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d91d39bc00 |
@@ -168,10 +168,13 @@ 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_15.3.app"
|
||||
XCODE_PATH="/Applications/Xcode_16.4.app"
|
||||
echo "> sudo xcode-select -s ${XCODE_PATH}"
|
||||
sudo xcode-select -s ${XCODE_PATH}
|
||||
echo "> g++ -v"
|
||||
|
||||
+5
-5
@@ -22,7 +22,7 @@ include:
|
||||
# the "needs" keyword and express the DAG of jobs for more efficiency.
|
||||
# - We use setup and setup_baseline phases to download content outside of mfem
|
||||
# directory.
|
||||
# - Allocate/Release is where ruby resource are allocated/released once for all.
|
||||
# - Allocate/Release is where Dane resource are allocated/released once for all.
|
||||
# - Build and Test is where we build and MFEM for multiple toolchains.
|
||||
# - Baseline_checks gathers baseline-type test suites execution
|
||||
# - Baseline_publish, only available on master, allows to update baseline
|
||||
@@ -53,7 +53,7 @@ variables:
|
||||
AUTOTEST_COMMIT: "YES"
|
||||
|
||||
# Trigger subpipelines:
|
||||
ruby-build-and-test:
|
||||
dane-build-and-test:
|
||||
stage: sub-pipelines
|
||||
variables:
|
||||
# Explicitly pass down values that we want to be able to set when triggering
|
||||
@@ -61,10 +61,10 @@ ruby-build-and-test:
|
||||
AUTOTEST: "${AUTOTEST}"
|
||||
AUTOTEST_COMMIT: "${AUTOTEST_COMMIT}"
|
||||
trigger:
|
||||
include: .gitlab/ruby-build-and-test.yml
|
||||
include: .gitlab/dane-build-and-test.yml
|
||||
strategy: depend
|
||||
|
||||
ruby-baseline:
|
||||
dane-baseline:
|
||||
stage: sub-pipelines
|
||||
variables:
|
||||
# Explicitly pass down values that we want to be able to set when triggering
|
||||
@@ -73,7 +73,7 @@ ruby-baseline:
|
||||
AUTOTEST: "${AUTOTEST}"
|
||||
AUTOTEST_COMMIT: "${AUTOTEST_COMMIT}"
|
||||
trigger:
|
||||
include: .gitlab/ruby-baseline.yml
|
||||
include: .gitlab/dane-baseline.yml
|
||||
strategy: depend
|
||||
|
||||
lassen-build-and-test:
|
||||
|
||||
+3
-3
@@ -24,7 +24,7 @@ and `test type`.
|
||||
|
||||
Machines typically include:
|
||||
|
||||
* Ruby: 2nd Gen Intel Xeon (Cascade Lake)
|
||||
* Dane: Intel Sapphire Rapids
|
||||
* 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 ruby for example resumes to:
|
||||
spack spec to use. Adding a job on Dane for example resumes to:
|
||||
|
||||
```yaml
|
||||
<job_name>:
|
||||
variables:
|
||||
SPEC: "<spack_spec>"
|
||||
extends: .build_and_test_on_ruby
|
||||
extends: .build_and_test_on_dane
|
||||
```
|
||||
|
||||
The remaining and non trivial work is to make sure this spec is working. To
|
||||
|
||||
@@ -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 ruby, there is only one allocation shared among jobs in order to
|
||||
# On LLNL's Dane, 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 Ruby machine at LLNL
|
||||
# GitLab pipelines configurations for the Dane machine at LLNL
|
||||
variables:
|
||||
MACHINE_NAME: ruby
|
||||
MACHINE_NAME: dane
|
||||
|
||||
.on_ruby:
|
||||
.on_dane:
|
||||
tags:
|
||||
- shell
|
||||
- ruby
|
||||
- dane
|
||||
rules:
|
||||
# Don't run ruby jobs if...
|
||||
- if: '$CI_COMMIT_BRANCH =~ /_qnone/ || $ON_RUBY == "OFF"'
|
||||
# Don't run dane jobs if...
|
||||
- if: '$CI_COMMIT_BRANCH =~ /_qnone/ || $ON_DANE == "OFF"'
|
||||
when: never
|
||||
# Don't run autotest update if...
|
||||
- if: '$CI_JOB_NAME =~ /report/ && $AUTOTEST != "YES"'
|
||||
@@ -40,13 +40,14 @@ variables:
|
||||
- when: on_success
|
||||
|
||||
# Spack helped builds
|
||||
# Generic ruby build job, extending build script
|
||||
.build_and_test_on_ruby:
|
||||
extends: [.on_ruby]
|
||||
# Generic dane build job, extending build script
|
||||
.build_and_test_on_dane:
|
||||
extends: [.on_dane]
|
||||
stage: build_and_test
|
||||
script:
|
||||
# THREADS is used by 'tests/gitlab/build_and_test', run below
|
||||
- export THREADS=16
|
||||
# Dane has 224 threads/node and we run 7 separate jobs: 224=7*32
|
||||
- export THREADS=28
|
||||
- echo ${ALLOC_NAME}
|
||||
- export JOBID=$(squeue -h --name=${ALLOC_NAME} --format=%A)
|
||||
- echo ${JOBID}
|
||||
@@ -18,7 +18,7 @@
|
||||
setup_baseline:
|
||||
tags:
|
||||
- shell
|
||||
- ruby
|
||||
- dane
|
||||
stage: setup
|
||||
variables:
|
||||
GIT_STRATEGY: none
|
||||
|
||||
@@ -16,7 +16,7 @@
|
||||
setup:
|
||||
tags:
|
||||
- shell
|
||||
- ruby
|
||||
- dane
|
||||
stage: setup
|
||||
variables:
|
||||
GIT_STRATEGY: none
|
||||
|
||||
@@ -19,8 +19,8 @@ stages:
|
||||
- cleanup
|
||||
- baseline_publish
|
||||
|
||||
baselinecheck_mfem_intel_ruby:
|
||||
extends: [.on_ruby]
|
||||
baselinecheck_mfem_intel_dane:
|
||||
extends: [.on_dane]
|
||||
stage: baseline_check
|
||||
variables:
|
||||
# TPLS_DIR is used in .gitlab/scripts/baseline to provide the tpls location
|
||||
@@ -31,8 +31,8 @@ baselinecheck_mfem_intel_ruby:
|
||||
script:
|
||||
- echo ${BUILD_ROOT}
|
||||
- echo ${TPLS_DIR}
|
||||
# Used by the tests in MFEM/tests:
|
||||
- export MFEM_TEST_NP=48
|
||||
# Used by the tests in MFEM/tests, dane has 224 threads/node:
|
||||
- export MFEM_TEST_NP=192
|
||||
# The next script uses the following environment variables:
|
||||
# * BASELINE_TEST, SYS_TYPE, CI_PROJECT_DIR, ARTIFACTS_DIR,
|
||||
# * BUILD_ROOT, TPLS_DIR, MACHINE_NAME
|
||||
@@ -44,7 +44,7 @@ baselinecheck_mfem_intel_ruby:
|
||||
allow_failure: true
|
||||
|
||||
cleanup:
|
||||
extends: .on_ruby
|
||||
extends: .on_dane
|
||||
stage: cleanup
|
||||
variables:
|
||||
GIT_STRATEGY: none
|
||||
@@ -53,7 +53,7 @@ cleanup:
|
||||
- rm -rf "${BUILD_ROOT}" || true
|
||||
|
||||
report_baseline:
|
||||
extends: [.on_ruby]
|
||||
extends: [.on_dane]
|
||||
stage: baseline_report
|
||||
script:
|
||||
- echo ${MACHINE_NAME}
|
||||
@@ -113,8 +113,8 @@ report_baseline:
|
||||
exit $err
|
||||
) 9> autotest.lock
|
||||
|
||||
baselinepublish_mfem_ruby:
|
||||
extends: [.on_ruby]
|
||||
baselinepublish_mfem_dane:
|
||||
extends: [.on_dane]
|
||||
stage: baseline_publish
|
||||
rules:
|
||||
# - if: '$CI_COMMIT_BRANCH == "master" || $REBASELINE == "YES"'
|
||||
@@ -129,5 +129,5 @@ baselinepublish_mfem_ruby:
|
||||
|
||||
include:
|
||||
- local: .gitlab/configs/common.yml
|
||||
- local: .gitlab/configs/ruby-config.yml
|
||||
- local: .gitlab/configs/dane-config.yml
|
||||
- local: .gitlab/configs/setup-baseline.yml
|
||||
@@ -19,54 +19,54 @@ stages:
|
||||
allocate_resource:
|
||||
variables:
|
||||
GIT_STRATEGY: none
|
||||
extends: .on_ruby
|
||||
extends: .on_dane
|
||||
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 Ruby machine at LLNL
|
||||
# GitLab jobs for the Dane machine at LLNL
|
||||
debug_ser_gcc_10:
|
||||
variables:
|
||||
SPEC: "%gcc@10.3.1 +debug~mpi"
|
||||
extends: .build_and_test_on_ruby
|
||||
extends: .build_and_test_on_dane
|
||||
|
||||
debug_par_gcc_10:
|
||||
variables:
|
||||
SPEC: "%gcc@10.3.1 +debug+mpi"
|
||||
extends: .build_and_test_on_ruby
|
||||
extends: .build_and_test_on_dane
|
||||
|
||||
opt_ser_gcc_10:
|
||||
variables:
|
||||
SPEC: "%gcc@10.3.1 ~mpi"
|
||||
extends: .build_and_test_on_ruby
|
||||
extends: .build_and_test_on_dane
|
||||
|
||||
opt_par_gcc_10:
|
||||
variables:
|
||||
SPEC: "%gcc@10.3.1"
|
||||
extends: .build_and_test_on_ruby
|
||||
extends: .build_and_test_on_dane
|
||||
|
||||
opt_par_gcc_10_sundials:
|
||||
variables:
|
||||
SPEC: "%gcc@10.3.1 +sundials"
|
||||
extends: .build_and_test_on_ruby
|
||||
extends: .build_and_test_on_dane
|
||||
|
||||
opt_par_gcc_10_petsc:
|
||||
variables:
|
||||
SPEC: "%gcc@10.3.1 +petsc ^petsc+mumps~superlu-dist"
|
||||
extends: .build_and_test_on_ruby
|
||||
extends: .build_and_test_on_dane
|
||||
|
||||
opt_par_gcc_10_pumi:
|
||||
variables:
|
||||
SPEC: "%gcc@10.3.1 +pumi"
|
||||
extends: .build_and_test_on_ruby
|
||||
extends: .build_and_test_on_dane
|
||||
|
||||
# Release
|
||||
release_resource:
|
||||
variables:
|
||||
GIT_STRATEGY: none
|
||||
extends: .on_ruby
|
||||
extends: .on_dane
|
||||
stage: release_resource_and_report
|
||||
script:
|
||||
- echo ${ALLOC_NAME}
|
||||
@@ -78,17 +78,17 @@ release_resource:
|
||||
report_job_success:
|
||||
stage: release_resource_and_report
|
||||
extends:
|
||||
- .on_ruby
|
||||
- .on_dane
|
||||
- .report_job_success
|
||||
|
||||
report_job_failure:
|
||||
stage: release_resource_and_report
|
||||
extends:
|
||||
- .on_ruby
|
||||
- .on_dane
|
||||
- .report_job_failure
|
||||
|
||||
include:
|
||||
- local: .gitlab/configs/common.yml
|
||||
- local: .gitlab/configs/ruby-config.yml
|
||||
- local: .gitlab/configs/dane-config.yml
|
||||
- local: .gitlab/configs/setup-build-and-test.yml
|
||||
- local: .gitlab/configs/report-build-and-test.yml
|
||||
@@ -14,7 +14,7 @@
|
||||
# locals
|
||||
glob_err=${BASELINE_TEST}.err
|
||||
base=${BASELINE_TEST}-${SYS_TYPE}
|
||||
if [[ "${MACHINE_NAME}" == "ruby" ]]; then
|
||||
if [[ "${MACHINE_NAME}" == "dane" ]]; 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}" == "ruby" ]]; then
|
||||
if [[ "${MACHINE_NAME}" == "dane" ]]; then
|
||||
salloc --nodes=1 --exclusive --reservation=ci ../runtest ../../mfem "${BASELINE_TEST} ${TPLS_DIR}"
|
||||
elif [[ ${MACHINE_NAME} == "corona" ]]; then
|
||||
salloc --nodes=1 -t 60 -p pbatch ../runtest ../../mfem "${BASELINE_TEST} ${TPLS_DIR}"
|
||||
|
||||
@@ -11,7 +11,7 @@
|
||||
# terms of the BSD-3 license. We welcome feedback and contributions, see file
|
||||
# CONTRIBUTING.md for details.
|
||||
|
||||
# There will be collision between corona and ruby baselines.
|
||||
# There will be collision between corona and dane baselines.
|
||||
# Once the corresponding files have been generated, we can switch to machine
|
||||
# specific ref.
|
||||
ARTIFACT_PATH=${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/baseline-${SYS_TYPE}
|
||||
@@ -21,7 +21,7 @@ PATCH_FILE=${ARTIFACT_PATH}.patch
|
||||
FULL_FILE=${ARTIFACT_PATH}.out
|
||||
DIFF_FILE=${ARTIFACT_PATH}.diff
|
||||
|
||||
# There will be collision between corona and ruby baselines.
|
||||
# There will be collision between corona and dane baselines.
|
||||
# Once the corresponding files have been generated, we can switch to machine
|
||||
# specific ref.
|
||||
SAVED_NAME=baseline-${SYS_TYPE}.saved
|
||||
|
||||
@@ -668,6 +668,7 @@ 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).
|
||||
|
||||
@@ -23,6 +23,9 @@
|
||||
#include "_config.hpp"
|
||||
#endif
|
||||
|
||||
#include <cstdint>
|
||||
#include <climits>
|
||||
|
||||
namespace mfem
|
||||
{
|
||||
|
||||
|
||||
@@ -1275,6 +1275,22 @@ 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)
|
||||
@@ -2337,6 +2353,31 @@ 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()
|
||||
|
||||
+26
-64
@@ -266,11 +266,7 @@ void PABilinearFormExtension::SetupRestrictionOperators(const L2FaceValues m)
|
||||
|
||||
// Gather the attributes on the host from all the elements
|
||||
const Mesh &mesh = *trial_fes->GetMesh();
|
||||
elem_attributes.SetSize(mesh.GetNE());
|
||||
for (int i = 0; i < mesh.GetNE(); ++i)
|
||||
{
|
||||
elem_attributes[i] = mesh.GetAttribute(i);
|
||||
}
|
||||
elem_attributes = &mesh.GetElementAttributes();
|
||||
}
|
||||
|
||||
// Construct face restriction operators only if the bilinear form has
|
||||
@@ -329,45 +325,7 @@ void PABilinearFormExtension::SetupRestrictionOperators(const L2FaceValues m)
|
||||
bdr_face_dYdn.SetSize(bdr_face_restrict_lex->Height());
|
||||
}
|
||||
|
||||
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.");
|
||||
}
|
||||
bdr_face_attributes = &trial_fes->GetMesh()->GetBdrFaceAttributes();
|
||||
}
|
||||
}
|
||||
|
||||
@@ -429,7 +387,7 @@ void PABilinearFormExtension::AssembleDiagonal(Vector &y) const
|
||||
mfem::forall(ne, [=] MFEM_HOST_DEVICE (int e)
|
||||
{
|
||||
const int attr = d_attr[e];
|
||||
if (d_m[attr - 1] == 0)
|
||||
if (attr <= 0 || d_m[attr - 1] == 0)
|
||||
{
|
||||
for (int i = 0; i < nd; ++i)
|
||||
{
|
||||
@@ -450,7 +408,7 @@ 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);
|
||||
@@ -476,7 +434,7 @@ 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);
|
||||
}
|
||||
}
|
||||
|
||||
@@ -489,7 +447,7 @@ 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_attributes, bdr_face_Y);
|
||||
*bdr_face_attributes, bdr_face_Y);
|
||||
}
|
||||
bdr_face_restrict_lex->AddAbsMultTranspose(bdr_face_Y, y);
|
||||
}
|
||||
@@ -588,7 +546,7 @@ 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)
|
||||
{
|
||||
@@ -690,8 +648,8 @@ 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_attributes,
|
||||
false, bdr_face_Y);
|
||||
AddMultWithMarkers(*bdr_integs[i], bdr_face_X, bdr_markers[i],
|
||||
*bdr_face_attributes, false, bdr_face_Y);
|
||||
}
|
||||
for (int i = 0; i < n_bdr_face_integs; ++i)
|
||||
{
|
||||
@@ -699,12 +657,14 @@ void PABilinearFormExtension::MultInternal(const Vector &x, Vector &y,
|
||||
{
|
||||
AddMultNormalDerivativesWithMarkers(
|
||||
*bdr_face_integs[i], bdr_face_X, bdr_face_dXdn,
|
||||
bdr_face_markers[i], bdr_attributes, bdr_face_Y, bdr_face_dYdn);
|
||||
bdr_face_markers[i], *bdr_face_attributes, bdr_face_Y,
|
||||
bdr_face_dYdn);
|
||||
}
|
||||
else
|
||||
{
|
||||
AddMultWithMarkers(*bdr_face_integs[i], bdr_face_X, bdr_face_markers[i],
|
||||
bdr_attributes, false, bdr_face_Y);
|
||||
AddMultWithMarkers(*bdr_face_integs[i], bdr_face_X,
|
||||
bdr_face_markers[i], *bdr_face_attributes, false,
|
||||
bdr_face_Y);
|
||||
}
|
||||
}
|
||||
bdr_face_restrict_lex->AddMultTransposeInPlace(bdr_face_Y, y);
|
||||
@@ -727,7 +687,7 @@ 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);
|
||||
@@ -774,13 +734,14 @@ 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_attributes,
|
||||
true, bdr_face_Y);
|
||||
AddMultWithMarkers(*bdr_integs[i], bdr_face_X, bdr_markers[i],
|
||||
*bdr_face_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_attributes, true, bdr_face_Y);
|
||||
AddMultWithMarkers(*bdr_face_integs[i], bdr_face_X,
|
||||
bdr_face_markers[i], *bdr_face_attributes, true,
|
||||
bdr_face_Y);
|
||||
}
|
||||
bdr_face_restrict_lex->AddMultTransposeInPlace(bdr_face_Y, y);
|
||||
}
|
||||
@@ -804,7 +765,7 @@ static void AddWithMarkers_(
|
||||
mfem::forall(ne, [=] MFEM_HOST_DEVICE (int e)
|
||||
{
|
||||
const int attr = d_attr[e];
|
||||
if (d_m[attr - 1] == 0) { return; }
|
||||
if (attr <= 0 || d_m[attr - 1] == 0) { return; }
|
||||
for (int i = 0; i < nd; ++i)
|
||||
{
|
||||
d_y(i, e) += d_x(i, e);
|
||||
@@ -920,7 +881,8 @@ void EABilinearFormExtension::Assemble()
|
||||
{
|
||||
const int i = idx % sz;
|
||||
const int e = idx / sz;
|
||||
const real_t val = d_m[d_a[e] - 1] ? d_ea_1(i, e) : 0.0;
|
||||
const real_t val =
|
||||
d_a[e] > 0 ? (d_m[d_a[e] - 1] ? d_ea_1(i, e) : 0) : 0;
|
||||
if (add)
|
||||
{
|
||||
d_ea_2(i, e) += val;
|
||||
@@ -953,7 +915,7 @@ 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);
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -982,7 +944,7 @@ 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_attributes, add);
|
||||
*bdr_face_attributes, add);
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -1031,7 +993,7 @@ void EABilinearFormExtension::Assemble()
|
||||
ea_data_tmp,
|
||||
add);
|
||||
add_with_markers(ea_data_tmp, ea_data_bdr, nf_bdr, *markers,
|
||||
bdr_attributes, add);
|
||||
*bdr_face_attributes, add);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@@ -69,7 +69,8 @@ class PABilinearFormExtension : public BilinearFormExtension
|
||||
protected:
|
||||
const FiniteElementSpace *trial_fes, *test_fes; // Not owned
|
||||
/// Attributes of all mesh elements.
|
||||
Array<int> elem_attributes, bdr_attributes;
|
||||
const Array<int> *elem_attributes; // Not owned
|
||||
const Array<int> *bdr_face_attributes; // Not owned
|
||||
mutable Vector tmp_evec; // Work array
|
||||
mutable Vector localX, localY;
|
||||
mutable Vector int_face_X, int_face_Y;
|
||||
|
||||
@@ -21,6 +21,11 @@ using namespace std;
|
||||
namespace mfem
|
||||
{
|
||||
|
||||
void BilinearFormIntegrator::Update()
|
||||
{
|
||||
// default no-op
|
||||
}
|
||||
|
||||
void BilinearFormIntegrator::AssemblePA(const FiniteElementSpace&)
|
||||
{
|
||||
MFEM_ABORT("BilinearFormIntegrator::AssemblePA(fes)\n"
|
||||
@@ -3460,6 +3465,12 @@ 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,
|
||||
|
||||
@@ -23,6 +23,8 @@
|
||||
|
||||
namespace mfem
|
||||
{
|
||||
class QuadratureSpace;
|
||||
class FaceQuadratureSpace;
|
||||
|
||||
/// Abstract base class BilinearFormIntegrator
|
||||
class BilinearFormIntegrator : public NonlinearFormIntegrator
|
||||
@@ -44,6 +46,10 @@ 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(). */
|
||||
@@ -3311,6 +3317,7 @@ 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
|
||||
@@ -3333,6 +3340,8 @@ 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,
|
||||
|
||||
+2
-2
@@ -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, MPI_INT,
|
||||
lengths.data(), 1, MPI_INT,
|
||||
MPI_Gather(&msg_len, 1, MPITypeMap<size_t>::mpi_type,
|
||||
lengths.data(), 1, MPITypeMap<size_t>::mpi_type,
|
||||
0, MPI_COMM_WORLD);
|
||||
|
||||
if (myrank == 0)
|
||||
|
||||
@@ -139,8 +139,6 @@ 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();
|
||||
@@ -148,6 +146,17 @@ 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();
|
||||
@@ -159,8 +168,6 @@ 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);
|
||||
|
||||
@@ -59,26 +59,23 @@ 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 = static_cast<int>(std::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)
|
||||
{
|
||||
MFEM_FOREACH_THREAD(i, x, NQ)
|
||||
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)
|
||||
{
|
||||
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);
|
||||
}
|
||||
});
|
||||
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);
|
||||
});
|
||||
}
|
||||
}
|
||||
|
||||
void MassIntegrator::AssemblePABoundary(const FiniteElementSpace &fes)
|
||||
@@ -109,50 +106,22 @@ void MassIntegrator::AssemblePABoundary(const FiniteElementSpace &fes)
|
||||
CoefficientVector coeff(Q, qs, CoefficientStorage::COMPRESSED);
|
||||
|
||||
const int NE = ne;
|
||||
const int Q1D = quad1D;
|
||||
const int NQ = nq;
|
||||
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(), 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 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)
|
||||
{
|
||||
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);
|
||||
}
|
||||
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);
|
||||
});
|
||||
}
|
||||
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)
|
||||
|
||||
+10
-32
@@ -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)
|
||||
@@ -93,13 +93,14 @@ void LinearFormExtension::Assemble()
|
||||
else
|
||||
{
|
||||
// scan the attributes to set the markers to 0 or 1
|
||||
const int NBE = bdr_attributes.Size();
|
||||
const auto attr = bdr_attributes.Read();
|
||||
const int NBE = bdr_face_attributes->Size();
|
||||
const auto attr = bdr_face_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_markers[attr[e]-1] == 1;
|
||||
markers_w[e] =
|
||||
attr[e] > 0 ? (attr_markers[attr[e] - 1] == 1) : false;
|
||||
});
|
||||
}
|
||||
|
||||
@@ -125,8 +126,7 @@ void LinearFormExtension::Update()
|
||||
//markers.UseDevice(true);
|
||||
|
||||
// Gather the attributes on the host from all the elements
|
||||
attributes.SetSize(NE);
|
||||
for (int i = 0; i < NE; ++i) { attributes[i] = mesh.GetAttribute(i); }
|
||||
attributes = &mesh.GetElementAttributes();
|
||||
|
||||
elem_restrict_lex = fes.GetElementRestriction(ordering);
|
||||
MFEM_VERIFY(elem_restrict_lex, "Element restriction not available");
|
||||
@@ -136,34 +136,12 @@ void LinearFormExtension::Update()
|
||||
|
||||
if (lf->boundary_integs.Size() > 0)
|
||||
{
|
||||
const int nf_bdr = fes.GetNFbyType(FaceType::Boundary);
|
||||
bdr_face_attributes = &mesh.GetBdrFaceAttributes();
|
||||
|
||||
const int nf_bdr = bdr_face_attributes->Size();
|
||||
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,
|
||||
|
||||
@@ -25,7 +25,8 @@ class LinearForm;
|
||||
class LinearFormExtension
|
||||
{
|
||||
/// Attributes of all mesh elements.
|
||||
Array<int> attributes, bdr_attributes;
|
||||
const Array<int> *attributes; // Not owned
|
||||
const Array<int> *bdr_face_attributes; // Not owned
|
||||
|
||||
/// Temporary markers for device kernels.
|
||||
Array<int> markers, bdr_markers;
|
||||
|
||||
+10
-10
@@ -214,16 +214,16 @@ public:
|
||||
inline void QuadratureFunction::GetValues(
|
||||
int idx, Vector &values)
|
||||
{
|
||||
const int s_offset = qspace->offsets[idx];
|
||||
const int sl_size = qspace->offsets[idx+1] - s_offset;
|
||||
const int s_offset = qspace->Offset(idx);
|
||||
const int sl_size = qspace->Offset(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->offsets[idx];
|
||||
const int sl_size = qspace->offsets[idx+1] - s_offset;
|
||||
const int s_offset = qspace->Offset(idx);
|
||||
const int sl_size = qspace->Offset(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->offsets[idx] * vdim + ip_num * vdim;
|
||||
const int s_offset = qspace->Offset(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->offsets[idx] * vdim + ip_num * vdim;
|
||||
const int s_offset = qspace->Offset(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->offsets[idx];
|
||||
const int sl_size = qspace->offsets[idx+1] - s_offset;
|
||||
const int s_offset = qspace->Offset(idx);
|
||||
const int sl_size = qspace->Offset(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->offsets[idx];
|
||||
const int sl_size = qspace->offsets[idx+1] - s_offset;
|
||||
const int s_offset = qspace->Offset(idx);
|
||||
const int sl_size = qspace->Offset(idx + 1) - s_offset;
|
||||
values.SetSize(vdim, sl_size);
|
||||
values.HostWrite();
|
||||
const real_t *q = HostRead() + vdim*s_offset;
|
||||
|
||||
+77
-58
@@ -17,8 +17,9 @@ namespace mfem
|
||||
{
|
||||
|
||||
QuadratureSpaceBase::QuadratureSpaceBase(Mesh &mesh_, Geometry::Type geom,
|
||||
const IntegrationRule &ir)
|
||||
: mesh(mesh_), order(ir.GetOrder())
|
||||
const IntegrationRule &ir,
|
||||
QSpaceStorage storage)
|
||||
: mesh(mesh_), order(ir.GetOrder()), storage(storage)
|
||||
{
|
||||
for (int g = 0; g < Geometry::NumGeom; g++)
|
||||
{
|
||||
@@ -96,27 +97,37 @@ void QuadratureSpaceBase::Integrate(VectorCoefficient &coeff,
|
||||
|
||||
void QuadratureSpace::ConstructOffsets()
|
||||
{
|
||||
const int num_elem = mesh.GetNE();
|
||||
offsets.SetSize(num_elem + 1);
|
||||
int offset = 0;
|
||||
for (int i = 0; i < num_elem; i++)
|
||||
const int num_elem = ne;
|
||||
|
||||
if (storage == QSpaceStorage::COMPRESSED &&
|
||||
mesh.GetNumGeometries(mesh.Dimension()) == 1)
|
||||
{
|
||||
offsets[i] = offset;
|
||||
int geom = mesh.GetElementBaseGeometry(i);
|
||||
MFEM_ASSERT(int_rule[geom] != NULL, "Missing integration rule.");
|
||||
offset += int_rule[geom]->GetNPoints();
|
||||
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[num_elem] = size = offset;
|
||||
}
|
||||
|
||||
void QuadratureSpace::Construct()
|
||||
{
|
||||
ConstructIntRules(mesh.Dimension());
|
||||
ConstructOffsets();
|
||||
}
|
||||
|
||||
QuadratureSpace::QuadratureSpace(Mesh *mesh_, std::istream &in)
|
||||
: QuadratureSpaceBase(*mesh_)
|
||||
QuadratureSpace::QuadratureSpace(Mesh *mesh_, std::istream &in,
|
||||
QSpaceStorage storage)
|
||||
: QuadratureSpaceBase(*mesh_, 0, storage)
|
||||
{
|
||||
const char *msg = "invalid input stream";
|
||||
std::string ident;
|
||||
@@ -135,15 +146,24 @@ QuadratureSpace::QuadratureSpace(Mesh *mesh_, std::istream &in)
|
||||
return;
|
||||
}
|
||||
|
||||
Construct();
|
||||
ne = mesh.GetNE();
|
||||
ConstructIntRules(mesh.Dimension());
|
||||
}
|
||||
|
||||
QuadratureSpace::QuadratureSpace(Mesh &mesh_, const IntegrationRule &ir)
|
||||
: QuadratureSpaceBase(mesh_, mesh_.GetTypicalElementGeometry(), ir)
|
||||
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)
|
||||
{
|
||||
MFEM_VERIFY(mesh.GetNumGeometries(mesh.Dimension()) <= 1,
|
||||
"Constructor not valid for mixed meshes");
|
||||
ConstructOffsets();
|
||||
ne = mesh.GetNE();
|
||||
}
|
||||
|
||||
void QuadratureSpace::Save(std::ostream &os) const
|
||||
@@ -165,54 +185,53 @@ const Vector &QuadratureSpace::GetGeometricFactorWeights() const
|
||||
}
|
||||
|
||||
FaceQuadratureSpace::FaceQuadratureSpace(Mesh &mesh_, int order_,
|
||||
FaceType face_type_)
|
||||
: QuadratureSpaceBase(mesh_, order_),
|
||||
face_type(face_type_),
|
||||
num_faces(mesh.GetNFbyType(face_type))
|
||||
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_))
|
||||
{
|
||||
Construct();
|
||||
ne = face_indices.Size();
|
||||
ConstructIntRules(mesh.Dimension() - 1);
|
||||
}
|
||||
|
||||
FaceQuadratureSpace::FaceQuadratureSpace(Mesh &mesh_, const IntegrationRule &ir,
|
||||
FaceType face_type_)
|
||||
: QuadratureSpaceBase(mesh_, mesh_.GetTypicalFaceGeometry(), ir),
|
||||
face_type(face_type_),
|
||||
num_faces(mesh.GetNFbyType(face_type))
|
||||
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_))
|
||||
{
|
||||
MFEM_VERIFY(mesh.GetNumGeometries(mesh.Dimension() - 1) <= 1,
|
||||
"Constructor not valid for mixed meshes");
|
||||
ConstructOffsets();
|
||||
ne = face_indices.Size();
|
||||
}
|
||||
|
||||
void FaceQuadratureSpace::ConstructOffsets()
|
||||
{
|
||||
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++)
|
||||
if (storage == QSpaceStorage::COMPRESSED &&
|
||||
mesh.GetNumGeometries(mesh.Dimension() - 1) == 1)
|
||||
{
|
||||
const Mesh::FaceInformation face = mesh.GetFaceInformation(i);
|
||||
if (face.IsNonconformingCoarse() || !face.IsOfFaceType(face_type))
|
||||
{
|
||||
continue;
|
||||
}
|
||||
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++;
|
||||
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)
|
||||
{
|
||||
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();
|
||||
}
|
||||
offsets[face_indices.Size()] = size = offset;
|
||||
}
|
||||
offsets[num_faces] = size = offset;
|
||||
}
|
||||
|
||||
void FaceQuadratureSpace::Construct()
|
||||
{
|
||||
ConstructIntRules(mesh.Dimension() - 1);
|
||||
ConstructOffsets();
|
||||
}
|
||||
|
||||
int FaceQuadratureSpace::GetPermutedIndex(int idx, int iq) const
|
||||
|
||||
+80
-25
@@ -19,35 +19,49 @@
|
||||
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; ///< Total number of quadrature points.
|
||||
int size = -1; ///< Total number of quadrature points. -1 indicates
|
||||
///< offsets/size not computed yet.
|
||||
int ne; ///< Actual number of entities
|
||||
mutable Vector weights; ///< Integration weights.
|
||||
mutable long nodes_sequence = 0; ///< Nodes counter for cache invalidation.
|
||||
|
||||
/// @brief Entity quadrature point offset array, of size num_entities + 1.
|
||||
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.
|
||||
///
|
||||
/// 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)
|
||||
: mesh(mesh_), order(order_) { }
|
||||
QuadratureSpaceBase(Mesh &mesh_, int order_ = 0,
|
||||
QSpaceStorage storage = QSpaceStorage::COMPRESSED)
|
||||
: mesh(mesh_), order(order_), storage(storage)
|
||||
{}
|
||||
|
||||
/// Protected constructor. Used by derived classes.
|
||||
QuadratureSpaceBase(Mesh &mesh_, Geometry::Type geom,
|
||||
const IntegrationRule &ir);
|
||||
const IntegrationRule &ir,
|
||||
QSpaceStorage storage = QSpaceStorage::COMPRESSED);
|
||||
|
||||
/// Fill the @ref int_rule array for each geometry type using @ref order.
|
||||
void ConstructIntRules(int dim);
|
||||
@@ -58,15 +72,55 @@ 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 { return size; }
|
||||
int GetSize() const
|
||||
{
|
||||
if (size < 0)
|
||||
{
|
||||
const_cast<QuadratureSpaceBase *>(this)->ConstructOffsets();
|
||||
}
|
||||
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 offsets.Size() - 1; }
|
||||
int GetNE() const { return ne; }
|
||||
|
||||
/// Returns the mesh.
|
||||
inline Mesh *GetMesh() const { return &mesh; }
|
||||
@@ -120,19 +174,20 @@ class QuadratureSpace : public QuadratureSpaceBase
|
||||
{
|
||||
protected:
|
||||
const Vector &GetGeometricFactorWeights() const override;
|
||||
void ConstructOffsets();
|
||||
void Construct();
|
||||
void ConstructOffsets() override;
|
||||
public:
|
||||
/// Create a QuadratureSpace based on the global rules from #IntRules.
|
||||
QuadratureSpace(Mesh *mesh_, int order_)
|
||||
: QuadratureSpaceBase(*mesh_, order_) { Construct(); }
|
||||
QuadratureSpace(Mesh *mesh_, int order_,
|
||||
QSpaceStorage storage = QSpaceStorage::COMPRESSED);
|
||||
|
||||
/// @brief Create a QuadratureSpace with an IntegrationRule, valid only when
|
||||
/// the mesh has one element type.
|
||||
QuadratureSpace(Mesh &mesh_, const IntegrationRule &ir);
|
||||
QuadratureSpace(Mesh &mesh_, const IntegrationRule &ir,
|
||||
QSpaceStorage storage = QSpaceStorage::COMPRESSED);
|
||||
|
||||
/// Read a QuadratureSpace from the stream @a in.
|
||||
QuadratureSpace(Mesh *mesh_, std::istream &in);
|
||||
QuadratureSpace(Mesh *mesh_, std::istream &in,
|
||||
QSpaceStorage storage = QSpaceStorage::COMPRESSED);
|
||||
|
||||
/// Returns number of elements in the mesh.
|
||||
inline int GetNE() const { return mesh.GetNE(); }
|
||||
@@ -169,29 +224,29 @@ 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.
|
||||
Array<int> face_indices;
|
||||
const Array<int> &face_indices;
|
||||
|
||||
/// Inverse of the map @a face_indices.
|
||||
std::unordered_map<int,int> face_indices_inv;
|
||||
const std::unordered_map<int,int> &face_indices_inv;
|
||||
|
||||
const Vector &GetGeometricFactorWeights() const override;
|
||||
void ConstructOffsets();
|
||||
void Construct();
|
||||
void ConstructOffsets() override;
|
||||
|
||||
public:
|
||||
/// Create a FaceQuadratureSpace based on the global rules from #IntRules.
|
||||
FaceQuadratureSpace(Mesh &mesh_, int order_, FaceType face_type_);
|
||||
FaceQuadratureSpace(Mesh &mesh_, int order_, FaceType face_type_,
|
||||
QSpaceStorage storage = QSpaceStorage::COMPRESSED);
|
||||
|
||||
/// @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_);
|
||||
FaceType face_type_,
|
||||
QSpaceStorage storage = QSpaceStorage::COMPRESSED);
|
||||
|
||||
/// Returns number of faces in the mesh.
|
||||
inline int GetNumFaces() const { return num_faces; }
|
||||
inline int GetNumFaces() const { return face_indices.Size(); }
|
||||
|
||||
/// Returns the face type (boundary or interior).
|
||||
FaceType GetFaceType() const { return face_type; }
|
||||
|
||||
@@ -211,6 +211,9 @@ 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();
|
||||
|
||||
@@ -935,6 +938,30 @@ 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()
|
||||
{
|
||||
|
||||
@@ -347,13 +347,23 @@ 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;
|
||||
const MPI_Datatype MPITypeMap<int64_t>::mpi_type = MPI_INT64_T;
|
||||
const MPI_Datatype MPITypeMap<uint64_t>::mpi_type = MPI_UINT64_T;
|
||||
|
||||
/// \endcond DO_NOT_DOCUMENT
|
||||
|
||||
GroupCommunicator::GroupCommunicator(const GroupTopology >, Mode m)
|
||||
: gtopo(gt), mode(m)
|
||||
|
||||
@@ -607,10 +607,50 @@ 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;
|
||||
@@ -619,15 +659,6 @@ 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).
|
||||
|
||||
@@ -225,6 +225,52 @@ 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)
|
||||
@@ -454,6 +500,42 @@ 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
|
||||
|
||||
|
||||
@@ -753,6 +835,83 @@ 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)
|
||||
{
|
||||
|
||||
@@ -0,0 +1,176 @@
|
||||
// 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
|
||||
+42
-1
@@ -14,6 +14,7 @@
|
||||
#include "../general/forall.hpp"
|
||||
#include "../general/reducers.hpp"
|
||||
#include "../general/hash.hpp"
|
||||
#include "../general/scan.hpp"
|
||||
#include "vector.hpp"
|
||||
|
||||
#ifdef MFEM_USE_OPENMP
|
||||
@@ -117,7 +118,7 @@ Vector::Vector(const Vector &v)
|
||||
UseDevice(v.UseDevice());
|
||||
}
|
||||
|
||||
Vector::Vector(Vector &&v)
|
||||
Vector::Vector(Vector &&v) : Vector()
|
||||
{
|
||||
*this = std::move(v);
|
||||
}
|
||||
@@ -1252,4 +1253,44 @@ 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
|
||||
|
||||
@@ -171,6 +171,12 @@ 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); }
|
||||
@@ -621,6 +627,18 @@ 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)
|
||||
{
|
||||
|
||||
+165
-23
@@ -32,6 +32,7 @@
|
||||
#include <cstring>
|
||||
#include <ctime>
|
||||
#include <functional>
|
||||
#include <set>
|
||||
#include <numeric>
|
||||
#include <unordered_map>
|
||||
#include <unordered_set>
|
||||
@@ -921,6 +922,103 @@ 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++)
|
||||
@@ -1804,8 +1902,15 @@ 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()
|
||||
@@ -1817,36 +1922,48 @@ 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()
|
||||
void Mesh::SetAttributes(bool elem_attrs_changed, bool bdr_face_attrs_changed)
|
||||
{
|
||||
Array<int> attribs;
|
||||
if (bdr_face_attrs_changed)
|
||||
{
|
||||
bdr_face_attrs_cache.SetSize(0); // Invalidate the cache
|
||||
|
||||
attribs.SetSize(GetNBE());
|
||||
for (int i = 0; i < attribs.Size(); i++)
|
||||
{
|
||||
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!");
|
||||
// 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.SetSize(GetNE());
|
||||
for (int i = 0; i < attribs.Size(); i++)
|
||||
if (elem_attrs_changed)
|
||||
{
|
||||
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!");
|
||||
// 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!");
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@@ -4454,6 +4571,10 @@ 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()
|
||||
@@ -7721,6 +7842,12 @@ 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);
|
||||
}
|
||||
|
||||
@@ -8055,6 +8182,12 @@ 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);
|
||||
@@ -10850,6 +10983,15 @@ 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,
|
||||
|
||||
+50
-3
@@ -107,6 +107,11 @@ 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(),
|
||||
@@ -273,6 +278,13 @@ 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;
|
||||
@@ -307,6 +319,11 @@ 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;
|
||||
|
||||
@@ -1122,13 +1139,14 @@ 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 and
|
||||
/// boundary elements.
|
||||
/// @brief Determine the sets of unique attribute values in domain if @a
|
||||
/// elem_attrs_changed and boundary elements if @a bdr_face_attrs_changed.
|
||||
///
|
||||
/// 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();
|
||||
virtual void SetAttributes(bool elem_attrs_changed = true,
|
||||
bool bdr_face_attrs_changed = true);
|
||||
|
||||
/// Check (and optionally attempt to fix) the orientation of the elements
|
||||
/** @param[in] fix_it If `true`, attempt to fix the orientations of some
|
||||
@@ -2267,6 +2285,35 @@ 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
|
||||
|
||||
+14
-8
@@ -1590,21 +1590,27 @@ void ParMesh::DistributeAttributes(Array<int> &attr)
|
||||
delete [] glb_attr_marker;
|
||||
}
|
||||
|
||||
void ParMesh::SetAttributes()
|
||||
void ParMesh::SetAttributes(bool elem_attrs_changed, bool bdr_attrs_changed)
|
||||
{
|
||||
// Determine the attributes occurring in local interior and boundary elements
|
||||
Mesh::SetAttributes();
|
||||
Mesh::SetAttributes(elem_attrs_changed, bdr_attrs_changed);
|
||||
|
||||
DistributeAttributes(bdr_attributes);
|
||||
if (bdr_attributes.Size() > 0 && bdr_attributes[0] <= 0)
|
||||
if (bdr_attrs_changed)
|
||||
{
|
||||
MFEM_WARNING("Non-positive boundary element attributes found!");
|
||||
DistributeAttributes(bdr_attributes);
|
||||
if (bdr_attributes.Size() > 0 && bdr_attributes[0] <= 0)
|
||||
{
|
||||
MFEM_WARNING("Non-positive boundary element attributes found!");
|
||||
}
|
||||
}
|
||||
|
||||
DistributeAttributes(attributes);
|
||||
if (attributes.Size() > 0 && attributes[0] <= 0)
|
||||
if (elem_attrs_changed)
|
||||
{
|
||||
MFEM_WARNING("Non-positive element attributes found!");
|
||||
DistributeAttributes(attributes);
|
||||
if (attributes.Size() > 0 && attributes[0] <= 0)
|
||||
{
|
||||
MFEM_WARNING("Non-positive element attributes found!");
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
+2
-1
@@ -394,7 +394,8 @@ public:
|
||||
|
||||
void Finalize(bool refine = false, bool fix_orientation = false) override;
|
||||
|
||||
void SetAttributes() override;
|
||||
void SetAttributes(bool elem_attrs_changed = true,
|
||||
bool bdr_attrs_changed = true) override;
|
||||
|
||||
/// Checks if any rank in the mesh has boundary elements
|
||||
bool HasBoundaryElements() const override;
|
||||
|
||||
@@ -22,6 +22,7 @@ set(UNIT_TESTS_SRCS
|
||||
dfem/test_mass.cpp
|
||||
general/test_array.cpp
|
||||
general/test_reduction.cpp
|
||||
general/test_scan.cpp
|
||||
general/test_arrays_by_name.cpp
|
||||
general/test_error.cpp
|
||||
general/test_mem.cpp
|
||||
|
||||
@@ -124,3 +124,19 @@ TEST_CASE("Array stl-interactions", "[Array]")
|
||||
CHECK(x[i] == y[i]);
|
||||
}
|
||||
}
|
||||
|
||||
TEST_CASE("Array delete at indices", "[Array]")
|
||||
{
|
||||
Array<int> test({0,1,2,3,4,5,6,7,8});
|
||||
Array<int> rm_indices({0, 3,4, 6, 8});
|
||||
Array<int> result({ 1,2, 5, 7 });
|
||||
|
||||
test.DeleteAt(rm_indices);
|
||||
|
||||
REQUIRE(test.Size() == result.Size());
|
||||
|
||||
for (int i = 0; i < test.Size(); i++)
|
||||
{
|
||||
CHECK(test[i] == result[i]);
|
||||
}
|
||||
}
|
||||
|
||||
@@ -0,0 +1,102 @@
|
||||
// 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 <algorithm>
|
||||
#include <limits>
|
||||
|
||||
#include "mfem.hpp"
|
||||
#include "unit_tests.hpp"
|
||||
|
||||
// must be included after mfem.hpp
|
||||
#include "general/scan.hpp"
|
||||
|
||||
using namespace mfem;
|
||||
|
||||
TEST_CASE("Inclusive Scan", "[Scan],[GPU]")
|
||||
{
|
||||
Array<char> workspace;
|
||||
Array<int> a(10);
|
||||
|
||||
for (int use_dev = 0; use_dev < 2; ++use_dev)
|
||||
{
|
||||
CAPTURE(use_dev);
|
||||
a.HostReadWrite();
|
||||
for (int i = 0; i < a.Size(); ++i)
|
||||
{
|
||||
a[i] = i;
|
||||
}
|
||||
auto dptr = a.ReadWrite(use_dev);
|
||||
InclusiveScan(use_dev, dptr, dptr, a.Size(), workspace);
|
||||
a.HostRead();
|
||||
for (int i = 0; i < a.Size(); ++i)
|
||||
{
|
||||
int expected = (i + 1) * i / 2;
|
||||
CAPTURE(i);
|
||||
REQUIRE(a[i] == expected);
|
||||
}
|
||||
a.HostReadWrite();
|
||||
for (int i = 0; i < a.Size(); ++i)
|
||||
{
|
||||
a[i] = i + 1;
|
||||
}
|
||||
a.ReadWrite(use_dev);
|
||||
InclusiveScan(use_dev, dptr, dptr, a.Size(), workspace, std::multiplies<> {});
|
||||
a.HostRead();
|
||||
int expected = 1;
|
||||
for (int i = 0; i < a.Size(); ++i)
|
||||
{
|
||||
expected *= i + 1;
|
||||
CAPTURE(i);
|
||||
REQUIRE(a[i] == expected);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
TEST_CASE("Exclusive Scan", "[Scan],[GPU]")
|
||||
{
|
||||
Array<char> workspace;
|
||||
Array<int> a(10);
|
||||
|
||||
for (int use_dev = 0; use_dev < 2; ++use_dev)
|
||||
{
|
||||
CAPTURE(use_dev);
|
||||
a.HostReadWrite();
|
||||
for (int i = 0; i < a.Size(); ++i)
|
||||
{
|
||||
a[i] = i;
|
||||
}
|
||||
auto dptr = a.ReadWrite(use_dev);
|
||||
ExclusiveScan(use_dev, dptr, dptr, a.Size(), 5, workspace);
|
||||
a.HostRead();
|
||||
for (int i = 0; i < a.Size(); ++i)
|
||||
{
|
||||
int expected = (i + 1) * i / 2 - i + 5;
|
||||
CAPTURE(i);
|
||||
REQUIRE(a[i] == expected);
|
||||
}
|
||||
a.HostReadWrite();
|
||||
for (int i = 0; i < a.Size(); ++i)
|
||||
{
|
||||
a[i] = i + 1;
|
||||
}
|
||||
a.ReadWrite(use_dev);
|
||||
ExclusiveScan(use_dev, dptr, dptr, a.Size(), 5, workspace,
|
||||
std::multiplies<> {});
|
||||
a.HostRead();
|
||||
int expected = 5;
|
||||
for (int i = 0; i < a.Size(); ++i)
|
||||
{
|
||||
CAPTURE(i);
|
||||
REQUIRE(a[i] == expected);
|
||||
expected *= i + 1;
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -247,3 +247,21 @@ TEST_CASE("Vector Sum", "[Vector],[GPU]")
|
||||
|
||||
REQUIRE(sum_1 == MFEM_Approx(sum_2));
|
||||
}
|
||||
|
||||
TEST_CASE("Vector delete at indices", "[Vector][GPU]")
|
||||
{
|
||||
Vector test({0,1,2,3,4,5,6,7,8});
|
||||
Array<int> rm_indices({0, 3,4, 6, 8});
|
||||
Vector result({ 1,2, 5, 7 });
|
||||
|
||||
test.UseDevice(true);
|
||||
test.DeleteAt(rm_indices);
|
||||
|
||||
REQUIRE(test.Size() == result.Size());
|
||||
|
||||
test.HostReadWrite();
|
||||
for (int i = 0; i < test.Size(); i++)
|
||||
{
|
||||
CHECK(test[i] == result[i]);
|
||||
}
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user