see file
// CONTRIBUTING.md for details.
#include "det.hpp"
#include "../quadinterpolator.hpp"
#include "../../general/forall.hpp"
#include "../../linalg/dtensor.hpp"
#include "../../fem/kernels.hpp"
#include "../../linalg/kernels.hpp"
using namespace mfem;
namespace mfem
{
namespace internal
{
namespace quadrature_interpolator
{
static void Det1D(const int NE,
const real_t *b,
const real_t *g,
const real_t *x,
real_t *y,
const int d1d,
const int q1d,
Vector *d_buff = nullptr)
{
MFEM_CONTRACT_VAR(b);
MFEM_CONTRACT_VAR(d_buff);
const auto G = Reshape(g, q1d, d1d);
const auto X = Reshape(x, d1d, NE);
auto Y = Reshape(y, q1d, NE);
mfem::forall(NE, [=] MFEM_HOST_DEVICE (int e)
{
for (int q = 0; q < q1d; q++)
{
real_t u = 0.0;
for (int d = 0; d < d1d; d++)
{
u += G(q, d) * X(d, e);
}
Y(q, e) = u;
}
});
}
template<int T_D1D = 0, int T_Q1D = 0>
static void Det2D(const int NE,
const real_t *b,
const real_t *g,
const real_t *x,
real_t *y,
const int d1d = 0,
const int q1d = 0,
Vector *d_buff = nullptr)
{
MFEM_CONTRACT_VAR(d_buff);
static constexpr int SDIM = 2;
static constexpr int NBZ = 1;
const int D1D = T_D1D ? T_D1D : d1d;
const int Q1D = T_Q1D ? T_Q1D : q1d;
const auto B = Reshape(b, Q1D, D1D);
const auto G = Reshape(g, Q1D, D1D);
const auto X = Reshape(x, D1D, D1D, SDIM, NE);
auto Y = Reshape(y, Q1D, Q1D, NE);
mfem::forall_2D_batch(NE, Q1D, Q1D, NBZ, [=] MFEM_HOST_DEVICE (int e)
{
constexpr int MQ1 = T_Q1D ? T_Q1D : DofQuadLimits::MAX_Q1D;
constexpr int MD1 = T_D1D ? T_D1D : DofQuadLimits::MAX_D1D;
const int D1D = T_D1D ? T_D1D : d1d;
const int Q1D = T_Q1D ? T_Q1D : q1d;
MFEM_SHARED real_t BG[2][MQ1*MD1];
MFEM_SHARED real_t XY[SDIM][NBZ][MD1*MD1];
MFEM_SHARED real_t DQ[2*SDIM][NBZ][MD1*MQ1];
MFEM_SHARED real_t QQ[2*SDIM][NBZ][MQ1*MQ1];
kernels::internal::LoadX<MD1,NBZ>(e,D1D,X,XY);
kernels::internal::LoadBG<MD1,MQ1>(D1D,Q1D,B,G,BG);
kernels::internal::GradX<MD1,MQ1,NBZ>(D1D,Q1D,BG,XY,DQ);
kernels::internal::GradY<MD1,MQ1,NBZ>(D1D,Q1D,BG,DQ,QQ);
MFEM_FOREACH_THREAD(qy,y,Q1D)
{
MFEM_FOREACH_THREAD(qx,x,Q1D)
{
real_t J[4];
kernels::internal::PullGrad<MQ1,NBZ>(Q1D,qx,qy,QQ,J);
Y(qx,qy,e) = kernels::Det<2>(J);
}
}
});
}
template<int T_D1D = 0, int T_Q1D = 0>
static void Det2DSurface(const int NE,
const real_t *b,
const real_t *g,
const real_t *x,
real_t *y,
const int d1d = 0,
const int q1d = 0,
Vector *d_buff = nullptr)
{
MFEM_CONTRACT_VAR(d_buff);
static constexpr int SDIM = 3;
static constexpr int NBZ = 1;
const int D1D = T_D1D ? T_D1D : d1d;
const int Q1D = T_Q1D ? T_Q1D : q1d;
const auto B = Reshape(b, Q1D, D1D);
const auto G = Reshape(g, Q1D, D1D);
const auto X = Reshape(x, D1D, D1D, SDIM, NE);
auto Y = Reshape(y, Q1D, Q1D, NE);
mfem::forall_2D_batch(NE, Q1D, Q1D, NBZ, [=] MFEM_HOST_DEVICE (int e)
{
constexpr int MQ1 = T_Q1D ? T_Q1D : DofQuadLimits::MAX_Q1D;
constexpr int MD1 = T_D1D ? T_D1D : DofQuadLimits::MAX_D1D;
const int D1D = T_D1D ? T_D1D : d1d;
const int Q1D = T_Q1D ? T_Q1D : q1d;
const int tidz = MFEM_THREAD_ID(z);
MFEM_SHARED real_t BG[2][MQ1*MD1];
MFEM_SHARED real_t XYZ[SDIM][NBZ][MD1*MD1];
MFEM_SHARED real_t DQ[2*SDIM][NBZ][MD1*MQ1];
kernels::internal::LoadBG<MD1,MQ1>(D1D,Q1D,B,G,BG);
// Load XYZ components
MFEM_FOREACH_THREAD(dy,y,D1D)
{
MFEM_FOREACH_THREAD(dx,x,D1D)
{
for (int d = 0; d < SDIM; ++d)
{
XYZ[d][tidz][dx + dy*D1D] = X(dx,dy,d,e);
}
}
}
MFEM_SYNC_THREAD;
ConstDeviceMatrix B_mat(BG[0], D1D, Q1D);
ConstDeviceMatrix G_mat(BG[1], D1D, Q1D);
// x contraction
MFEM_FOREACH_THREAD(dy,y,D1D)
{
MFEM_FOREACH_THREAD(qx,x,Q1D)
{
for (int d = 0; d < SDIM; ++d)
{
real_t u = 0.0;
real_t v = 0.0;
for (int dx = 0; dx < D1D; ++dx)
{
const real_t xval = XYZ[d][tidz][dx + dy*D1D];
u += xval * G_mat(dx,qx);
v += xval * B_mat(dx,qx);
}
DQ[d][tidz][dy + qx*D1D] = u;
DQ[3 + d][tidz][dy + qx*D1D] = v;
}
}
}
MFEM_SYNC_THREAD;
// y contraction and determinant computation
MFEM_FOREACH_THREAD(qy,y,Q1D)
{
MFEM_FOREACH_THREAD(qx,x,Q1D)
{
real_t J_[6] = {0.0, 0.0, 0.0, 0.0, 0.0, 0.0};
for (int d = 0; d < SDIM; ++d)
{
for (int dy = 0; dy < D1D; ++dy)
{
J_[d] += DQ[d][tidz][dy + qx*D1D] * B_mat(dy,qy);
J_[3 + d] += DQ[3 + d][tidz][dy + qx*D1D] * G_mat(dy,qy);
}
}
DeviceTensor<2> J(J_, 3, 2);
const real_t E = J(0,0)*J(0,0) + J(1,0)*J(1,0) + J(2,0)*J(2,0);
const real_t F = J(0,0)*J(0,1) + J(1,0)*J(1,1) + J(2,0)*J(2,1);
const real_t G = J(0,1)*J(0,1) + J(1,1)*J(1,1) + J(2,1)*J(2,1);
Y(qx,qy,e) = std::sqrt(E*G - F*F);
}
}
});
}
template<int T_D1D = 0, int T_Q1D = 0, bool SMEM = true>
static void Det3D(const int NE,
const real_t *b,
const real_t *g,
const real_t *x,
real_t *y,
const int d1d = 0,
const int q1d = 0,
Vector *d_buff = nullptr) // used only with SMEM = false
{
constexpr int DIM = 3;
static constexpr int GRID = SMEM ? 0 : 128;
const int D1D = T_D1D ? T_D1D : d1d;
const int Q1D = T_Q1D ? T_Q1D : q1d;
const auto B = Reshape(b, Q1D, D1D);
const auto G = Reshape(g, Q1D, D1D);
const auto X = Reshape(x, D1D, D1D, D1D, DIM, NE);
auto Y = Reshape(y, Q1D, Q1D, Q1D, NE);
real_t *GM = nullptr;
if (!SMEM)
{
const DeviceDofQuadLimits &limits = DeviceDofQuadLimits::Get();
const int max_q1d = T_Q1D ? T_Q1D : limits.MAX_Q1D;
const int max_d1d = T_D1D ? T_D1D : limits.MAX_D1D;
const int max_qd = std::max(max_q1d, max_d1d);
const int mem_size = max_qd * max_qd * max_qd * 9;
d_buff->SetSize(2*mem_size*GRID);
GM = d_buff->Write();
}
mfem::forall_3D_grid(NE, Q1D, Q1D, Q1D, GRID, [=] MFEM_HOST_DEVICE (int e)
{
static constexpr int MQ1 = T_Q1D ? T_Q1D :
(SMEM ? DofQuadLimits::MAX_DET_1D : DofQuadLimits::MAX_Q1D);
static constexpr int MD1 = T_D1D ? T_D1D :
(SMEM ? DofQuadLimits::MAX_DET_1D : DofQuadLimits::MAX_D1D);
static constexpr int MDQ = MQ1 > MD1 ? MQ1 : MD1;
static constexpr int MSZ = MDQ * MDQ * MDQ * 9;
const int bid = MFEM_BLOCK_ID(x);
MFEM_SHARED real_t BG[2][MQ1*MD1];
MFEM_SHARED real_t SM0[SMEM?MSZ:1];
MFEM_SHARED real_t SM1[SMEM?MSZ:1];
real_t *lm0 = SMEM ? SM0 : GM + MSZ*bid;
real_t *lm1 = SMEM ? SM1 : GM + MSZ*(GRID+bid);
real_t (*DDD)[MD1*MD1*MD1] = (real_t (*)[MD1*MD1*MD1]) (lm0);
real_t (*DDQ)[MD1*MD1*MQ1] = (real_t (*)[MD1*MD1*MQ1]) (lm1);
real_t (*DQQ)[MD1*MQ1*MQ1] = (real_t (*)[MD1*MQ1*MQ1]) (lm0);
real_t (*QQQ)[MQ1*MQ1*MQ1] = (real_t (*)[MQ1*MQ1*MQ1]) (lm1);
kernels::internal::LoadX<MD1>(e,D1D,X,DDD);
kernels::internal::LoadBG<MD1,MQ1>(D1D,Q1D,B,G,BG);
kernels::internal::GradX<MD1,MQ1>(D1D,Q1D,BG,DDD,DDQ);
kernels::internal::GradY<MD1,MQ1>(D1D,Q1D,BG,DDQ,DQQ);
kernels::internal::GradZ<MD1,MQ1>(D1D,Q1D,BG,DQQ,QQQ);
MFEM_FOREACH_THREAD(qz,z,Q1D)
{
MFEM_FOREACH_THREAD(qy,y,Q1D)
{
MFEM_FOREACH_THREAD(qx,x,Q1D)
{
real_t J[9];
kernels::internal::PullGrad<MQ1>(Q1D, qx,qy,qz, QQQ, J);
Y(qx,qy,qz,e) = kernels::Det<3>(J);
}
}
}
});
}
void InitDetKernels()
{
using k = QuadratureInterpolator::DetKernels;
@@ -40,12 +302,27 @@ void InitDetKernels()
}
} // namespace quadrature_interpolator
} // namespace internal
/// @cond Suppress_Doxygen_warnings
QuadratureInterpolator::DetKernelType
QuadratureInterpolator::DetKernels::Fallback(
namespace
{
using DetKernel = QuadratureInterpolator::DetKernelType;
}
template<int DIM, int SDIM, int D1D, int Q1D>
DetKernel QuadratureInterpolator::DetKernels::Kernel()
{
if (DIM == 1) { return internal::quadrature_interpolator::Det1D; }
else if (DIM == 2 && SDIM == 2) { return internal::quadrature_interpolator::Det2D<D1D, Q1D>; }
else if (DIM == 2 && SDIM == 3) { return internal::quadrature_interpolator::Det2DSurface<D1D, Q1D>; }
else if (DIM == 3) { return internal::quadrature_interpolator::Det3D<D1D, Q1D>; }
else { MFEM_ABORT(""); }
}
DetKernel QuadratureInterpolator::DetKernels::Fallback(
int DIM, int SDIM, int D1D, int Q1D)
{
if (DIM == 1) { return internal::quadrature_interpolator::Det1D; }
-304
View File
@@ -1,304 +0,0 @@
// Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
// LICENSE and NOTICE for details. LLNL-CODE-806117.
//
// This file is part of the MFEM library. For more information and source code
// availability visit https://mfem.org.
//
// MFEM is free software; you can redistribute it and/or modify it under the
// terms of the BSD-3 license. We welcome feedback and contributions, see file
// CONTRIBUTING.md for details.
#ifndef MFEM_QUADINTERP_DET_HPP
#define MFEM_QUADINTERP_DET_HPP
#include "../quadinterpolator.hpp"
#include "../../general/forall.hpp"
#include "../../linalg/dtensor.hpp"
#include "../../fem/kernels.hpp"
#include "../../linalg/kernels.hpp"
namespace mfem
{
namespace internal
{
namespace quadrature_interpolator
{
inline void Det1D(const int NE,
const real_t *b,
const real_t *g,
const real_t *x,
real_t *y,
const int d1d,
const int q1d,
Vector *d_buff = nullptr)
{
MFEM_CONTRACT_VAR(b);
MFEM_CONTRACT_VAR(d_buff);
const auto G = Reshape(g, q1d, d1d);
const auto X = Reshape(x, d1d, NE);
auto Y = Reshape(y, q1d, NE);
mfem::forall(NE, [=] MFEM_HOST_DEVICE (int e)
{
for (int q = 0; q < q1d; q++)
{
real_t u = 0.0;
for (int d = 0; d < d1d; d++)
{
u += G(q, d) * X(d, e);
}
Y(q, e) = u;
}
});
}
template<int T_D1D = 0, int T_Q1D = 0>
inline void Det2D(const int NE,
const real_t *b,
const real_t *g,
const real_t *x,
real_t *y,
const int d1d = 0,
const int q1d = 0,
Vector *d_buff = nullptr)
{
MFEM_CONTRACT_VAR(d_buff);
static constexpr int SDIM = 2;
static constexpr int NBZ = 1;
const int D1D = T_D1D ? T_D1D : d1d;
const int Q1D = T_Q1D ? T_Q1D : q1d;
const auto B = Reshape(b, Q1D, D1D);
const auto G = Reshape(g, Q1D, D1D);
const auto X = Reshape(x, D1D, D1D, SDIM, NE);
auto Y = Reshape(y, Q1D, Q1D, NE);
mfem::forall_2D_batch(NE, Q1D, Q1D, NBZ, [=] MFEM_HOST_DEVICE (int e)
{
constexpr int MQ1 = T_Q1D ? T_Q1D : DofQuadLimits::MAX_Q1D;
constexpr int MD1 = T_D1D ? T_D1D : DofQuadLimits::MAX_D1D;
const int D1D = T_D1D ? T_D1D : d1d;
const int Q1D = T_Q1D ? T_Q1D : q1d;
MFEM_SHARED real_t BG[2][MQ1*MD1];
MFEM_SHARED real_t XY[SDIM][NBZ][MD1*MD1];
MFEM_SHARED real_t DQ[2*SDIM][NBZ][MD1*MQ1];
MFEM_SHARED real_t QQ[2*SDIM][NBZ][MQ1*MQ1];
kernels::internal::LoadX<MD1,NBZ>(e,D1D,X,XY);
kernels::internal::LoadBG<MD1,MQ1>(D1D,Q1D,B,G,BG);
kernels::internal::GradX<MD1,MQ1,NBZ>(D1D,Q1D,BG,XY,DQ);
kernels::internal::GradY<MD1,MQ1,NBZ>(D1D,Q1D,BG,DQ,QQ);
MFEM_FOREACH_THREAD(qy,y,Q1D)
{
MFEM_FOREACH_THREAD(qx,x,Q1D)
{
real_t J[4];
kernels::internal::PullGrad<MQ1,NBZ>(Q1D,qx,qy,QQ,J);
Y(qx,qy,e) = kernels::Det<2>(J);
}
}
});
}
template<int T_D1D = 0, int T_Q1D = 0>
inline void Det2DSurface(const int NE,
const real_t *b,
const real_t *g,
const real_t *x,
real_t *y,
const int d1d = 0,
const int q1d = 0,
Vector *d_buff = nullptr)
{
MFEM_CONTRACT_VAR(d_buff);
static constexpr int SDIM = 3;
static constexpr int NBZ = 1;
const int D1D = T_D1D ? T_D1D : d1d;
const int Q1D = T_Q1D ? T_Q1D : q1d;
const auto B = Reshape(b, Q1D, D1D);
const auto G = Reshape(g, Q1D, D1D);
const auto X = Reshape(x, D1D, D1D, SDIM, NE);
auto Y = Reshape(y, Q1D, Q1D, NE);
mfem::forall_2D_batch(NE, Q1D, Q1D, NBZ, [=] MFEM_HOST_DEVICE (int e)
{
constexpr int MQ1 = T_Q1D ? T_Q1D : DofQuadLimits::MAX_Q1D;
constexpr int MD1 = T_D1D ? T_D1D : DofQuadLimits::MAX_D1D;
const int D1D = T_D1D ? T_D1D : d1d;
const int Q1D = T_Q1D ? T_Q1D : q1d;
const int tidz = MFEM_THREAD_ID(z);
MFEM_SHARED real_t BG[2][MQ1*MD1];
MFEM_SHARED real_t XYZ[SDIM][NBZ][MD1*MD1];
MFEM_SHARED real_t DQ[2*SDIM][NBZ][MD1*MQ1];
kernels::internal::LoadBG<MD1,MQ1>(D1D,Q1D,B,G,BG);
// Load XYZ components
MFEM_FOREACH_THREAD(dy,y,D1D)
{
MFEM_FOREACH_THREAD(dx,x,D1D)
{
for (int d = 0; d < SDIM; ++d)
{
XYZ[d][tidz][dx + dy*D1D] = X(dx,dy,d,e);
}
}
}
MFEM_SYNC_THREAD;
ConstDeviceMatrix B_mat(BG[0], D1D, Q1D);
ConstDeviceMatrix G_mat(BG[1], D1D, Q1D);
// x contraction
MFEM_FOREACH_THREAD(dy,y,D1D)
{
MFEM_FOREACH_THREAD(qx,x,Q1D)
{
for (int d = 0; d < SDIM; ++d)
{
real_t u = 0.0;
real_t v = 0.0;
for (int dx = 0; dx < D1D; ++dx)
{
const real_t xval = XYZ[d][tidz][dx + dy*D1D];
u += xval * G_mat(dx,qx);
v += xval * B_mat(dx,qx);
}
DQ[d][tidz][dy + qx*D1D] = u;
DQ[3 + d][tidz][dy + qx*D1D] = v;
}
}
}
MFEM_SYNC_THREAD;
// y contraction and determinant computation
MFEM_FOREACH_THREAD(qy,y,Q1D)
{
MFEM_FOREACH_THREAD(qx,x,Q1D)
{
real_t J_[6] = {0.0, 0.0, 0.0, 0.0, 0.0, 0.0};
for (int d = 0; d < SDIM; ++d)
{
for (int dy = 0; dy < D1D; ++dy)
{
J_[d] += DQ[d][tidz][dy + qx*D1D] * B_mat(dy,qy);
J_[3 + d] += DQ[3 + d][tidz][dy + qx*D1D] * G_mat(dy,qy);
}
}
DeviceTensor<2> J(J_, 3, 2);
const real_t E = J(0,0)*J(0,0) + J(1,0)*J(1,0) + J(2,0)*J(2,0);
const real_t F = J(0,0)*J(0,1) + J(1,0)*J(1,1) + J(2,0)*J(2,1);
const real_t G = J(0,1)*J(0,1) + J(1,1)*J(1,1) + J(2,1)*J(2,1);
Y(qx,qy,e) = std::sqrt(E*G - F*F);
}
}
});
}
template<int T_D1D = 0, int T_Q1D = 0, bool SMEM = true>
inline void Det3D(const int NE,
const real_t *b,
const real_t *g,
const real_t *x,
real_t *y,
const int d1d = 0,
const int q1d = 0,
Vector *d_buff = nullptr) // used only with SMEM = false
{
constexpr int DIM = 3;
static constexpr int GRID = SMEM ? 0 : 128;
const int D1D = T_D1D ? T_D1D : d1d;
const int Q1D = T_Q1D ? T_Q1D : q1d;
const auto B = Reshape(b, Q1D, D1D);
const auto G = Reshape(g, Q1D, D1D);
const auto X = Reshape(x, D1D, D1D, D1D, DIM, NE);
auto Y = Reshape(y, Q1D, Q1D, Q1D, NE);
real_t *GM = nullptr;
if (!SMEM)
{
const DeviceDofQuadLimits &limits = DeviceDofQuadLimits::Get();
const int max_q1d = T_Q1D ? T_Q1D : limits.MAX_Q1D;
const int max_d1d = T_D1D ? T_D1D : limits.MAX_D1D;
const int max_qd = std::max(max_q1d, max_d1d);
const int mem_size = max_qd * max_qd * max_qd * 9;
d_buff->SetSize(2*mem_size*GRID);
GM = d_buff->Write();
}
mfem::forall_3D_grid(NE, Q1D, Q1D, Q1D, GRID, [=] MFEM_HOST_DEVICE (int e)
{
static constexpr int MQ1 = T_Q1D ? T_Q1D :
(SMEM ? DofQuadLimits::MAX_DET_1D : DofQuadLimits::MAX_Q1D);
static constexpr int MD1 = T_D1D ? T_D1D :
(SMEM ? DofQuadLimits::MAX_DET_1D : DofQuadLimits::MAX_D1D);
static constexpr int MDQ = MQ1 > MD1 ? MQ1 : MD1;
static constexpr int MSZ = MDQ * MDQ * MDQ * 9;
const int bid = MFEM_BLOCK_ID(x);
MFEM_SHARED real_t BG[2][MQ1*MD1];
MFEM_SHARED real_t SM0[SMEM?MSZ:1];
MFEM_SHARED real_t SM1[SMEM?MSZ:1];
real_t *lm0 = SMEM ? SM0 : GM + MSZ*bid;
real_t *lm1 = SMEM ? SM1 : GM + MSZ*(GRID+bid);
real_t (*DDD)[MD1*MD1*MD1] = (real_t (*)[MD1*MD1*MD1]) (lm0);
real_t (*DDQ)[MD1*MD1*MQ1] = (real_t (*)[MD1*MD1*MQ1]) (lm1);
real_t (*DQQ)[MD1*MQ1*MQ1] = (real_t (*)[MD1*MQ1*MQ1]) (lm0);
real_t (*QQQ)[MQ1*MQ1*MQ1] = (real_t (*)[MQ1*MQ1*MQ1]) (lm1);
kernels::internal::LoadX<MD1>(e,D1D,X,DDD);
kernels::internal::LoadBG<MD1,MQ1>(D1D,Q1D,B,G,BG);
kernels::internal::GradX<MD1,MQ1>(D1D,Q1D,BG,DDD,DDQ);
kernels::internal::GradY<MD1,MQ1>(D1D,Q1D,BG,DDQ,DQQ);
kernels::internal::GradZ<MD1,MQ1>(D1D,Q1D,BG,DQQ,QQQ);
MFEM_FOREACH_THREAD(qz,z,Q1D)
{
MFEM_FOREACH_THREAD(qy,y,Q1D)
{
MFEM_FOREACH_THREAD(qx,x,Q1D)
{
real_t J[9];
kernels::internal::PullGrad<MQ1>(Q1D, qx,qy,qz, QQQ, J);
Y(qx,qy,qz,e) = kernels::Det<3>(J);
}
}
}
});
}
} // namespace quadrature_interpolator
} // namespace internal
/// @cond Suppress_Doxygen_warnings
template<int DIM, int SDIM, int D1D, int Q1D>
QuadratureInterpolator::DetKernelType
QuadratureInterpolator::DetKernels::Kernel()
{
if (DIM == 1) { return internal::quadrature_interpolator::Det1D; }
else if (DIM == 2 && SDIM == 2) { return internal::quadrature_interpolator::Det2D<D1D, Q1D>; }
else if (DIM == 2 && SDIM == 3) { return internal::quadrature_interpolator::Det2DSurface<D1D, Q1D>; }
else if (DIM == 3) { return internal::quadrature_interpolator::Det3D<D1D, Q1D>; }
else { MFEM_ABORT(""); }
}
/// @endcond
} // namespace mfem
#endif // MFEM_QUADINTERP_DET_HPP
+56 -75
View File
@@ -17,9 +17,8 @@ namespace mfem
{
QuadratureSpaceBase::QuadratureSpaceBase(Mesh &mesh_, Geometry::Type geom,
const IntegrationRule &ir,
QSpaceStorage storage)
: mesh(mesh_), order(ir.GetOrder()), storage(storage)
const IntegrationRule &ir)
: mesh(mesh_), order(ir.GetOrder())
{
for (int g = 0; g < Geometry::NumGeom; g++)
{
@@ -97,37 +96,27 @@ void QuadratureSpaceBase::Integrate(VectorCoefficient &coeff,
void QuadratureSpace::ConstructOffsets()
{
const int num_elem = ne;
if (storage == QSpaceStorage::COMPRESSED &&
mesh.GetNumGeometries(mesh.Dimension()) == 1)
const int num_elem = mesh.GetNE();
offsets.SetSize(num_elem + 1);
int offset = 0;
for (int i = 0; i < num_elem; i++)
{
Array<Geometry::Type> geoms;
mesh.GetGeometries(mesh.Dimension(), geoms);
offsets.SetSize(1);
offsets.HostWrite();
offsets[0] = int_rule[geoms[0]]->GetNPoints();
size = num_elem * offsets[0];
}
else
{
offsets.SetSize(num_elem + 1);
int offset = 0;
for (int i = 0; i < num_elem; i++)
{
offsets[i] = offset;
const Geometry::Type geom = mesh.GetElementBaseGeometry(i);
MFEM_ASSERT(int_rule[geom] != NULL, "Missing integration rule.");
offset += int_rule[geom]->GetNPoints();
}
offsets[num_elem] = offset;
size = offsets.Last();
offsets[i] = offset;
int geom = mesh.GetElementBaseGeometry(i);
MFEM_ASSERT(int_rule[geom] != NULL, "Missing integration rule.");
offset += int_rule[geom]->GetNPoints();
}
offsets[num_elem] = size = offset;
}
QuadratureSpace::QuadratureSpace(Mesh *mesh_, std::istream &in,
QSpaceStorage storage)
: QuadratureSpaceBase(*mesh_, 0, storage)
void QuadratureSpace::Construct()
{
ConstructIntRules(mesh.Dimension());
ConstructOffsets();
}
QuadratureSpace::QuadratureSpace(Mesh *mesh_, std::istream &in)
: QuadratureSpaceBase(*mesh_)
{
const char *msg = "invalid input stream";
std::string ident;
@@ -146,24 +135,15 @@ QuadratureSpace::QuadratureSpace(Mesh *mesh_, std::istream &in,
return;
}
ne = mesh.GetNE();
ConstructIntRules(mesh.Dimension());
Construct();
}
QuadratureSpace::QuadratureSpace(Mesh *mesh_, int order_, QSpaceStorage storage)
: QuadratureSpaceBase(*mesh_, order_, storage)
{
ne = mesh.GetNE();
ConstructIntRules(mesh.Dimension());
}
QuadratureSpace::QuadratureSpace(Mesh &mesh_, const IntegrationRule &ir,
QSpaceStorage storage)
: QuadratureSpaceBase(mesh_, mesh_.GetTypicalElementGeometry(), ir, storage)
QuadratureSpace::QuadratureSpace(Mesh &mesh_, const IntegrationRule &ir)
: QuadratureSpaceBase(mesh_, mesh_.GetTypicalElementGeometry(), ir)
{
MFEM_VERIFY(mesh.GetNumGeometries(mesh.Dimension()) <= 1,
"Constructor not valid for mixed meshes");
ne = mesh.GetNE();
ConstructOffsets();
}
void QuadratureSpace::Save(std::ostream &os) const
@@ -185,53 +165,54 @@ const Vector &QuadratureSpace::GetGeometricFactorWeights() const
}
FaceQuadratureSpace::FaceQuadratureSpace(Mesh &mesh_, int order_,
FaceType face_type_,
QSpaceStorage storage)
: QuadratureSpaceBase(mesh_, order_, storage), face_type(face_type_),
face_indices(mesh.GetFaceIndices(face_type_)),
face_indices_inv(mesh.GetInvFaceIndices(face_type_))
FaceType face_type_)
: QuadratureSpaceBase(mesh_, order_),
face_type(face_type_),
num_faces(mesh.GetNFbyType(face_type))
{
ne = face_indices.Size();
ConstructIntRules(mesh.Dimension() - 1);
Construct();
}
FaceQuadratureSpace::FaceQuadratureSpace(Mesh &mesh_, const IntegrationRule &ir,
FaceType face_type_,
QSpaceStorage storage)
: QuadratureSpaceBase(mesh_, mesh_.GetTypicalFaceGeometry(), ir, storage),
face_type(face_type_), face_indices(mesh.GetFaceIndices(face_type_)),
face_indices_inv(mesh.GetInvFaceIndices(face_type_))
FaceType face_type_)
: QuadratureSpaceBase(mesh_, mesh_.GetTypicalFaceGeometry(), ir),
face_type(face_type_),
num_faces(mesh.GetNFbyType(face_type))
{
MFEM_VERIFY(mesh.GetNumGeometries(mesh.Dimension() - 1) <= 1,
"Constructor not valid for mixed meshes");
ne = face_indices.Size();
ConstructOffsets();
}
void FaceQuadratureSpace::ConstructOffsets()
{
if (storage == QSpaceStorage::COMPRESSED &&
mesh.GetNumGeometries(mesh.Dimension() - 1) == 1)
face_indices.SetSize(num_faces);
offsets.SetSize(num_faces + 1);
int offset = 0;
int f_idx = 0;
for (int i = 0; i < mesh.GetNumFacesWithGhost(); i++)
{
Array<Geometry::Type> geoms;
mesh.GetGeometries(mesh.Dimension() - 1, geoms);
offsets.SetSize(1);
offsets.HostWrite();
offsets[0] = int_rule[geoms[0]]->GetNPoints();
size = ne * offsets[0];
}
else
{
offsets.SetSize(face_indices.Size() + 1);
int offset = 0;
for (int i = 0; i < mesh.GetNFbyType(face_type); ++i)
const Mesh::FaceInformation face = mesh.GetFaceInformation(i);
if (face.IsNonconformingCoarse() || !face.IsOfFaceType(face_type))
{
offsets[i] = offset;
Geometry::Type geom = mesh.GetFaceGeometry(face_indices[i]);
MFEM_ASSERT(int_rule[geom] != NULL, "Missing integration rule");
offset += int_rule[geom]->GetNPoints();
continue;
}
offsets[face_indices.Size()] = size = offset;
face_indices[f_idx] = i;
face_indices_inv[i] = f_idx;
offsets[f_idx] = offset;
Geometry::Type geom = mesh.GetFaceGeometry(i);
MFEM_ASSERT(int_rule[geom] != NULL, "Missing integration rule");
offset += int_rule[geom]->GetNPoints();
f_idx++;
}
offsets[num_faces] = size = offset;
}
void FaceQuadratureSpace::Construct()
{
ConstructIntRules(mesh.Dimension() - 1);
ConstructOffsets();
}
int FaceQuadratureSpace::GetPermutedIndex(int idx, int iq) const
+25 -80
View File
@@ -19,49 +19,35 @@
namespace mfem
{
enum class QSpaceStorage
{
FULL,
COMPRESSED
};
/// Abstract base class for QuadratureSpace and FaceQuadratureSpace.
/** This class represents the storage layout for QuadratureFunction%s, that may
be defined either on mesh elements or mesh faces. */
class QuadratureSpaceBase
{
protected:
friend class QuadratureFunction; // Uses the offsets.
Mesh &mesh; ///< The underlying mesh.
int order; ///< The order of integration rule.
int size = -1; ///< Total number of quadrature points. -1 indicates
///< offsets/size not computed yet.
int ne; ///< Actual number of entities
int size; ///< Total number of quadrature points.
mutable Vector weights; ///< Integration weights.
mutable long nodes_sequence = 0; ///< Nodes counter for cache invalidation.
QSpaceStorage storage;
/// @brief Entity quadrature point offset array.
///
/// Supports a constant compression scheme for meshes which have a single
/// geometry type. When compressed, will have a single value. The true offset
/// can be computed as i * offsets[0], where i is the entity index. Otherwise
/// has size num_entities + 1. Lazily constructed.
/// @brief Entity quadrature point offset array, of size num_entities + 1.
///
/// The quadrature point values for entity i are stored in the indices between
/// offsets[i] and offsets[i+1].
Array<int> offsets;
/// The quadrature rules used for each geometry type.
const IntegrationRule *int_rule[Geometry::NumGeom];
/// Protected constructor. Used by derived classes.
QuadratureSpaceBase(Mesh &mesh_, int order_ = 0,
QSpaceStorage storage = QSpaceStorage::COMPRESSED)
: mesh(mesh_), order(order_), storage(storage)
{}
QuadratureSpaceBase(Mesh &mesh_, int order_ = 0)
: mesh(mesh_), order(order_) { }
/// Protected constructor. Used by derived classes.
QuadratureSpaceBase(Mesh &mesh_, Geometry::Type geom,
const IntegrationRule &ir,
QSpaceStorage storage = QSpaceStorage::COMPRESSED);
const IntegrationRule &ir);
/// Fill the @ref int_rule array for each geometry type using @ref order.
void ConstructIntRules(int dim);
@@ -72,55 +58,15 @@ protected:
/// Compute the integration weights.
void ConstructWeights() const;
virtual void ConstructOffsets() = 0;
public:
QSpaceStorage StorageType() const { return storage; }
/// @brief Gets the offset for a given entity @a idx.
///
/// The quadrature point values for entity i are stored in the indices
/// between Offset(i) and Offset(i+1)
int Offset(int idx) const
{
if (size < 0)
{
const_cast<QuadratureSpaceBase *>(this)->ConstructOffsets();
}
return (offsets.Size() == 1) ? (idx * offsets[0]) : offsets[idx];
}
/// @brief Entity quadrature point offset array.
///
/// Supports a constant compression scheme for meshes which have a single
/// geometry type. When compressed, will have a single value. The true offset
/// can be computed as i * offsets[0], where i is the entity index. Otherwise
/// has size num_entities + 1.
///
const Array<int> &Offsets() const
{
if (size < 0)
{
const_cast<QuadratureSpaceBase *>(this)->ConstructOffsets();
}
return offsets;
}
/// Return the total number of quadrature points.
int GetSize() const
{
if (size < 0)
{
const_cast<QuadratureSpaceBase *>(this)->ConstructOffsets();
}
return size;
}
int GetSize() const { return size; }
/// Return the order of the quadrature rule(s) used by all elements.
int GetOrder() const { return order; }
/// Return the number of entities.
int GetNE() const { return ne; }
int GetNE() const { return offsets.Size() - 1; }
/// Returns the mesh.
inline Mesh *GetMesh() const { return &mesh; }
@@ -174,20 +120,19 @@ class QuadratureSpace : public QuadratureSpaceBase
{
protected:
const Vector &GetGeometricFactorWeights() const override;
void ConstructOffsets() override;
void ConstructOffsets();
void Construct();
public:
/// Create a QuadratureSpace based on the global rules from #IntRules.
QuadratureSpace(Mesh *mesh_, int order_,
QSpaceStorage storage = QSpaceStorage::COMPRESSED);
QuadratureSpace(Mesh *mesh_, int order_)
: QuadratureSpaceBase(*mesh_, order_) { Construct(); }
/// @brief Create a QuadratureSpace with an IntegrationRule, valid only when
/// the mesh has one element type.
QuadratureSpace(Mesh &mesh_, const IntegrationRule &ir,
QSpaceStorage storage = QSpaceStorage::COMPRESSED);
QuadratureSpace(Mesh &mesh_, const IntegrationRule &ir);
/// Read a QuadratureSpace from the stream @a in.
QuadratureSpace(Mesh *mesh_, std::istream &in,
QSpaceStorage storage = QSpaceStorage::COMPRESSED);
QuadratureSpace(Mesh *mesh_, std::istream &in);
/// Returns number of elements in the mesh.
inline int GetNE() const { return mesh.GetNE(); }
@@ -224,29 +169,29 @@ public:
class FaceQuadratureSpace : public QuadratureSpaceBase
{
FaceType face_type; ///< Is the space defined on interior or boundary faces?
const int num_faces; ///< Number of faces.
/// Map from boundary or interior face indices to mesh face indices.
const Array<int> &face_indices;
Array<int> face_indices;
/// Inverse of the map @a face_indices.
const std::unordered_map<int,int> &face_indices_inv;
std::unordered_map<int,int> face_indices_inv;
const Vector &GetGeometricFactorWeights() const override;
void ConstructOffsets() override;
void ConstructOffsets();
void Construct();
public:
/// Create a FaceQuadratureSpace based on the global rules from #IntRules.
FaceQuadratureSpace(Mesh &mesh_, int order_, FaceType face_type_,
QSpaceStorage storage = QSpaceStorage::COMPRESSED);
FaceQuadratureSpace(Mesh &mesh_, int order_, FaceType face_type_);
/// @brief Create a FaceQuadratureSpace with an IntegrationRule, valid only
/// when the mesh has one type of face geometry.
FaceQuadratureSpace(Mesh &mesh_, const IntegrationRule &ir,
FaceType face_type_,
QSpaceStorage storage = QSpaceStorage::COMPRESSED);
FaceType face_type_);
/// Returns number of faces in the mesh.
inline int GetNumFaces() const { return face_indices.Size(); }
inline int GetNumFaces() const { return num_faces; }
/// Returns the face type (boundary or interior).
FaceType GetFaceType() const { return face_type; }
+27 -9
View File
@@ -5122,32 +5122,33 @@ real_t TMOP_Integrator::GetSurfaceFittingWeight()
void TMOP_Integrator::EnableNormalization(const GridFunction &x)
{
ComputeNormalizationEnergies(x, metric_normal, lim_normal);
ComputeNormalizationEnergies(x, metric_normal, lim_normal, surf_fit_normal);
metric_normal = 1.0 / metric_normal;
lim_normal = 1.0 / lim_normal;
//if (surf_fit_gf) { surf_fit_normal = 1.0 / surf_fit_normal; }
if (surf_fit_gf || surf_fit_pos) { surf_fit_normal = lim_normal; }
}
#ifdef MFEM_USE_MPI
void TMOP_Integrator::ParEnableNormalization(const ParGridFunction &x)
{
real_t loc[2];
ComputeNormalizationEnergies(x, loc[0], loc[1]);
real_t rdc[2];
MPI_Allreduce(loc, rdc, 2, MPITypeMap<real_t>::mpi_type, MPI_SUM,
real_t loc[3];
ComputeNormalizationEnergies(x, loc[0], loc[1], loc[2]);
real_t rdc[3];
MPI_Allreduce(loc, rdc, 3, MPITypeMap<real_t>::mpi_type, MPI_SUM,
x.ParFESpace()->GetComm());
metric_normal = 1.0 / rdc[0];
lim_normal = 1.0 / rdc[1];
// if (surf_fit_gf) { surf_fit_normal = 1.0 / rdc[2]; }
if (surf_fit_gf || surf_fit_pos) { surf_fit_normal = lim_normal; }
}
#endif
void TMOP_Integrator::ComputeNormalizationEnergies(const GridFunction &x,
real_t &metric_energy,
real_t &lim_energy)
real_t &lim_energy,
real_t &surf_fit_gf_energy)
{
metric_energy = 0.0;
lim_energy = 0.0;
if (PA.enabled)
{
MFEM_VERIFY(PA.E.Size() > 0, "Must be called after AssemblePA!");
@@ -5190,6 +5191,9 @@ void TMOP_Integrator::ComputeNormalizationEnergies(const GridFunction &x,
Jpr.SetSize(dim);
Jpt.SetSize(dim);
metric_energy = 0.0;
lim_energy = 0.0;
surf_fit_gf_energy = 0.0;
for (int i = 0; i < fes->GetNE(); i++)
{
const FiniteElement *fe = fes->GetFE(i);
@@ -5221,7 +5225,21 @@ void TMOP_Integrator::ComputeNormalizationEnergies(const GridFunction &x,
lim_energy += weight;
}
// TODO: Normalization of the surface fitting term.
// Normalization of the surface fitting term.
if (surf_fit_gf)
{
Array<int> dofs;
Vector sigma_e;
surf_fit_gf->FESpace()->GetElementDofs(i, dofs);
surf_fit_gf->GetSubVector(dofs, sigma_e);
for (int s = 0; s < dofs.Size(); s++)
{
if ((*surf_fit_marker)[dofs[s]] == true)
{
surf_fit_gf_energy += sigma_e(s) * sigma_e(s);
}
}
}
}
// Cases when integration is not over the target element, or when the
+2 -1
View File
@@ -2038,7 +2038,8 @@ protected:
} PA;
void ComputeNormalizationEnergies(const GridFunction &x,
real_t &metric_energy, real_t &lim_energy);
real_t &metric_energy, real_t &lim_energy,
real_t &surf_fit_gf_energy);
void AssembleElementVectorExact(const FiniteElement &el,
ElementTransformation &T,
+1 -32
View File
@@ -211,9 +211,6 @@ public:
/// Delete the first entry with value == 'el'.
inline void DeleteFirst(const T &el);
/// Delete entries at @a indices, and resize.
inline void DeleteAt(const Array<int> &indices);
/// Delete the whole array.
inline void DeleteAll();
@@ -329,11 +326,7 @@ public:
the Size to match this Capacity after this.*/
template <typename U>
inline void CopyFrom(const U *src)
{
if (!begin() || size == 0) { return; }
MFEM_ASSERT(begin() && src, "Error in Array::CopyFrom");
std::memcpy(begin(), src, MemoryUsage());
}
{ std::memcpy(begin(), src, MemoryUsage()); }
/// STL-like begin. Returns pointer to the first element of the array.
inline T* begin() { return data; }
@@ -938,30 +931,6 @@ inline void Array<T>::DeleteFirst(const T &el)
}
}
template <class T>
inline void Array<T>::DeleteAt(const Array<int> &indices)
{
// Make a copy of the indices, sorted.
Array<int> sorted_indices(indices);
sorted_indices.Sort();
int rm_count = 0;
for (int i = 0; i < size; i++)
{
if (rm_count < sorted_indices.Size() && i == sorted_indices[rm_count])
{
rm_count++;
}
else
{
data[i-rm_count] = data[i]; // shift data rm_count
}
}
// Resize to remove tail
size -= rm_count;
}
template <class T>
inline void Array<T>::DeleteAll()
{
+6 -7
View File
@@ -14,7 +14,7 @@
#include "../config/config.hpp"
#if defined(MFEM_USE_CUDA) && defined(__CUDACC__)
#ifdef MFEM_USE_CUDA
#include <cusparse.h>
#include <library_types.h>
#include <cuda_runtime.h>
@@ -22,7 +22,7 @@
#endif
#include "cuda.hpp"
#if defined(MFEM_USE_HIP) && defined(__HIP__)
#ifdef MFEM_USE_HIP
#include <hip/hip_runtime.h>
#endif
#include "hip.hpp"
@@ -43,7 +43,7 @@
#endif
#endif
#if !defined(MFEM_USE_CUDA_OR_HIP)
#if !(defined(MFEM_USE_CUDA) || defined(MFEM_USE_HIP))
#define MFEM_DEVICE
#define MFEM_HOST
#define MFEM_LAMBDA
@@ -55,18 +55,17 @@
#endif
#if !((defined(MFEM_USE_CUDA) && defined(__CUDA_ARCH__)) || \
(defined(MFEM_USE_HIP) && defined(__HIP_DEVICE_COMPILE__)))
(defined(MFEM_USE_HIP) && defined(__HIP_DEVICE_COMPILE__)))
#define MFEM_SHARED
#define MFEM_SYNC_THREAD
#define MFEM_BLOCK_ID(k) 0
#define MFEM_THREAD_ID(k) 0
#define MFEM_THREAD_SIZE(k) 1
#define MFEM_FOREACH_THREAD(i,k,N) for(int i=0; i<N; i++)
#define MFEM_FOREACH_THREAD_DIRECT(i,k,N) MFEM_FOREACH_THREAD(i,k,N)
#endif
// 'double' and 'float' atomicAdd implementation for previous versions of CUDA
#if defined(MFEM_USE_CUDA) && defined(__CUDA_ARCH__) && (__CUDA_ARCH__ < 600)
#if defined(MFEM_USE_CUDA) && defined(__CUDA_ARCH__) && __CUDA_ARCH__ < 600
MFEM_DEVICE inline mfem::real_t atomicAdd(mfem::real_t *add, mfem::real_t val)
{
unsigned long long int *ptr = (unsigned long long int *) add;
@@ -94,7 +93,7 @@ template <typename T>
MFEM_HOST_DEVICE T AtomicAdd(T &add, const T val)
{
#if ((defined(MFEM_USE_CUDA) && defined(__CUDA_ARCH__)) || \
(defined(MFEM_USE_HIP) && defined(__HIP_DEVICE_COMPILE__)))
(defined(MFEM_USE_HIP) && defined(__HIP_DEVICE_COMPILE__)))
return atomicAdd(&add,val);
#else
T old = add;
+3 -13
View File
@@ -347,23 +347,13 @@ void GroupTopology::Swap(GroupTopology &other)
mfem::Swap(group_mgroup, other.group_mgroup);
}
/// \cond DO_NOT_DOCUMENT
// Initialize the static mpi_type for the specializations of MPITypeMap:
const MPI_Datatype MPITypeMap<bool>::mpi_type = MFEM_MPI_CXX_BOOL;
const MPI_Datatype MPITypeMap<char>::mpi_type = MPI_CHAR;
const MPI_Datatype MPITypeMap<unsigned char>::mpi_type = MPI_UNSIGNED_CHAR;
const MPI_Datatype MPITypeMap<short>::mpi_type = MPI_SHORT;
const MPI_Datatype MPITypeMap<unsigned short>::mpi_type = MPI_UNSIGNED_SHORT;
const MPI_Datatype MPITypeMap<int>::mpi_type = MPI_INT;
const MPI_Datatype MPITypeMap<unsigned int>::mpi_type = MPI_UNSIGNED;
const MPI_Datatype MPITypeMap<long>::mpi_type = MPI_LONG;
const MPI_Datatype MPITypeMap<unsigned long>::mpi_type = MPI_UNSIGNED_LONG;
const MPI_Datatype MPITypeMap<long long>::mpi_type = MPI_LONG_LONG;
const MPI_Datatype MPITypeMap<unsigned long long>::mpi_type =
MPI_UNSIGNED_LONG_LONG;
const MPI_Datatype MPITypeMap<float>::mpi_type = MPI_FLOAT;
const MPI_Datatype MPITypeMap<double>::mpi_type = MPI_DOUBLE;
/// \endcond DO_NOT_DOCUMENT
const MPI_Datatype MPITypeMap<int64_t>::mpi_type = MPI_INT64_T;
const MPI_Datatype MPITypeMap<uint64_t>::mpi_type = MPI_UINT64_T;
GroupCommunicator::GroupCommunicator(const GroupTopology &gt, Mode m)
: gtopo(gt), mode(m)
+17 -56
View File
@@ -425,24 +425,16 @@ public:
~GroupCommunicator();
};
/// General MPI message tags used by MFEM
enum MessageTag
{
DEREFINEMENT_MATRIX_CONSTRUCTION_DATA =
291, /// ParFiniteElementSpace ParallelDerefinementMatrix and
/// ParDerefineMatrixOp
};
enum VarMessageTag
{
NEIGHBOR_ELEMENT_RANK_VM, ///< NeighborElementRankMessage
NEIGHBOR_ORDER_VM, ///< NeighborOrderMessage
NEIGHBOR_DEREFINEMENT_VM, ///< NeighborDerefinementMessage
NEIGHBOR_REFINEMENT_VM, ///< NeighborRefinementMessage
NEIGHBOR_PREFINEMENT_VM, ///< NeighborPRefinementMessage
NEIGHBOR_ROW_VM, ///< NeighborRowMessage
REBALANCE_VM, ///< RebalanceMessage
REBALANCE_DOF_VM, ///< RebalanceDofMessage
NEIGHBOR_ELEMENT_RANK_VM, ///< NeighborElementRankMessage
NEIGHBOR_ORDER_VM, ///< NeighborOrderMessage
NEIGHBOR_DEREFINEMENT_VM, ///< NeighborDerefinementMessage
NEIGHBOR_REFINEMENT_VM, ///< NeighborRefinementMessage
NEIGHBOR_PREFINEMENT_VM, ///< NeighborPRefinementMessage
NEIGHBOR_ROW_VM, ///< NeighborRowMessage
REBALANCE_VM, ///< RebalanceMessage
REBALANCE_DOF_VM ///< RebalanceDofMessage
};
/// \brief Variable-length MPI message containing unspecific binary data.
@@ -607,50 +599,10 @@ protected:
template <typename Type> struct MPITypeMap;
// Specializations of MPITypeMap; mpi_type initialized in communication.cpp:
template<> struct MPITypeMap<bool>
{
static MFEM_EXPORT const MPI_Datatype mpi_type;
};
template<> struct MPITypeMap<char>
{
static MFEM_EXPORT const MPI_Datatype mpi_type;
};
template<> struct MPITypeMap<unsigned char>
{
static MFEM_EXPORT const MPI_Datatype mpi_type;
};
template<> struct MPITypeMap<short>
{
static MFEM_EXPORT const MPI_Datatype mpi_type;
};
template<> struct MPITypeMap<unsigned short>
{
static MFEM_EXPORT const MPI_Datatype mpi_type;
};
template<> struct MPITypeMap<int>
{
static MFEM_EXPORT const MPI_Datatype mpi_type;
};
template<> struct MPITypeMap<unsigned int>
{
static MFEM_EXPORT const MPI_Datatype mpi_type;
};
template<> struct MPITypeMap<long>
{
static MFEM_EXPORT const MPI_Datatype mpi_type;
};
template<> struct MPITypeMap<unsigned long>
{
static MFEM_EXPORT const MPI_Datatype mpi_type;
};
template<> struct MPITypeMap<long long>
{
static MFEM_EXPORT const MPI_Datatype mpi_type;
};
template<> struct MPITypeMap<unsigned long long>
{
static MFEM_EXPORT const MPI_Datatype mpi_type;
};
template<> struct MPITypeMap<double>
{
static MFEM_EXPORT const MPI_Datatype mpi_type;
@@ -659,6 +611,15 @@ template<> struct MPITypeMap<float>
{
static MFEM_EXPORT const MPI_Datatype mpi_type;
};
template<> struct MPITypeMap<int64_t>
{
static MFEM_EXPORT const MPI_Datatype mpi_type;
};
template<> struct MPITypeMap<uint64_t>
{
static MFEM_EXPORT const MPI_Datatype mpi_type;
};
/** Reorder MPI ranks to follow the Z-curve within the physical machine topology
(provided that functions to query physical node coordinates are available).
+1 -1
View File
@@ -24,7 +24,7 @@ void mfem_cuda_error(cudaError_t err, const char *expr, const char *func,
const char *file, int line)
{
mfem::err << "\n\nCUDA error: (" << expr << ") failed with error:\n --> "
<< cudaGetErrorString(err) << " [code: " << (int)err << ']'
<< cudaGetErrorString(err)
<< "\n ... in function: " << func
<< "\n ... in file: " << file << ':' << line << '\n';
mfem_error();
+5 -6
View File
@@ -18,7 +18,7 @@
// CUDA block size used by MFEM.
#define MFEM_CUDA_BLOCKS 256
#if defined(MFEM_USE_CUDA) && defined(__CUDACC__)
#ifdef MFEM_USE_CUDA
#define MFEM_USE_CUDA_OR_HIP
#define MFEM_DEVICE __device__
#define MFEM_HOST __host__
@@ -37,23 +37,22 @@
__FILE__, __LINE__); \
} \
} while (0)
#endif // MFEM_USE_CUDA
// Define the MFEM inner threading macros
#if defined(__CUDA_ARCH__)
#if defined(MFEM_USE_CUDA) && defined(__CUDA_ARCH__)
#define MFEM_SHARED __shared__
#define MFEM_SYNC_THREAD __syncthreads()
#define MFEM_BLOCK_ID(k) blockIdx.k
#define MFEM_THREAD_ID(k) threadIdx.k
#define MFEM_THREAD_SIZE(k) blockDim.k
#define MFEM_FOREACH_THREAD(i,k,N) for(int i=threadIdx.k; i<N; i+=blockDim.k)
#define MFEM_FOREACH_THREAD_DIRECT(i,k,N) if(const int i=threadIdx.k; i<N)
#endif // defined(__CUDA_ARCH__)
#endif // defined(MFEM_USE_CUDA) && defined(__CUDACC__)
#endif
namespace mfem
{
#if defined(MFEM_USE_CUDA) && defined(__CUDACC__)
#ifdef MFEM_USE_CUDA
// Function used by the macro MFEM_GPU_CHECK.
void mfem_cuda_error(cudaError_t err, const char *expr, const char *func,
const char *file, int line);
+1 -37
View File
@@ -16,7 +16,6 @@
#include "../fem/ceed/interface/util.hpp"
#endif
#ifdef MFEM_USE_MPI
#include "communication.hpp"
#include "../linalg/hypre.hpp"
#endif
@@ -146,11 +145,6 @@ Device::Device()
Configure(device);
device_env = true;
}
if (GetEnv("MFEM_GPU_AWARE_MPI"))
{
SetGPUAwareMPI(true);
}
}
Device::~Device()
@@ -202,29 +196,6 @@ void Device::Configure(const std::string &device, const int device_id)
{
bmap[internal::backend_name[i]] = internal::backend_list[i];
}
// auto-detect GPU configurations
// assumes only one of HIP or CUDA are available
#ifdef MFEM_USE_HIP
bmap["gpu"] = Backend::HIP;
#ifdef MFEM_USE_RAJA
bmap["raja-gpu"] = Backend::RAJA_HIP;
#endif
#ifdef MFEM_USE_CEED
bmap["ceed-gpu"] = Backend::CEED_HIP;
#endif
// no OCCA+HIP?
#elif defined(MFEM_USE_CUDA)
bmap["gpu"] = Backend::CUDA;
#ifdef MFEM_USE_RAJA
bmap["raja-gpu"] = Backend::RAJA_CUDA;
#endif
#ifdef MFEM_USE_CEED
bmap["ceed-gpu"] = Backend::CEED_CUDA;
#endif
#ifdef MFEM_USE_OCCA
bmap["occa-gpu"] = Backend::OCCA_CUDA;
#endif
#endif
std::string device_option;
std::string::size_type beg = 0, end;
while (1)
@@ -342,13 +313,6 @@ void Device::Print(std::ostream &os)
{
os << ',' << MemoryTypeName[static_cast<int>(device_mem_type)];
}
#ifdef MFEM_USE_MPI
if (Allows(Backend::DEVICE_MASK) &&
Mpi::IsInitialized() && !Mpi::IsFinalized())
{
os << "\nUse GPU-aware MPI: " << (GetGPUAwareMPI() ? "yes" : "no");
}
#endif
os << std::endl;
}
@@ -615,7 +579,7 @@ void Device::Setup(const std::string &device_option, const int device_id)
if (Allows(Backend::DEBUG_DEVICE)) { ngpu = 1; }
}
MemoryType Device::QueryMemoryType(const void* ptr)
MemoryType Device::QueryMemoryType(void *ptr)
{
// from HYPRE's hypre_GetPointerLocation
MemoryType res = MemoryType::HOST;
+3 -7
View File
@@ -198,10 +198,6 @@ public:
'ceed-hip', 'hip', 'debug',
'occa-omp', 'raja-omp', 'omp',
'ceed-cpu', 'occa-cpu', 'raja-cpu', 'cpu'.
- The following backend aliases are also available: 'ceed-gpu',
'occa-gpu', 'raja-gpu', and 'gpu' where they alias their respective
'*-cuda' or '*-hip' backends depending on the MFEM build-time
configuration.
- Multiple backends can be configured at the same time.
- Only one 'occa-*' backend can be configured at a time.
- The backend 'occa-cuda' enables the 'cuda' backend unless 'raja-cuda'
@@ -297,9 +293,9 @@ public:
/// Get the status of GPU-aware MPI flag.
static bool GetGPUAwareMPI() { return Get().mpi_gpu_aware; }
/** Query the device driver for what memory type a given @a ptr is allocated
* with. */
static MemoryType QueryMemoryType(const void* ptr);
/** @brief Query the device driver for what memory type a given @a ptr is
allocated with. */
static MemoryType QueryMemoryType(void *ptr);
/** @brief The number of hardware compute units/streaming multiprocessors
available on a given compute device @a device_id. */
+1 -1
View File
@@ -176,7 +176,7 @@ __device__ void abort_msg(T & msg)
printf(__VA_ARGS__); \
asm("trap;"); \
}
#elif defined(__HIP_DEVICE_COMPILE__)
#elif defined(MFEM_USE_HIP)
#define MFEM_ABORT_KERNEL(...) \
{ \
printf(__VA_ARGS__); \
+12 -171
View File
@@ -158,8 +158,8 @@ private:
#define MFEM_PRAGMA(X) _Pragma(#X)
// MFEM_UNROLL pragma macro that can be used inside MFEM_FORALL macros.
#if defined(MFEM_USE_CUDA) && defined(__CUDA_ARCH__) // Clang cuda or nvcc
#ifdef __NVCC__ // nvcc specifically
#if defined(MFEM_USE_CUDA) && defined(__CUDA_ARCH__)
#ifdef __NVCC__
#define MFEM_UNROLL(N) MFEM_PRAGMA(unroll(N))
#else // Assuming Clang CUDA
#define MFEM_UNROLL(N) MFEM_PRAGMA(unroll N)
@@ -169,12 +169,12 @@ private:
#endif
// MFEM_GPU_FORALL: "parallel for" executed with CUDA or HIP based on the MFEM
// build-time configuration (MFEM_USE_CUDA or MFEM_USE_HIP), and if compiling
// with CUDA/HIP language. Otherwise, this macro is a no-op.
#if defined(MFEM_USE_CUDA) && defined(__CUDACC__)
// build-time configuration (MFEM_USE_CUDA or MFEM_USE_HIP). If neither CUDA nor
// HIP is enabled, this macro is a no-op.
#if defined(MFEM_USE_CUDA)
#define MFEM_GPU_FORALL(i, N,...) CuWrap1D(N, [=] MFEM_DEVICE \
(int i) {__VA_ARGS__})
#elif defined(MFEM_USE_HIP) && defined(__HIP__)
#elif defined(MFEM_USE_HIP)
#define MFEM_GPU_FORALL(i, N,...) HipWrap1D(N, [=] MFEM_DEVICE \
(int i) {__VA_ARGS__})
#else
@@ -225,52 +225,6 @@ void OmpWrap(const int N, HBODY &&h_body)
#endif
}
template <typename HBODY>
void OmpWrap2D(const int Nx, const int Ny, HBODY &&h_body)
{
#ifdef MFEM_USE_OPENMP
// requires OpenMP 3.1
#pragma omp parallel for collapse(2)
for (int j = 0; j < Ny; j++)
{
for (int i = 0; i < Nx; i++)
{
h_body(i, j);
}
}
#else
MFEM_CONTRACT_VAR(Nx);
MFEM_CONTRACT_VAR(Ny);
MFEM_CONTRACT_VAR(h_body);
MFEM_ABORT("OpenMP requested for MFEM but OpenMP is not enabled!");
#endif
}
template <typename HBODY>
void OmpWrap3D(const int Nx, const int Ny, const int Nz, HBODY &&h_body)
{
#ifdef MFEM_USE_OPENMP
// requires OpenMP 3.1
#pragma omp parallel for collapse(3)
for (int k = 0; k < Nz; k++)
{
for (int j = 0; j < Ny; j++)
{
for (int i = 0; i < Nx; i++)
{
h_body(i, j, k);
}
}
}
#else
MFEM_CONTRACT_VAR(Nx);
MFEM_CONTRACT_VAR(Ny);
MFEM_CONTRACT_VAR(Nz);
MFEM_CONTRACT_VAR(h_body);
MFEM_ABORT("OpenMP requested for MFEM but OpenMP is not enabled!");
#endif
}
/// RAJA Cuda and Hip backends
#if defined(MFEM_USE_RAJA) && defined(RAJA_ENABLE_CUDA)
@@ -500,42 +454,6 @@ void RajaOmpWrap(const int N, HBODY &&h_body)
RAJA::forall<RAJA::omp_parallel_for_exec>(RAJA::RangeSegment(0,N), h_body);
}
template <typename HBODY>
void RajaOmpWrap2D(const int Nx, const int Ny, HBODY &&h_body)
{
using omp_launch_policy = RAJA::LaunchPolicy<RAJA::omp_launch_t>;
using global_thread_xy = RAJA::LoopPolicy<RAJA::omp_for_exec>;
RAJA::RangeSegment xrange(0, Nx);
RAJA::RangeSegment yrange(0, Ny);
RAJA::launch<omp_launch_policy>(RAJA::ExecPlace::HOST, RAJA::LaunchParams(),
[=](RAJA::LaunchContext ctx)
{
// contiguous in x
RAJA::expt::loop<global_thread_xy>(ctx, xrange, yrange, [&](int i, int j)
{
h_body(i, j);
});
});
}
template <typename HBODY>
void RajaOmpWrap3D(const int Nx, const int Ny, const int Nz, HBODY &&h_body)
{
using omp_launch_policy = RAJA::LaunchPolicy<RAJA::omp_launch_t>;
using global_thread_xyz = RAJA::LoopPolicy<RAJA::omp_for_exec>;
RAJA::RangeSegment xrange(0, Nx);
RAJA::RangeSegment yrange(0, Ny);
RAJA::RangeSegment zrange(0, Nz);
RAJA::launch<omp_launch_policy>(RAJA::ExecPlace::HOST, RAJA::LaunchParams(),
[=](RAJA::LaunchContext ctx)
{
// contiguous in x
RAJA::expt::loop<global_thread_xyz>(ctx, xrange, yrange, zrange,
[&](int i, int j, int k)
{ h_body(i, j, k); });
});
}
#endif
@@ -563,7 +481,7 @@ void RajaSeqWrap(const int N, HBODY &&h_body)
/// CUDA backend
#if defined(MFEM_USE_CUDA) && defined(__CUDACC__)
#ifdef MFEM_USE_CUDA
template <typename BODY> __global__ static
void CuKernel1D(const int N, BODY body)
@@ -655,11 +573,11 @@ struct CuWrap<3>
}
};
#endif // defined(MFEM_USE_CUDA) && defined(__CUDACC__)
#endif // MFEM_USE_CUDA
/// HIP backend
#if defined(MFEM_USE_HIP) && defined(__HIP__)
#ifdef MFEM_USE_HIP
template <typename BODY> __global__ static
void HipKernel1D(const int N, BODY body)
@@ -750,7 +668,7 @@ struct HipWrap<3>
}
};
#endif // defined(MFEM_USE_HIP) && defined(__HIP__)
#endif // MFEM_USE_HIP
/// The forall kernel body wrapper
@@ -783,7 +701,7 @@ inline void ForallWrap(const bool use_dev, const int N,
}
#endif
#if defined(MFEM_USE_CUDA) && defined(__CUDACC__)
#ifdef MFEM_USE_CUDA
// If Backend::CUDA is allowed, use it
if (Device::Allows(Backend::CUDA))
{
@@ -791,7 +709,7 @@ inline void ForallWrap(const bool use_dev, const int N,
}
#endif
#if defined(MFEM_USE_HIP) && defined(__HIP__)
#ifdef MFEM_USE_HIP
// If Backend::HIP is allowed, use it
if (Device::Allows(Backend::HIP))
{
@@ -835,83 +753,6 @@ inline void ForallWrap(const bool use_dev, const int N, lambda &&body,
template<typename lambda>
inline void forall(int N, lambda &&body) { ForallWrap<1>(true, N, body); }
template<typename lambda>
inline void forall(int Nx, int Ny, lambda &&body)
{
if (Device::Allows(Backend::DEVICE_MASK))
{
forall(Nx * Ny, [=] MFEM_HOST_DEVICE(int idx)
{
int j = idx / Nx;
int i = idx % Nx;
body(i, j);
});
}
#if defined(MFEM_USE_RAJA) && defined(RAJA_ENABLE_OPENMP)
else if (Device::Allows(Backend::RAJA_OMP))
{
return RajaOmpWrap2D(Nx, Ny, body);
}
#endif
#ifdef MFEM_USE_OPENMP
else if (Device::Allows(Backend::OMP))
{
return OmpWrap2D(Nx, Ny, body);
}
#endif
else
{
for (int j = 0; j < Ny; ++j)
{
for (int i = 0; i < Nx; ++i)
{
body(i, j);
}
}
}
}
template<typename lambda>
inline void forall(int Nx, int Ny, int Nz, lambda &&body)
{
if (Device::Allows(Backend::DEVICE_MASK))
{
forall(Nx * Ny * Nz, [=] MFEM_HOST_DEVICE(int idx)
{
int i = idx % Nx;
int j = idx / Nx;
int k = j / Ny;
j = j % Ny;
body(i, j, k);
});
}
#if defined(MFEM_USE_RAJA) && defined(RAJA_ENABLE_OPENMP)
else if (Device::Allows(Backend::RAJA_OMP))
{
return RajaOmpWrap3D(Nx, Ny, Nz, body);
}
#endif
#ifdef MFEM_USE_OPENMP
else if (Device::Allows(Backend::OMP))
{
return OmpWrap3D(Nx, Ny, Nz, body);
}
#endif
else
{
for (int k = 0; k < Nz; ++k)
{
for (int j = 0; j < Ny; ++j)
{
for (int i = 0; i < Nx; ++i)
{
body(i, j, k);
}
}
}
}
}
template<typename lambda>
inline void forall_switch(bool use_dev, int N, lambda &&body)
{
+1 -1
View File
@@ -24,7 +24,7 @@ void mfem_hip_error(hipError_t err, const char *expr, const char *func,
const char *file, int line)
{
mfem::err << "\n\nHIP error: (" << expr << ") failed with error:\n --> "
<< hipGetErrorString(err) << " [code: " << (int)err << ']'
<< hipGetErrorString(err)
<< "\n ... in function: " << func
<< "\n ... in file: " << file << ':' << line << '\n';
mfem_error();
+5 -7
View File
@@ -18,7 +18,7 @@
// HIP block size used by MFEM.
#define MFEM_HIP_BLOCKS 256
#if defined(MFEM_USE_HIP) && defined(__HIP__)
#ifdef MFEM_USE_HIP
#define MFEM_USE_CUDA_OR_HIP
#define MFEM_DEVICE __device__
#define MFEM_HOST __host__
@@ -37,20 +37,18 @@
__FILE__, __LINE__); \
} \
} while (0)
#endif // MFEM_USE_HIP
// Define the MFEM inner threading macros
#if defined(__HIP_DEVICE_COMPILE__)
#if defined(MFEM_USE_HIP) && defined(__HIP_DEVICE_COMPILE__)
#define MFEM_SHARED __shared__
#define MFEM_SYNC_THREAD __syncthreads()
#define MFEM_BLOCK_ID(k) hipBlockIdx_ ##k
#define MFEM_THREAD_ID(k) hipThreadIdx_ ##k
#define MFEM_THREAD_SIZE(k) hipBlockDim_ ##k
#define MFEM_FOREACH_THREAD(i,k,N) \
for(int i=hipThreadIdx_ ##k; i<N; i+=hipBlockDim_ ##k)
#define MFEM_FOREACH_THREAD_DIRECT(i,k,N) \
if(const int i=hipThreadIdx_ ##k; i<N)
#endif // defined(__HIP_DEVICE_COMPILE__)
#endif // defined(MFEM_USE_HIP) && defined(__HIP__)
for(int i=hipThreadIdx_ ##k; i<N; i+=hipBlockDim_ ##k)
#endif
namespace mfem
{
+8 -2
View File
@@ -513,7 +513,10 @@ public:
void *HtoD(void *dst, const void *src, size_t bytes) override
{ return HipMemcpyHtoD(dst, src, bytes); }
void *DtoD(void* dst, const void* src, size_t bytes) override
{ return HipMemcpyDtoD(dst, src, bytes); }
// Unlike cudaMemcpy(DtoD), hipMemcpy(DtoD) causes a host-side synchronization so
// instead we use hipMemcpyAsync to get similar behavior.
// for more info see: https://github.com/mfem/mfem/pull/2780
{ return HipMemcpyDtoDAsync(dst, src, bytes); }
void *DtoH(void *dst, const void *src, size_t bytes) override
{ return HipMemcpyDtoH(dst, src, bytes); }
};
@@ -655,7 +658,10 @@ public:
return CuMemcpyDtoD(dst, src, bytes);
#endif
#ifdef MFEM_USE_HIP
return HipMemcpyDtoD(dst, src, bytes);
// Unlike cudaMemcpy(DtoD), hipMemcpy(DtoD) causes a host-side synchronization so
// instead we use hipMemcpyAsync to get similar behavior.
// for more info see: https://github.com/mfem/mfem/pull/2780
return HipMemcpyDtoDAsync(dst, src, bytes);
#endif
// rm.copy(dst, const_cast<void*>(src), bytes); return dst;
}
+1 -3
View File
@@ -896,7 +896,6 @@ inline HYPRE_MemoryLocation GetHypreMemoryLocation()
#elif MFEM_HYPRE_VERSION < 23100
return HYPRE_MEMORY_DEVICE;
#else // HYPRE_USING_GPU is defined and MFEM_HYPRE_VERSION >= 23100
if (!HYPRE_Initialized()) { return HYPRE_MEMORY_HOST; }
HYPRE_MemoryLocation loc;
HYPRE_GetMemoryLocation(&loc);
return loc;
@@ -1058,8 +1057,7 @@ inline void Memory<T>::MakeAlias(const Memory &base, int offset, int size)
// register the 'base' if the MemoryManager::Exists():
MemoryManager::Exists()
#else // HYPRE_USING_GPU is defined and MFEM_HYPRE_VERSION >= 23100
IsDeviceMemory(MemoryManager::GetDeviceMemoryType()) ||
(MemoryManager::Exists() && HypreUsingGPU())
MemoryManager::Exists() && HypreUsingGPU()
#endif
)
{
+1 -1
View File
@@ -537,7 +537,7 @@ void reduce(int N, T &res, B &&body, const R &reducer, bool use_dev,
return;
}
#if defined(MFEM_USE_CUDA_OR_HIP)
#if defined(MFEM_USE_HIP) || defined(MFEM_USE_CUDA)
if (use_dev &&
mfem::Device::Allows(Backend::CUDA | Backend::HIP | Backend::RAJA_CUDA |
Backend::RAJA_HIP))
-176
View File
@@ -1,176 +0,0 @@
// Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
// LICENSE and NOTICE for details. LLNL-CODE-806117.
//
// This file is part of the MFEM library. For more information and source code
// availability visit https://mfem.org.
//
// MFEM is free software; you can redistribute it and/or modify it under the
// terms of the BSD-3 license. We welcome feedback and contributions, see file
// CONTRIBUTING.md for details.
#ifndef MFEM_SCAN_HPP
#define MFEM_SCAN_HPP
#ifdef MFEM_USE_CUDA
#include <cub/device/device_scan.cuh>
#define MFEM_CUB_NAMESPACE cub
#elif MFEM_USE_HIP
#include <hipcub/device/device_scan.hpp>
#define MFEM_CUB_NAMESPACE hipcub
#endif
#include <functional>
#include <numeric>
namespace mfem
{
/// Equivalent to InclusiveScan(use_dev, d_in, d_out, num_items, workspace,
/// std::plus<>{})
template <class InputIt, class OutputIt>
void InclusiveScan(bool use_dev, InputIt d_in, OutputIt d_out, size_t num_items,
Array<char> &workspace)
{
// forward to InclusiveSum for potentially faster kernels
#if defined(MFEM_USE_CUDA) || defined(MFEM_USE_HIP)
if (use_dev && mfem::Device::Allows(Backend::CUDA_MASK | Backend::HIP_MASK))
{
size_t bytes = workspace.Size();
if (bytes)
{
auto err = MFEM_CUB_NAMESPACE::DeviceScan::InclusiveSum(
workspace.Write(), bytes, d_in, d_out, num_items);
#if defined(MFEM_USE_CUDA)
if (err == cudaSuccess)
{
return;
}
#elif defined(MFEM_USE_HIP)
if (err == hipSuccess)
{
return;
}
#endif
}
// try allocating a larger buffer
bytes = 0;
MFEM_GPU_CHECK(MFEM_CUB_NAMESPACE::DeviceScan::InclusiveSum(
nullptr, bytes, d_in, d_out, num_items));
workspace.SetSize(bytes);
MFEM_GPU_CHECK(MFEM_CUB_NAMESPACE::DeviceScan::InclusiveSum(
workspace.Write(), bytes, d_in, d_out, num_items));
return;
}
#endif
std::inclusive_scan(d_in, d_in + num_items, d_out);
}
/// Performs an inclusive scan of [d_in, d_in+num_items) -> [d_out,
/// d_out+num_items). This call is potentially asynchronous on the device.
/// @a d_in input start.
/// @a d_out output start. Can perform in-place scans with d_out = d_in
/// @a workspace temporary workspace used for device scans. TODO: replace with
/// internal temporary workspace once that's added to the memory manager.
/// @a scan_op binary scan functor. Must be associative. If only weakly
/// associative (i.e. floating point addition) results are not deterministic. On
/// device this must also be commutative.
template <class InputIt, class OutputIt, class ScanOp>
void InclusiveScan(bool use_dev, InputIt d_in, OutputIt d_out, size_t num_items,
Array<char> &workspace, ScanOp scan_op)
{
#if defined(MFEM_USE_CUDA) || defined(MFEM_USE_HIP)
if (use_dev && mfem::Device::Allows(Backend::CUDA_MASK | Backend::HIP_MASK))
{
size_t bytes = workspace.Size();
if (bytes)
{
auto err = MFEM_CUB_NAMESPACE::DeviceScan::InclusiveScan(
workspace.Write(), bytes, d_in, d_out, scan_op, num_items);
#if defined(MFEM_USE_CUDA)
if (err == cudaSuccess)
{
return;
}
#elif defined(MFEM_USE_HIP)
if (err == hipSuccess)
{
return;
}
#endif
}
// try allocating a larger buffer
bytes = 0;
MFEM_GPU_CHECK(MFEM_CUB_NAMESPACE::DeviceScan::InclusiveScan(
nullptr, bytes, d_in, d_out, scan_op, num_items));
workspace.SetSize(bytes);
MFEM_GPU_CHECK(MFEM_CUB_NAMESPACE::DeviceScan::InclusiveScan(
workspace.Write(), bytes, d_in, d_out, scan_op, num_items));
return;
}
#endif
std::inclusive_scan(d_in, d_in + num_items, d_out, scan_op);
}
/// Performs an exclusive scan of [d_in, d_in+num_items) -> [d_out,
/// d_out+num_items). This call is potentially asynchronous on the device.
/// @a d_in input start.
/// @a d_out output start. Can perform in-place scans with d_out = d_in
/// @a workspace temporary workspace used for device scans. TODO: replace with
/// internal temporary workspace once that's added to the memory manager.
/// @a scan_op binary scan functor. Must be associative. If only weakly
/// associative (i.e. floating point addition) results are not deterministic. On
/// device this must also be commutative.
template <class InputIt, class OutputIt, class T, class ScanOp>
void ExclusiveScan(bool use_dev, InputIt d_in, OutputIt d_out, size_t num_items,
T init_value, Array<char> &workspace, ScanOp scan_op)
{
#if defined(MFEM_USE_CUDA) || defined(MFEM_USE_HIP)
if (use_dev && mfem::Device::Allows(Backend::CUDA_MASK | Backend::HIP_MASK))
{
size_t bytes = workspace.Size();
if (bytes)
{
auto err = MFEM_CUB_NAMESPACE::DeviceScan::ExclusiveScan(
workspace.Write(), bytes, d_in, d_out, scan_op, init_value,
num_items);
#if defined(MFEM_USE_CUDA)
if (err == cudaSuccess)
{
return;
}
#elif defined(MFEM_USE_HIP)
if (err == hipSuccess)
{
return;
}
#endif
}
// try allocating a larger buffer
bytes = 0;
MFEM_GPU_CHECK(MFEM_CUB_NAMESPACE::DeviceScan::ExclusiveScan(
nullptr, bytes, d_in, d_out, scan_op, init_value, num_items));
workspace.SetSize(bytes);
MFEM_GPU_CHECK(MFEM_CUB_NAMESPACE::DeviceScan::ExclusiveScan(
workspace.Write(), bytes, d_in, d_out, scan_op, init_value,
num_items));
return;
}
#endif
std::exclusive_scan(d_in, d_in + num_items, d_out, init_value, scan_op);
}
/// Equivalent to ExclusiveScan(use_dev, d_in, d_out, num_items, init_value,
/// workspace, std::plus<>{})
template <class InputIt, class OutputIt, class T>
void ExclusiveScan(bool use_dev, InputIt d_in, OutputIt d_out, size_t num_items,
T init_value, Array<char> &workspace)
{
ExclusiveScan(use_dev, d_in, d_out, num_items, init_value, workspace,
std::plus<> {});
}
} // namespace mfem
#undef MFEM_CUB_NAMESPACE
#endif
-28
View File
@@ -4405,32 +4405,4 @@ void BatchLUSolve(const DenseTensor &Mlu, const Array<int> &P, Vector &X)
BatchedLinAlg::LUSolve(Mlu, P, X);
}
#ifdef MFEM_USE_LAPACK
void BandedSolve(int KL, int KU, DenseMatrix &AB, DenseMatrix &B,
Array<int> &ipiv)
{
int LDAB = (2*KL) + KU + 1;
int N = AB.NumCols();
int NRHS = B.NumCols();
int info;
ipiv.SetSize(N);
MFEM_LAPACK_PREFIX(gbsv_)(&N, &KL, &KU, &NRHS, AB.GetData(), &LDAB,
ipiv.GetData(), B.GetData(), &N, &info);
MFEM_ASSERT(info == 0, "BandedSolve failed in LAPACK");
}
void BandedFactorizedSolve(int KL, int KU, DenseMatrix &AB, DenseMatrix &B,
bool transpose, Array<int> &ipiv)
{
int LDAB = (2*KL) + KU + 1;
int N = AB.NumCols();
int NRHS = B.NumCols();
char trans = transpose ? 'T' : 'N';
int info;
MFEM_LAPACK_PREFIX(gbtrs_)(&trans, &N, &KL, &KU, &NRHS, AB.GetData(), &LDAB,
ipiv.GetData(), B.GetData(), &N, &info);
MFEM_ASSERT(info == 0, "BandedFactorizedSolve failed in LAPACK");
}
#endif
} // namespace mfem
-7
View File
@@ -1329,13 +1329,6 @@ void BatchLUFactor(DenseTensor &Mlu, Array<int> &P, const real_t TOL = 0.0);
dimension m x n. */
void BatchLUSolve(const DenseTensor &Mlu, const Array<int> &P, Vector &X);
#ifdef MFEM_USE_LAPACK
void BandedSolve(int KL, int KU, DenseMatrix &AB, DenseMatrix &B,
Array<int> &ipiv);
void BandedFactorizedSolve(int KL, int KU, DenseMatrix &AB, DenseMatrix &B,
bool transpose, Array<int> &ipiv);
#endif
// Inline methods
inline real_t &DenseMatrix::operator()(int i, int j)
-12
View File
@@ -2574,18 +2574,6 @@ void HypreParMatrix::EliminateBC(const Array<int> &ess_dofs,
#if defined(HYPRE_USING_GPU)
if (HypreUsingGPU())
{
#if defined(HYPRE_WITH_GPU_AWARE_MPI) || defined(HYPRE_USING_GPU_AWARE_MPI)
// hypre_GetGpuAwareMPI() was introduced in v2.31.0, however, its value
// is not checked in hypre_ParCSRCommHandleCreate_v2() before v2.33.0,
// instead only HYPRE_WITH_GPU_AWARE_MPI is checked.
#if MFEM_HYPRE_VERSION >= 23300
if (hypre_GetGpuAwareMPI())
#endif
{
// ensure int_buf_data has been computed before sending it
MFEM_STREAM_SYNC;
}
#endif
// Try to use device-aware MPI for the communication if available
comm_handle = hypre_ParCSRCommHandleCreate_v2(
11, comm_pkg, HYPRE_MEMORY_DEVICE, int_buf_data,
-7
View File
@@ -42,13 +42,6 @@ extern "C" void
MFEM_LAPACK_PREFIX(getri_)(int *N, real_t *A, int *LDA, int *IPIV, real_t *WORK,
int *LWORK, int *INFO);
extern "C" void
MFEM_LAPACK_PREFIX(gbsv_)(int *, int *, int *, int *, real_t *, int *, int *,
real_t *, int *, int *);
extern "C" void
MFEM_LAPACK_PREFIX(gbtrs_)(char *, int *, int *, int *, int *, real_t *, int *,
int *, real_t *, int *, int *);
extern "C" void
MFEM_LAPACK_PREFIX(syevr_)(char *JOBZ, char *RANGE, char *UPLO, int *N,
real_t *A, int *LDA, real_t *VL, real_t *VU, int *IL,
int *IU, real_t *ABSTOL, int *M, real_t *W,
+1 -42
View File
@@ -14,7 +14,6 @@
#include "../general/forall.hpp"
#include "../general/reducers.hpp"
#include "../general/hash.hpp"
#include "../general/scan.hpp"
#include "vector.hpp"
#ifdef MFEM_USE_OPENMP
@@ -118,7 +117,7 @@ Vector::Vector(const Vector &v)
UseDevice(v.UseDevice());
}
Vector::Vector(Vector &&v) : Vector()
Vector::Vector(Vector &&v)
{
*this = std::move(v);
}
@@ -1253,44 +1252,4 @@ real_t Vector::Sum() const
return res;
}
void Vector::DeleteAt(const Array<int> &indices)
{
const bool use_dev = UseDevice();
Array<int> flag(size);
const auto d_flag = flag.Write(use_dev);
mfem::forall_switch(use_dev, size, [=] MFEM_HOST_DEVICE (int i)
{
d_flag[i] = true;
});
const auto d_indices = indices.Read(use_dev);
mfem::forall_switch(use_dev, indices.Size(), [=] MFEM_HOST_DEVICE (int i)
{
d_flag[d_indices[i]] = false;
});
Array<int> out_idx(size);
auto d_out_idx = out_idx.Write(use_dev);
Array<char> workspace;
// Perform inclusive scan so that the last entry is the new size.
InclusiveScan(use_dev, d_flag, d_out_idx, size, workspace);
Vector copy(*this);
auto d_in = copy.Read(use_dev);
auto d_out = Write(use_dev);
mfem::forall_switch(use_dev, size, [=] MFEM_HOST_DEVICE (int i)
{
if (d_flag[i])
{
// Transform inclusive scan to exclusive by shifting.
const int j = (i > 0) ? d_out_idx[i - 1] : 0;
d_out[j] = d_in[i];
}
});
// Get the new size of the vector. Copy only the last entry.
Memory<int> submem(out_idx.GetMemory(), out_idx.Size() - 1, 1);
size = submem.Read(MemoryClass::HOST, 1)[0];
}
} // namespace mfem
-18
View File
@@ -171,12 +171,6 @@ public:
/// Resize the vector to size @a s using the MemoryType of @a v.
void SetSize(int s, const Vector &v) { SetSize(s, v.GetMemory().GetMemoryType()); }
/// Update \ref Capacity() to @a res (if less than current), keeping existing entries.
void Reserve(int res);
/// Delete entries at @a indices and resize vector accordingly.
void DeleteAt(const Array<int> &indices);
/// Set the Vector data.
/// @warning This method should be called only when OwnsData() is false.
void SetData(real_t *d) { data.Wrap(d, data.Capacity(), false); }
@@ -627,18 +621,6 @@ inline void Vector::SetSize(int s, MemoryType mt)
data.UseDevice(use_dev);
}
inline void Vector::Reserve(int res)
{
if (res > Capacity())
{
Memory<real_t> p(res, data.GetMemoryType());
p.CopyFrom(data, size);
p.UseDevice(data.UseDevice());
data.Delete();
data = p;
}
}
inline void Vector::NewMemoryAndSize(const Memory<real_t> &mem, int s,
bool own_mem)
{
+27 -35
View File
@@ -26,12 +26,6 @@
}\
}
#if defined(MFEM_USE_DOUBLE)
#define MFEM_NETCDF_REAL_T NC_DOUBLE
#elif defined(MFEM_USE_SINGLE)
#define MFEM_NETCDF_REAL_T NC_FLOAT
#endif
namespace mfem
{
@@ -141,18 +135,18 @@ public:
/// @brief Writes the mesh to an ExodusII file.
/// @param fpath The path to the file.
/// @param flags NC_CLOBBER will overwrite existing file.
void PrintExodusII(const std::string &fpath, int flags = NC_CLOBBER);
void PrintExodusII(std::string fpath, int flags = NC_CLOBBER);
/// @brief Static method for writing a mesh to an ExodusII file.
/// @param mesh The mesh to write to the file.
/// @param fpath The path to the file.
/// @param flags NetCDF file flags.
static void PrintExodusII(Mesh & mesh, const std::string &fpath,
static void PrintExodusII(Mesh & mesh, std::string fpath,
int flags = NC_CLOBBER);
protected:
/// @brief Closes any open file and creates a NetCDF file using selected flags.
void OpenExodusII(const std::string &fpath, int flags);
void OpenExodusII(std::string fpath, int flags);
/// @brief Closes any open file.
void CloseExodusII();
@@ -173,9 +167,9 @@ protected:
std::unordered_set<int> GenerateUniqueNodeIDs();
/// @brief Populates vectors with x, y, z coordinates from mesh.
void ExtractVertexCoordinates(std::vector<real_t> &coordx,
std::vector<real_t> &coordy,
std::vector<real_t> &coordz);
void ExtractVertexCoordinates(std::vector<double> & coordx,
std::vector<double> & coordy,
std::vector<double> & coordz);
/// @brief Writes node connectivity for a particular block.
/// @param block_id The block to write to the file.
@@ -193,7 +187,7 @@ protected:
/// @brief Writes the number of elements in the mesh.
void WriteNumOfElements();
/// @brief Writes the floating-point word size (sizeof(real_t)).
/// @brief Writes the floating-point word size (4 == float; 8 == double).
void WriteFloatingPointWordSize();
/// @brief Writes the API version.
@@ -297,7 +291,7 @@ private:
std::map<int, std::vector<int>> exodusII_side_ids_for_boundary_id;
};
void Mesh::PrintExodusII(const std::string &fpath)
void Mesh::PrintExodusII(const std::string fpath)
{
ExodusIIWriter::PrintExodusII(*this, fpath);
}
@@ -368,7 +362,7 @@ void ExodusIIWriter::WriteExodusIIMeshInformation()
WriteNodeSets();
}
void ExodusIIWriter::PrintExodusII(const std::string &fpath, int flags)
void ExodusIIWriter::PrintExodusII(std::string fpath, int flags)
{
OpenExodusII(fpath, flags);
@@ -380,7 +374,7 @@ void ExodusIIWriter::PrintExodusII(const std::string &fpath, int flags)
mfem::out << "Mesh successfully written to Exodus II file" << std::endl;
}
void ExodusIIWriter::PrintExodusII(Mesh &mesh, const std::string &fpath,
void ExodusIIWriter::PrintExodusII(Mesh & mesh, std::string fpath,
int flags)
{
ExodusIIWriter writer(mesh);
@@ -388,7 +382,7 @@ void ExodusIIWriter::PrintExodusII(Mesh &mesh, const std::string &fpath,
writer.PrintExodusII(fpath, flags);
}
void ExodusIIWriter::OpenExodusII(const std::string &fpath, int flags)
void ExodusIIWriter::OpenExodusII(std::string fpath, int flags)
{
CloseExodusII(); // Close any open files.
@@ -428,7 +422,7 @@ void ExodusIIWriter::WriteNumOfElements()
void ExodusIIWriter::WriteFloatingPointWordSize()
{
const int word_size = sizeof(real_t);
const int word_size = 8;
PutAtt(NC_GLOBAL, ExodusIILabels::EXODUS_FLOATING_POINT_WORD_SIZE_LABEL,
NC_INT, 1,
&word_size);
@@ -436,15 +430,13 @@ void ExodusIIWriter::WriteFloatingPointWordSize()
void ExodusIIWriter::WriteAPIVersion()
{
PutAtt(NC_GLOBAL, ExodusIILabels::EXODUS_API_VERSION_LABEL, MFEM_NETCDF_REAL_T,
1,
PutAtt(NC_GLOBAL, ExodusIILabels::EXODUS_API_VERSION_LABEL, NC_FLOAT, 1,
&ExodusIILabels::EXODUS_API_VERSION);
}
void ExodusIIWriter::WriteDatabaseVersion()
{
PutAtt(NC_GLOBAL, ExodusIILabels::EXODUS_DATABASE_VERSION_LABEL,
MFEM_NETCDF_REAL_T, 1,
PutAtt(NC_GLOBAL, ExodusIILabels::EXODUS_DATABASE_VERSION_LABEL, NC_FLOAT, 1,
&ExodusIILabels::EXODUS_DATABASE_VERSION);
}
@@ -615,25 +607,25 @@ void ExodusIIWriter::WriteNodalCoordinates()
DefineDimension("num_nodes", num_nodes, &num_nodes_id);
// 3. Extract the nodal coordinates.
// NB: writes in format real_t (double or float); ndims = 1 (vector).
// NB: assume doubles (could be floats!); ndims = 1 (vector).
// https://docs.unidata.ucar.edu/netcdf-c/current/group__variables.html#gac7e8662c51f3bb07d1fc6d6c6d9052c8
std::vector<real_t> coordx(num_nodes);
std::vector<real_t> coordy(num_nodes);
std::vector<real_t> coordz(mesh.Dimension() == 3 ? num_nodes : 0);
std::vector<double> coordx(num_nodes);
std::vector<double> coordy(num_nodes);
std::vector<double> coordz(mesh.Dimension() == 3 ? num_nodes : 0);
ExtractVertexCoordinates(coordx, coordy, coordz);
// 4. Define and put the nodal coordinates.
DefineAndPutVar(ExodusIILabels::EXODUS_COORDX_LABEL, MFEM_NETCDF_REAL_T, 1,
DefineAndPutVar(ExodusIILabels::EXODUS_COORDX_LABEL, NC_DOUBLE, 1,
&num_nodes_id,
coordx.data());
DefineAndPutVar(ExodusIILabels::EXODUS_COORDY_LABEL, MFEM_NETCDF_REAL_T, 1,
DefineAndPutVar(ExodusIILabels::EXODUS_COORDY_LABEL, NC_DOUBLE, 1,
&num_nodes_id,
coordy.data());
if (mesh.Dimension() == 3)
{
DefineAndPutVar(ExodusIILabels::EXODUS_COORDZ_LABEL, MFEM_NETCDF_REAL_T, 1,
DefineAndPutVar(ExodusIILabels::EXODUS_COORDZ_LABEL, NC_DOUBLE, 1,
&num_nodes_id,
coordz.data());
}
@@ -778,9 +770,9 @@ void ExodusIIWriter::WriteNodeConnectivityForBlock(const int block_id)
}
void ExodusIIWriter::ExtractVertexCoordinates(std::vector<real_t> & coordx,
std::vector<real_t> & coordy,
std::vector<real_t> & coordz)
void ExodusIIWriter::ExtractVertexCoordinates(std::vector<double> & coordx,
std::vector<double> & coordy,
std::vector<double> & coordz)
{
if (mesh.GetNodes()) // Higher-order.
{
@@ -790,7 +782,7 @@ void ExodusIIWriter::ExtractVertexCoordinates(std::vector<real_t> & coordx,
sorted_node_ids.assign(unordered_node_ids.begin(), unordered_node_ids.end());
std::sort(sorted_node_ids.begin(), sorted_node_ids.end());
real_t coordinates[3];
double coordinates[3];
for (size_t i = 0; i < sorted_node_ids.size(); i++)
{
int node_id = sorted_node_ids[i];
@@ -810,7 +802,7 @@ void ExodusIIWriter::ExtractVertexCoordinates(std::vector<real_t> & coordx,
{
for (int ivertex = 0; ivertex < mesh.GetNV(); ivertex++)
{
real_t *coordinates = mesh.GetVertex(ivertex);
double * coordinates = mesh.GetVertex(ivertex);
coordx[ivertex] = coordinates[0];
coordy[ivertex] = coordinates[1];
@@ -1088,4 +1080,4 @@ void ExodusIIWriter::CheckNodalFESpaceIsSecondOrderH1() const
#endif
}
}
+25 -168
View File
@@ -32,7 +32,6 @@
#include <cstring>
#include <ctime>
#include <functional>
#include <set>
#include <numeric>
#include <unordered_map>
#include <unordered_set>
@@ -922,103 +921,6 @@ const FaceGeometricFactors* Mesh::GetFaceGeometricFactors(
return gf;
}
const Array<int>& Mesh::GetBdrFaceAttributes() const
{
if (bdr_face_attrs_cache.Size() == 0)
{
std::unordered_map<int, int> f_to_be;
for (int i = 0; i < GetNBE(); ++i)
{
const int f = GetBdrElementFaceIndex(i);
f_to_be[f] = i;
}
const int nf_bdr = GetNFbyType(FaceType::Boundary);
// MFEM_VERIFY(size_t(nf_bdr) == f_to_be.size(), "Incompatible sizes");
bdr_face_attrs_cache.SetSize(nf_bdr);
int f_ind = 0;
const int nf = GetNumFaces();
for (int f = 0; f < nf; ++f)
{
if (!GetFaceInformation(f).IsOfFaceType(FaceType::Boundary))
{
continue;
}
int attribute = -1; // default value
auto iter = f_to_be.find(f);
if (iter != f_to_be.end())
{
const int be = iter->second;
attribute = GetBdrAttribute(be);
}
else
{
// If a boundary face does not correspond to the a boundary element,
// we assign it the default attribute of -1.
}
bdr_face_attrs_cache[f_ind] = attribute;
++f_ind;
}
}
return bdr_face_attrs_cache;
}
const Array<int>& Mesh::GetElementAttributes() const
{
if (elem_attrs_cache.Size() == 0)
{
// re-compute cache
elem_attrs_cache.SetSize(GetNE());
elem_attrs_cache.HostWrite();
for (int i = 0; i < GetNE(); ++i)
{
elem_attrs_cache[i] = GetAttribute(i);
MFEM_ASSERT(elem_attrs_cache[i] > 0,
"Negative attribute on element " << i);
}
}
return elem_attrs_cache;
}
void Mesh::ComputeFaceInfo(FaceType ftype) const
{
auto &fidcs = face_indices[static_cast<int>(ftype)];
auto &ifidcs = inv_face_indices[static_cast<int>(ftype)];
fidcs.SetSize(GetNFbyType(ftype));
fidcs.HostWrite();
ifidcs.reserve(fidcs.Size());
int f_idx = 0;
for (int i = 0; i < GetNumFacesWithGhost(); ++i)
{
const FaceInformation face = GetFaceInformation(i);
if (face.IsNonconformingCoarse() || !face.IsOfFaceType(ftype))
{
continue;
}
fidcs[f_idx] = i;
ifidcs[i] = f_idx;
++f_idx;
}
}
const Array<int> &Mesh::GetFaceIndices(FaceType ftype) const
{
if (face_indices[static_cast<int>(ftype)].Size() == 0)
{
ComputeFaceInfo(ftype);
}
return face_indices[static_cast<int>(ftype)];
}
const std::unordered_map<int, int> &
Mesh::GetInvFaceIndices(FaceType ftype) const
{
if (inv_face_indices[static_cast<int>(ftype)].empty())
{
ComputeFaceInfo(ftype);
}
return inv_face_indices[static_cast<int>(ftype)];
}
void Mesh::DeleteGeometricFactors()
{
for (int i = 0; i < geom_factors.Size(); i++)
@@ -1902,15 +1804,8 @@ void Mesh::Destroy()
TetMemory.Clear();
#endif
elem_attrs_cache.DeleteAll();
bdr_face_attrs_cache.DeleteAll();
attributes.DeleteAll();
bdr_attributes.DeleteAll();
face_indices[0].DeleteAll();
face_indices[1].DeleteAll();
inv_face_indices[0] = std::unordered_map<int, int>();
inv_face_indices[1] = std::unordered_map<int, int>();
}
void Mesh::ResetLazyData()
@@ -1922,48 +1817,36 @@ void Mesh::ResetLazyData()
DeleteGeometricFactors();
nbInteriorFaces = -1;
nbBoundaryFaces = -1;
// set size to 0 so re-computations can potentially avoid a new allocation
bdr_face_attrs_cache.SetSize(0);
elem_attrs_cache.SetSize(0);
}
void Mesh::SetAttributes(bool elem_attrs_changed, bool bdr_face_attrs_changed)
void Mesh::SetAttributes()
{
if (bdr_face_attrs_changed)
Array<int> attribs;
attribs.SetSize(GetNBE());
for (int i = 0; i < attribs.Size(); i++)
{
bdr_face_attrs_cache.SetSize(0); // Invalidate the cache
// Get sorted list of unique boundary element attributes
std::set<int> attribs;
for (int i = 0; i < GetNBE(); i++)
{
attribs.emplace(GetBdrAttribute(i));
}
bdr_attributes.SetSize(attribs.size());
bdr_attributes.HostWrite();
std::copy(attribs.begin(), attribs.end(), bdr_attributes.begin());
if (bdr_attributes.Size() > 0 && bdr_attributes[0] <= 0)
{
MFEM_WARNING("Non-positive attributes on the boundary!");
}
attribs[i] = GetBdrAttribute(i);
}
attribs.Sort();
attribs.Unique();
attribs.Copy(bdr_attributes);
if (bdr_attributes.Size() > 0 && bdr_attributes[0] <= 0)
{
MFEM_WARNING("Non-positive attributes on the boundary!");
}
if (elem_attrs_changed)
attribs.SetSize(GetNE());
for (int i = 0; i < attribs.Size(); i++)
{
// Re-compute the attributes cache
elem_attrs_cache.SetSize(0);
GetElementAttributes();
// Get sorted list of unique element attributes
std::set<int> attribs(elem_attrs_cache.begin(), elem_attrs_cache.end());
attributes.SetSize(attribs.size());
attributes.HostWrite();
std::copy(attribs.begin(), attribs.end(), attributes.begin());
if (attributes.Size() > 0 && attributes[0] <= 0)
{
MFEM_WARNING("Non-positive attributes in the domain!");
}
attribs[i] = GetAttribute(i);
}
attribs.Sort();
attribs.Unique();
attribs.Copy(attributes);
if (attributes.Size() > 0 && attributes[0] <= 0)
{
MFEM_WARNING("Non-positive attributes in the domain!");
}
}
@@ -3111,7 +2994,6 @@ void Mesh::DoNodeReorder(DSTable *old_v_to_v, Table *old_elem_vert)
const int num_edge_dofs = old_dofs.Size();
// Save the original nodes
Nodes->HostReadWrite(); // for "(*Nodes)() = "
const Vector onodes = *Nodes;
// vertex dofs do not need to be moved
@@ -4571,10 +4453,6 @@ Mesh::Mesh(const Mesh &mesh, bool copy_nodes)
Nodes = mesh.Nodes;
own_nodes = 0;
}
// copy attribute caches
elem_attrs_cache = mesh.elem_attrs_cache;
bdr_face_attrs_cache = mesh.bdr_face_attrs_cache;
}
Mesh::Mesh(Mesh &&mesh) : Mesh()
@@ -7842,12 +7720,6 @@ void Mesh::GetBdrElementAdjacentElement2(
void Mesh::SetAttribute(int i, int attr)
{
elements[i]->SetAttribute(attr);
if (elem_attrs_cache.Size() == GetNE())
{
// update the existing cache instead of deleting it
elem_attrs_cache.HostReadWrite();
elem_attrs_cache[i] = attr;
}
if (ncmesh) ncmesh->SetAttribute(i, attr);
}
@@ -8182,12 +8054,6 @@ void Mesh::GenerateFaces()
FreeElement(f);
}
// delete caches
face_indices[0].SetSize(0);
face_indices[1].SetSize(0);
inv_face_indices[0].clear();
inv_face_indices[1].clear();
// (re)generate the interior faces and the info for them
faces.SetSize(nfaces);
faces_info.SetSize(nfaces);
@@ -10983,15 +10849,6 @@ void Mesh::Swap(Mesh& other, bool non_geometry)
mfem::Swap(nodes_sequence, other.nodes_sequence);
mfem::Swap(last_operation, other.last_operation);
}
// copy attribute caches
mfem::Swap(elem_attrs_cache, other.elem_attrs_cache);
mfem::Swap(bdr_face_attrs_cache, other.bdr_face_attrs_cache);
mfem::Swap(face_indices[0], other.face_indices[0]);
mfem::Swap(face_indices[1], other.face_indices[1]);
inv_face_indices[0].swap(other.inv_face_indices[0]);
inv_face_indices[1].swap(other.inv_face_indices[1]);
}
void Mesh::GetElementData(const Array<Element*> &elem_array, int geom,
@@ -13399,7 +13256,7 @@ void Mesh::ScaleElements(real_t sf)
delete [] vn;
}
void Mesh::Transform(std::function<void(const Vector &, Vector&)> f)
void Mesh::Transform(void (*f)(const Vector&, Vector&))
{
// TODO: support for different new spaceDim.
if (Nodes == NULL)
@@ -13412,7 +13269,7 @@ void Mesh::Transform(std::function<void(const Vector &, Vector&)> f)
vold(j) = vertices[i](j);
}
vnew.SetData(vertices[i]());
f(vold, vnew);
(*f)(vold, vnew);
}
}
else
+12 -62
View File
@@ -107,11 +107,6 @@ protected:
Array<Element *> boundary;
Array<Element *> faces;
/// internal cache for element attributes
mutable Array<int> elem_attrs_cache;
/// internal cache for boundary element attributes
mutable Array<int> bdr_face_attrs_cache;
/** @brief This structure stores the low level information necessary to
interpret the configuration of elements on a specific face. This
information can be accessed using methods like GetFaceElements(),
@@ -278,13 +273,6 @@ protected:
// used during NC mesh initialization only
Array<Triple<int, int, int> > tmp_vertex_parents;
/// cache for FaceIndices(ftype)
mutable Array<int> face_indices[2];
/// cache for FaceIndices(ftype)
mutable std::unordered_map<int, int> inv_face_indices[2];
/// compute face_indices[ftype] and inv_face_indices[type]
void ComputeFaceInfo(FaceType ftype) const;
public:
typedef Geometry::Constants<Geometry::SEGMENT> seg_t;
@@ -319,11 +307,6 @@ public:
// (true) is set in mesh_readers.cpp.
static bool remove_unused_vertices;
/// Map from boundary or interior face indices to mesh face indices.
const Array<int>& GetFaceIndices(FaceType ftype) const;
/// Inverse of the map FaceIndices(ftype)
const std::unordered_map<int, int>& GetInvFaceIndices(FaceType ftype) const;
protected:
Operation last_operation;
@@ -605,10 +588,9 @@ protected:
void Loader(std::istream &input, int generate_edges = 0,
std::string parse_tag = "");
/** @brief If NURBS mesh, write NURBS format. If NCMesh, write mfem v1.1
format. If section_delimiter is empty, write mfem v1.0 format. Otherwise,
write mfem v1.2 format with the given section_delimiter at the end.
/** If NURBS mesh, write NURBS format. If NCMesh, write mfem v1.1 format.
If section_delimiter is empty, write mfem v1.0 format. Otherwise, write
mfem v1.2 format with the given section_delimiter at the end.
If @a comments is non-empty, it will be printed after the first line of
the file, and each line should begin with '#'. */
void Printer(std::ostream &os = mfem::out,
@@ -1139,14 +1121,13 @@ public:
Mesh vertices or nodes are set. */
virtual void Finalize(bool refine = false, bool fix_orientation = false);
/// @brief Determine the sets of unique attribute values in domain if @a
/// elem_attrs_changed and boundary elements if @a bdr_face_attrs_changed.
/// @brief Determine the sets of unique attribute values in domain and
/// boundary elements.
///
/// Separately scan the domain and boundary elements to generate unique,
/// sorted sets of the element attribute values present in the mesh and
/// store these in the Mesh::attributes and Mesh::bdr_attributes arrays.
virtual void SetAttributes(bool elem_attrs_changed = true,
bool bdr_face_attrs_changed = true);
virtual void SetAttributes();
/// Check (and optionally attempt to fix) the orientation of the elements
/** @param[in] fix_it If `true`, attempt to fix the orientations of some
@@ -2272,7 +2253,7 @@ public:
void ScaleSubdomains (real_t sf);
void ScaleElements (real_t sf);
void Transform(std::function<void(const Vector &, Vector&)> f);
void Transform(void (*f)(const Vector&, Vector&));
void Transform(VectorCoefficient &deformation);
/** @brief This function should be called after the mesh node coordinates
@@ -2285,35 +2266,6 @@ public:
method does not modify the nodes. */
void NodesUpdated() { DeleteGeometricFactors(); }
/// @brief Returns the attributes for all elements in this mesh. The i'th
/// entry of the array is the attribute of the i'th element of the mesh.
///
/// The returned array points to an internal object that may be invalidated
/// by mesh operations such as refinement or any element attributes are
/// modified. Since not all such modifications can be tracked by the Mesh
/// class (e.g. if a user calls GetElement() then changes the element
/// attribute directly), one needs to account for such changes by calling the
/// method SetAttributes().
const Array<int>& GetElementAttributes() const;
/// @brief Returns the attributes for all boundary elements in this mesh.
///
/// The face restriction will give "face E-vectors" on the boundary that
/// are numbered in the order of the faces of mesh. This numbering will be
/// different than the numbering of the boundary elements. We compute
/// mappings so that the array `bdr_attributes[i]` gives the boundary
/// attribute of the `i`th boundary face in the mesh face order.
/// Attributes <= 0 indicate there is no boundary element and should be
/// skipped.
///
/// The returned array points to an internal object that may be invalidated
/// by mesh operations such as refinement or any element attributes are
/// modified. Since not all such modifications can be tracked by the Mesh
/// class (e.g. if a user calls GetElement() then changes the element
/// attribute directly), one needs to account for such changes by calling the
/// method SetAttributes().
const Array<int>& GetBdrFaceAttributes() const;
/// @}
/// @anchor mfem_Mesh_gf_nodes
@@ -2530,12 +2482,10 @@ public:
/// Print the mesh to the given stream using Netgen/Truegrid format.
virtual void PrintXG(std::ostream &os = mfem::out) const;
/** @brief Print the mesh to the given stream using the default MFEM mesh
format.
\see mfem::ofgzstream() for on-the-fly compression of ascii outputs. If
@a comments is non-empty, it will be printed after the first line of the
file, and each line should begin with '#'. */
/// Print the mesh to the given stream using the default MFEM mesh format.
/// \see mfem::ofgzstream() for on-the-fly compression of ascii outputs. If
/// @a comments is non-empty, it will be printed after the first line of the
/// file, and each line should begin with '#'.
virtual void Print(std::ostream &os = mfem::out,
const std::string &comments = "") const
{ Printer(os, "", comments); }
@@ -2587,7 +2537,7 @@ public:
#ifdef MFEM_USE_NETCDF
/// @brief Export a mesh to an Exodus II file.
void PrintExodusII(const std::string &fpath);
void PrintExodusII(const std::string fpath);
#endif
/** @brief Prints the mesh with boundary elements given by the boundary of
+13 -3
View File
@@ -802,11 +802,21 @@ struct BufferReader : BufferReaderBase
{
// Each "data block" is preceded by a header that is either UInt32 or
// UInt64. The rest of the data follows.
MFEM_VERIFY(sizeof(F)*n == ReadHeaderEntry(header_buf),
"AppendedData: wrong data size");
uint64_t data_size;
if (header_type == UINT32_HEADER)
{
uint32_t *data_size_32 = (uint32_t *)header_buf;
data_size = *data_size_32;
}
else
{
uint64_t *data_size_64 = (uint64_t *)header_buf;
data_size = *data_size_64;
}
MFEM_VERIFY(sizeof(F)*n == data_size, "AppendedData: wrong data size");
}
if (std::is_same_v<T, F>)
if (std::is_same<T, F>::value)
{
// Special case: no type conversions necessary, so can just memcpy
memcpy(dest, buf, sizeof(T)*n);
+27 -99
View File
@@ -9,13 +9,8 @@
// terms of the BSD-3 license. We welcome feedback and contributions, see file
// CONTRIBUTING.md for details.
#include "nurbs.hpp"
#include "point.hpp"
#include "segment.hpp"
#include "quadrilateral.hpp"
#include "hexahedron.hpp"
#include "../fem/gridfunc.hpp"
#include "mesh_headers.hpp"
#include "../fem/fem.hpp"
#include "../general/text.hpp"
#include <fstream>
@@ -38,7 +33,6 @@ KnotVector::KnotVector(istream &input)
knot.Load(input, NumOfControlPoints + Order + 1);
GetElements();
coarse = false;
}
KnotVector::KnotVector(int order, int NCP)
@@ -47,13 +41,12 @@ KnotVector::KnotVector(int order, int NCP)
NumOfControlPoints = NCP;
knot.SetSize(NumOfControlPoints + Order + 1);
NumOfElements = 0;
coarse = false;
knot = -1.;
}
KnotVector::KnotVector(int order, const Vector& intervals,
const Array<int>& continuity)
const Array<int>& continuity )
{
// NOTE: This may need to be generalized to support periodicity
// in the future.
@@ -93,7 +86,6 @@ KnotVector::KnotVector(int order, const Vector& intervals,
++NumOfElements;
}
}
coarse = false;
}
KnotVector &KnotVector::operator=(const KnotVector &kv)
@@ -151,7 +143,7 @@ void KnotVector::UniformRefinement(Vector &newknots, int rf) const
{
for (int m = 1; m < rf; ++m)
{
newknots(j) = ((1.0 - (m * h)) * knot(i)) + (m * h * knot(i+1));
newknots(j) = m * h * (knot(i) + knot(i+1));
j++;
}
}
@@ -340,7 +332,7 @@ void KnotVector::PrintFunctions(std::ostream &os, int samples) const
}
}
// Routine from "The NURBS Book" - 2nd ed - Piegl and Tiller
// Routine from "The NURBS book" - 2nd ed - Piegl and Tiller
// Algorithm A2.2 p. 70
void KnotVector::CalcShape(Vector &shape, int i, real_t xi) const
{
@@ -367,7 +359,7 @@ void KnotVector::CalcShape(Vector &shape, int i, real_t xi) const
}
}
// Routine from "The NURBS Book" - 2nd ed - Piegl and Tiller
// Routine from "The NURBS book" - 2nd ed - Piegl and Tiller
// Algorithm A2.3 p. 72
void KnotVector::CalcDShape(Vector &grad, int i, real_t xi) const
{
@@ -425,7 +417,7 @@ void KnotVector::CalcDShape(Vector &grad, int i, real_t xi) const
}
}
// Routine from "The NURBS Book" - 2nd ed - Piegl and Tiller
// Routine from "The NURBS book" - 2nd ed - Piegl and Tiller
// Algorithm A2.3 p. 72
void KnotVector::CalcDnShape(Vector &gradn, int n, int i, real_t xi) const
{
@@ -545,11 +537,11 @@ void KnotVector::FindMaxima(Array<int> &ks, Vector &xi, Vector &u) const
int i = j - d;
if (isElement(i))
{
arg1 = std::numeric_limits<real_t>::epsilon() / 2_r;
arg1 = 1e-16;
CalcShape(shape, i, arg1);
max1 = shape[d];
arg2 = 1_r - arg1;
arg2 = 1-(1e-16);
CalcShape(shape, i, arg2);
max2 = shape[d];
@@ -587,9 +579,9 @@ void KnotVector::FindMaxima(Array<int> &ks, Vector &xi, Vector &u) const
}
}
// Routine from "The NURBS Book" - 2nd ed - Piegl and Tiller
// Routine from "The NURBS book" - 2nd ed - Piegl and Tiller
// Algorithm A9.1 p. 369
void KnotVector::FindInterpolant(Array<Vector*> &x, bool reuse_inverse)
void KnotVector::FindInterpolant(Array<Vector*> &x)
{
int order = GetOrder();
int ncp = GetNCP();
@@ -597,93 +589,29 @@ void KnotVector::FindInterpolant(Array<Vector*> &x, bool reuse_inverse)
// Find interpolation points
Vector xi_args, u_args;
Array<int> i_args;
FindMaxima(i_args, xi_args, u_args);
FindMaxima(i_args,xi_args, u_args);
// Assemble collocation matrix
#ifdef MFEM_USE_LAPACK
// If using LAPACK, we use banded matrix storage (order + 1 nonzeros per row).
// Find banded structure of matrix.
int KL = 0; // Number of subdiagonals
int KU = 0; // Number of superdiagonals
Vector shape(order+1);
DenseMatrix A(ncp,ncp);
A = 0.0;
for (int i = 0; i < ncp; i++)
{
CalcShape(shape, i_args[i], xi_args[i]);
for (int p = 0; p < order+1; p++)
{
const int col = i_args[i] + p;
if (col < i)
{
KL = std::max(KL, i - col);
}
else if (i < col)
{
KU = std::max(KU, col - i);
}
A(i,i_args[i] + p) = shape[p];
}
}
const int LDAB = (2*KL) + KU + 1;
const int N = ncp;
fact_AB.SetSize(LDAB, N);
#else
// Without LAPACK, we store and invert a DenseMatrix (inefficient).
if (!reuse_inverse)
{
A_coll_inv.SetSize(ncp, ncp);
A_coll_inv = 0.0;
}
#endif
Vector shape(order+1);
if (!reuse_inverse) // Set collocation matrix entries
{
for (int i = 0; i < ncp; i++)
{
CalcShape(shape, i_args[i], xi_args[i]);
for (int p = 0; p < order+1; p++)
{
const int j = i_args[i] + p;
#ifdef MFEM_USE_LAPACK
fact_AB(KL+KU+i-j,j) = shape[p];
#else
A_coll_inv(i,j) = shape[p];
#endif
}
}
}
// Solve the system
#ifdef MFEM_USE_LAPACK
const int NRHS = x.Size();
DenseMatrix B(N, NRHS);
for (int j=0; j<NRHS; ++j)
{
for (int i=0; i<N; ++i) { B(i, j) = (*x[j])[i]; }
}
if (reuse_inverse)
{
BandedFactorizedSolve(KL, KU, fact_AB, B, false, fact_ipiv);
}
else
{
BandedSolve(KL, KU, fact_AB, B, fact_ipiv);
}
for (int j=0; j<NRHS; ++j)
{
for (int i=0; i<N; ++i) { (*x[j])[i] = B(i, j); }
}
#else
if (!reuse_inverse) { A_coll_inv.Invert(); }
// Solve problems
A.Invert();
Vector tmp;
for (int i = 0; i < x.Size(); i++)
for (int i= 0; i < x.Size(); i++)
{
tmp = *x[i];
A_coll_inv.Mult(tmp, *x[i]);
A.Mult(tmp,*x[i]);
}
#endif
}
int KnotVector::findKnotSpan(real_t u) const
@@ -1485,7 +1413,7 @@ void NURBSPatch::DegreeElevate(int t)
}
}
// Routine from "The NURBS Book" - 2nd ed - Piegl and Tiller
// Routine from "The NURBS book" - 2nd ed - Piegl and Tiller
void NURBSPatch::DegreeElevate(int dir, int t)
{
if (dir >= kv.Size() || dir < 0)
@@ -1503,8 +1431,8 @@ void NURBSPatch::DegreeElevate(int dir, int t)
KnotVector &oldkv = *kv[dir];
oldkv.GetElements();
auto *newpatch = new NURBSPatch(this, dir, oldkv.GetOrder() + t,
oldkv.GetNCP() + oldkv.GetNE()*t);
NURBSPatch *newpatch = new NURBSPatch(this, dir, oldkv.GetOrder() + t,
oldkv.GetNCP() + oldkv.GetNE()*t);
NURBSPatch &newp = *newpatch;
KnotVector &newkv = *newp.GetKV(dir);
@@ -2449,7 +2377,7 @@ NURBSExtension::NURBSExtension(Mesh *mesh_array[], int num_pieces)
}
NURBSExtension::NURBSExtension(const Mesh *patch_topology,
const Array<const NURBSPatch*> &patches_)
const Array<const NURBSPatch*> patches_)
{
// Basic topology checks
MFEM_VERIFY(patches_.Size() > 0, "Must have at least one patch");
@@ -4659,7 +4587,7 @@ void NURBSExtension::KnotInsert(Array<Vector *> &kv)
// Flip vector
int size = pkvc[d]->Size();
int ns = static_cast<int>(ceil(size/2.0));
int ns = ceil(size/2.0);
for (int j = 0; j < ns; j++)
{
real_t tmp = apb - pkvc[d]->Elem(j);
@@ -4719,7 +4647,7 @@ void NURBSExtension::KnotRemove(Array<Vector *> &kv, real_t tol)
// Flip vector
int size = pkvc[d]->Size();
int ns = static_cast<int>(ceil(size/2.0));
int ns = ceil(size/2.0);
for (int j = 0; j < ns; j++)
{
real_t tmp = apb - pkvc[d]->Elem(j);
+7 -20
View File
@@ -22,6 +22,7 @@
#include "../general/communication.hpp"
#endif
#include <iostream>
#include <set>
namespace mfem
{
@@ -54,7 +55,7 @@ protected:
public:
/// Create an empty KnotVector.
KnotVector() = default;
KnotVector() { }
/** @brief Create a KnotVector by reading data from stream @a input. Two
integers are read, for order and number of control points. */
@@ -73,7 +74,7 @@ public:
polynomial degree). Periodicity is not supported.
*/
KnotVector(int order, const Vector& intervals,
const Array<int>& continuity);
const Array<int>& continuity );
/// Copy constructor.
KnotVector(const KnotVector &kv) { (*this) = kv; }
@@ -143,13 +144,8 @@ public:
/** @brief Global curve interpolation through the points @a x (overwritten).
@a x is an array with the length of the spatial dimension containing
vectors with spatial coordinates. The control points of the interpolated
curve are returned in @a x in the same form.
The inverse of the collocation matrix, used in the interpolation, is
stored for repeated calls and used if @a reuse_inverse is true. Reuse is
valid only if this KnotVector has not changed since the initial call with
@a reuse_inverse false. */
void FindInterpolant(Array<Vector*> &x, bool reuse_inverse = false);
curve are returned in @a x in the same form. */
void FindInterpolant(Array<Vector*> &x);
/** Set @a diff, comprised of knots in @a kv not contained in this KnotVector.
@a kv must be of the same order as this KnotVector. The current
@@ -207,14 +203,6 @@ public:
/** Flag to indicate whether the KnotVector has been coarsened, which means
it is ready for non-nested refinement. */
bool coarse;
#ifdef MFEM_USE_LAPACK
// Data for reusing banded matrix factorization in FindInterpolant().
DenseMatrix fact_AB; /// Banded matrix factorization
Array<int> fact_ipiv; /// Row pivot indices
#else
DenseMatrix A_coll_inv; /// Collocation matrix inverse
#endif
};
@@ -298,7 +286,7 @@ public:
includes the weight. The array of control point coordinates stores each
point's coordinates contiguously, and points are ordered in a standard
ijk grid ordering. */
NURBSPatch(Array<const KnotVector *> &kv_, int dim_,
NURBSPatch(Array<const KnotVector *> &kv_, int dim_,
const real_t* control_points);
/// Constructor for a patch of dimension equal to the size of @a kv.
@@ -713,8 +701,7 @@ public:
NURBSExtension(Mesh *mesh_array[], int num_pieces);
NURBSExtension(const Mesh *patch_topology,
const Array<const NURBSPatch*> &patches_);
NURBSExtension(const Mesh *patch_topology, const Array<const NURBSPatch*> p);
/// Copy assignment not supported.
NURBSExtension& operator=(const NURBSExtension&) = delete;
+9 -16
View File
@@ -1590,27 +1590,21 @@ void ParMesh::DistributeAttributes(Array<int> &attr)
delete [] glb_attr_marker;
}
void ParMesh::SetAttributes(bool elem_attrs_changed, bool bdr_attrs_changed)
void ParMesh::SetAttributes()
{
// Determine the attributes occurring in local interior and boundary elements
Mesh::SetAttributes(elem_attrs_changed, bdr_attrs_changed);
Mesh::SetAttributes();
if (bdr_attrs_changed)
DistributeAttributes(bdr_attributes);
if (bdr_attributes.Size() > 0 && bdr_attributes[0] <= 0)
{
DistributeAttributes(bdr_attributes);
if (bdr_attributes.Size() > 0 && bdr_attributes[0] <= 0)
{
MFEM_WARNING("Non-positive boundary element attributes found!");
}
MFEM_WARNING("Non-positive boundary element attributes found!");
}
if (elem_attrs_changed)
DistributeAttributes(attributes);
if (attributes.Size() > 0 && attributes[0] <= 0)
{
DistributeAttributes(attributes);
if (attributes.Size() > 0 && attributes[0] <= 0)
{
MFEM_WARNING("Non-positive element attributes found!");
}
MFEM_WARNING("Non-positive element attributes found!");
}
}
@@ -3138,12 +3132,11 @@ void ParMesh::GetFaceNbrElementTransformation(
pNodes->ParFESpace()->GetFaceNbrElementVDofs(FaceNo, vdofs);
int n = vdofs.Size()/spaceDim;
pointmat.SetSize(spaceDim, n);
pNodes->FaceNbrData().HostRead();
for (int k = 0; k < spaceDim; k++)
{
for (int j = 0; j < n; j++)
{
pointmat(k,j) = AsConst(pNodes->FaceNbrData())(vdofs[n*k+j]);
pointmat(k,j) = (pNodes->FaceNbrData())(vdofs[n*k+j]);
}
}
+1 -2
View File
@@ -394,8 +394,7 @@ public:
void Finalize(bool refine = false, bool fix_orientation = false) override;
void SetAttributes(bool elem_attrs_changed = true,
bool bdr_attrs_changed = true) override;
void SetAttributes() override;
/// Checks if any rank in the mesh has boundary elements
bool HasBoundaryElements() const override;
+9 -1
View File
@@ -257,7 +257,15 @@ template <typename SubMeshT>
void AddBoundaryElements(SubMeshT &mesh,
const std::unordered_map<int,int> &lface_to_boundary_attribute)
{
const int num_codim_1 = mesh.GetNumFaces();
mesh.Dimension();
const int num_codim_1 = [&mesh]()
{
auto Dim = mesh.Dimension();
if (Dim == 1) { return mesh.GetNV(); }
else if (Dim == 2) { return mesh.GetNEdges(); }
else if (Dim == 3) { return mesh.GetNFaces(); }
else { MFEM_ABORT("Invalid dimension."); return -1; }
}();
if (mesh.Dimension() == 3)
{
+42 -44
View File
@@ -84,7 +84,7 @@ void VTKHDF::EnsureSteps()
}
hid_t VTKHDF::EnsureDataset(hid_t f, const std::string &name, hid_t type,
Dims &dims)
int ndims)
{
const char *name_c = name.c_str();
@@ -94,23 +94,20 @@ hid_t VTKHDF::EnsureDataset(hid_t f, const std::string &name, hid_t type,
if (status == 0)
{
// Dataset does not exist, create it.
const int ndims = dims.ndims;
// The dataset is allowed to grow in the first dimension, but is fixed
// in size in all other dimesions; the maximum dataset size is same as
// dims, but unlimited in first dimension.
Dims max_dims = dims;
max_dims[0] = H5S_UNLIMITED;
const hid_t fspace = H5Screate_simple(ndims, dims, max_dims);
Dims dims(ndims);
Dims maxdims(ndims, H5S_UNLIMITED);
const hid_t fspace = H5Screate_simple(ndims, dims, maxdims);
Dims chunk(ndims);
size_t chunk_size_bytes = 1024 * 1024 / 2; // 0.5 MB
const size_t t_bytes = H5Tget_size(type);
for (int i = 1; i < ndims; ++i)
{
chunk[i] = dims[i];
chunk_size_bytes /= dims[i];
chunk[i] = 16;
chunk_size_bytes /= 16;
}
chunk[0] = chunk_size_bytes / t_bytes;
for (int i = 1; i < ndims; ++i) { chunk[i] = 16; }
const hid_t dcpl = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_chunk(dcpl, ndims, chunk);
if (compression_level >= 0)
@@ -127,19 +124,7 @@ hid_t VTKHDF::EnsureDataset(hid_t f, const std::string &name, hid_t type,
else if (status > 0)
{
// Dataset exists, open it.
const hid_t d = H5Dopen2(f, name_c, H5P_DEFAULT);
// Resize the dataset, set dims to its new size.
Dims old_dims(dims.ndims);
const hid_t dspace = H5Dget_space(d);
const int ndims_dset = H5Sget_simple_extent_ndims(dspace);
MFEM_VERIFY(ndims_dset == dims.ndims, "");
H5Sget_simple_extent_dims(dspace, old_dims, NULL);
H5Sclose(dspace);
dims[0] += old_dims[0];
H5Dset_extent(d, dims);
return d;
return H5Dopen2(f, name_c, H5P_DEFAULT);
}
else
{
@@ -175,13 +160,27 @@ void VTKHDF::AppendParData(hid_t f, const std::string &name, hsize_t locsize,
hsize_t offset, Dims globsize, T *data)
{
const int ndims = globsize.ndims;
Dims dims = globsize;
const hid_t d = EnsureDataset(f, name, GetTypeID<T>(), dims);
const hid_t d = EnsureDataset(f, name, GetTypeID<T>(), ndims);
// Resize the dataset, set dims to its new size.
hsize_t old_size;
Dims dims(ndims);
{
const hid_t dspace = H5Dget_space(d);
const int ndims_dset = H5Sget_simple_extent_ndims(dspace);
MFEM_VERIFY(ndims_dset == ndims, "");
H5Sget_simple_extent_dims(dspace, dims, NULL);
H5Sclose(dspace);
old_size = dims[0];
dims[0] += globsize[0];
for (int i = 1; i < ndims; ++i) { dims[i] = globsize[i]; }
H5Dset_extent(d, dims);
}
// Write the new entry.
const hid_t dspace = H5Dget_space(d);
Dims start(ndims);
start[0] = dims[0] - globsize[0] + offset;
start[0] = old_size + offset;
Dims count(ndims);
count[0] = locsize;
for (int i = 1; i < ndims; ++i) { count[i] = globsize[i]; }
@@ -335,14 +334,14 @@ void VTKHDF::Truncate(const real_t t)
}
// Index of found time index (may be 'one-past-the-end' if not found)
const ptrdiff_t i = std::distance(tvals.begin(), it);
const int i = std::distance(tvals.begin(), it);
// Only truncate if needed
const bool truncate = it != tvals.end();
// Number of steps we are keeping
nsteps = i;
H5LTset_attribute_ulong(vtk, "Steps", "NSteps", &nsteps, 1);
H5LTset_attribute_int(vtk, "Steps", "NSteps", &nsteps, 1);
// We want to continue writing immediately after step 'i - 1'. If i = 0,
// then this is at the beginning of the file, and the offsets do not need
@@ -510,7 +509,7 @@ void VTKHDF::UpdateSteps(real_t t)
// Set the NSteps attribute
++nsteps;
H5LTset_attribute_ulong(steps, ".", "NSteps", &nsteps, 1);
H5LTset_attribute_int(steps, ".", "NSteps", &nsteps, 1);
AppendValue(steps, "Values", t);
AppendValue(steps, "PartOffsets", part_offset);
@@ -619,16 +618,16 @@ void VTKHDF::SaveMesh(const Mesh &mesh, bool high_order, int ref)
for (int i = 0; i < pmat.Width(); i++)
{
points.push_back(FP_T(pmat(0,i)));
if (pmat.Height() > 1) { points.push_back(FP_T(pmat(1,i))); }
points.push_back(pmat(0,i));
if (pmat.Height() > 1) { points.push_back(pmat(1,i)); }
else { points.push_back(0.0); }
if (pmat.Height() > 2) { points.push_back(FP_T(pmat(2,i))); }
if (pmat.Height() > 2) { points.push_back(pmat(2,i)); }
else { points.push_back(0.0); }
}
}
}
const int ne_0 = mesh.GetNE();
const hsize_t ne_0 = mesh.GetNE();
const hsize_t ne = high_order ? ne_0 : ne_ref;
AppendParData(vtk, "NumberOfPoints", 1, mpi_rank, mpi_dims, &np);
@@ -658,7 +657,7 @@ void VTKHDF::SaveMesh(const Mesh &mesh, bool high_order, int ref)
if (high_order)
{
Array<int> local_connectivity;
for (int e = 0; e < int(ne); ++e)
for (size_t e = 0; e < ne; ++e)
{
offsets[e] = off;
const Geometry::Type geom = mesh.GetElementGeometry(e);
@@ -676,7 +675,7 @@ void VTKHDF::SaveMesh(const Mesh &mesh, bool high_order, int ref)
{
int off_0 = 0;
int e_ref = 0;
for (int e = 0; e < ne_0; ++e)
for (hsize_t e = 0; e < ne_0; ++e)
{
const Geometry::Type geom = mesh.GetElementGeometry(e);
const int nv = get_nv(e);
@@ -715,13 +714,12 @@ void VTKHDF::SaveMesh(const Mesh &mesh, bool high_order, int ref)
const int *vtk_geom_map =
high_order ? VTKGeometry::HighOrderMap : VTKGeometry::Map;
int e_ref = 0;
for (int e = 0; e < ne_0; ++e)
for (hsize_t e = 0; e < ne_0; ++e)
{
const int ne_ref_e = get_ne_ref(e, ref_0);
for (int i = 0; i < ne_ref_e; ++i, ++e_ref)
const int ne_ref = get_ne_ref(e, ref_0);
for (int i = 0; i < ne_ref; ++i, ++e_ref)
{
cell_types[e_ref] = static_cast<unsigned char>(
vtk_geom_map[mesh.GetElementGeometry(e)]);
cell_types[e_ref] = vtk_geom_map[mesh.GetElementGeometry(e)];
}
}
AppendParData(vtk, "Types", ne, e_offset, Dims({ne_total}),
@@ -734,11 +732,11 @@ void VTKHDF::SaveMesh(const Mesh &mesh, bool high_order, int ref)
EnsureGroup("CellData", cell_data);
std::vector<int> attributes(ne);
hsize_t e_ref = 0;
for (int e = 0; e < ne_0; ++e)
for (hsize_t e = 0; e < ne_0; ++e)
{
const int attr = mesh.GetAttribute(e);
const int ne_ref_e = get_ne_ref(e, ref_0);
for (int i = 0; i < ne_ref_e; ++i, ++e_ref)
const int ne_ref = get_ne_ref(e, ref_0);
for (int i = 0; i < ne_ref; ++i, ++e_ref)
{
attributes[e_ref] = attr;
}
@@ -774,7 +772,7 @@ void VTKHDF::SaveGridFunction(const GridFunction &gf, const std::string &name)
{
for (int vd = 0; vd < vdim; ++vd)
{
point_values[off] = FP_T(vec_val(vd, i));
point_values[off] = vec_val(vd, i);
++off;
}
}

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