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156a93937f |
@@ -0,0 +1,61 @@
|
||||
# Configuration for probot-stale - https://github.com/probot/stale
|
||||
|
||||
# Number of days of inactivity before an Issue or Pull Request becomes stale
|
||||
daysUntilStale: 30
|
||||
|
||||
# Number of days of inactivity before an Issue or Pull Request with the stale
|
||||
# label is closed. Set to false to disable. If disabled, issues still need to
|
||||
# be closed manually, but will remain marked as stale.
|
||||
daysUntilClose: 7
|
||||
|
||||
# Only issues or pull requests with all of these labels are check if stale.
|
||||
# Defaults to `[]` (disabled)
|
||||
onlyLabels: []
|
||||
|
||||
# Issues or Pull Requests with these labels will never be considered stale. Set
|
||||
# to `[]` to disable
|
||||
exemptLabels:
|
||||
- bug
|
||||
- WIP
|
||||
- ready-for-review
|
||||
- in-review
|
||||
- in-next
|
||||
|
||||
# Set to true to ignore issues in a project (defaults to false)
|
||||
exemptProjects: false
|
||||
|
||||
# Set to true to ignore issues in a milestone (defaults to false)
|
||||
exemptMilestones: false
|
||||
|
||||
# Set to true to ignore issues with an assignee (defaults to false)
|
||||
exemptAssignees: false
|
||||
|
||||
# Label to use when marking an issue as stale
|
||||
staleLabel: stale
|
||||
|
||||
# Comment to post when marking an issue as stale. Set to `false` to disable
|
||||
markComment: >
|
||||
:warning: This issue or PR has been automatically marked as stale because it has not
|
||||
had any activity in the last month. *If no activity occurs in the next week, it will
|
||||
be automatically closed.* Thank you for your contributions.
|
||||
|
||||
# Comment to post when closing a stale issue. Set to `false` to disable
|
||||
closeComment: false
|
||||
|
||||
# Limit the number of actions per hour, from 1-30. Default is 30
|
||||
limitPerRun: 30
|
||||
|
||||
# Limit to only `issues` or `pulls`
|
||||
# only: issues
|
||||
|
||||
# Optionally, specify configuration settings that are specific to just 'issues' or 'pulls':
|
||||
# pulls:
|
||||
# daysUntilStale: 30
|
||||
# markComment: >
|
||||
# This pull request has been automatically marked as stale because it has not had
|
||||
# recent activity. It will be closed if no further activity occurs. Thank you
|
||||
# for your contributions.
|
||||
|
||||
# issues:
|
||||
# exemptLabels:
|
||||
# - confirmed
|
||||
@@ -102,28 +102,29 @@ examples/ex25.mesh
|
||||
examples/ex25-*.gf
|
||||
examples/ex25p-*.*
|
||||
|
||||
examples/sundials/ex9
|
||||
examples/sundials/ex1[06]
|
||||
examples/sundials/ex9p
|
||||
examples/sundials/ex1[06]p
|
||||
examples/amgx/ex1
|
||||
examples/amgx/ex1p
|
||||
examples/amgx/.logamgx
|
||||
examples/amgx/refined.mesh
|
||||
examples/amgx/sol.gf
|
||||
examples/amgx/mesh.*
|
||||
examples/amgx/sol.*
|
||||
|
||||
examples/sundials/ex9.mesh
|
||||
examples/sundials/ex9-mesh.*
|
||||
examples/sundials/ex9-init.*
|
||||
examples/sundials/ex9-final.*
|
||||
examples/sundials/Example9*
|
||||
examples/sundials/deformed.*
|
||||
examples/sundials/velocity.*
|
||||
examples/sundials/elastic_energy.*
|
||||
examples/sundials/ex16.mesh
|
||||
examples/sundials/ex16-mesh.*
|
||||
examples/sundials/ex16-init.*
|
||||
examples/sundials/ex16-final.*
|
||||
examples/sundials/Example16*
|
||||
examples/gingko/ex1
|
||||
examples/gingko/refined.mesh
|
||||
examples/gingko/sol.gf
|
||||
examples/gingko/mesh.*
|
||||
examples/gingko/sol.*
|
||||
|
||||
examples/hiop/ex9
|
||||
examples/hiop/ex9p
|
||||
examples/hiop/ex9.mesh
|
||||
examples/hiop/ex9-mesh.*
|
||||
examples/hiop/ex9-init.*
|
||||
examples/hiop/ex9-final.*
|
||||
|
||||
examples/petsc/ex[1-69]p
|
||||
examples/petsc/ex1[0-1]p
|
||||
|
||||
examples/petsc/mesh.*
|
||||
examples/petsc/sol.*
|
||||
examples/petsc/sol_p.*
|
||||
@@ -141,28 +142,51 @@ examples/petsc/mode_*
|
||||
|
||||
examples/pumi/ex1
|
||||
examples/pumi/ex[126]p
|
||||
|
||||
examples/hiop/ex9.mesh
|
||||
examples/hiop/ex9-mesh.*
|
||||
examples/hiop/ex9-init.*
|
||||
examples/hiop/ex9-final.*
|
||||
|
||||
examples/pumi/refined.mesh
|
||||
examples/pumi/sol.gf
|
||||
examples/pumi/mesh.*
|
||||
examples/pumi/sol.*
|
||||
examples/pumi/displaced.mesh
|
||||
|
||||
examples/sundials/ex9
|
||||
examples/sundials/ex1[06]
|
||||
examples/sundials/ex9p
|
||||
examples/sundials/ex1[06]p
|
||||
examples/sundials/ex9.mesh
|
||||
examples/sundials/ex9-mesh.*
|
||||
examples/sundials/ex9-init.*
|
||||
examples/sundials/ex9-final.*
|
||||
examples/sundials/Example9*
|
||||
examples/sundials/deformed.*
|
||||
examples/sundials/velocity.*
|
||||
examples/sundials/elastic_energy.*
|
||||
examples/sundials/ex16.mesh
|
||||
examples/sundials/ex16-mesh.*
|
||||
examples/sundials/ex16-init.*
|
||||
examples/sundials/ex16-final.*
|
||||
examples/sundials/Example16*
|
||||
|
||||
examples/superlu/ex1p
|
||||
examples/superlu/mesh.*
|
||||
examples/superlu/sol.*
|
||||
|
||||
miniapps/adjoint/cvsRoberts_ASAi_dns
|
||||
miniapps/adjoint/adjoint_advection_diffusion
|
||||
|
||||
miniapps/electromagnetics/volta
|
||||
miniapps/electromagnetics/tesla
|
||||
miniapps/electromagnetics/maxwell
|
||||
miniapps/electromagnetics/joule
|
||||
|
||||
miniapps/electromagnetics/Volta-AMR*
|
||||
miniapps/electromagnetics/Tesla-AMR*
|
||||
miniapps/electromagnetics/Maxwell-Parallel*
|
||||
miniapps/electromagnetics/Joule_*
|
||||
|
||||
miniapps/gslib/field-diff
|
||||
miniapps/gslib/field-interp
|
||||
miniapps/gslib/findpts
|
||||
miniapps/gslib/pfindpts
|
||||
|
||||
miniapps/meshing/mobius-strip
|
||||
miniapps/meshing/klein-bottle
|
||||
miniapps/meshing/toroid
|
||||
@@ -176,7 +200,6 @@ miniapps/meshing/pmesh-optimizer
|
||||
miniapps/meshing/minimal-surface
|
||||
miniapps/meshing/pminimal-surface
|
||||
miniapps/meshing/polar-nc
|
||||
|
||||
miniapps/meshing/mobius-strip.mesh
|
||||
miniapps/meshing/klein-bottle.mesh
|
||||
miniapps/meshing/toroid-*.mesh
|
||||
@@ -190,9 +213,26 @@ miniapps/meshing/optimized*
|
||||
miniapps/meshing/perturbed*
|
||||
miniapps/meshing/polar-nc.mesh
|
||||
|
||||
miniapps/navier/navier_mms
|
||||
miniapps/navier/navier_kovasznay
|
||||
miniapps/navier/navier_kovasznay_vs
|
||||
miniapps/navier/navier_tgv
|
||||
miniapps/navier/navier_shear
|
||||
miniapps/navier/navier_3dfoc
|
||||
miniapps/navier/tgv_out*.txt
|
||||
miniapps/navier/*_output
|
||||
|
||||
miniapps/nurbs/nurbs_ex1
|
||||
miniapps/nurbs/nurbs_ex1p
|
||||
miniapps/nurbs/nurbs_ex11p
|
||||
miniapps/nurbs/refined.mesh
|
||||
miniapps/nurbs/mesh.*
|
||||
miniapps/nurbs/sol.*
|
||||
miniapps/nurbs/mode_*
|
||||
miniapps/nurbs/Example1*
|
||||
|
||||
miniapps/performance/ex1
|
||||
miniapps/performance/ex1p
|
||||
|
||||
miniapps/performance/refined.mesh
|
||||
miniapps/performance/mesh.*
|
||||
miniapps/performance/sol.*
|
||||
@@ -210,7 +250,6 @@ miniapps/toys/rubik
|
||||
miniapps/toys/snake
|
||||
miniapps/toys/lissajous
|
||||
miniapps/toys/mondrian
|
||||
|
||||
miniapps/toys/snake-init.mesh
|
||||
miniapps/toys/snake-user.mesh
|
||||
miniapps/toys/snake-joined.mesh
|
||||
@@ -225,37 +264,13 @@ miniapps/toys/lissajous.mesh
|
||||
miniapps/toys/lissajous.gf
|
||||
miniapps/toys/mondrian.mesh
|
||||
|
||||
miniapps/nurbs/nurbs_ex1
|
||||
miniapps/nurbs/nurbs_ex1p
|
||||
miniapps/nurbs/nurbs_ex11p
|
||||
miniapps/nurbs/refined.mesh
|
||||
miniapps/nurbs/mesh.*
|
||||
miniapps/nurbs/sol.*
|
||||
miniapps/nurbs/mode_*
|
||||
miniapps/nurbs/Example1*
|
||||
|
||||
miniapps/gslib/field-diff
|
||||
miniapps/gslib/field-interp
|
||||
miniapps/gslib/findpts
|
||||
miniapps/gslib/pfindpts
|
||||
|
||||
miniapps/navier/navier_mms
|
||||
miniapps/navier/navier_kovasznay
|
||||
miniapps/navier/navier_tgv
|
||||
miniapps/navier/navier_shear
|
||||
miniapps/navier/navier_3dfoc
|
||||
miniapps/navier/tgv_out*.txt
|
||||
miniapps/navier/*_output
|
||||
|
||||
miniapps/adjoint/cvsRoberts_ASAi_dns
|
||||
miniapps/adjoint/adjoint_advection_diffusion
|
||||
|
||||
# Unit test binary and outputs
|
||||
tests/unit/output_meshes
|
||||
tests/unit/unit_tests
|
||||
tests/unit/punit_tests
|
||||
tests/unit/sedov_tests_*
|
||||
tests/unit/psedov_tests_*
|
||||
tests/unit/ceed_tests
|
||||
|
||||
# Test script output
|
||||
tests/scripts/*.err
|
||||
|
||||
@@ -76,7 +76,7 @@ stages:
|
||||
- baseline_check
|
||||
- baseline_publish
|
||||
|
||||
# The setup job in setup stage don’t rely on MFEM git repo. It prepares a
|
||||
# The setup job in setup stage don't rely on MFEM git repo. It prepares a
|
||||
# pipeline-wide working directory downloading/updating external repos.
|
||||
# TODO: updating tests and tpls is not necessary anymore since pipelines are
|
||||
# now using unique directories so repo are never shared with another pipeline.
|
||||
@@ -226,7 +226,7 @@ setup:
|
||||
echo "${BASELINE_TEST}: Differences found, replacement file generated"
|
||||
cp ${_base_out} ${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/${_base_out}.txt
|
||||
fi
|
||||
# _base_diff won’t even exist if there is no difference.
|
||||
# _base_diff won't even exist if there is no difference.
|
||||
if [[ -f ${_base_diff} ]]
|
||||
then
|
||||
echo "${BASELINE_TEST}: Relevant differences (filtered diff) ..."
|
||||
|
||||
@@ -37,7 +37,7 @@ build_mfem_debug_ser_lassen:
|
||||
- mkdir -p ${BUILD_PATH}
|
||||
- cp -r ${CI_PROJECT_DIR} ${BUILD_PATH}/${CI_PROJECT_NAME}_lassen_ser_debug
|
||||
- cd ${BUILD_PATH}/${CI_PROJECT_NAME}_lassen_ser_debug
|
||||
- lalloc 1 -W 5 -q pdebug make -j cuda MFEM_DEBUG="YES" CUDA_ARCH=sm_70
|
||||
- lalloc 1 -W 5 -q pdebug make -j cuda MFEM_DEBUG="YES" CPPFLAGS=-O2 CUDA_ARCH=sm_70
|
||||
|
||||
# Sanity check
|
||||
sanitycheck_mfem_ser_lassen:
|
||||
|
||||
@@ -5,12 +5,186 @@
|
||||
| | | | | || _|| __/| | | | | |
|
||||
|_| |_| |_||_| \___||_| |_| |_|
|
||||
|
||||
http://mfem.org
|
||||
https://mfem.org
|
||||
|
||||
|
||||
Version 4.1.1 (development)
|
||||
Version 4.2.1 (development)
|
||||
===========================
|
||||
|
||||
- Added matrix-free GPU-enabled implementations of GradientInterpolator and
|
||||
IdentityInterpolator.
|
||||
|
||||
- Added interface to MUMPS direct solver. Its usage is demonstrated in ex25p.
|
||||
See http://mumps.enseeiht.fr/ for more details. Supported versions >= 5.1.1.
|
||||
|
||||
- Added three ESDIRK time integrators: implicit trapezoid rule, L-stable
|
||||
ESDIRK-32, and A-stable ESDIRK-33.
|
||||
|
||||
- Added a "scaled Jacobian" visualization option in the Mesh Explorer miniapp to
|
||||
help identify elements with poor mesh quality.
|
||||
|
||||
- Added support for the "BR2" discontinuous Galerkin discretization for
|
||||
diffusion via DGDiffusionBR2Integrator (see Example 14/14p).
|
||||
|
||||
- Generalized the Multigrid class to support non-geometric multigrid. The
|
||||
previous functionality, based on FiniteElementSpaceHierarchy, is now available
|
||||
in the derived class GeometricMultigrid.
|
||||
|
||||
- Upgraded the Catch unit test framework from version 2.13.0 to version 2.13.2.
|
||||
|
||||
- Implemented a filter method for the Navier miniapp to stabilize highly
|
||||
turbulent flows in direct numerical simulation.
|
||||
|
||||
- Added support for reading high-order Lagrange meshes in VTK format. Arbitrary-
|
||||
orders and all element types are supported. See the VTK blog for more info:
|
||||
https://blog.kitware.com/wp-content/uploads/2018/09/Source_Issue_43.pdf
|
||||
|
||||
- Added support for reading VTK meshes in XML format.
|
||||
|
||||
- Added partial assembly and device support to Example 25/25p, with diagonal
|
||||
preconditioning.
|
||||
|
||||
- Implemented a variable step-size IMEX (VSSIMEX) method for the Navier miniapp.
|
||||
|
||||
- Added new mesh quality metrics and improved the untangling capabilities of the
|
||||
TMOP-based mesh optimization algorithms.
|
||||
|
||||
- Changed the interface for the error estimator.
|
||||
|
||||
- Implemented the parallel Kelly error indicator for scalar-valued problems.
|
||||
|
||||
- Added new classes DenseSymmetricMatrix and SymmetricMatrixCoefficient for
|
||||
efficient evaluation of symmetric matrix coefficients. This replaces the now
|
||||
deprecated EvalSymmetric in MatrixCoefficient. Added DiagonalMatrixCoefficient
|
||||
for clarity, which is a typedef of VectorCoefficient.
|
||||
|
||||
- Added support for AMG preconditioners for non-symmetric systems (e.g.
|
||||
advection-dominated problems) using hypre's approximate ideal restriction
|
||||
(AIR) AMG. Requires hypre version 2.14.0 or newer. Usage is illustrated in
|
||||
example 9/9p.
|
||||
|
||||
- Implemented an adaptive linear solver tolerance option for NewtonSolver based
|
||||
on the algorithm of Eisenstat and Walker.
|
||||
|
||||
- Extending support for L2 basis functions using MapTypes VALUE and INTEGRAL in
|
||||
linear interpolators and GridFunction "GetValue" methods.
|
||||
|
||||
|
||||
Version 4.2, released on October 30, 2020
|
||||
=========================================
|
||||
|
||||
High-Performance Computing
|
||||
--------------------------
|
||||
- Added support for explicit vectorization in the high-performance templated
|
||||
code, which can now take advantage of specific classes on the following
|
||||
architectures:
|
||||
* x86 (SSE/AVX/AVX2/AVX512),
|
||||
* Power8 & Power9 (VSX),
|
||||
* BG/Q (QPX).
|
||||
These are disabled by default, but can be enabled with MFEM_USE_SIMD=YES.
|
||||
See the new file linalg/simd.hpp and the new directory linalg/simd.
|
||||
|
||||
- Added an Element Assembly mode compatible with GPU device execution for H1 and
|
||||
L2 spaces in the mass, convection, diffusion, transpose, and the face DG trace
|
||||
integrators. See option '-ea' in Example 9. When enabled, this assembly level
|
||||
stores independent dense matrices for the elements, and independent dense
|
||||
matrices for the faces in the DG case.
|
||||
|
||||
- Added a Full Assembly mode compatible with GPU device execution. This assembly
|
||||
level builds on top of the Element Assembly kernels to compute a global sparse
|
||||
matrix. All integrators supported by element assembly are also supported by
|
||||
full assembly. See the '-fa' option in Example 9.
|
||||
|
||||
- Optimized the AMD/HIP kernel support and enabled HIP support in the libCEED
|
||||
integration. This is now available via the "ceed-hip" device backend.
|
||||
|
||||
- Improved the libCEED integration to support:
|
||||
* AssemblyLevel::NONE for Mass, Diffusion, VectorMass, and VectorDiffusion
|
||||
Integrators. This level computes the full operator evaluation "on the fly".
|
||||
* VectorMassIntegrator and VectorDiffusionIntegrator.
|
||||
* All types of (scalar) Coefficients.
|
||||
|
||||
- Added partial assembly / device support for:
|
||||
* H(div) bilinear forms and VectorFEDivergenceIntegrator.
|
||||
* BlockOperator, see the updated Example 5.
|
||||
* Complex operators, see the updated Example 22.
|
||||
* Chebyshev accelerated polynomial smoother.
|
||||
* Convergent diagonal preconditioning on non-conforming adaptively refined
|
||||
meshes, see Example 6/6p.
|
||||
|
||||
- Added CUDA support for:
|
||||
* Sparse matrix-vector multiplication with cuSPARSE,
|
||||
* SUNDIALS ODE integrators, see updated SUNDIALS modification of Example 9/9p.
|
||||
|
||||
Linear and nonlinear solvers
|
||||
----------------------------
|
||||
- Added a new solver class for simple integration with NVIDIA's multigrid
|
||||
library, AmgX. The AmgX class is designed to work as a standalone solver or
|
||||
preconditioner for existing MFEM solvers. It uses MFEM's sparse matrix format
|
||||
for serial runs and the HypreParMatrix format for parallel runs. The new
|
||||
solver may be configured to run with one GPU per MPI rank or with more MPI
|
||||
ranks than GPUs. In the latter case, matrices and vectors are consolidated to
|
||||
ranks communicating with the GPUs and the solution is then broadcasted.
|
||||
|
||||
Although CUDA is required to build, the AmgX support is compatible with the
|
||||
MFEM CPU device configuration. The examples/amgx folder illustrates how to
|
||||
integrate AmgX in existing MFEM applications. The AmgX solver class is
|
||||
partially based on: "AmgXWrapper: An interface between PETSc and the NVIDIA
|
||||
AmgX library", by Pi-Yueh Chuang and Lorena A. Barba, doi:10.21105/joss.00280.
|
||||
|
||||
- Added initial support for geometric h- and p-multigrid preconditioners for
|
||||
matrix-based and matrix-free discretizations with basic GPU capability, see
|
||||
Example 26/26p.
|
||||
|
||||
- Added support for the CVODES package in SUNDIALS which provides ODE solvers
|
||||
with sensitivity analysis capabilities. See the CVODESSolver class and the new
|
||||
adjoint miniapps in the miniapps/adjoint directory.
|
||||
|
||||
- Added an interface to the MKL CPardiso solver, an MPI-parallel sparse direct
|
||||
solver developed by Intel. See Example 11p for an illustration of its usage.
|
||||
|
||||
- Added support for the SLEPc eigensolver package, https://slepc.upv.es.
|
||||
|
||||
- Upgraded SuperLU interface to use SuperLU_DIST 6.3.1. Added a simple SuperLU
|
||||
example in the new directory examples/superlu.
|
||||
|
||||
- Extended the KINSOL (SUNDIALS) nonlinear solver interface to support the
|
||||
Jacobian-free Newton-Krylov method. A usage example is shown in Example 10p.
|
||||
|
||||
- Block arrays of parallel matrices can now be merged into a single parallel
|
||||
matrix with the function HypreParMatrixFromBlocks. This could be useful for
|
||||
solving block systems with parallel direct solvers such as STRUMPACK.
|
||||
|
||||
- Added wrappers for hypre's flexible GMRES solver and the new parallel ILU
|
||||
preconditioner. The latter requires hypre version 2.19.0 or later.
|
||||
|
||||
Discretization improvements
|
||||
---------------------------
|
||||
- Extended GSLIB-FindPoints integration to support simplices and interpolation
|
||||
of functions from L2, H(div) and H(curl) spaces.
|
||||
|
||||
- Added support for computing asymptotic error estimates and convergence rates
|
||||
for the whole de Rham sequence based on the new class ConvergenceStudy and new
|
||||
member methods in GridFunction and ParGridFunction. See the rates.cpp file in
|
||||
the tests/convergence directory for sample usage.
|
||||
|
||||
- Extended the GetValue and GetVectorValue methods of GridFunction to support
|
||||
evaluation on boundary elements and, in the continuous field case, arbitrary
|
||||
mesh edges and faces. This requires passing an ElementTransformation argument.
|
||||
|
||||
- Added support for matrix-free interpolation and restriction operators between
|
||||
continuous H1 finite element spaces of different order on the same mesh or
|
||||
with the same order on uniformly refined meshes.
|
||||
|
||||
- The Coefficient classes based on a C-function pointer (FunctionCoefficient,
|
||||
VectorFunctionCoefficient and MatrixFunctionCoefficient) now use the more
|
||||
general std::function class template. This allows the classes to be backward
|
||||
compatible (i.e. they can still work with C-functions) and, in addition,
|
||||
support any "callable", e.g. lambda functions.
|
||||
|
||||
- Non-conforming meshes are now supported with block nonlinear forms. See the
|
||||
updated Example 19/19p.
|
||||
|
||||
Meshing improvements
|
||||
--------------------
|
||||
- The graph linear ordering library Gecko, previously an external dependency, is
|
||||
@@ -18,146 +192,55 @@ Meshing improvements
|
||||
always available. The interface has also been improved, see for example the
|
||||
Mesh Explorer miniapp.
|
||||
|
||||
- Improved Gmsh reader (version 2.2), which now supports both high-order and
|
||||
periodic meshes. Segments, triangles, quadrilaterals, and tetrahedra are
|
||||
supported up to order 10. Wedges and hexahedra are supported up to order 9.
|
||||
For sample periodic meshes, see the periodic*.msh files in the data directory.
|
||||
|
||||
- Added support for finite difference-based gradient and Hessian approximation
|
||||
in the TMOP mesh optimization algorithms. This improves the accuracy of the
|
||||
Hessian for r-adaptivity using discrete fields, and allows use of skewness
|
||||
and orientation based metrics.
|
||||
|
||||
- Added support for r-adaptivity with more than one discrete field. This allows
|
||||
the user to specify different discrete functions for controlling the
|
||||
size, aspect-ratio, orientation, and skew of elements in the mesh.
|
||||
- Improved Gmsh reader (version 2.2), which now supports both high-order and
|
||||
periodic meshes. Segments, triangles, quadrilaterals, and tetrahedra are
|
||||
supported up to order 10. Wedges and hexahedra are supported up to order 9.
|
||||
For sample periodic meshes, see the periodic*.msh files in the data directory.
|
||||
|
||||
- Added TMOP capability for approximate tangential mesh relaxation. Added
|
||||
support and examples for using TMOP on mixed meshes.
|
||||
|
||||
- Added complete action of the TMOP Integrator to account for the spatial
|
||||
derivatives of discrete and analytic targets.
|
||||
|
||||
- Added support for initialization of (serial) non-conforming meshes. Hanging
|
||||
- Added support for construction of (serial) non-conforming meshes. Hanging
|
||||
nodes can be marked with Mesh::AddVertexParents when building the mesh with
|
||||
the "init" constructor. The usage is demonstrated in a new meshing miniapp
|
||||
(polar-nc) which generates meshes that are non-conforming from the start.
|
||||
the "init" constructor. The usage is demonstrated in a new meshing miniapp,
|
||||
Polar NC, which generates meshes that are non-conforming from the start.
|
||||
|
||||
Performance improvements
|
||||
------------------------
|
||||
- Added support for explicit vectorization in the high-performance templated
|
||||
code, which can now take advantage of specific intrinsics classes on the
|
||||
following architectures:
|
||||
- x86 (SSE/AVX/AVX2/AVX512),
|
||||
- Power8 & Power9 (VSX),
|
||||
- BG/Q (QPX).
|
||||
These are disabled by default, and can be enabled with MFEM_USE_SIMD=YES.
|
||||
See the new file linalg/simd.hpp and the new directory linalg/simd.
|
||||
- Added support for r-adaptivity with more than one discrete field. This allows
|
||||
the user to specify different discrete functions for controlling the size,
|
||||
aspect-ratio, orientation, and skew of elements in the mesh.
|
||||
|
||||
Improved GPU capabilities
|
||||
-------------------------
|
||||
- Added support for Chebyshev accelerated polynomial smoother on GPU.
|
||||
|
||||
- Optimized AMD/HIP kernel support.
|
||||
|
||||
- Added a Full Assembly mode compatible with Device kernel execution. This
|
||||
assembly level builds on top of the current Element Assembly kernels to
|
||||
compute a global sparse matrix. All integrators supported by element assembly
|
||||
are also supported by full assembly. See the '-fa' option in Example 9.
|
||||
|
||||
- Added CUDA support for sparse matrix-vector multiplication with cuSPARSE.
|
||||
|
||||
- Added AmgX solver class for simple integration with NVIDIA's multigrid library.
|
||||
|
||||
- Added support for BlockOperator on GPU. See the updated Example 5.
|
||||
|
||||
- Added partial assembly and GPU support for complex operators, including the
|
||||
classes ComplexOperator, [Par]ComplexGridFunction, [Par]ComplexLinearForm, and
|
||||
[Par]SesquilinearForm. See the updated Example 22.
|
||||
|
||||
Discretization improvements
|
||||
---------------------------
|
||||
- Added support for matrix-free interpolation and restriction operators between
|
||||
continuous H1 finite element spaces of different order on the same mesh or
|
||||
with the same order on uniformly refined meshes.
|
||||
|
||||
- Added support for simplices in GSLIB-FindPoints.
|
||||
|
||||
- Added support for H1 and L2 element matrix assembly in the mass, convection,
|
||||
diffusion, transpose, and the face DG trace integrators. This is compatible
|
||||
with GPU device execution and is illustrated in Example 9/9p, see the option
|
||||
'-ea'. When enabled, this level of assembly stores independent dense matrices
|
||||
for the elements, and independent dense matrices for the faces in the DG case.
|
||||
|
||||
- Added new partial assembly kernels for H(div) bilinear forms, as well as
|
||||
VectorFEDivergenceIntegrator.
|
||||
|
||||
- Improved the documentation of the GridFunction GetValue and GetVectorValue
|
||||
methods. Expanded the GetValue and GetVectorValue methods which accept an
|
||||
ElementTransformation argument to support evaluation on boundary elements
|
||||
and, in the continuous field case, arbitrary mesh edges and faces.
|
||||
|
||||
- Added new coefficient and vector coefficient classes for QuadratureFunctions.
|
||||
Additionally, new LinearForm integrators were also added which make use of
|
||||
these new QuadratureFunction coefficient classes.
|
||||
|
||||
- Added support face integrals on the boundaries of NURBS meshes.
|
||||
|
||||
- Added support for interpolation of functions in L2, H(div) and H(curl)
|
||||
spaces using GSLIB-FindPoints.
|
||||
|
||||
- Added support for computing asymptotic error estimates and convergence rates
|
||||
for the whole de Rham sequence based on the new class ConvergenceStudy and new
|
||||
member methods in GridFunction and ParGridFunction. See the rates.cpp file in
|
||||
the tests/convergence directory for sample usage.
|
||||
|
||||
Linear and nonlinear solvers
|
||||
----------------------------
|
||||
- Added power method to iteratively estimate the largest eigenvalue and the
|
||||
corresponding eigenvector of an operator.
|
||||
|
||||
- Added initial support for h- and p-multigrid solvers and preconditioners for
|
||||
matrix-based and matrix-free discretizations with basic GPU capability.
|
||||
|
||||
- Added a new IterativeSolverMonitor class that allows to monitor the residual
|
||||
and solution during the solving process of an IterativeSolver after every
|
||||
iteration.
|
||||
|
||||
- Added support for the CVODES package in SUNDIALS which provides ODE
|
||||
solvers with sensitivity analysis capabilities. See the CVODESSolver
|
||||
class and the new adjoint miniapps below.
|
||||
|
||||
- Block arrays of parallel matrices can now be merged into a single parallel
|
||||
matrix with the function HypreParMatrixFromBlocks. This could be useful for
|
||||
solving block systems with parallel direct solvers such as STRUMPACK.
|
||||
|
||||
- In SLISolver, changed the residual inner product from (Br,r) to (Br,Br) so the
|
||||
solver can work with non-SPD preconditioner B.
|
||||
|
||||
- Added support for the SLEPc eigensolver package.
|
||||
|
||||
- Added partially assembled convergent diagonal preconditioner for adaptively
|
||||
refined meshes (i.e. non-conforming finite element spaces), see Example 6/6p.
|
||||
- Additional TMOP improvements:
|
||||
* Capability for approximate tangential mesh relaxation.
|
||||
* Support and examples for using TMOP on mixed meshes.
|
||||
* Complete integrator action accounting for spatial derivatives of discrete
|
||||
and analytic targets.
|
||||
|
||||
New and updated examples and miniapps
|
||||
-------------------------------------
|
||||
- Added a new example, Example 25/25p, to demonstrate the use of a Perfectly
|
||||
Matched Layer (PML) for the simulation of electromagnetic wave propagation.
|
||||
The example defines and solves several indefinite Maxwell problems.
|
||||
|
||||
- Added a new Example 26/26p to demonstrate the construction of a matrix-free
|
||||
geometric and p-multigrid preconditioner for the Laplace problem.
|
||||
|
||||
- Added a new example, Example 27/27p, to demonstrate the enforcement of various
|
||||
boundary conditions with the Laplace operator. The example shows the procedure
|
||||
for applying Dirichlet, Neumann (both homogeneous and inhomogeneous), Robin,
|
||||
and periodic boundary conditions with either H1 or DG discretizations.
|
||||
|
||||
- Added a new miniapp, Navier, that solves the time-dependent Navier-Stokes
|
||||
equations of incompressible fluid dynamics. See the miniapps/navier directory
|
||||
for more details.
|
||||
|
||||
- Added a new miniapps/adjoint directory with two miniapps demonstrating how to
|
||||
- Added 10 new example codes:
|
||||
* Example 25/25p demonstrates the use of a Perfectly Matched Layer (PML) for
|
||||
electromagnetic wave propagation (indefinite Maxwell).
|
||||
* Example 26/26p shows how to construct matrix-free geometric and p-multigrid
|
||||
preconditioner for the Laplace problem.
|
||||
* Example 27/27p demonstrates the enforcement of Dirichlet, Neumann, Robin,
|
||||
and periodic boundary conditions with either H1 or DG Laplace problems.
|
||||
* Versions of Example 1/1p in examples/amgx demonstrating the use of AmgX,
|
||||
to solve the Laplace problem with AMG preconditioning on GPUs.
|
||||
* A version of Example 11p in examples/petsc demonstrating the use of SLEPc,
|
||||
to solve the Laplace eigenproblem with shift-and-invert transformation.
|
||||
* A version of Example 1 in examples/superlu demonstrating the use of SuperLU
|
||||
to solve the Laplace problem.
|
||||
|
||||
- Added a new Field Interpolation miniapp in miniapps/gslib that demonstrates
|
||||
transfer of grid functions between different meshes using GSLIB-FindPoints.
|
||||
|
||||
- Added 2 miniapps in the new miniapps/adjoint directory demonstrating how to
|
||||
solve adjoint problems in MFEM using the CVODES package in SUNDIALS. Both of
|
||||
these miniapps require the MFEM_USE_SUNDIALS configuration option.
|
||||
* The cvsRoberts_ASAi_dns miniapp solves a backward adjoint problem for a
|
||||
@@ -165,73 +248,73 @@ New and updated examples and miniapps
|
||||
* The adjoint_advection_diffusion miniapp solves a backward adjoint problem
|
||||
for an advection diffusion PDE, evaluating adjoint quadratures in parallel.
|
||||
|
||||
- Ported Example 11p to SLEPc, to demonstrate solving the Laplace eigenvalue
|
||||
equation with the shift-and-invert spectral transformation method.
|
||||
- Added 4 additional meshing miniapps:
|
||||
* The Minimal Surface miniapp solves Plateau's problem: the Dirichlet problem
|
||||
for the minimal surface equation.
|
||||
* The Twist miniapp demonstrates how to stitch together opposite surfaces of a
|
||||
mesh to create a topologically periodic mesh.
|
||||
* The Trimmer miniapp trims away parts of a mesh based on element attributes.
|
||||
* Polar NC shows the construction of polar non-conforming meshes.
|
||||
|
||||
- Added a simple meshing miniapp, Twist, which demonstrates MFEM's strategy of
|
||||
stitching together opposite surfaces of a mesh to create a topologically
|
||||
periodic mesh.
|
||||
- Several examples and miniapps were updated to include:
|
||||
* Full and element assembly support in Example 9/9p.
|
||||
* Partial assembly with diagonal preconditioning in Examples 4/4p/5/5p/22/22p.
|
||||
* Diagonal preconditioner in Example 6/6p for partial assembly with AMR.
|
||||
* The option to plot a function in Mesh Explorer.
|
||||
* A new test problem showing a mixed bilinear form for H1, H(curl), H(div) and
|
||||
L2, with partial assembly support in Example 24/24p.
|
||||
* Weak Dirichlet boundary conditions (Nitsche) to the NURBS miniapp.
|
||||
|
||||
- Added a new meshing miniapp, Minimal Surface, which solves Plateau's problem:
|
||||
the Dirichlet problem for the minimal surface equation.
|
||||
Data management and Visualization
|
||||
---------------------------------
|
||||
- Added support for ADIOS2 for parallel I/O with ParaView visualization. See
|
||||
Examples 5, 9, 12, 16. The classes adios2stream and ADIOS2DataCollection
|
||||
provide the interface to generate ADIOS2 Binary Pack (BP4) directory datasets.
|
||||
|
||||
- Added a new meshing miniapp, Polar NC, which demonstrates the construction of
|
||||
polar non-conforming meshes.
|
||||
|
||||
- Added partial assembly support to Example 4/4p and Example 5/5p, with diagonal
|
||||
preconditioning.
|
||||
|
||||
- Added full assembly support in Example 9/9p.
|
||||
|
||||
- Added a new test problem in Example 24/24p, demonstrating a mixed bilinear
|
||||
form for H1, H(curl), H(div) and L_2, with partial assembly support.
|
||||
|
||||
- Added weak Dirichlet boundary conditions (Nitsche) to the NURBS miniapp.
|
||||
|
||||
- Added a simple mesh editing miniapp, Trimmer, which trims away portions of a
|
||||
mesh based on element attributes. Any newly exposed boundary elements are
|
||||
assigned attribute numbers related to the trimmed element attributes.
|
||||
|
||||
- Added a new miniapp (field-interp) that demonstrates transfer of grid function
|
||||
between different meshes using GSLIB-FindPoints.
|
||||
|
||||
- Added diagonal preconditioner in Example 6/6p for partial assembly with AMR.
|
||||
|
||||
- Added device support in Example 5/5p.
|
||||
|
||||
- Added partial assembly and device support to Example 22/22p, with diagonal
|
||||
preconditioning.
|
||||
|
||||
- Added the option to plot a function in Mesh Explorer.
|
||||
- Added VTU output of boundary elements and attributes and parallel VTU (PVTU)
|
||||
output of parallel meshes for visualization using ParaView.
|
||||
|
||||
Improved testing
|
||||
----------------
|
||||
- Upgraded the Catch unit test framework from version 1.6.1 to version 2.13.0.
|
||||
|
||||
- Added a GitLab pipeline that automates PR testing on supercomputing systems
|
||||
and Linux clusters at Lawrence Livermore National Lab (LLNL). This can be
|
||||
triggered only by LLNL developers, see .gitlab-ci.yml, the .gitlab directory
|
||||
and the updated CONTRIBUTING.md file.
|
||||
|
||||
- Added testing of the parallel mesh format in tests/par-mesh-format.
|
||||
- Added additional testing for convergence, the parallel mesh I/O, and for the
|
||||
libCEED integration in MFEM in the tests/ directory.
|
||||
|
||||
- Upgraded the Catch unit test framework from version 1.6.1 to version 2.13.0.
|
||||
|
||||
Miscellaneous
|
||||
-------------
|
||||
- Added support for ADIOS2 for parallel I/O with ParaView visualization. The
|
||||
classes adios2stream and ADIOS2DataCollection are introduced in mfem as the
|
||||
interfaces to generate ADIOS2 Binary Pack (BP4) directory datasets for the
|
||||
entire spatial and temporal node data. Cell centered data is accessible by
|
||||
ADIOS2 data readers (e.g. Python), but currently not yet implement as of
|
||||
ParaView v5.8.1. In addition, ADIOS2 allows for setting a user-defined number
|
||||
of data substreams/subfiles at scale. See examples 5, 9, 12, 16.
|
||||
- Renamed "Backend::DEBUG" to "Backend::DEBUG_DEVICE" to avoid conflicts,
|
||||
as DEBUG is sometimes used as a macro.
|
||||
|
||||
- Added a new IterativeSolverMonitor class that allows to monitor the residual
|
||||
and solution with an IterativeSolver after every iteration.
|
||||
|
||||
- Added power method to iteratively estimate the largest eigenvalue and the
|
||||
corresponding eigenvector of an operator.
|
||||
|
||||
- Added support for face integrals on the boundaries of NURBS meshes.
|
||||
|
||||
- In SLISolver, changed the residual inner product from (Br,r) to (Br,Br) so the
|
||||
solver can work with non-SPD preconditioner B.
|
||||
|
||||
- Added new coefficient and vector coefficient classes for QuadratureFunctions,
|
||||
with new LinearForm integrators which use them.
|
||||
|
||||
- The integration order used in the ComputeLpError and ComputeElementLpError
|
||||
methods of class GridFunction has been increased.
|
||||
|
||||
- Various other simplifications, extensions, and bugfixes in the code.
|
||||
- Change the IntegrationRule inside VectorDiffusionIntegrator to use the same
|
||||
quadrature as DiffusionIntegrator.
|
||||
|
||||
- Renamed "Backend::DEBUG" to "Backend::DEBUG_DEVICE" to avoid conflicts,
|
||||
as DEBUG is sometimes used as a macro.
|
||||
- The README.html files previously included in several source directories have
|
||||
been removed. Use the corresponding pages at mfem.org instead.
|
||||
|
||||
- Various other simplifications, extensions, and bugfixes in the code.
|
||||
|
||||
|
||||
Version 4.1, released on March 10, 2020
|
||||
@@ -563,7 +646,7 @@ Other meshing improvements
|
||||
follows precisely the paper:
|
||||
|
||||
D. Arnold, A. Mukherjee, and L. Pouly, "Locally Adapted Tetrahedral Meshes
|
||||
Using Bisection", SIAM J. Sci. Comput. 22 (2000), 431–448.
|
||||
Using Bisection", SIAM J. Sci. Comput. 22 (2000), 431-448.
|
||||
|
||||
This guarantees that the shape regularity of the elements will be preserved
|
||||
under refinement.
|
||||
@@ -708,7 +791,7 @@ Discretization improvements
|
||||
|
||||
- New specialized time integrators: symplectic integrators of orders 1-4 for
|
||||
systems of first order ODEs derived from a Hamiltonian and generalized-alpha
|
||||
ODE solver for the filtered Navier–Stokes equations with stabilization. See
|
||||
ODE solver for the filtered Navier-Stokes equations with stabilization. See
|
||||
classes SIASolver and GeneralizedAlphaSolver in linalg/ode.hpp.
|
||||
|
||||
- Inherit finite element classes from the new base class TensorBasisElement,
|
||||
@@ -1198,7 +1281,7 @@ New and improved linear solvers
|
||||
it can only be enabled along with MFEM_USE_MPI. When MFEM is configured with
|
||||
MFEM_USE_SUPERLU, one also needs to alter the version of METIS, since SuperLU
|
||||
requires ParMETIS (which comes packaged with a serial version of METIS). See
|
||||
http://http://crd-legacy.lbl.gov/~xiaoye/SuperLU for SuperLU_DIST details.
|
||||
http://crd-legacy.lbl.gov/~xiaoye/SuperLU for SuperLU_DIST details.
|
||||
|
||||
- Added a wrapper for the KLU solver in SuiteSparse see
|
||||
http://faculty.cse.tamu.edu/davis/suitesparse.html for details of KLU.
|
||||
|
||||
@@ -9,7 +9,8 @@
|
||||
# terms of the BSD-3 license. We welcome feedback and contributions, see file
|
||||
# CONTRIBUTING.md for details.
|
||||
|
||||
cmake_minimum_required(VERSION 2.8.11)
|
||||
# The variable CMAKE_CXX_STANDARD and related were introduced in CMake v3.1
|
||||
cmake_minimum_required(VERSION 3.1)
|
||||
set(USER_CONFIG "${CMAKE_CURRENT_SOURCE_DIR}/config/user.cmake" CACHE PATH
|
||||
"Path to optional user configuration file.")
|
||||
|
||||
@@ -50,7 +51,7 @@ project(mfem NONE)
|
||||
# Current version of MFEM, see also `makefile`.
|
||||
# mfem_VERSION = (string)
|
||||
# MFEM_VERSION = (int) [automatically derived from mfem_VERSION]
|
||||
set(${PROJECT_NAME}_VERSION 4.1.1)
|
||||
set(${PROJECT_NAME}_VERSION 4.2.1)
|
||||
|
||||
# Prohibit in-source build
|
||||
if (${PROJECT_SOURCE_DIR} STREQUAL ${PROJECT_BINARY_DIR})
|
||||
@@ -185,7 +186,7 @@ if (MFEM_USE_MPI)
|
||||
endif()
|
||||
endif()
|
||||
else()
|
||||
set(PKGS_NEED_MPI SUPERLU PETSC SLEPC STRUMPACK PUMI)
|
||||
set(PKGS_NEED_MPI SUPERLU MUMPS PETSC SLEPC STRUMPACK PUMI)
|
||||
foreach(PKG IN LISTS PKGS_NEED_MPI)
|
||||
if (MFEM_USE_${PKG})
|
||||
message(STATUS "Disabling package ${PKG} - requires MPI")
|
||||
@@ -240,12 +241,14 @@ endif()
|
||||
|
||||
# SUNDIALS
|
||||
if (MFEM_USE_SUNDIALS)
|
||||
if (NOT MFEM_USE_MPI)
|
||||
find_package(SUNDIALS REQUIRED NVector_Serial CVODES ARKODE KINSOL)
|
||||
else()
|
||||
find_package(SUNDIALS REQUIRED
|
||||
NVector_Serial NVector_Parallel NVector_ParHyp CVODES ARKODE KINSOL)
|
||||
set(SUNDIALS_COMPONENTS CVODES ARKODE KINSOL NVector_Serial)
|
||||
if (MFEM_USE_MPI)
|
||||
list(APPEND SUNDIALS_COMPONENTS NVector_Parallel NVector_MPIPlusX)
|
||||
endif()
|
||||
if (MFEM_USE_CUDA)
|
||||
list(APPEND SUNDIALS_COMPONENTS NVector_Cuda)
|
||||
endif()
|
||||
find_package(SUNDIALS REQUIRED ${SUNDIALS_COMPONENTS})
|
||||
endif()
|
||||
|
||||
# Mesquite
|
||||
@@ -262,6 +265,15 @@ if (MFEM_USE_SUPERLU)
|
||||
endif()
|
||||
endif()
|
||||
|
||||
# MUMPS can only be enabled in parallel
|
||||
if (MFEM_USE_MUMPS)
|
||||
if (MFEM_USE_MPI)
|
||||
find_package(MUMPS REQUIRED mumps_common pord)
|
||||
else()
|
||||
message(FATAL_ERROR " *** MUMPS requires that MPI be enabled.")
|
||||
endif()
|
||||
endif()
|
||||
|
||||
# STRUMPACK can only be enabled in parallel
|
||||
if (MFEM_USE_STRUMPACK)
|
||||
if (MFEM_USE_MPI)
|
||||
@@ -296,8 +308,7 @@ if (MFEM_USE_CEED)
|
||||
endif()
|
||||
|
||||
if (MFEM_USE_AMGX)
|
||||
include_directories(${AMGX_DIR}/include)
|
||||
link_directories(${AMGX_DIR}/lib64 -L${AMGX_DIR}/lib -Xlinker=-rpath=${CUDA_HOME}/lib64)
|
||||
find_package(AMGX REQUIRED)
|
||||
endif()
|
||||
|
||||
if (MFEM_USE_CONDUIT)
|
||||
@@ -351,6 +362,12 @@ if (MFEM_USE_ADIOS2)
|
||||
find_package(ADIOS2 REQUIRED)
|
||||
endif()
|
||||
|
||||
if (MFEM_USE_MKL_CPARDISO)
|
||||
if (MFEM_USE_MPI)
|
||||
find_package(MKL_CPARDISO REQUIRED MKL_SEQUENTIAL MKL_LP64 MKL_MPI_WRAPPER)
|
||||
endif()
|
||||
endif()
|
||||
|
||||
# MFEM_TIMER_TYPE
|
||||
if (NOT DEFINED MFEM_TIMER_TYPE)
|
||||
if (APPLE)
|
||||
@@ -375,9 +392,9 @@ endif()
|
||||
# integers, the METIS header (with 32-bit indices, as used by mfem) needs to
|
||||
# be before SuiteSparse.
|
||||
set(MFEM_TPLS MPI_CXX OPENMP BLAS LAPACK METIS HYPRE SuiteSparse SUNDIALS PETSC
|
||||
SLEPC MESQUITE SuperLUDist STRUMPACK AXOM CONDUIT Ginkgo GNUTLS GSLIB NETCDF
|
||||
SLEPC MESQUITE SuperLUDist MUMPS STRUMPACK AXOM CONDUIT Ginkgo GNUTLS GSLIB NETCDF
|
||||
MPFR PUMI HIOP POSIXCLOCKS MFEMBacktrace ZLIB OCCA CEED RAJA UMPIRE ADIOS2
|
||||
CUSPARSE AMGX)
|
||||
CUSPARSE MKL_CPARDISO AMGX)
|
||||
# Add all *_FOUND libraries in the variable TPL_LIBRARIES.
|
||||
set(TPL_LIBRARIES "")
|
||||
set(TPL_INCLUDE_DIRS "")
|
||||
|
||||
@@ -1,12 +1,12 @@
|
||||
<p align="center">
|
||||
<a href="http://mfem.org/"><img alt="mfem" src="http://mfem.org/img/logo-300.png"></a>
|
||||
<a href="https://mfem.org/"><img alt="mfem" src="https://mfem.org/img/logo-300.png"></a>
|
||||
</p>
|
||||
|
||||
<p align="center">
|
||||
<a href="https://github.com/mfem/mfem/blob/master/LICENSE"><img alt="License" src="https://img.shields.io/badge/License-BSD-brightgreen.svg"></a>
|
||||
<a href="https://travis-ci.org/mfem/mfem"><img alt="Build Status" src="https://travis-ci.org/mfem/mfem.svg?branch=master"></a>
|
||||
<a href="https://ci.appveyor.com/project/mfem/mfem"><img alt="Build Status" src="https://ci.appveyor.com/api/projects/status/19non9sqm6msi2wy?svg=true"></a>
|
||||
<a href="http://mfem.github.io/doxygen/html/index.html"><img alt="Doxygen" src="https://img.shields.io/badge/code-documented-brightgreen.svg"></a>
|
||||
<a href="https://mfem.github.io/doxygen/html/index.html"><img alt="Doxygen" src="https://img.shields.io/badge/code-documented-brightgreen.svg"></a>
|
||||
</p>
|
||||
|
||||
|
||||
@@ -26,7 +26,7 @@ request (PR) toward the `mfem:master` branch to propose your contribution. If
|
||||
you are planning significant code changes or have questions, you may want to
|
||||
open an [issue](https://github.com/mfem/mfem/issues) before issuing a PR. In
|
||||
addition to technical contributions, we are also interested in your results and
|
||||
[simulation images](http://mfem.org/gallery/), which you can share via a pull
|
||||
[simulation images](https://mfem.org/gallery/), which you can share via a pull
|
||||
request in the [mfem/web](https://github.com/mfem/web) repo.
|
||||
|
||||
See the [Quick Summary](#quick-summary) section for the main highlights of our
|
||||
@@ -51,7 +51,7 @@ back to them before issuing pull requests:
|
||||
Contributing to MFEM requires knowledge of Git and, likely, finite elements. If
|
||||
you are new to Git, see the [GitHub learning
|
||||
resources](https://help.github.com/articles/git-and-github-learning-resources/).
|
||||
To learn more about the finite element method, see our [FEM page](http://mfem.org/fem).
|
||||
To learn more about the finite element method, see our [FEM page](https://mfem.org/fem).
|
||||
|
||||
*By submitting a pull request, you are affirming the [Developer's Certificate of
|
||||
Origin](#developers-certificate-of-origin-11) at the end of this file.*
|
||||
@@ -92,21 +92,22 @@ The MFEM source code has the following structure:
|
||||
.
|
||||
├── config
|
||||
│ └── cmake
|
||||
│ └── modules
|
||||
│ └── ...
|
||||
├── data
|
||||
├── doc
|
||||
│ └── web
|
||||
│ └── examples
|
||||
├── examples
|
||||
│ ├── amgx
|
||||
│ ├── ginkgo
|
||||
│ ├── hiop
|
||||
│ ├── petsc
|
||||
│ ├── pumi
|
||||
│ └── sundials
|
||||
│ ├── sundials
|
||||
| └── superlu
|
||||
├── fem
|
||||
│ └── libceed
|
||||
├── general
|
||||
├── linalg
|
||||
│ └── simd
|
||||
├── mesh
|
||||
├── miniapps
|
||||
│ ├── adjoint
|
||||
@@ -114,15 +115,17 @@ The MFEM source code has the following structure:
|
||||
│ ├── electromagnetics
|
||||
│ ├── gslib
|
||||
│ ├── meshing
|
||||
│ ├── navier
|
||||
│ ├── nurbs
|
||||
│ ├── performance
|
||||
│ ├── tools
|
||||
│ └── toys
|
||||
└── tests
|
||||
├── convergence
|
||||
├── par-mesh-format
|
||||
├── scripts
|
||||
├── unit
|
||||
│ ├── ...
|
||||
└── ...
|
||||
└── unit
|
||||
└── ...
|
||||
```
|
||||
|
||||
#### Main directories and classes
|
||||
@@ -132,24 +135,24 @@ classes implementing the finite element, mesh and linear algebra concepts
|
||||
respectively.
|
||||
|
||||
- The main mesh classes are:
|
||||
+ [`Mesh`](http://mfem.github.io/doxygen/html/classmfem_1_1Mesh.html)
|
||||
+ [`NCMesh`](http://mfem.github.io/doxygen/html/classmfem_1_1NCMesh.html)
|
||||
+ [`Element`](http://mfem.github.io/doxygen/html/classmfem_1_1Element.html)
|
||||
+ [`ElementTransformation`](http://mfem.github.io/doxygen/html/classmfem_1_1ElementTransformation.html)
|
||||
+ [`Mesh`](https://mfem.github.io/doxygen/html/classmfem_1_1Mesh.html)
|
||||
+ [`NCMesh`](https://mfem.github.io/doxygen/html/classmfem_1_1NCMesh.html)
|
||||
+ [`Element`](https://mfem.github.io/doxygen/html/classmfem_1_1Element.html)
|
||||
+ [`ElementTransformation`](https://mfem.github.io/doxygen/html/classmfem_1_1ElementTransformation.html)
|
||||
|
||||
- The main finite element classes are:
|
||||
+ [`FiniteElement`](http://mfem.github.io/doxygen/html/classmfem_1_1FiniteElement.html)
|
||||
+ [`FiniteElementCollection`](http://mfem.github.io/doxygen/html/classmfem_1_1FiniteElement.html)
|
||||
+ [`FiniteElementSpace`](http://mfem.github.io/doxygen/html/classmfem_1_1FiniteElementSpace.html)
|
||||
+ [`GridFunction`](http://mfem.github.io/doxygen/html/classmfem_1_1GridFunction.html)
|
||||
+ [`BilinearFormIntegrator`](http://mfem.github.io/doxygen/html/classmfem_1_1BilinearFormIntegrator.html) and [`LinearFormIntegrator`](http://mfem.github.io/doxygen/html/classmfem_1_1LinearFormIntegrator.html)
|
||||
+ [`LinearForm`](http://mfem.github.io/doxygen/html/classmfem_1_1LinearFormIntegrator.html), [`BilinearForm`](http://mfem.github.io/doxygen/html/classmfem_1_1BilinearForm.html) and [`MixedBilinearForm`](http://mfem.github.io/doxygen/html/classmfem_1_1MixedBilinearForm.html)
|
||||
+ [`FiniteElement`](https://mfem.github.io/doxygen/html/classmfem_1_1FiniteElement.html)
|
||||
+ [`FiniteElementCollection`](https://mfem.github.io/doxygen/html/classmfem_1_1FiniteElement.html)
|
||||
+ [`FiniteElementSpace`](https://mfem.github.io/doxygen/html/classmfem_1_1FiniteElementSpace.html)
|
||||
+ [`GridFunction`](https://mfem.github.io/doxygen/html/classmfem_1_1GridFunction.html)
|
||||
+ [`BilinearFormIntegrator`](https://mfem.github.io/doxygen/html/classmfem_1_1BilinearFormIntegrator.html) and [`LinearFormIntegrator`](https://mfem.github.io/doxygen/html/classmfem_1_1LinearFormIntegrator.html)
|
||||
+ [`LinearForm`](https://mfem.github.io/doxygen/html/classmfem_1_1LinearFormIntegrator.html), [`BilinearForm`](https://mfem.github.io/doxygen/html/classmfem_1_1BilinearForm.html) and [`MixedBilinearForm`](https://mfem.github.io/doxygen/html/classmfem_1_1MixedBilinearForm.html)
|
||||
|
||||
- The main linear algebra classes and sources are
|
||||
+ [`Operator`](http://mfem.github.io/doxygen/html/classmfem_1_1Operator.html) and [`BilinearForm`](http://mfem.github.io/doxygen/html/classmfem_1_1BilinearForm.html)
|
||||
+ [`Vector`](http://mfem.github.io/doxygen/html/classmfem_1_1BilinearForm.html) and [`LinearForm`](http://mfem.github.io/doxygen/html/classmfem_1_1LinearForm.html)
|
||||
+ [`DenseMatrix`](http://mfem.github.io/doxygen/html/classmfem_1_1DenseMatrix.html) and [`SparseMatrix`](http://mfem.github.io/doxygen/html/classmfem_1_1SparseMatrix.html)
|
||||
+ Sparse [smoothers](http://mfem.github.io/doxygen/html/sparsesmoothers_8hpp.html) and linear [solvers](http://mfem.github.io/doxygen/html/solvers_8hpp.html)
|
||||
+ [`Operator`](https://mfem.github.io/doxygen/html/classmfem_1_1Operator.html) and [`BilinearForm`](https://mfem.github.io/doxygen/html/classmfem_1_1BilinearForm.html)
|
||||
+ [`Vector`](https://mfem.github.io/doxygen/html/classmfem_1_1BilinearForm.html) and [`LinearForm`](https://mfem.github.io/doxygen/html/classmfem_1_1LinearForm.html)
|
||||
+ [`DenseMatrix`](https://mfem.github.io/doxygen/html/classmfem_1_1DenseMatrix.html) and [`SparseMatrix`](https://mfem.github.io/doxygen/html/classmfem_1_1SparseMatrix.html)
|
||||
+ Sparse [smoothers](https://mfem.github.io/doxygen/html/sparsesmoothers_8hpp.html) and linear [solvers](https://mfem.github.io/doxygen/html/solvers_8hpp.html)
|
||||
|
||||
#### Parallel implementation
|
||||
|
||||
@@ -159,13 +162,13 @@ shared geometric entities between different tasks. The parallel source files
|
||||
have a `p` prefix, e.g. `pmesh.cpp` vs. the serial `mesh.cpp`.
|
||||
|
||||
- The main parallel classes are
|
||||
+ [`ParMesh`](http://mfem.github.io/doxygen/html/solvers_8hpp.html)
|
||||
+ [`ParNCMesh`](http://mfem.github.io/doxygen/html/classmfem_1_1ParMesh.html)
|
||||
+ [`ParFiniteElementSpace`](http://mfem.github.io/doxygen/html/classmfem_1_1ParFiniteElementSpace.html)
|
||||
+ [`ParGridFunction`](http://mfem.github.io/doxygen/html/classmfem_1_1ParGridFunction.html)
|
||||
+ [`ParBilinearForm`](http://mfem.github.io/doxygen/html/classmfem_1_1ParBilinearForm.html) and [`ParLinearForm`](http://mfem.github.io/doxygen/html/classmfem_1_1ParLinearForm.html)
|
||||
+ [`HypreParMatrix`](http://mfem.github.io/doxygen/html/classmfem_1_1HypreParMatrix.html) and [`HypreParVector`](http://mfem.github.io/doxygen/html/classmfem_1_1HypreParVector.html)
|
||||
+ [`HypreSolver`](http://mfem.github.io/doxygen/html/classmfem_1_1HypreSolver.html) and other [hypre classes](http://mfem.github.io/doxygen/html/hypre_8hpp.html)
|
||||
+ [`ParMesh`](https://mfem.github.io/doxygen/html/solvers_8hpp.html)
|
||||
+ [`ParNCMesh`](https://mfem.github.io/doxygen/html/classmfem_1_1ParMesh.html)
|
||||
+ [`ParFiniteElementSpace`](https://mfem.github.io/doxygen/html/classmfem_1_1ParFiniteElementSpace.html)
|
||||
+ [`ParGridFunction`](https://mfem.github.io/doxygen/html/classmfem_1_1ParGridFunction.html)
|
||||
+ [`ParBilinearForm`](https://mfem.github.io/doxygen/html/classmfem_1_1ParBilinearForm.html) and [`ParLinearForm`](https://mfem.github.io/doxygen/html/classmfem_1_1ParLinearForm.html)
|
||||
+ [`HypreParMatrix`](https://mfem.github.io/doxygen/html/classmfem_1_1HypreParMatrix.html) and [`HypreParVector`](https://mfem.github.io/doxygen/html/classmfem_1_1HypreParVector.html)
|
||||
+ [`HypreSolver`](https://mfem.github.io/doxygen/html/classmfem_1_1HypreSolver.html) and other [hypre classes](https://mfem.github.io/doxygen/html/hypre_8hpp.html)
|
||||
|
||||
#### GPU and general device support
|
||||
|
||||
@@ -174,10 +177,10 @@ backends (CUDA, OCCA, RAJA, OpenMP, etc.) and an internal lightweight
|
||||
device/host memory manager.
|
||||
|
||||
- The main device-relevant classes and sources are:
|
||||
+ [`Device`](http://mfem.github.io/doxygen/html/device_8hpp.html)
|
||||
+ [`MemoryManager`](http://mfem.github.io/doxygen/html/mem_manager_8hpp.html)
|
||||
+ the [`MFEM_FORALL`](http://mfem.github.io/doxygen/html/forall_8hpp.html) macro
|
||||
+ the [`cuda.hpp`](http://mfem.github.io/doxygen/html/cuda_8hpp.html) and [`occa.hpp`](http://mfem.github.io/doxygen/html/occa_8hpp.html) files
|
||||
+ [`Device`](https://mfem.github.io/doxygen/html/device_8hpp.html)
|
||||
+ [`MemoryManager`](https://mfem.github.io/doxygen/html/mem_manager_8hpp.html)
|
||||
+ the [`MFEM_FORALL`](https://mfem.github.io/doxygen/html/forall_8hpp.html) macro
|
||||
+ the [`cuda.hpp`](https://mfem.github.io/doxygen/html/cuda_8hpp.html) and [`occa.hpp`](https://mfem.github.io/doxygen/html/occa_8hpp.html) files
|
||||
|
||||
#### Utilities, building and documentation
|
||||
- The `general/` directory contains C++ classes that serve as utilities for
|
||||
@@ -186,7 +189,7 @@ device/host memory manager.
|
||||
Makefile and the CMake build options.
|
||||
- The `doc/` directory contains configuration for the Doxygen code documentation
|
||||
that can either be built locally or browsed online at
|
||||
http://mfem.github.io/doxygen/html/index.html.
|
||||
https://mfem.github.io/doxygen/html/index.html.
|
||||
|
||||
#### Examples and tests
|
||||
- `examples` and `miniapps` respectively gather simple and more fully-featured
|
||||
@@ -195,7 +198,7 @@ device/host memory manager.
|
||||
- The `tests/` directory contains a unit test suite and will later contain more
|
||||
tests that run example codes.
|
||||
|
||||
See also the [code overview](http://mfem.org/code-overview/) section on the MFEM
|
||||
See also the [code overview](https://mfem.org/code-overview/) section on the MFEM
|
||||
website.
|
||||
|
||||
## GitHub Workflow
|
||||
@@ -435,7 +438,6 @@ Before a PR can be merged, it should satisfy the following:
|
||||
- [ ] Run `make unittest` to make sure all unit tests pass.
|
||||
- [ ] Run the tests in `tests/scripts`.
|
||||
- [ ] (LLNL only) After merging:
|
||||
- [ ] Regenerate `README.html` files from companion documentation pull requests.
|
||||
- [ ] Update internal tests to include the new features.
|
||||
|
||||
### Master/Next Workflow
|
||||
@@ -508,7 +510,10 @@ MFEM uses a `master`/`next`-branch workflow as described below:
|
||||
- [ ] Check that continuous integration server configurations reflect the dependency version requirements of the new release
|
||||
- [ ] `.travis.yml`
|
||||
- [ ] `.appveyor.yml`
|
||||
- [ ] (LLNL only) Make sure all `README.html` files in the source repo are up to date.
|
||||
- [ ] Update the `CHANGELOG` to organize all release contributions
|
||||
- [ ] Review the whole source code once over
|
||||
- [ ] Ask MFEM-based applications to test the pre-release branch
|
||||
- [ ] Test on additional platforms and compilers
|
||||
- [ ] Tag the repository:
|
||||
|
||||
```
|
||||
@@ -519,14 +524,13 @@ MFEM uses a `master`/`next`-branch workflow as described below:
|
||||
- [ ] Recreate the `next` branch as described in previous section.
|
||||
- [ ] Update and push documentation to `mfem/doxygen`.
|
||||
- [ ] Update URL shortlinks:
|
||||
- [ ] Create a shortlink at [http://bit.ly/](http://bit.ly/) for the release tarball, e.g. http://mfem.github.io/releases/mfem-3.1.tgz.
|
||||
- [ ] Create a shortlink at [http://bit.ly/](http://bit.ly/) for the release tarball, e.g. https://mfem.github.io/releases/mfem-3.1.tgz.
|
||||
- [ ] (LLNL only) Add and commit the new shortlink in the `links` and `links-mfem` files of the internal `mfem/downloads` repo.
|
||||
- [ ] Add the new shortlinks to the MFEM packages in `spack`, `homebrew/science`, `VisIt`, etc.
|
||||
- [ ] Update website in `mfem/web` repo:
|
||||
- Update version and shortlinks in `src/index.md` and `src/download.md`.
|
||||
- Use [cloc-1.62.pl](http://cloc.sourceforge.net/) and `ls -lh` to estimate the SLOC and the tarball size in `src/download.md`.
|
||||
|
||||
|
||||
## LLNL Workflow
|
||||
|
||||
### Mirroring on Bitbucket
|
||||
|
||||
@@ -5,7 +5,7 @@
|
||||
| | | | | || _|| __/| | | | | |
|
||||
|_| |_| |_||_| \___||_| |_| |_|
|
||||
|
||||
http://mfem.org
|
||||
https://mfem.org
|
||||
|
||||
The MFEM library has a serial and an MPI-based parallel version, which largely
|
||||
share the same code base. The only prerequisite for building the serial version
|
||||
@@ -19,10 +19,10 @@ requires an MPI C++ compiler, as well as the following external libraries:
|
||||
http://glaros.dtc.umn.edu/gkhome/metis/metis/overview
|
||||
|
||||
The hypre dependency can be downloaded as a tarball from GitHub or from the
|
||||
project webpage https://www.llnl.gov/casc/hypre. For example, the 2.16.0 release
|
||||
project webpage https://www.llnl.gov/casc/hypre. For example, the 2.20.0 release
|
||||
of hypre is available at
|
||||
|
||||
https://github.com/hypre-space/hypre/archive/v2.16.0.tar.gz
|
||||
https://github.com/hypre-space/hypre/archive/v2.20.0.tar.gz
|
||||
|
||||
The METIS dependency can be disabled but that is not generally recommended, see
|
||||
the option MFEM_USE_METIS.
|
||||
@@ -62,7 +62,7 @@ following package managers:
|
||||
|
||||
We also recommend downloading and building the MFEM-based GLVis visualization
|
||||
tool which can be used to visualize the meshes and solution in MFEM's examples
|
||||
and miniapps. See http://glvis.org and http://mfem.org/building.
|
||||
and miniapps. See https://glvis.org and https://mfem.org/building.
|
||||
|
||||
Quick start with GNU make
|
||||
=========================
|
||||
@@ -344,24 +344,33 @@ MFEM_USE_SUPERLU = YES/NO
|
||||
SuperLURowLocMatrix a distributed CSR matrix class needed by SuperLU. When
|
||||
enabled, this option uses the SUPERLU_* library options, see below.
|
||||
|
||||
MFEM_USE_SUPERLU5 = YES/NO
|
||||
If SuperLU functionality is enabled, use the older 5.1.0 version rather than
|
||||
the more recent 6+ versions.
|
||||
|
||||
MFEM_USE_MUMPS = YES/NO
|
||||
Enable MFEM functionality based on the MUMPS library. Currently, this
|
||||
option adds the class MUMPSSolver (a parallel sparse direct solver).
|
||||
When enabled, this option uses the MUMPS_* library options, see
|
||||
below.
|
||||
|
||||
MFEM_USE_STRUMPACK = YES/NO
|
||||
Enable MFEM functionality based on the STRUMPACK sparse direct solver and
|
||||
preconditioner through the STRUMPACKSolver and STRUMPACKRowLocMatrix
|
||||
classes. When enabled, this option uses the STRUMPACK_* library options, see
|
||||
below.
|
||||
|
||||
MFEM_USE_AMGX = YES/NO
|
||||
Enable MFEM functionality based on the AMGX multigrid library from
|
||||
NVIDIA. When enabled, this options enables the user to use SparseMatrices
|
||||
and HypreParMatrices to solve linear systems using routines from the AMGX
|
||||
library.
|
||||
|
||||
MFEM_USE_GINKGO = YES/NO
|
||||
Enable MFEM functionality based on the Ginkgo library, which provides
|
||||
iterative linear solvers and preconditioners with OpenMP, CUDA backends, see
|
||||
https://github.com/ginkgo-project/ginkgo. When enabled, the user can use
|
||||
Ginkgo's solvers and preconditioners as shown in examples/ginkgo/.
|
||||
|
||||
MFEM_USE_AMGX = YES/NO
|
||||
Enable MFEM functionality based on the AmgX multigrid library from NVIDIA.
|
||||
Allows the user to use SparseMatrices and HypreParMatrices to solve linear
|
||||
systems with the routines from the AmgX library.
|
||||
|
||||
MFEM_USE_GNUTLS = YES/NO
|
||||
Enable secure socket support in class socketstream, using the auxiliary
|
||||
GnuTLS_* classes, based on the GnuTLS library. This option may be useful in
|
||||
@@ -492,6 +501,13 @@ MFEM_USE_CEED = YES/NO
|
||||
library for performant high-order operator evaluation developed by the Center
|
||||
for Efficient Exascale Discretizations in the Exascale Computing Project.
|
||||
|
||||
MFEM_USE_MKL_CPARDISO = YES/NO
|
||||
Enables the interface to MKL CPardiso: the Intel MKL Parallel Direct Sparse
|
||||
Solver for Clusters. Make sure to set the correct values for MKL_MPI_WRAPPER
|
||||
and MKL_LIBRARY_SUBDIR as shown in defaults.mk. If you configure MFEM with
|
||||
MFEM_USE_LAPACK=YES, verify that the MKL LAPACK libraries are used. The
|
||||
OpenMP capabilities are disabled at link time.
|
||||
|
||||
MFEM_BUILD_TAG = (any value)
|
||||
An optional tag to characterize the build. Exported to config/config.mk.
|
||||
Can be used to identify the MFEM build from other makefiles.
|
||||
@@ -541,15 +557,19 @@ The specific libraries and their options are:
|
||||
Beginning with MFEM v3.3, SUNDIALS v2.7.0 is supported.
|
||||
Beginning with MFEM v3.3.2, SUNDIALS v3.0.0 is also supported.
|
||||
Beginning with MFEM v4.1, only SUNDIALS v5.0.0+ is supported.
|
||||
When MFEM_USE_CUDA is enabled, only SUNDIALS v5.4.0+ is supported.
|
||||
If MFEM_USE_MPI is enabled, we expect that SUNDIALS is built with support for
|
||||
both MPI and hypre.
|
||||
If MFEM_USE_CUDA is enabled, we expect that SUNDIALS is built with support
|
||||
for CUDA.
|
||||
URL: http://computation.llnl.gov/projects/sundials/sundials-software
|
||||
Options: SUNDIALS_OPT, SUNDIALS_LIB.
|
||||
Versions: SUNDIALS >= 5.0.0.
|
||||
Versions: SUNDIALS >= 5.0.0, SUNDIALS >= 5.4.0 for CUDA support.
|
||||
|
||||
- Mesquite (optional), used when MFEM_USE_MESQUITE = YES.
|
||||
URL: http://trilinos.org/oldsite/packages/mesquite
|
||||
Options: MESQUITE_OPT, MESQUITE_LIB.
|
||||
The Mesquite support is deprecated and will be removed in the future.
|
||||
|
||||
- SuiteSparse (optional), used when MFEM_USE_SUITESPARSE = YES.
|
||||
URL: http://faculty.cse.tamu.edu/davis/suitesparse.html
|
||||
@@ -559,11 +579,17 @@ The specific libraries and their options are:
|
||||
- SuperLU_DIST (optional), used when MFEM_USE_SUPERLU = YES. Note that
|
||||
SuperLU_DIST requires ParMETIS, which includes METIS 5 in its distribution.
|
||||
Both ParMETIS and the included METIS 5 should be built and installed in the
|
||||
same location.
|
||||
same location. If using SuperLU_Dist v5, set MFEM_USE_SUPERLU5=YES.
|
||||
URL: http://crd-legacy.lbl.gov/~xiaoye/SuperLU
|
||||
Options: SUPERLU_OPT, SUPERLU_LIB.
|
||||
Versions: SuperLU_DIST >= 5.1.0.
|
||||
|
||||
- MUMPS (optional), used when MFEM_USE_MUMPS = YES. Note that MUMPS
|
||||
requires LAPACK, SCALAPACK and a reordering package such as PORD or METIS.
|
||||
URL: http://mumps.enseeiht.fr
|
||||
Options: MUMPS_OPT, MUMPS_LIB.
|
||||
Versions: MUMPS >= 5.1.1
|
||||
|
||||
- STRUMPACK (optional), used when MFEM_USE_STRUMPACK = YES. Note that STRUMPACK
|
||||
requires the PT-Scotch and Scalapack libraries as well as ParMETIS, which
|
||||
includes METIS 5 in its distribution. Starting with STRUMPACK v2.2.0, ParMETIS
|
||||
@@ -572,7 +598,7 @@ The specific libraries and their options are:
|
||||
2.0.0 or later.
|
||||
URL: http://portal.nersc.gov/project/sparse/strumpack
|
||||
Options: STRUMPACK_OPT, STRUMPACK_LIB.
|
||||
Versions: STRUMPACK >= 3.0.0, requires HYPRE < 2.16.0.
|
||||
Versions: STRUMPACK >= 3.0.0.
|
||||
|
||||
- Ginkgo (optional), used when MFEM_USE_GINKGO = YES. Note that Ginkgo needs a
|
||||
C++ compiler that supports the C++-11 standard. For additional requirements
|
||||
@@ -580,6 +606,11 @@ The specific libraries and their options are:
|
||||
URL: https://ginkgo-project.github.io
|
||||
Options: GINKGO_OPT (Not used), GINKGO_LIB.
|
||||
|
||||
- AmgX (optional), used when MFEM_USE_AMGX = YES.
|
||||
URL: https://github.com/NVIDIA/AMGX
|
||||
Options: AMGX_OPT, AMGX_LIB.
|
||||
Versions: AmgX >= 2.1, older versions may work too.
|
||||
|
||||
- GnuTLS (optional), used when MFEM_USE_GNUTLS = YES. On most Linux systems,
|
||||
GnuTLS is available as a development package, e.g. gnutls-devel. On Mac OS X,
|
||||
one can get the library through the Homebrew package manager (http://brew.sh).
|
||||
@@ -630,16 +661,18 @@ The specific libraries and their options are:
|
||||
|
||||
- ADIOS2 (optional) used when MFEM_USE_ADIOS2 = YES.
|
||||
URL: https://adios2.readthedocs.io/
|
||||
Versions: ADIOS >= 2.5.0.
|
||||
|
||||
- PUMI (optional), used when MFEM_USE_PUMI = YES.
|
||||
URL: https://scorec.rpi.edu/pumi
|
||||
https://github.com/SCOREC/core
|
||||
Options: PUMI_OPT, PUMI_LIB.
|
||||
Versions: PUMI >= 2.2.3.
|
||||
Versions: PUMI == 2.2.3.
|
||||
|
||||
- HiOp (optional), used when MFEM_USE_HIOP = YES.
|
||||
URL: https://github.com/LLNL/hiop
|
||||
Options: HIOP_OPT, HIOP_LIB.
|
||||
Versions: HIOP >= 0.1.
|
||||
|
||||
- GSLIB (optional), used when MFEM_USE_GSLIB = YES. The gslib library must be
|
||||
built prior to the MFEM build, as follows: download gslib-1.0.5, untar it at
|
||||
@@ -651,16 +684,16 @@ The specific libraries and their options are:
|
||||
Options: GSLIB_OPT, GSLIB_LIB.
|
||||
Versions: GSLIB >= 1.0.5.
|
||||
|
||||
- MKL CPardiso (optional), used when MFEM_USE_MKL_CPARDISO = YES.
|
||||
URL: https://software.intel.com/content/www/us/en/develop/tools/math-kernel-library.html
|
||||
Options: MKL_CPARDISO_OPT, MKL_CPARDISO_LIB.
|
||||
Versions: Intel MKL >= 2020.
|
||||
|
||||
- CUDA (optional), used when MFEM_USE_CUDA = YES.
|
||||
URL: https://developer.nvidia.com/cuda-toolkit
|
||||
Options: CUDA_CXX, CUDA_ARCH, CUDA_OPT, CUDA_LIB.
|
||||
Versions: CUDA >= 9.1, older versions may work too.
|
||||
|
||||
- AMGX (optional), used when MFEM_USE_AMGX = YES.
|
||||
URL: https://github.com/NVIDIA/AMGX
|
||||
Options: AMGX_OPT, AMGX_LIB.
|
||||
Versions: AMGX >= 2.1, older versions may work too.
|
||||
|
||||
- HIP (optional), used when MFEM_USE_HIP = YES.
|
||||
URL: https://rocm.github.io/ROCmInstall.html
|
||||
Options: HIP_CXX, HIP_ARCH, HIP_OPT, HIP_LIB.
|
||||
@@ -668,19 +701,19 @@ The specific libraries and their options are:
|
||||
- OCCA (optional), used when MFEM_USE_OCCA = YES.
|
||||
URL: https://libocca.org
|
||||
Options: OCCA_DIR, OCCA_OPT, OCCA_LIB.
|
||||
Versions: OCCA >= 1.0.9.
|
||||
Versions: OCCA >= 1.1.0.
|
||||
|
||||
- libCEED (optional), used when MFEM_USE_CEED = YES.
|
||||
URL: https://github.com/CEED/libCEED
|
||||
https://ceed.exascaleproject.org/libceed
|
||||
Options: CEED_DIR, CEED_OPT, CEED_LIB.
|
||||
Versions: libCEED > 0.6, git-hash bdfed75.
|
||||
Versions: libCEED >= 0.7.
|
||||
|
||||
- RAJA (optional), used when MFEM_USE_RAJA = YES.
|
||||
Beginning with MFEM v4.1, only RAJA v0.10.0+ is supported.
|
||||
Beginning with MFEM v4.3, only RAJA v0.13.0+ is supported.
|
||||
URL: https://github.com/LLNL/RAJA
|
||||
Options: RAJA_DIR, RAJA_OPT, RAJA_LIB.
|
||||
Versions: RAJA >= 0.10.0.
|
||||
Versions: RAJA >= 0.13.0.
|
||||
|
||||
- Umpire, used when MFEM_USE_UMPIRE = YES.
|
||||
URL: https://github.com/LLNL/Umpire
|
||||
@@ -816,9 +849,10 @@ MFEM_TIMER_TYPE - Set automatically, can be overwritten.
|
||||
MFEM_USE_MESQUITE
|
||||
MFEM_USE_SUITESPARSE
|
||||
MFEM_USE_SUPERLU
|
||||
MFEM_USE_MUMPS
|
||||
MFEM_USE_STRUMPACK
|
||||
MFEM_USE_AMGX
|
||||
MFEM_USE_GINKGO
|
||||
MFEM_USE_AMGX
|
||||
MFEM_USE_GNUTLS
|
||||
MFEM_USE_NETCDF
|
||||
MFEM_USE_MPFR
|
||||
@@ -867,11 +901,12 @@ The CMake build system adds auto-detection for the following packages/libraries:
|
||||
|
||||
- HYPRE
|
||||
- METIS - The option MFEM_USE_METIS_5 is auto-detected.
|
||||
- ParMETIS
|
||||
- MESQUITE
|
||||
- SuiteSparse
|
||||
- SuperLUDist, STRUMPACK
|
||||
- ParMETIS
|
||||
- Ginkgo
|
||||
- AMGX
|
||||
- GNUTLS - Extends the built-in CMake support, to search GNUTLS_DIR as well.
|
||||
- NETCDF
|
||||
- MPFR
|
||||
|
||||
@@ -25,7 +25,9 @@ This project distributes the sources of several external software products with
|
||||
their own respective licenses which can be found in their code and attached
|
||||
license files. These software products and their licenses are as follows:
|
||||
|
||||
* AmgXWrapper (linalg/amgxsolver.{hpp,cpp}) -- MIT license
|
||||
* Catch++ (tests/unit/catch.hpp) -- Boost 1.0 license
|
||||
* Gecko (general/gecko.{cpp,hpp}) -- BSD 3-clause license
|
||||
* Picojson (fem/picojson.h) -- Custom 2-clause license
|
||||
* Catch++ (tests/unit/catch.hpp) -- Boost 1.0 license
|
||||
* TinyXML2 (general/tinyxml2.{cpp,h}) -- zlib license
|
||||
* Zstr (general/zstr.hpp) -- MIT license
|
||||
|
||||
@@ -5,7 +5,7 @@
|
||||
| | | | | || _|| __/| | | | | |
|
||||
|_| |_| |_||_| \___||_| |_| |_|
|
||||
|
||||
http://mfem.org
|
||||
https://mfem.org
|
||||
|
||||
MFEM is a modular parallel C++ library for finite element methods. Its goal is
|
||||
to enable high-performance scalable finite element discretization research and
|
||||
@@ -16,8 +16,8 @@ supercomputers.
|
||||
|
||||
* Copyright and licensing information can be found in files LICENSE and NOTICE.
|
||||
|
||||
* The best starting point for new users interested in MFEM's features is the
|
||||
interactive documentation in examples/README.html.
|
||||
* The best starting point for new users interested in MFEM's features is to
|
||||
review the examples and miniapps at https://mfem.org/examples.
|
||||
|
||||
* Developers interested in contributing to the library, should read the
|
||||
instructions and documentation in the CONTRIBUTING.md file.
|
||||
@@ -49,17 +49,17 @@ library. Nonlinear solvers (the Newton method), eigensolvers (LOBPCG), and
|
||||
several explicit and implicit Runge-Kutta time integrators are also available.
|
||||
|
||||
MFEM supports MPI-based parallelism throughout the library, and can readily be
|
||||
used as a scalable unstructured finite element problem generator. As of version
|
||||
4.0, MFEM offers initial support for GPU acceleration, and programming models,
|
||||
such as CUDA, OCCA, RAJA and OpenMP. MFEM-based applications require minimal
|
||||
changes to switch from a serial to a high-performing MPI-parallel version of the
|
||||
code, where they can take advantage of the integrated linear solvers from the
|
||||
hypre library. Comprehensive support for other external packages, e.g. PETSc
|
||||
and SUNDIALS is also included, giving access to many additional linear and
|
||||
nonlinear solvers, preconditioners, time integrators, etc.
|
||||
used as a scalable unstructured finite element problem generator. Starting with
|
||||
version 4.0, MFEM offers support for GPU acceleration, and programming models,
|
||||
such as CUDA, HIP, OCCA, RAJA and OpenMP. MFEM-based applications require
|
||||
minimal changes to switch from a serial to a highly-performant MPI-parallel
|
||||
version of the code, where they can take advantage of the integrated linear
|
||||
solvers from the hypre library. Comprehensive support for other external
|
||||
packages, e.g. PETSc, SUNDIALS and libCEED is also included, giving access to
|
||||
additional linear and nonlinear solvers, preconditioners, time integrators, etc.
|
||||
|
||||
For examples of using MFEM, see the examples/ and miniapps/ directories, as well
|
||||
as the OpenGL visualization tool GLVis which is available at http://glvis.org.
|
||||
as the OpenGL visualization tool GLVis which is available at https://glvis.org.
|
||||
|
||||
MFEM is distributed under the terms of the BSD-3 license. All new contributions
|
||||
must be made under this license. See LICENSE and NOTICE for details.
|
||||
|
||||
@@ -32,8 +32,11 @@ set(MFEM_USE_SUNDIALS @MFEM_USE_SUNDIALS@)
|
||||
set(MFEM_USE_MESQUITE @MFEM_USE_MESQUITE@)
|
||||
set(MFEM_USE_SUITESPARSE @MFEM_USE_SUITESPARSE@)
|
||||
set(MFEM_USE_SUPERLU @MFEM_USE_SUPERLU@)
|
||||
set(MFEM_USE_MUMPS @MFEM_USE_MUMPS@)
|
||||
set(MFEM_USE_STRUMPACK @MFEM_USE_STRUMPACK@)
|
||||
set(MFEM_USE_GINKGO @MFEM_USE_GINKGO@)
|
||||
set(MFEM_USE_AMGX @MFEM_USE_AMGX@)
|
||||
set(MFEM_USE_HIOP @MFEM_USE_HIOP@)
|
||||
set(MFEM_USE_GNUTLS @MFEM_USE_GNUTLS@)
|
||||
set(MFEM_USE_GSLIB @MFEM_USE_GSLIB@)
|
||||
set(MFEM_USE_NETCDF @MFEM_USE_NETCDF@)
|
||||
|
||||
@@ -74,6 +74,9 @@
|
||||
// [Deprecated] Enable experimental OpenMP support. Requires MFEM_THREAD_SAFE.
|
||||
#cmakedefine MFEM_USE_LEGACY_OPENMP
|
||||
|
||||
// Internal MFEM option: enable group/batch allocation for some small objects.
|
||||
#cmakedefine MFEM_USE_MEMALLOC
|
||||
|
||||
// Enable MFEM functionality based on the Mesquite library.
|
||||
#cmakedefine MFEM_USE_MESQUITE
|
||||
|
||||
@@ -83,15 +86,18 @@
|
||||
// Enable MFEM functionality based on the SuperLU_DIST library.
|
||||
#cmakedefine MFEM_USE_SUPERLU
|
||||
|
||||
// Enable MFEM functionality based on the MUMPS library.
|
||||
#cmakedefine MFEM_USE_MUMPS
|
||||
|
||||
// Enable MFEM functionality based on the STRUMPACK library.
|
||||
#cmakedefine MFEM_USE_STRUMPACK
|
||||
|
||||
// Internal MFEM option: enable group/batch allocation for some small objects.
|
||||
#cmakedefine MFEM_USE_MEMALLOC
|
||||
|
||||
// Enable functionality based on the Ginkgo library
|
||||
#cmakedefine MFEM_USE_GINKGO
|
||||
|
||||
// Enable MFEM functionality based on the AmgX library
|
||||
#cmakedefine MFEM_USE_AMGX
|
||||
|
||||
// Enable MFEM functionality based on the GnuTLS library
|
||||
#cmakedefine MFEM_USE_GNUTLS
|
||||
|
||||
@@ -126,9 +132,6 @@
|
||||
// Requires a CUDA compiler (nvcc).
|
||||
#cmakedefine MFEM_USE_CUDA
|
||||
|
||||
// Enable MFEM functionality based on the AMGX library
|
||||
#cmakedefine MFEM_USE_AMGX
|
||||
|
||||
// Enable MFEM functionality based on the RAJA library
|
||||
#cmakedefine MFEM_USE_RAJA
|
||||
|
||||
@@ -159,4 +162,7 @@
|
||||
// library.
|
||||
#cmakedefine MFEM_USE_SIMMETRIX
|
||||
|
||||
// Enable interface to the MKL CPardiso library.
|
||||
#cmakedefine MFEM_USE_MKL_CPARDISO
|
||||
|
||||
#endif // MFEM_CONFIG_HEADER
|
||||
|
||||
@@ -38,19 +38,19 @@ if(NOT ADIOS2_FOUND)
|
||||
endif()
|
||||
|
||||
find_path(ADIOS2_INCLUDE_DIR adios2.h ${ADIOS2_INCLUDE_OPTS})
|
||||
|
||||
# adios2 version 2.5.0
|
||||
|
||||
# adios2 version 2.5.0
|
||||
find_library(ADIOS2_LIBRARY NAMES adios2 ${ADIOS2_LIBRARY_OPTS})
|
||||
|
||||
|
||||
# adios2 version 2.6.0 and onwards
|
||||
if(NOT ADIOS2_LIBRARY)
|
||||
find_library(ADIOS2_CXX11_MPI_LIBRARY NAMES adios2_cxx11_mpi ${ADIOS2_LIBRARY_OPTS})
|
||||
find_library(ADIOS2_CXX11_LIBRARY NAMES adios2_cxx11 ${ADIOS2_LIBRARY_OPTS})
|
||||
set(ADIOS2_LIBRARY ${ADIOS2_CXX11_MPI_LIBRARY} ${ADIOS2_CXX11_LIBRARY})
|
||||
if(MFEM_USE_MPI)
|
||||
add_definitions(-DADIOS2_USE_MPI)
|
||||
endif()
|
||||
endif()
|
||||
find_library(ADIOS2_CXX11_MPI_LIBRARY NAMES adios2_cxx11_mpi ${ADIOS2_LIBRARY_OPTS})
|
||||
find_library(ADIOS2_CXX11_LIBRARY NAMES adios2_cxx11 ${ADIOS2_LIBRARY_OPTS})
|
||||
set(ADIOS2_LIBRARY ${ADIOS2_CXX11_MPI_LIBRARY} ${ADIOS2_CXX11_LIBRARY})
|
||||
if(MFEM_USE_MPI)
|
||||
add_definitions(-DADIOS2_USE_MPI)
|
||||
endif()
|
||||
endif()
|
||||
|
||||
include(FindPackageHandleStandardArgs)
|
||||
find_package_handle_standard_args(ADIOS2
|
||||
|
||||
@@ -0,0 +1,20 @@
|
||||
# Copyright (c) 2010-2020, 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.
|
||||
|
||||
# Defines the following variables:
|
||||
# - AMGX_FOUND
|
||||
# - AMGX_LIBRARIES
|
||||
# - AMGX_INCLUDE_DIRS
|
||||
|
||||
include(MfemCmakeUtilities)
|
||||
set(AMGX_REQUIRED_LIBRARIES cusparse cusolver cublas nvToolsExt)
|
||||
mfem_find_package(AMGX AMGX AMGX_DIR "include" "amgx_c.h" "lib" "amgx"
|
||||
"Paths to headers required by AMGX." "Libraries required by AMGX.")
|
||||
@@ -25,16 +25,16 @@ mfem_find_package(METIS METIS METIS_DIR "include;Lib" "metis.h"
|
||||
|
||||
int main()
|
||||
{
|
||||
int n = 10;
|
||||
int nparts = 5;
|
||||
int edgecut;
|
||||
int* partitioning = new int[10];
|
||||
int* I = partitioning,
|
||||
idx_t n = 10;
|
||||
idx_t nparts = 5;
|
||||
idx_t edgecut;
|
||||
idx_t* partitioning = new idx_t[10];
|
||||
idx_t* I = partitioning,
|
||||
* J = partitioning;
|
||||
|
||||
int ncon = 1;
|
||||
idx_t ncon = 1;
|
||||
int err;
|
||||
int options[40];
|
||||
idx_t options[40];
|
||||
|
||||
METIS_SetDefaultOptions(options);
|
||||
options[10] = 1; // set METIS_OPTION_CONTIG
|
||||
|
||||
@@ -0,0 +1,32 @@
|
||||
# Copyright (c) 2010-2020, 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.
|
||||
|
||||
# Defines the following variables:
|
||||
# - MKL_CPARDISO_FOUND
|
||||
# - MKL_CPARDISO_LIBRARIES
|
||||
# - MKL_CPARDISO_INCLUDE_DIRS
|
||||
|
||||
if(NOT MKL_MPI_WRAPPER_LIB)
|
||||
message(FATAL_ERROR "MKL CPardiso enabled but no MKL MPI Wrapper lib specified")
|
||||
endif()
|
||||
|
||||
if(NOT MKL_LIBRARY_DIR)
|
||||
message(WARNING "Using default MKL library path. Double check the variable MKL_LIBRARY_DIR")
|
||||
set(MKL_LIBRARY_DIR "lib")
|
||||
endif()
|
||||
|
||||
include(MfemCmakeUtilities)
|
||||
mfem_find_package(MKL_CPARDISO MKL_CPARDISO
|
||||
MKL_CPARDISO_DIR "include" mkl_cluster_sparse_solver.h ${MKL_LIBRARY_DIR} mkl_core
|
||||
"Paths to headers required by MKL CPardiso." "Libraries required by MKL CPARDISO."
|
||||
ADD_COMPONENT MKL_LP64 "include" "" ${MKL_LIBRARY_DIR} mkl_intel_lp64
|
||||
ADD_COMPONENT MKL_SEQUENTIAL "include" "" ${MKL_LIBRARY_DIR} mkl_sequential
|
||||
ADD_COMPONENT MKL_MPI_WRAPPER "include" "" ${MKL_LIBRARY_DIR} ${MKL_MPI_WRAPPER_LIB})
|
||||
@@ -0,0 +1,23 @@
|
||||
# Copyright (c) 2010-2020, 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.
|
||||
|
||||
# Sets the following variables:
|
||||
# - MUMPS_FOUND
|
||||
# - MUMPS_INCLUDE_DIRS
|
||||
# - MUMPS_LIBRARIES
|
||||
|
||||
include(MfemCmakeUtilities)
|
||||
mfem_find_package(MUMPS MUMPS MUMPS_DIR
|
||||
"include" dmumps_c.h "lib" dmumps
|
||||
"Paths to headers required by MUMPS."
|
||||
"Libraries required by MUMPS."
|
||||
ADD_COMPONENT mumps_common "include" dmumps_c.h "lib" mumps_common
|
||||
ADD_COMPONENT pord "include" dmumps_c.h "lib" pord)
|
||||
@@ -20,10 +20,14 @@ mfem_find_package(SUNDIALS SUNDIALS SUNDIALS_DIR
|
||||
"Paths to headers required by SUNDIALS." "Libraries required by SUNDIALS."
|
||||
ADD_COMPONENT NVector_Serial
|
||||
"include" nvector/nvector_serial.h "lib" sundials_nvecserial
|
||||
ADD_COMPONENT NVector_Parallel
|
||||
"include" nvector/nvector_parallel.h "lib" sundials_nvecparallel
|
||||
ADD_COMPONENT NVector_Cuda
|
||||
"include" nvector/nvector_cuda.h "lib" sundials_nveccuda
|
||||
ADD_COMPONENT NVector_ParHyp
|
||||
"include" nvector/nvector_parhyp.h "lib" sundials_nvecparhyp
|
||||
ADD_COMPONENT NVector_Parallel
|
||||
"include" nvector/nvector_parallel.h "lib" sundials_nvecparallel
|
||||
ADD_COMPONENT NVector_MPIPlusX
|
||||
"include" nvector/nvector_mpiplusx.h "lib" sundials_nvecmpiplusx
|
||||
ADD_COMPONENT CVODE "include" cvode/cvode.h "lib" sundials_cvode
|
||||
ADD_COMPONENT CVODES "include" cvodes/cvodes.h "lib" sundials_cvodes
|
||||
ADD_COMPONENT ARKODE "include" arkode/arkode.h "lib" sundials_arkode
|
||||
|
||||
@@ -235,7 +235,7 @@ endfunction(mfem_find_component)
|
||||
# code snippets. Additionally, a list of required/optional/alternative
|
||||
# packages (given by ${Name}_REQUIRED_PACKAGES) are searched for and added to
|
||||
# the ${Prefix}_INCLUDE_DIRS and ${Prefix}_LIBRARIES lists. The variable
|
||||
# ${Name}_REQUIRED_LIBRARIES can be set to spcecify any additional libraries
|
||||
# ${Name}_REQUIRED_LIBRARIES can be set to specify any additional libraries
|
||||
# that are needed. This function defines the following CACHE variables:
|
||||
#
|
||||
# ${Prefix}_FOUND
|
||||
@@ -733,15 +733,16 @@ function(mfem_export_mk_files)
|
||||
set(shared_link_flag "-Wl,-rpath,")
|
||||
endif()
|
||||
|
||||
# Convert Boolean vars to YES/NO without writting the values to cache
|
||||
# Convert Boolean vars to YES/NO without writing the values to cache
|
||||
set(CONFIG_MK_BOOL_VARS MFEM_USE_MPI MFEM_USE_METIS MFEM_USE_METIS_5
|
||||
MFEM_DEBUG MFEM_USE_EXCEPTIONS MFEM_USE_ZLIB MFEM_USE_LIBUNWIND
|
||||
MFEM_USE_LAPACK MFEM_THREAD_SAFE MFEM_USE_OPENMP MFEM_USE_LEGACY_OPENMP
|
||||
MFEM_USE_MEMALLOC MFEM_USE_SUNDIALS MFEM_USE_MESQUITE MFEM_USE_SUITESPARSE
|
||||
MFEM_USE_SUPERLU MFEM_USE_STRUMPACK MFEM_USE_GNUTLS
|
||||
MFEM_USE_GSLIB MFEM_USE_NETCDF MFEM_USE_PETSC MFEM_USE_SLEPC MFEM_USE_MPFR MFEM_USE_SIDRE
|
||||
MFEM_USE_CONDUIT MFEM_USE_PUMI MFEM_USE_CUDA MFEM_USE_OCCA MFEM_USE_RAJA
|
||||
MFEM_USE_UMPIRE MFEM_USE_SIMD MFEM_USE_ADIOS2)
|
||||
MFEM_USE_SUPERLU MFEM_USE_STRUMPACK MFEM_USE_GINKGO MFEM_USE_AMGX
|
||||
MFEM_USE_GNUTLS MFEM_USE_GSLIB MFEM_USE_NETCDF MFEM_USE_PETSC
|
||||
MFEM_USE_SLEPC MFEM_USE_MPFR MFEM_USE_SIDRE MFEM_USE_CONDUIT MFEM_USE_PUMI
|
||||
MFEM_USE_CUDA MFEM_USE_OCCA MFEM_USE_RAJA MFEM_USE_UMPIRE MFEM_USE_SIMD
|
||||
MFEM_USE_ADIOS2)
|
||||
foreach(var ${CONFIG_MK_BOOL_VARS})
|
||||
if (${var})
|
||||
set(${var} YES)
|
||||
@@ -753,7 +754,13 @@ function(mfem_export_mk_files)
|
||||
set(MFEM_CXX ${CMAKE_CXX_COMPILER})
|
||||
set(MFEM_HOST_CXX ${MFEM_CXX})
|
||||
set(MFEM_CPPFLAGS "")
|
||||
string(STRIP "${CMAKE_CXX_FLAGS_${BUILD_TYPE}} ${CMAKE_CXX_FLAGS}"
|
||||
get_target_property(cxx_std mfem CXX_STANDARD)
|
||||
# For now, we ignore the setting of the CXX_EXTENSIONS property. If this
|
||||
# property is set, then we need to use a variable like:
|
||||
# CMAKE_CXX11_EXTENSION_COMPILE_OPTION
|
||||
set(cxx_std_flag ${CMAKE_CXX${cxx_std}_STANDARD_COMPILE_OPTION})
|
||||
string(STRIP
|
||||
"${cxx_std_flag} ${CMAKE_CXX_FLAGS_${BUILD_TYPE}} ${CMAKE_CXX_FLAGS}"
|
||||
MFEM_CXXFLAGS)
|
||||
set(MFEM_TPLFLAGS "")
|
||||
foreach(dir ${MFEM_TPL_INCLUDE_DIRS})
|
||||
@@ -819,7 +826,7 @@ function(mfem_export_mk_files)
|
||||
string(REGEX REPLACE "^SCOREC::" "" libname ${pumilib})
|
||||
string(FIND "${pumilib}" ".a" staticlib)
|
||||
string(FIND "${pumilib}" ".so" sharedlib)
|
||||
find_library(lib ${libname} PATHS ${PUMI_DIR}/lib NO_DEFUALT_PATH)
|
||||
find_library(lib ${libname} PATHS ${PUMI_DIR}/lib NO_DEFAULT_PATH)
|
||||
if (NOT "${sharedlib}" MATCHES "-1" OR
|
||||
NOT "${staticlib}" MATCHES "-1" )
|
||||
set(MFEM_EXT_LIBS "${pumilib} ${MFEM_EXT_LIBS}")
|
||||
|
||||
@@ -34,6 +34,12 @@
|
||||
// Macro needed to get defines like M_PI from <cmath>. (Visual Studio C++ only?)
|
||||
#define _USE_MATH_DEFINES
|
||||
#endif
|
||||
// On Cygwin the option -std=c++11 prevents the definition of M_PI. Defining
|
||||
// the following macro allows us to get M_PI and some needed functions, e.g.
|
||||
// posix_memalign(), strdup(), strerror_r().
|
||||
#ifdef __CYGWIN__
|
||||
#define _XOPEN_SOURCE 600
|
||||
#endif
|
||||
|
||||
// Check dependencies:
|
||||
|
||||
@@ -42,9 +48,15 @@
|
||||
#ifdef MFEM_USE_SUPERLU
|
||||
#error Building with SuperLU_DIST (MFEM_USE_SUPERLU=YES) requires MPI (MFEM_USE_MPI=YES)
|
||||
#endif
|
||||
#ifdef MFEM_USE_MUMPS
|
||||
#error Building with MUMPS (MFEM_USE_MUMPS=YES) requires MPI (MFEM_USE_MPI=YES)
|
||||
#endif
|
||||
#ifdef MFEM_USE_STRUMPACK
|
||||
#error Building with STRUMPACK (MFEM_USE_STRUMPACK=YES) requires MPI (MFEM_USE_MPI=YES)
|
||||
#endif
|
||||
#ifdef MFEM_USE_MKL_CPARDISO
|
||||
#error Building with MKL CPARDISO (MFEM_USE_MKL_CPARDISO=YES) requires MPI (MFEM_USE_MPI=YES)
|
||||
#endif
|
||||
#ifdef MFEM_USE_PETSC
|
||||
#error Building with PETSc (MFEM_USE_PETSC=YES) requires MPI (MFEM_USE_MPI=YES)
|
||||
#endif
|
||||
|
||||
@@ -93,6 +93,11 @@
|
||||
|
||||
// Enable MFEM functionality based on the SuperLU library.
|
||||
// #define MFEM_USE_SUPERLU
|
||||
// #define MFEM_USE_SUPERLU5
|
||||
|
||||
// Enable MFEM functionality based on the MUMPS library.
|
||||
// #define MFEM_USE_MUMPS
|
||||
// #define MFEM_MUMPS_VERSION @MFEM_MUMPS_VERSION@
|
||||
|
||||
// Enable MFEM functionality based on the STRUMPACK library.
|
||||
// #define MFEM_USE_STRUMPACK
|
||||
@@ -100,6 +105,9 @@
|
||||
// Enable MFEM features based on the Ginkgo library
|
||||
// #define MFEM_USE_GINKGO
|
||||
|
||||
// Enable MFEM functionality based on the AmgX library.
|
||||
// #define MFEM_USE_AMGX
|
||||
|
||||
// Enable secure socket streams based on the GNUTLS library
|
||||
// #define MFEM_USE_GNUTLS
|
||||
|
||||
@@ -137,9 +145,6 @@
|
||||
// Requires a CUDA compiler (nvcc).
|
||||
// #define MFEM_USE_CUDA
|
||||
|
||||
// Enable MFEM functionality based on the AMGX library.
|
||||
// #define MFEM_USE_AMGX
|
||||
|
||||
// Build the AMD GPU/HIP-enabled version of the MFEM library.
|
||||
// Requires a HIP compiler (hipcc).
|
||||
// #define MFEM_USE_HIP
|
||||
@@ -166,4 +171,7 @@
|
||||
// library.
|
||||
// #define MFEM_USE_SIMMETRIX
|
||||
|
||||
// Enable interface to the MKL CPardiso library.
|
||||
// #define MFEM_USE_MKL_CPARDISO
|
||||
|
||||
#endif // MFEM_CONFIG_HEADER
|
||||
|
||||
@@ -32,8 +32,11 @@ MFEM_USE_SUNDIALS = @MFEM_USE_SUNDIALS@
|
||||
MFEM_USE_MESQUITE = @MFEM_USE_MESQUITE@
|
||||
MFEM_USE_SUITESPARSE = @MFEM_USE_SUITESPARSE@
|
||||
MFEM_USE_SUPERLU = @MFEM_USE_SUPERLU@
|
||||
MFEM_USE_SUPERLU5 = @MFEM_USE_SUPERLU5@
|
||||
MFEM_USE_MUMPS = @MFEM_USE_MUMPS@
|
||||
MFEM_USE_STRUMPACK = @MFEM_USE_STRUMPACK@
|
||||
MFEM_USE_GINKGO = @MFEM_USE_GINKGO@
|
||||
MFEM_USE_AMGX = @MFEM_USE_AMGX@
|
||||
MFEM_USE_GNUTLS = @MFEM_USE_GNUTLS@
|
||||
MFEM_USE_NETCDF = @MFEM_USE_NETCDF@
|
||||
MFEM_USE_PETSC = @MFEM_USE_PETSC@
|
||||
@@ -45,7 +48,6 @@ MFEM_USE_PUMI = @MFEM_USE_PUMI@
|
||||
MFEM_USE_HIOP = @MFEM_USE_HIOP@
|
||||
MFEM_USE_GSLIB = @MFEM_USE_GSLIB@
|
||||
MFEM_USE_CUDA = @MFEM_USE_CUDA@
|
||||
MFEM_USE_AMGX = @MFEM_USE_AMGX@
|
||||
MFEM_USE_HIP = @MFEM_USE_HIP@
|
||||
MFEM_USE_RAJA = @MFEM_USE_RAJA@
|
||||
MFEM_USE_OCCA = @MFEM_USE_OCCA@
|
||||
@@ -53,6 +55,7 @@ MFEM_USE_CEED = @MFEM_USE_CEED@
|
||||
MFEM_USE_UMPIRE = @MFEM_USE_UMPIRE@
|
||||
MFEM_USE_SIMD = @MFEM_USE_SIMD@
|
||||
MFEM_USE_ADIOS2 = @MFEM_USE_ADIOS2@
|
||||
MFEM_USE_MKL_CPARDISO = @MFEM_USE_MKL_CPARDISO@
|
||||
|
||||
# Compiler, compile options, and link options
|
||||
MFEM_CXX = @MFEM_CXX@
|
||||
|
||||
@@ -33,8 +33,11 @@ option(MFEM_USE_SUNDIALS "Enable SUNDIALS usage" OFF)
|
||||
option(MFEM_USE_MESQUITE "Enable MESQUITE usage" OFF)
|
||||
option(MFEM_USE_SUITESPARSE "Enable SuiteSparse usage" OFF)
|
||||
option(MFEM_USE_SUPERLU "Enable SuperLU_DIST usage" OFF)
|
||||
option(MFEM_USE_SUPERLU5 "Use the old SuperLU_DIST 5.1 version" OFF)
|
||||
option(MFEM_USE_MUMPS "Enable MUMPS usage" OFF)
|
||||
option(MFEM_USE_STRUMPACK "Enable STRUMPACK usage" OFF)
|
||||
option(MFEM_USE_GINKGO "Enable Ginkgo usage" OFF)
|
||||
option(MFEM_USE_AMGX "Enable AmgX usage" OFF)
|
||||
option(MFEM_USE_GNUTLS "Enable GNUTLS usage" OFF)
|
||||
option(MFEM_USE_GSLIB "Enable GSLIB usage" OFF)
|
||||
option(MFEM_USE_NETCDF "Enable NETCDF usage" OFF)
|
||||
@@ -52,6 +55,7 @@ option(MFEM_USE_CEED "Enable CEED" OFF)
|
||||
option(MFEM_USE_UMPIRE "Enable Umpire" OFF)
|
||||
option(MFEM_USE_SIMD "Enable use of SIMD intrinsics" OFF)
|
||||
option(MFEM_USE_ADIOS2 "Enable ADIOS2" OFF)
|
||||
option(MFEM_USE_MKL_CPARDISO "Enable MKL CPardiso" OFF)
|
||||
|
||||
set(MFEM_MPI_NP 4 CACHE STRING "Number of processes used for MPI tests")
|
||||
|
||||
@@ -88,7 +92,7 @@ set(METIS_DIR "${MFEM_DIR}/../metis-4.0" CACHE PATH "Path to the METIS library."
|
||||
|
||||
set(LIBUNWIND_DIR "" CACHE PATH "Path to Libunwind.")
|
||||
|
||||
# For sundials_nvecparhyp and nvecparallel remember to build with MPI_ENABLED=ON
|
||||
# For sundials_nvecmpiplusx and nvecparallel remember to build with MPI_ENABLE=ON
|
||||
# and modify cmake variables for hypre for sundials
|
||||
set(SUNDIALS_DIR "${MFEM_DIR}/../sundials-5.0.0/instdir" CACHE PATH
|
||||
"Path to the SUNDIALS library.")
|
||||
@@ -109,12 +113,21 @@ set(ParMETIS_DIR "${MFEM_DIR}/../parmetis-4.0.3" CACHE PATH
|
||||
set(ParMETIS_REQUIRED_PACKAGES "METIS" CACHE STRING
|
||||
"Additional packages required by ParMETIS.")
|
||||
|
||||
set(SuperLUDist_DIR "${MFEM_DIR}/../SuperLU_DIST_5.1.0" CACHE PATH
|
||||
set(SuperLUDist_DIR "${MFEM_DIR}/../SuperLU_DIST_6.3.1" CACHE PATH
|
||||
"Path to the SuperLU_DIST library.")
|
||||
# SuperLU_DIST may also depend on "OpenMP", depending on how it was compiled.
|
||||
set(SuperLUDist_REQUIRED_PACKAGES "MPI" "BLAS" "ParMETIS" CACHE STRING
|
||||
"Additional packages required by SuperLU_DIST.")
|
||||
|
||||
set(MUMPS_DIR "${MFEM_DIR}/../MUMPS_5.2.0" CACHE PATH
|
||||
"Path to the MUMPS library.")
|
||||
# Packages required by MUMPS, depending on how it was compiled.
|
||||
set(MUMPS_REQUIRED_PACKAGES "MPI" "BLAS" "METIS" "ScaLAPACK" CACHE STRING
|
||||
"Additional packages required by MUMPS.")
|
||||
# If the MPI package does not find all required Fortran libraries:
|
||||
# set(MUMPS_REQUIRED_LIBRARIES "gfortran" "mpi_mpifh" CACHE STRING
|
||||
# "Additional libraries required by MUMPS.")
|
||||
|
||||
set(STRUMPACK_DIR "${MFEM_DIR}/../STRUMPACK-build" CACHE PATH
|
||||
"Path to the STRUMPACK library.")
|
||||
# STRUMPACK may also depend on "OpenMP", depending on how it was compiled.
|
||||
@@ -145,6 +158,8 @@ set(ScaLAPACK_TARGET_NAMES scalapack)
|
||||
|
||||
set(Ginkgo_DIR "${MFEM_DIR}/../ginkgo" CACHE PATH "Path to the Ginkgo library.")
|
||||
|
||||
set(AMGX_DIR "${MFEM_DIR}/../amgx" CACHE PATH "Path to AmgX")
|
||||
|
||||
set(GNUTLS_DIR "" CACHE PATH "Path to the GnuTLS library.")
|
||||
|
||||
set(GSLIB_DIR "" CACHE PATH "Path to the GSLIB library.")
|
||||
@@ -180,9 +195,12 @@ set(HIOP_DIR "${MFEM_DIR}/../hiop/install" CACHE STRING
|
||||
set(HIOP_REQUIRED_PACKAGES "BLAS" "LAPACK" CACHE STRING
|
||||
"Packages that HiOp depends on.")
|
||||
|
||||
set(MKL_CPARDISO_DIR "" CACHE STRING "MKL installation path.")
|
||||
set(MKL_MPI_WRAPPER_LIB "mkl_blacs_mpich_lp64" CACHE STRING "MKL MPI wrapper library")
|
||||
set(MKL_LIBRARY_DIR "" CACHE STRING "Custom library subdirectory")
|
||||
|
||||
set(OCCA_DIR "${MFEM_DIR}/../occa" CACHE PATH "Path to OCCA")
|
||||
set(RAJA_DIR "${MFEM_DIR}/../raja" CACHE PATH "Path to RAJA")
|
||||
set(AMGX_DIR "${MFEM_DIR}/../amgx" CACHE PATH "Path to AMGX")
|
||||
set(CEED_DIR "${MFEM_DIR}/../libCEED" CACHE PATH "Path to libCEED")
|
||||
set(UMPIRE_DIR "${MFEM_DIR}/../umpire" CACHE PATH "Path to Umpire")
|
||||
|
||||
|
||||
@@ -53,6 +53,8 @@ HIP_CXX = hipcc
|
||||
# gfx900, gfx1010, etc.
|
||||
HIP_ARCH = gfx900
|
||||
HIP_FLAGS = --amdgpu-target=$(HIP_ARCH)
|
||||
HIP_XCOMPILER =
|
||||
HIP_XLINKER = -Wl,
|
||||
|
||||
ifneq ($(NOTMAC),)
|
||||
AR = ar
|
||||
@@ -120,8 +122,11 @@ MFEM_USE_SUNDIALS = NO
|
||||
MFEM_USE_MESQUITE = NO
|
||||
MFEM_USE_SUITESPARSE = NO
|
||||
MFEM_USE_SUPERLU = NO
|
||||
MFEM_USE_SUPERLU5 = NO
|
||||
MFEM_USE_MUMPS = NO
|
||||
MFEM_USE_STRUMPACK = NO
|
||||
MFEM_USE_GINKGO = NO
|
||||
MFEM_USE_AMGX = NO
|
||||
MFEM_USE_GNUTLS = NO
|
||||
MFEM_USE_NETCDF = NO
|
||||
MFEM_USE_PETSC = NO
|
||||
@@ -133,7 +138,6 @@ MFEM_USE_PUMI = NO
|
||||
MFEM_USE_HIOP = NO
|
||||
MFEM_USE_GSLIB = NO
|
||||
MFEM_USE_CUDA = NO
|
||||
MFEM_USE_AMGX = NO
|
||||
MFEM_USE_HIP = NO
|
||||
MFEM_USE_RAJA = NO
|
||||
MFEM_USE_OCCA = NO
|
||||
@@ -141,12 +145,23 @@ MFEM_USE_CEED = NO
|
||||
MFEM_USE_UMPIRE = NO
|
||||
MFEM_USE_SIMD = NO
|
||||
MFEM_USE_ADIOS2 = NO
|
||||
MFEM_USE_MKL_CPARDISO = NO
|
||||
|
||||
# MPI library compile and link flags
|
||||
# These settings are used only when building MFEM with MPI + HIP
|
||||
ifeq ($(MFEM_USE_MPI)$(MFEM_USE_HIP),YESYES)
|
||||
# We determine MPI_DIR assuming $(MPICXX) is in $(MPI_DIR)/bin
|
||||
MPI_DIR := $(patsubst %/,%,$(dir $(shell which $(MPICXX))))
|
||||
MPI_DIR := $(patsubst %/,%,$(dir $(MPI_DIR)))
|
||||
MPI_OPT = -I$(MPI_DIR)/include
|
||||
MPI_LIB = -L$(MPI_DIR)/lib $(XLINKER)-rpath,$(MPI_DIR)/lib -lmpi
|
||||
endif
|
||||
|
||||
# Compile and link options for zlib.
|
||||
ZLIB_DIR =
|
||||
ZLIB_OPT = $(if $(ZLIB_DIR),-I$(ZLIB_DIR)/include)
|
||||
ZLIB_LIB = $(if $(ZLIB_DIR),$(ZLIB_RPATH) -L$(ZLIB_DIR)/lib ,)-lz
|
||||
ZLIB_RPATH = -Wl,-rpath,$(ZLIB_DIR)/lib
|
||||
ZLIB_RPATH = $(XLINKER)-rpath,$(ZLIB_DIR)/lib
|
||||
|
||||
LIBUNWIND_OPT = -g
|
||||
LIBUNWIND_LIB = $(if $(NOTMAC),-lunwind -ldl,)
|
||||
@@ -157,7 +172,7 @@ HYPRE_OPT = -I$(HYPRE_DIR)/include
|
||||
HYPRE_LIB = -L$(HYPRE_DIR)/lib -lHYPRE
|
||||
|
||||
# METIS library configuration
|
||||
ifeq ($(MFEM_USE_SUPERLU)$(MFEM_USE_STRUMPACK),NONO)
|
||||
ifeq ($(MFEM_USE_SUPERLU)$(MFEM_USE_STRUMPACK)$(MFEM_USE_MUMPS),NONONO)
|
||||
ifeq ($(MFEM_USE_METIS_5),NO)
|
||||
METIS_DIR = @MFEM_DIR@/../metis-4.0
|
||||
METIS_OPT =
|
||||
@@ -190,15 +205,19 @@ OPENMP_LIB =
|
||||
POSIX_CLOCKS_LIB = -lrt
|
||||
|
||||
# SUNDIALS library configuration
|
||||
# For sundials_nvecparhyp and nvecparallel remember to build with MPI_ENABLED=ON
|
||||
# For sundials_nvecmpiplusx and nvecparallel remember to build with MPI_ENABLE=ON
|
||||
# and modify cmake variables for hypre for sundials
|
||||
SUNDIALS_DIR = @MFEM_DIR@/../sundials-5.0.0/instdir
|
||||
SUNDIALS_OPT = -I$(SUNDIALS_DIR)/include
|
||||
SUNDIALS_LIB = -Wl,-rpath,$(SUNDIALS_DIR)/lib64 -L$(SUNDIALS_DIR)/lib64\
|
||||
SUNDIALS_DIR = @MFEM_DIR@/../sundials-5.0.0/instdir
|
||||
SUNDIALS_OPT = -I$(SUNDIALS_DIR)/include
|
||||
SUNDIALS_LIBDIR = $(wildcard $(SUNDIALS_DIR)/lib*)
|
||||
SUNDIALS_LIB = $(XLINKER)-rpath,$(SUNDIALS_LIBDIR) -L$(SUNDIALS_LIBDIR)\
|
||||
-lsundials_arkode -lsundials_cvodes -lsundials_nvecserial -lsundials_kinsol
|
||||
|
||||
ifeq ($(MFEM_USE_MPI),YES)
|
||||
SUNDIALS_LIB += -lsundials_nvecparhyp -lsundials_nvecparallel
|
||||
SUNDIALS_LIB += -lsundials_nvecparallel -lsundials_nvecmpiplusx
|
||||
endif
|
||||
ifeq ($(MFEM_USE_CUDA),YES)
|
||||
SUNDIALS_LIB += -lsundials_nveccuda
|
||||
endif
|
||||
# If SUNDIALS was built with KLU:
|
||||
# MFEM_USE_SUITESPARSE = YES
|
||||
@@ -212,14 +231,22 @@ MESQUITE_LIB = -L$(MESQUITE_DIR)/lib -lmesquite
|
||||
LIB_RT = $(if $(NOTMAC),-lrt,)
|
||||
SUITESPARSE_DIR = @MFEM_DIR@/../SuiteSparse
|
||||
SUITESPARSE_OPT = -I$(SUITESPARSE_DIR)/include
|
||||
SUITESPARSE_LIB = -Wl,-rpath,$(SUITESPARSE_DIR)/lib -L$(SUITESPARSE_DIR)/lib\
|
||||
-lklu -lbtf -lumfpack -lcholmod -lcolamd -lamd -lcamd -lccolamd\
|
||||
-lsuitesparseconfig $(LIB_RT) $(METIS_LIB) $(LAPACK_LIB)
|
||||
SUITESPARSE_LIB = $(XLINKER)-rpath,$(SUITESPARSE_DIR)/lib\
|
||||
-L$(SUITESPARSE_DIR)/lib -lklu -lbtf -lumfpack -lcholmod -lcolamd -lamd -lcamd\
|
||||
-lccolamd -lsuitesparseconfig $(LIB_RT) $(METIS_LIB) $(LAPACK_LIB)
|
||||
|
||||
# SuperLU library configuration
|
||||
SUPERLU_DIR = @MFEM_DIR@/../SuperLU_DIST_5.1.0
|
||||
SUPERLU_OPT = -I$(SUPERLU_DIR)/SRC
|
||||
SUPERLU_LIB = -Wl,-rpath,$(SUPERLU_DIR)/lib -L$(SUPERLU_DIR)/lib -lsuperlu_dist_5.1.0
|
||||
ifeq ($(MFEM_USE_SUPERLU5),YES)
|
||||
SUPERLU_DIR = @MFEM_DIR@/../SuperLU_DIST_5.1.0
|
||||
SUPERLU_OPT = -I$(SUPERLU_DIR)/include
|
||||
SUPERLU_LIB = $(XLINKER)-rpath,$(SUPERLU_DIR)/lib -L$(SUPERLU_DIR)/lib\
|
||||
-lsuperlu_dist_5.1.0
|
||||
else
|
||||
SUPERLU_DIR = @MFEM_DIR@/../SuperLU_DIST_6.3.1
|
||||
SUPERLU_OPT = -I$(SUPERLU_DIR)/include
|
||||
SUPERLU_LIB = $(XLINKER)-rpath,$(SUPERLU_DIR)/lib64 -L$(SUPERLU_DIR)/lib64\
|
||||
-lsuperlu_dist -lblas
|
||||
endif
|
||||
|
||||
# SCOTCH library configuration (required by STRUMPACK <= v2.1.0, optional in
|
||||
# STRUMPACK >= v2.2.0)
|
||||
@@ -228,12 +255,12 @@ SCOTCH_OPT = -I$(SCOTCH_DIR)/include
|
||||
SCOTCH_LIB = -L$(SCOTCH_DIR)/lib -lptscotch -lptscotcherr -lscotch -lscotcherr\
|
||||
-lpthread
|
||||
|
||||
# SCALAPACK library configuration (required by STRUMPACK)
|
||||
# SCALAPACK library configuration (required by STRUMPACK and MUMPS)
|
||||
SCALAPACK_DIR = @MFEM_DIR@/../scalapack-2.0.2
|
||||
SCALAPACK_OPT = -I$(SCALAPACK_DIR)/SRC
|
||||
SCALAPACK_LIB = -L$(SCALAPACK_DIR)/lib -lscalapack $(LAPACK_LIB)
|
||||
|
||||
# MPI Fortran library, needed e.g. by STRUMPACK
|
||||
# MPI Fortran library, needed e.g. by STRUMPACK or MUMPS
|
||||
# MPICH:
|
||||
MPI_FORTRAN_LIB = -lmpifort
|
||||
# OpenMPI:
|
||||
@@ -241,6 +268,12 @@ MPI_FORTRAN_LIB = -lmpifort
|
||||
# Additional Fortan library:
|
||||
# MPI_FORTRAN_LIB += -lgfortran
|
||||
|
||||
# MUMPS library configuration
|
||||
MUMPS_DIR = @MFEM_DIR@/../MUMPS_5.2.0
|
||||
MUMPS_OPT = -I$(MUMPS_DIR)/include
|
||||
MUMPS_LIB = $(XLINKER)-rpath,$(MUMPS_DIR)/lib -L$(MUMPS_DIR)/lib -ldmumps\
|
||||
-lmumps_common -lpord $(SCALAPACK_LIB) $(LAPACK_LIB) $(MPI_FORTRAN_LIB)
|
||||
|
||||
# STRUMPACK library configuration
|
||||
STRUMPACK_DIR = @MFEM_DIR@/../STRUMPACK-build
|
||||
STRUMPACK_OPT = -I$(STRUMPACK_DIR)/include $(SCOTCH_OPT)
|
||||
@@ -252,7 +285,13 @@ STRUMPACK_LIB = -L$(STRUMPACK_DIR)/lib -lstrumpack $(MPI_FORTRAN_LIB)\
|
||||
# Ginkgo library configuration (currently not needed)
|
||||
GINKGO_DIR = @MFEM_DIR@/../ginkgo/install
|
||||
GINKGO_OPT = -isystem $(GINKGO_DIR)/include
|
||||
GINKGO_LIB = $(XLINKER)-rpath,$(GINKGO_DIR)/lib -L$(GINKGO_DIR)/lib -lginkgo -lginkgo_omp -lginkgo_cuda -lginkgo_reference
|
||||
GINKGO_LIB = $(XLINKER)-rpath,$(GINKGO_DIR)/lib -L$(GINKGO_DIR)/lib -lginkgo\
|
||||
-lginkgo_omp -lginkgo_cuda -lginkgo_reference
|
||||
|
||||
# AmgX library configuration
|
||||
AMGX_DIR = @MFEM_DIR@/../amgx
|
||||
AMGX_OPT = -I$(AMGX_DIR)/include
|
||||
AMGX_LIB = -lcusparse -lcusolver -lcublas -lnvToolsExt -L$(AMGX_DIR)/lib -lamgx
|
||||
|
||||
# GnuTLS library configuration
|
||||
GNUTLS_OPT =
|
||||
@@ -262,8 +301,8 @@ GNUTLS_LIB = -lgnutls
|
||||
NETCDF_DIR = $(HOME)/local
|
||||
HDF5_DIR = $(HOME)/local
|
||||
NETCDF_OPT = -I$(NETCDF_DIR)/include -I$(HDF5_DIR)/include $(ZLIB_OPT)
|
||||
NETCDF_LIB = -Wl,-rpath,$(NETCDF_DIR)/lib -L$(NETCDF_DIR)/lib\
|
||||
-Wl,-rpath,$(HDF5_DIR)/lib -L$(HDF5_DIR)/lib\
|
||||
NETCDF_LIB = $(XLINKER)-rpath,$(NETCDF_DIR)/lib -L$(NETCDF_DIR)/lib\
|
||||
$(XLINKER)-rpath,$(HDF5_DIR)/lib -L$(HDF5_DIR)/lib\
|
||||
-lnetcdf -lhdf5_hl -lhdf5 $(ZLIB_LIB)
|
||||
|
||||
# PETSc library configuration (version greater or equal to 3.8 or the dev branch)
|
||||
@@ -275,9 +314,10 @@ PETSC_INC_VAR = PETSC_CC_INCLUDES
|
||||
PETSC_LIB_VAR = PETSC_EXTERNAL_LIB_BASIC
|
||||
ifeq ($(PETSC_FOUND),YES)
|
||||
PETSC_OPT := $(shell sed -n "s/$(PETSC_INC_VAR) = *//p" $(PETSC_VARS))
|
||||
PETSC_LIB := $(shell sed -n "s/$(PETSC_LIB_VAR) = *//p" $(PETSC_VARS))
|
||||
PETSC_LIB := -Wl,-rpath,$(abspath $(PETSC_DIR))/lib\
|
||||
-L$(abspath $(PETSC_DIR))/lib -lpetsc $(PETSC_LIB)
|
||||
PETSC_DEP := $(shell sed -n "s/$(PETSC_LIB_VAR) = *//p" $(PETSC_VARS))
|
||||
PETSC_LIB = $(XLINKER)-rpath,$(abspath $(PETSC_DIR))/lib\
|
||||
-L$(abspath $(PETSC_DIR))/lib -lpetsc\
|
||||
$(subst $(CXX_XLINKER),$(XLINKER),$(PETSC_DEP))
|
||||
endif
|
||||
|
||||
SLEPC_DIR := $(MFEM_DIR)/../slepc
|
||||
@@ -289,9 +329,10 @@ ifeq ($(SLEPC_FOUND),YES)
|
||||
SLEPC_OPT := $(shell sed -n "s/$(SLEPC_INC_VAR) *= *//p" $(SLEPC_VARS))
|
||||
# Some additional external libraries might be defined in this file
|
||||
-include ${SLEPC_DIR}/${PETSC_ARCH}/lib/slepc/conf/slepcvariables
|
||||
SLEPC_LIB := $(shell sed -n "s/$(SLEPC_LIB_VAR) *= *//p" $(SLEPC_VARS))
|
||||
SLEPC_LIB := -Wl,-rpath,$(abspath $(SLEPC_DIR))/$(PETSC_ARCH)/lib\
|
||||
-L$(abspath $(SLEPC_DIR))/$(PETSC_ARCH)/lib -lslepc $(SLEPC_LIB)
|
||||
SLEPC_DEP := $(shell sed -n "s/$(SLEPC_LIB_VAR) *= *//p" $(SLEPC_VARS))
|
||||
SLEPC_LIB = $(XLINKER)-rpath,$(abspath $(SLEPC_DIR))/$(PETSC_ARCH)/lib\
|
||||
-L$(abspath $(SLEPC_DIR))/$(PETSC_ARCH)/lib -lslepc\
|
||||
$(subst $(CXX_XLINKER),$(XLINKER),$(SLEPC_DEP))
|
||||
endif
|
||||
|
||||
# MPFR library configuration
|
||||
@@ -302,7 +343,7 @@ MPFR_LIB = -lmpfr
|
||||
CONDUIT_DIR = @MFEM_DIR@/../conduit
|
||||
CONDUIT_OPT = -I$(CONDUIT_DIR)/include/conduit
|
||||
CONDUIT_LIB = \
|
||||
-Wl,-rpath,$(CONDUIT_DIR)/lib -L$(CONDUIT_DIR)/lib \
|
||||
$(XLINKER)-rpath,$(CONDUIT_DIR)/lib -L$(CONDUIT_DIR)/lib \
|
||||
-lconduit -lconduit_relay -lconduit_blueprint -ldl
|
||||
|
||||
# Check if Conduit was built with hdf5 support, by looking
|
||||
@@ -310,7 +351,7 @@ CONDUIT_LIB = \
|
||||
CONDUIT_HDF5_HEADER=$(CONDUIT_DIR)/include/conduit/conduit_relay_hdf5.hpp
|
||||
ifneq (,$(wildcard $(CONDUIT_HDF5_HEADER)))
|
||||
CONDUIT_OPT += -I$(HDF5_DIR)/include
|
||||
CONDUIT_LIB += -Wl,-rpath,$(HDF5_DIR)/lib -L$(HDF5_DIR)/lib \
|
||||
CONDUIT_LIB += $(XLINKER)-rpath,$(HDF5_DIR)/lib -L$(HDF5_DIR)/lib \
|
||||
-lhdf5 $(ZLIB_LIB)
|
||||
endif
|
||||
|
||||
@@ -320,9 +361,9 @@ SIDRE_DIR = @MFEM_DIR@/../axom
|
||||
SIDRE_OPT = -I$(SIDRE_DIR)/include -I$(CONDUIT_DIR)/include/conduit\
|
||||
-I$(HDF5_DIR)/include
|
||||
SIDRE_LIB = \
|
||||
-Wl,-rpath,$(SIDRE_DIR)/lib -L$(SIDRE_DIR)/lib \
|
||||
-Wl,-rpath,$(CONDUIT_DIR)/lib -L$(CONDUIT_DIR)/lib \
|
||||
-Wl,-rpath,$(HDF5_DIR)/lib -L$(HDF5_DIR)/lib \
|
||||
$(XLINKER)-rpath,$(SIDRE_DIR)/lib -L$(SIDRE_DIR)/lib \
|
||||
$(XLINKER)-rpath,$(CONDUIT_DIR)/lib -L$(CONDUIT_DIR)/lib \
|
||||
$(XLINKER)-rpath,$(HDF5_DIR)/lib -L$(HDF5_DIR)/lib \
|
||||
-laxom -lconduit -lconduit_relay -lconduit_blueprint -lhdf5 $(ZLIB_LIB) -ldl
|
||||
|
||||
# PUMI
|
||||
@@ -373,10 +414,14 @@ UMPIRE_DIR = @MFEM_DIR@/../umpire
|
||||
UMPIRE_OPT = -I$(UMPIRE_DIR)/include
|
||||
UMPIRE_LIB = -L$(UMPIRE_DIR)/lib -lumpire
|
||||
|
||||
# AMGX library configuration
|
||||
AMGX_DIR = @MFEM_DIR@/../amgx
|
||||
AMGX_OPT = -I$(AMGX_DIR)/include
|
||||
AMGX_LIB = -L$(CUDA_HOME)/lib64 -lcusparse -lcusolver -lcublas -lnvToolsExt -L$(AMGX_DIR)/lib -lamgx -Xlinker=-rpath=$(CUDA_HOME)/lib64
|
||||
# MKL CPardiso library configuration
|
||||
MKL_CPARDISO_DIR ?=
|
||||
MKL_MPI_WRAPPER ?= mkl_blacs_mpich_lp64
|
||||
MKL_LIBRARY_SUBDIR ?= lib
|
||||
MKL_CPARDISO_OPT = -I$(MKL_CPARDISO_DIR)/include
|
||||
MKL_CPARDISO_LIB = $(XLINKER)-rpath,$(MKL_CPARDISO_DIR)/$(MKL_LIBRARY_SUBDIR)\
|
||||
-L$(MKL_CPARDISO_DIR)/$(MKL_LIBRARY_SUBDIR) -l$(MKL_MPI_WRAPPER)\
|
||||
-lmkl_intel_lp64 -lmkl_sequential -lmkl_core
|
||||
|
||||
# If YES, enable some informational messages
|
||||
VERBOSE = NO
|
||||
|
||||
@@ -0,0 +1,33 @@
|
||||
// Copyright (c) 2010-2020, 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 "dmumps_c.h"
|
||||
#include <string>
|
||||
#include <iostream>
|
||||
#include <algorithm>
|
||||
|
||||
// Macros to expand a macro as a string
|
||||
#define STR_EXPAND(s) #s
|
||||
#define STR(s) STR_EXPAND(s)
|
||||
|
||||
int main()
|
||||
{
|
||||
#ifdef MUMPS_VERSION
|
||||
const char *ptr = STR(MUMPS_VERSION);
|
||||
std::string s(ptr);
|
||||
s.erase(std::remove(s.begin(), s.end(), '"'), s.end());
|
||||
s.erase(std::remove(s.begin(), s.end(), '.'), s.end());
|
||||
std::cout << s << "\n";
|
||||
return 0;
|
||||
#else
|
||||
return -1;
|
||||
#endif
|
||||
}
|
||||
@@ -42,6 +42,10 @@ GHV_FLAGS = $(subst @MFEM_DIR@,$(if $(MFEM_DIR),$(MFEM_DIR),..),$(HYPRE_OPT))
|
||||
SMX = $(if $(MFEM_USE_PUMI:NO=),MFEM_USE_SIMMETRIX)
|
||||
SMX_PATH = $(PUMI_DIR)/include/gmi_sim.h
|
||||
SMX_FILE = $(subst @MFEM_DIR@,$(if $(MFEM_DIR),$(MFEM_DIR),..),$(SMX_PATH))
|
||||
MUMPS = $(MFEM_USE_MUMPS:NO=)
|
||||
GMV_CXX ?= $(MFEM_CXX)
|
||||
GMV = get_mumps_version
|
||||
GMV_FLAGS = $(subst @MFEM_DIR@,$(if $(MFEM_DIR),$(MFEM_DIR),..),$(MUMPS_OPT))
|
||||
|
||||
$(GHV): $(SRC)$(GHV).cpp
|
||||
$(call mfem-info, Determining HYPRE version ...)
|
||||
@@ -50,6 +54,13 @@ $(GHV).out: $(GHV)
|
||||
./$(GHV) > $(GHV).out
|
||||
.INTERMEDIATE: $(GHV) $(GHV).out
|
||||
|
||||
$(GMV): $(SRC)$(GMV).cpp
|
||||
$(call mfem-info, Determining MUMPS version ...)
|
||||
$(GMV_CXX) ${GMV_FLAGS} $(SRC)$(GMV).cpp -o $(GMV)
|
||||
$(GMV).out: $(GMV)
|
||||
./$(GMV) > $(GMV).out
|
||||
.INTERMEDIATE: $(GMV) $(GMV).out
|
||||
|
||||
get-hypre-version: $(GHV).out
|
||||
$(eval MFEM_HYPRE_VERSION:=$(shell cat $(GHV).out))
|
||||
$(if $(MFEM_HYPRE_VERSION),$(eval export MFEM_HYPRE_VERSION)\
|
||||
@@ -62,10 +73,18 @@ check-smx:
|
||||
$(call mfem-info, MFEM_USE_SIMMETRIX = $(MFEM_USE_SIMMETRIX))
|
||||
$(eval export MFEM_USE_SIMMETRIX)
|
||||
|
||||
header: $(if $(MPI),get-hypre-version,) $(if $(SMX),check-smx)
|
||||
get-mumps-version: $(GMV).out
|
||||
$(eval MFEM_MUMPS_VERSION:=$(shell cat $(GMV).out))
|
||||
$(if $(MFEM_MUMPS_VERSION),$(eval export MFEM_MUMPS_VERSION)\
|
||||
$(info MUMPS version: $(MFEM_MUMPS_VERSION)),\
|
||||
$(error Unable to determine MUMPS version))
|
||||
|
||||
header: $(if $(MPI),get-hypre-version,) $(if $(SMX),check-smx,) \
|
||||
$(if $(MUMPS),get-mumps-version,)
|
||||
$(call mfem-info, Writing $(CONFIG_HPP) ...)
|
||||
@set -- && \
|
||||
for def in $${MFEM_DEFINES} $(if $(MPI),MFEM_HYPRE_VERSION) $(SMX); do \
|
||||
for def in $${MFEM_DEFINES} $(if $(MPI),MFEM_HYPRE_VERSION) $(SMX) \
|
||||
$(if $(MUMPS),MFEM_MUMPS_VERSION); do \
|
||||
eval var=\$$$$def && \
|
||||
if [ "NO" != "$${var}" ]; then \
|
||||
set -- "$$@" -e "s|// \(#define $${def} \)|\1|" && \
|
||||
|
||||
@@ -48,6 +48,10 @@ groups_serial=(
|
||||
"miniapps/meshing"
|
||||
"mobius-strip.cpp klein-bottle.cpp extruder.cpp toroid.cpp
|
||||
mesh-optimizer.cpp minimal-surface.cpp"'
|
||||
'"convergence"
|
||||
"Convergence tests:"
|
||||
"tests/convergence"
|
||||
"rates.cpp"'
|
||||
)
|
||||
# Parallel groups
|
||||
groups_parallel=(
|
||||
@@ -81,7 +85,7 @@ groups_parallel=(
|
||||
'"convergence"
|
||||
"Convergence tests:"
|
||||
"tests/convergence"
|
||||
"diffusion.cpp"'
|
||||
"prates.cpp"'
|
||||
'"par-mesh-format"
|
||||
"Parallel mesh tests:"
|
||||
"tests/par-mesh-format"
|
||||
@@ -118,7 +122,7 @@ groups_all=(
|
||||
'"convergence"
|
||||
"Convergence tests:"
|
||||
"tests/convergence"
|
||||
"diffusion.cpp"'
|
||||
"{,p}rates.cpp"'
|
||||
'"par-mesh-format"
|
||||
"Parallel mesh tests:"
|
||||
"tests/par-mesh-format"
|
||||
|
||||
@@ -31,14 +31,14 @@ POINTS 27 double
|
||||
7 0.5 1
|
||||
8 0.5 1
|
||||
CELLS 8 56
|
||||
6 0 9 18 1 10 19
|
||||
6 1 10 19 2 11 20
|
||||
6 2 11 20 3 12 21
|
||||
6 3 12 21 4 13 22
|
||||
6 4 13 22 5 14 23
|
||||
6 5 14 23 6 15 24
|
||||
6 6 15 24 7 16 25
|
||||
6 7 16 25 8 17 26
|
||||
6 0 18 9 1 19 10
|
||||
6 1 19 10 2 20 11
|
||||
6 2 20 11 3 21 12
|
||||
6 3 21 12 4 22 13
|
||||
6 4 22 13 5 23 14
|
||||
6 5 23 14 6 24 15
|
||||
6 6 24 15 7 25 16
|
||||
6 7 25 16 8 26 17
|
||||
CELL_TYPES 8
|
||||
13
|
||||
13
|
||||
|
||||
@@ -16,7 +16,6 @@ if (DOXYGEN_FOUND)
|
||||
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/CodeDocumentation.conf.in
|
||||
${CMAKE_CURRENT_BINARY_DIR}/CodeDocumentation.conf @ONLY)
|
||||
|
||||
|
||||
add_custom_target(doc
|
||||
COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/CodeDocumentation.conf
|
||||
COMMAND echo "<meta http-equiv=\"REFRESH\" content=\"0;URL=CodeDocumentation/html/index.html\">" > ${CMAKE_CURRENT_BINARY_DIR}/CodeDocumentation.html
|
||||
@@ -32,5 +31,4 @@ if (DOXYGEN_FOUND)
|
||||
COMMENT "Removing API documentation"
|
||||
VERBATIM)
|
||||
|
||||
|
||||
endif (DOXYGEN_FOUND)
|
||||
|
||||
@@ -38,7 +38,7 @@ PROJECT_NAME = "MFEM"
|
||||
# could be handy for archiving the generated documentation or if some version
|
||||
# control system is used.
|
||||
|
||||
PROJECT_NUMBER = v4.1.1
|
||||
PROJECT_NUMBER = v4.2.1
|
||||
|
||||
# Using the PROJECT_BRIEF tag one can provide an optional one line description
|
||||
# for a project that appears at the top of each page and should give viewer a
|
||||
@@ -51,7 +51,7 @@ PROJECT_BRIEF = "Finite element discretization library"
|
||||
# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
|
||||
# the logo to the output directory.
|
||||
|
||||
PROJECT_LOGO = web/logo-small.png
|
||||
PROJECT_LOGO = logo-small.png
|
||||
|
||||
# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
|
||||
# into which the generated documentation will be written. If a relative path is
|
||||
@@ -766,11 +766,14 @@ INPUT = @MFEM_SOURCE_DIR@/doc/CodeDocumentation.dox \
|
||||
@MFEM_SOURCE_DIR@/mesh \
|
||||
@MFEM_SOURCE_DIR@/fem \
|
||||
@MFEM_SOURCE_DIR@/examples \
|
||||
@MFEM_SOURCE_DIR@/examples/amgx \
|
||||
@MFEM_SOURCE_DIR@/examples/ginkgo \
|
||||
@MFEM_SOURCE_DIR@/examples/hiop \
|
||||
@MFEM_SOURCE_DIR@/examples/petsc \
|
||||
@MFEM_SOURCE_DIR@/examples/pumi \
|
||||
@MFEM_SOURCE_DIR@/examples/hiop \
|
||||
@MFEM_SOURCE_DIR@/examples/sundials \
|
||||
@MFEM_SOURCE_DIR@/miniapps/adjoint \
|
||||
@MFEM_SOURCE_DIR@/examples/superlu \
|
||||
@MFEM_SOURCE_DIR@/miniapps/adjoint \
|
||||
@MFEM_SOURCE_DIR@/miniapps/common \
|
||||
@MFEM_SOURCE_DIR@/miniapps/electromagnetics \
|
||||
@MFEM_SOURCE_DIR@/miniapps/gslib \
|
||||
@@ -816,7 +819,9 @@ RECURSIVE = NO
|
||||
# run.
|
||||
|
||||
EXCLUDE = @MFEM_SOURCE_DIR@/config/_config.hpp \
|
||||
@MFEM_SOURCE_DIR@/config/get_hypre_version.cpp
|
||||
@MFEM_SOURCE_DIR@/config/get_hypre_version.cpp \
|
||||
@MFEM_SOURCE_DIR@/general/tinyxml2.h \
|
||||
@MFEM_SOURCE_DIR@/general/tinyxml2.cpp
|
||||
|
||||
# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
|
||||
# directories that are symbolic links (a Unix file system feature) are excluded
|
||||
@@ -2334,7 +2339,7 @@ PLANTUML_INCLUDE_PATH =
|
||||
# Minimum value: 0, maximum value: 10000, default value: 50.
|
||||
# This tag requires that the tag HAVE_DOT is set to YES.
|
||||
|
||||
DOT_GRAPH_MAX_NODES = 10
|
||||
DOT_GRAPH_MAX_NODES = 50
|
||||
|
||||
# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the graphs
|
||||
# generated by dot. A depth value of 3 means that only nodes reachable from the
|
||||
|
||||
@@ -62,7 +62,7 @@ namespace mfem {
|
||||
* - <a class="el" href="ex9p_8cpp_source.html">Example 9p</a>: parallel Discontinuous Galerkin (DG) time-dependent advection
|
||||
* - <a class="el" href="ex10_8cpp_source.html">Example 10</a>: time-dependent implicit nonlinear elasticity
|
||||
* - <a class="el" href="ex10p_8cpp_source.html">Example 10p</a>: parallel time-dependent implicit nonlinear elasticity
|
||||
* - <a class="el" href="examples_2ex11p_8cpp_source.html">Example 11p</a>: parallel Laplace eigensolver
|
||||
* - <a class="el" href="ex11p_8cpp_source.html">Example 11p</a>: parallel Laplace eigensolver
|
||||
* - <a class="el" href="ex12p_8cpp_source.html">Example 12p</a>: parallel linear elasticity eigensolver
|
||||
* - <a class="el" href="ex13p_8cpp_source.html">Example 13p</a>: parallel Maxwell eigensolver
|
||||
* - <a class="el" href="ex14_8cpp_source.html">Example 14</a>: Discontinuous Galerkin (DG) for the Laplace problem
|
||||
@@ -90,20 +90,25 @@ namespace mfem {
|
||||
* - <a class="el" href="ex25p_8cpp_source.html">Example 25p</a>: parallel simulation of electromagnetic wave propagation using a Perfectly Matched Layer (PML)
|
||||
* - <a class="el" href="ex26_8cpp_source.html">Example 26</a>: multigrid preconditioner for the Laplace problem using nodal H1 FEM
|
||||
* - <a class="el" href="ex26p_8cpp_source.html">Example 26p</a>: parallel multigrid preconditioner for the Laplace problem using nodal H1 FEM
|
||||
* - <a class="el" href="ex27_8cpp_source.html">Example 27</a>: boundary conditions for the Laplace problem
|
||||
* - <a class="el" href="ex27p_8cpp_source.html">Example 27p</a>: parallel boundary conditions for the Laplace problem
|
||||
*
|
||||
* <H4>SUNDIALS Examples</H4>
|
||||
* <H4>AmgX Examples</H4>
|
||||
* - Variants of Examples
|
||||
* <a class="el" href="sundials_2ex9_8cpp_source.html">9</a>,
|
||||
* <a class="el" href="sundials_2ex9p_8cpp_source.html">9p</a>,
|
||||
* <a class="el" href="sundials_2ex10_8cpp_source.html">10</a>,
|
||||
* <a class="el" href="sundials_2ex10p_8cpp_source.html">10p</a>,
|
||||
* <a class="el" href="sundials_2ex16_8cpp_source.html">16</a>,
|
||||
* and
|
||||
* <a class="el" href="sundials_2ex16p_8cpp_source.html">16p</a>
|
||||
* demonstrating the use of MFEM's \link sundials.hpp SUNDIALS classes\endlink
|
||||
* - CVODES adjoint examples:
|
||||
* <a class="el" href="cvsRoberts__ASAi__dns_8cpp_source.html">serial ODE system</a>,
|
||||
* <a class="el" href="adjoint__advection__diffusion_8cpp_source.html">parallel advection-diffusion</a>
|
||||
* <a class="el" href="examples_2amgx_2ex1_8cpp_source.html">1</a> and
|
||||
* <a class="el" href="examples_2amgx_2ex1p_8cpp_source.html">1p</a>,
|
||||
* demonstrating the use of MFEM's \link amgxsolver.hpp AmgX integration\endlink.
|
||||
*
|
||||
* <H4>Ginkgo Examples</H4>
|
||||
* - Variants of Example
|
||||
* <a class="el" href="examples_2ginkgo_2ex1_8cpp_source.html">1</a>,
|
||||
* demonstrating the use of MFEM's \link ginkgo.hpp Ginkgo integration\endlink.
|
||||
*
|
||||
* <H4>HiOp Examples</H4>
|
||||
* - Variants of Examples
|
||||
* <a class="el" href="hiop_2ex9_8cpp_source.html">9</a> and
|
||||
* <a class="el" href="hiop_2ex9p_8cpp_source.html">9p</a>,
|
||||
* demonstrating the use of MFEM's \link hiop.hpp HiOp integration\endlink.
|
||||
*
|
||||
* <H4>PETSc Examples</H4>
|
||||
* - Variants of Examples
|
||||
@@ -115,8 +120,8 @@ namespace mfem {
|
||||
* <a class="el" href="petsc_2ex6p_8cpp_source.html">6p</a>,
|
||||
* <a class="el" href="petsc_2ex9p_8cpp_source.html">9p</a>,
|
||||
* and
|
||||
* <a class="el" href="petsc_2ex10p_8cpp_source.html">10p</a>
|
||||
* demonstrating the use of MFEM's \link petsc.hpp PETSc classes\endlink
|
||||
* <a class="el" href="petsc_2ex10p_8cpp_source.html">10p</a>,
|
||||
* demonstrating the use of MFEM's \link petsc.hpp PETSc integration\endlink.
|
||||
*
|
||||
* <H4>PUMI Examples</H4>
|
||||
* - Variants of Examples
|
||||
@@ -124,19 +129,27 @@ namespace mfem {
|
||||
* <a class="el" href="examples_2pumi_2ex1p_8cpp_source.html">1p</a>,
|
||||
* <a class="el" href="pumi_2ex2_8cpp_source.html">2</a>,
|
||||
* and
|
||||
* <a class="el" href="pumi_2ex6p_8cpp_source.html">6p</a>
|
||||
* demonstrating the use of MFEM's \link pumi.hpp PUMI classes\endlink
|
||||
* <a class="el" href="pumi_2ex6p_8cpp_source.html">6p</a>,
|
||||
* demonstrating the use of MFEM's \link pumi.hpp PUMI integration\endlink.
|
||||
*
|
||||
* <H4>HiOp Examples</H4>
|
||||
* <H4>SUNDIALS Examples</H4>
|
||||
* - Variants of Examples
|
||||
* <a class="el" href="hiop_2ex9_8cpp_source.html">9</a> and
|
||||
* <a class="el" href="hiop_2ex9p_8cpp_source.html">9p</a>,
|
||||
* demonstrating the use of MFEM's \link hiop.hpp HiOp classes\endlink
|
||||
* <a class="el" href="sundials_2ex9_8cpp_source.html">9</a>,
|
||||
* <a class="el" href="sundials_2ex9p_8cpp_source.html">9p</a>,
|
||||
* <a class="el" href="sundials_2ex10_8cpp_source.html">10</a>,
|
||||
* <a class="el" href="sundials_2ex10p_8cpp_source.html">10p</a>,
|
||||
* <a class="el" href="sundials_2ex16_8cpp_source.html">16</a>,
|
||||
* and
|
||||
* <a class="el" href="sundials_2ex16p_8cpp_source.html">16p</a>,
|
||||
* demonstrating the use of MFEM's \link sundials.hpp SUNDIALS integration\endlink.
|
||||
* - CVODES adjoint miniapps:
|
||||
* <a class="el" href="cvsRoberts__ASAi__dns_8cpp_source.html">serial ODE system</a>,
|
||||
* <a class="el" href="adjoint__advection__diffusion_8cpp_source.html">parallel advection-diffusion</a>.
|
||||
*
|
||||
* <H4>Ginkgo Examples</H4>
|
||||
* <H4>SuperLU Examples</H4>
|
||||
* - Variants of Example
|
||||
* <a class="el" href="ginkgo_2ex1_8cpp_source.html">1</a>
|
||||
* demonstrating the use of MFEM's \link ginkgo.hpp Ginkgo classes\endlink
|
||||
* <a class="el" href="examples_2superlu_2ex1p_8cpp_source.html">1p</a>,
|
||||
* demonstrating the use of MFEM's \link superlu.hpp SuperLU integration\endlink.
|
||||
*
|
||||
* <H3>Miniapps</H3>
|
||||
* - <a class="el" href="volta_8cpp_source.html">Volta</a>: simple electrostatics simulation code
|
||||
@@ -162,11 +175,11 @@ namespace mfem {
|
||||
* - <a class="el" href="lor-transfer_8cpp_source.html">LOR Transfer</a>: map functions between high-order and low-order refined spaces
|
||||
* - <a class="el" href="findpts_8cpp_source.html">Find Points</a>: evaluate grid function in physical space, <a class="el" href="findpts_8cpp_source.html">serial</a> and <a class="el" href="pfindpts_8cpp_source.html">parallel</a> versions
|
||||
* - <a class="el" href="field-diff_8cpp_source.html">Field Diff</a>: compare grid functions on different meshes
|
||||
* - <a class="el" href="field-interp_8cpp_source.html">Field Interp</a>: transfer a grid functions betwen meshes
|
||||
* - <a class="el" href="field-interp_8cpp_source.html">Field Interp</a>: transfer a grid functions between meshes
|
||||
* - <a class="el" href="miniapps_2performance_2ex1_8cpp_source.html">HPC Example 1</a>: high-performance nodal H1 FEM for the Laplace problem
|
||||
* - <a class="el" href="miniapps_2performance_2ex1p_8cpp_source.html">HPC Example 1p</a>: high-performance parallel nodal H1 FEM for the Laplace problem
|
||||
*
|
||||
* See also the <a class="el" href="../../../examples/README.html">README</a> in the <code>examples/</code> directory
|
||||
* See also the <a class="el" href="https://mfem.org/examples/">examples documentation</a> online.
|
||||
*/
|
||||
|
||||
}
|
||||
|
||||
@@ -5,7 +5,7 @@
|
||||
| | | | | || _|| __/| | | | | |
|
||||
|_| |_| |_||_| \___||_| |_| |_|
|
||||
|
||||
http://mfem.org
|
||||
https://mfem.org
|
||||
|
||||
This directory contains Doxygen configuration files for building HTML
|
||||
documentation of the MFEM sources (including the example codes and miniapps).
|
||||
@@ -21,7 +21,7 @@ create the file CodeDocumentation.html, which can be viewed in any web browser.
|
||||
|
||||
Alternatively, the (pre-build) documentation can be browsed directly online at
|
||||
|
||||
http://mfem.github.io/doxygen/html/index.html
|
||||
https://mfem.github.io/doxygen/html/index.html
|
||||
|
||||
|
||||
Some building considerations:
|
||||
|
||||
|
Before Width: | Height: | Size: 12 KiB After Width: | Height: | Size: 12 KiB |
@@ -13,7 +13,6 @@ SHELL = /bin/bash
|
||||
MFEM_DIR ?= ..
|
||||
DOXYGEN_CONF = CodeDocumentation.conf
|
||||
|
||||
|
||||
# doxygen uses: graphviz, latex
|
||||
html: $(DOXYGEN_CONF)
|
||||
@# Generate the html documentation
|
||||
|
||||
|
Before Width: | Height: | Size: 184 KiB |
@@ -1,208 +0,0 @@
|
||||
body {
|
||||
padding-top: 70px;
|
||||
}
|
||||
|
||||
/* hack to increase height of headers to make #anchors work with the top nav-bar,
|
||||
(note: we only want this on pages with TOC, otherwise there are other problems) */
|
||||
div.col-md-9 h1[id]::before,
|
||||
div.col-md-9 h2[id]::before,
|
||||
div.col-md-9 h3[id]::before,
|
||||
div.col-md-9 h4[id]::before,
|
||||
div.col-md-9 h5[id]::before,
|
||||
div.col-md-9 h6[id]::before {
|
||||
content: "";
|
||||
display: block;
|
||||
margin-top: -75px;
|
||||
height: 75px;
|
||||
}
|
||||
|
||||
img {
|
||||
max-width: 100%;
|
||||
height: auto;
|
||||
}
|
||||
|
||||
pre {
|
||||
overflow-x: auto;
|
||||
}
|
||||
|
||||
pre code {
|
||||
overflow-wrap: normal;
|
||||
white-space: pre;
|
||||
font-size: 13.5px;
|
||||
}
|
||||
|
||||
label {
|
||||
font-weight: normal;
|
||||
}
|
||||
|
||||
ul.nav li.main {
|
||||
font-weight: bold;
|
||||
}
|
||||
|
||||
div.col-md-3 {
|
||||
padding-right: 0;
|
||||
}
|
||||
|
||||
div.col-md-9, div.col-md-12 {
|
||||
padding-bottom: 100px;
|
||||
}
|
||||
|
||||
div.source-links {
|
||||
float: right;
|
||||
}
|
||||
|
||||
img {
|
||||
display: block;
|
||||
margin-left: auto;
|
||||
margin-right: auto;
|
||||
margin-top: 25px;
|
||||
margin-bottom: 25px;
|
||||
}
|
||||
|
||||
img.floatright {
|
||||
display: block;
|
||||
float: right;
|
||||
margin-top: 0;
|
||||
margin-left: 25px;
|
||||
margin-bottom: 25px;
|
||||
}
|
||||
|
||||
img.teamphoto {
|
||||
box-shadow: 4px 4px 4px #999;
|
||||
}
|
||||
|
||||
p.centered {
|
||||
margin-left: auto;
|
||||
margin-right: auto;
|
||||
text-align: center;
|
||||
}
|
||||
|
||||
/*label {
|
||||
display: inline-block;
|
||||
margin-bottom: 5px;
|
||||
font-weight: normal;
|
||||
}*/
|
||||
|
||||
/*
|
||||
* Side navigation
|
||||
*
|
||||
* Scrollspy and affixed enhanced navigation to highlight sections and secondary
|
||||
* sections of docs content.
|
||||
*/
|
||||
|
||||
/* By default it's not affixed in mobile views, so undo that */
|
||||
.bs-sidebar.affix {
|
||||
position: static;
|
||||
}
|
||||
|
||||
.bs-sidebar.well {
|
||||
padding: 0;
|
||||
}
|
||||
|
||||
/* First level of nav */
|
||||
.bs-sidenav {
|
||||
/*margin-top: 10px;
|
||||
margin-bottom: 10px;*/
|
||||
padding-top: 10px;
|
||||
padding-bottom: 10px;
|
||||
border-radius: 5px;
|
||||
}
|
||||
|
||||
/* All levels of nav */
|
||||
.bs-sidebar .nav > li > a {
|
||||
display: block;
|
||||
padding: 5px 20px;
|
||||
z-index: 1;
|
||||
}
|
||||
.bs-sidebar .nav > li > a:hover,
|
||||
.bs-sidebar .nav > li > a:focus {
|
||||
text-decoration: none;
|
||||
border-right: 1px solid;
|
||||
}
|
||||
.bs-sidebar .nav > .active > a,
|
||||
.bs-sidebar .nav > .active:hover > a,
|
||||
.bs-sidebar .nav > .active:focus > a {
|
||||
font-weight: bold;
|
||||
background-color: transparent;
|
||||
border-right: 1px solid;
|
||||
}
|
||||
|
||||
/* Nav: second level (shown on .active) */
|
||||
.bs-sidebar .nav .nav {
|
||||
display: none; /* Hide by default, but at >768px, show it */
|
||||
margin-bottom: 8px;
|
||||
}
|
||||
.bs-sidebar .nav .nav > li > a {
|
||||
padding-top: 3px;
|
||||
padding-bottom: 3px;
|
||||
padding-left: 30px;
|
||||
font-size: 90%;
|
||||
}
|
||||
|
||||
/* Show and affix the side nav when space allows it */
|
||||
@media (min-width: 992px) {
|
||||
.bs-sidebar .nav > .active > ul {
|
||||
display: block;
|
||||
}
|
||||
/* Widen the fixed sidebar */
|
||||
.bs-sidebar.affix,
|
||||
.bs-sidebar.affix-bottom {
|
||||
width: 213px;
|
||||
}
|
||||
.bs-sidebar.affix {
|
||||
position: fixed; /* Undo the static from mobile first approach */
|
||||
top: 80px;
|
||||
}
|
||||
.bs-sidebar.affix-bottom {
|
||||
position: absolute; /* Undo the static from mobile first approach */
|
||||
}
|
||||
.bs-sidebar.affix-bottom .bs-sidenav,
|
||||
.bs-sidebar.affix .bs-sidenav {
|
||||
margin-top: 0;
|
||||
margin-bottom: 0;
|
||||
}
|
||||
}
|
||||
@media (min-width: 1200px) {
|
||||
/* Widen the fixed sidebar again */
|
||||
.bs-sidebar.affix-bottom,
|
||||
.bs-sidebar.affix {
|
||||
width: 263px;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/* Sticky footer styles
|
||||
-------------------------------------------------- */
|
||||
html {
|
||||
position: relative;
|
||||
min-height: 100%;
|
||||
}
|
||||
body {
|
||||
/* Margin bottom by footer height */
|
||||
margin-bottom: 50px;
|
||||
}
|
||||
.footer {
|
||||
position: absolute;
|
||||
bottom: 0;
|
||||
width: 100%;
|
||||
/* Set the fixed height of the footer here */
|
||||
height: 50px;
|
||||
background-color: #eeeeee;
|
||||
overflow: hidden;
|
||||
}
|
||||
|
||||
|
||||
/* Custom page CSS
|
||||
-------------------------------------------------- */
|
||||
/* Not required for template or sticky footer method. */
|
||||
|
||||
.container .text-muted {
|
||||
margin-top: 17px;
|
||||
margin-bottom: 0;
|
||||
}
|
||||
.container .alignleft {
|
||||
float: left;
|
||||
}
|
||||
.container .alignright {
|
||||
float: right;
|
||||
}
|
||||
|
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|
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@@ -34,6 +34,7 @@ list(APPEND ALL_EXE_SRCS
|
||||
ex25.cpp
|
||||
ex26.cpp
|
||||
ex27.cpp
|
||||
ex91.cpp
|
||||
)
|
||||
|
||||
if (MFEM_USE_MPI)
|
||||
@@ -117,16 +118,21 @@ if (MFEM_USE_SUPERLU)
|
||||
${MPIEXEC_POSTFLAGS})
|
||||
endif()
|
||||
|
||||
# Include the examples/sundials directory if SUNDIALS is enabled.
|
||||
if (MFEM_USE_SUNDIALS)
|
||||
add_subdirectory(sundials)
|
||||
# Include the examples/amgx directory if AmgX is enabled
|
||||
if (MFEM_USE_AMGX)
|
||||
add_subdirectory(amgx)
|
||||
endif()
|
||||
|
||||
# Include the examples/sundials directory if SUNDIALS is enabled.
|
||||
# Include the examples/ginkgo directory if GINKGO is enabled.
|
||||
if (MFEM_USE_GINKGO)
|
||||
add_subdirectory(ginkgo)
|
||||
endif()
|
||||
|
||||
# Include the examples/hiop directory if HiOp is enabled
|
||||
if (MFEM_USE_HIOP)
|
||||
add_subdirectory(hiop)
|
||||
endif()
|
||||
|
||||
# Include the examples/petsc directory if PETSc is enabled.
|
||||
if (MFEM_USE_PETSC)
|
||||
add_subdirectory(petsc)
|
||||
@@ -137,7 +143,12 @@ if (MFEM_USE_PUMI)
|
||||
add_subdirectory(pumi)
|
||||
endif()
|
||||
|
||||
if (MFEM_USE_HIOP)
|
||||
add_subdirectory(hiop)
|
||||
# Include the examples/sundials directory if SUNDIALS is enabled.
|
||||
if (MFEM_USE_SUNDIALS)
|
||||
add_subdirectory(sundials)
|
||||
endif()
|
||||
|
||||
# Include the examples/superlu directory if SUPERLU is enabled.
|
||||
if (MFEM_USE_SUPERLU)
|
||||
add_subdirectory(superlu)
|
||||
endif()
|
||||
|
||||
@@ -0,0 +1,79 @@
|
||||
# Copyright (c) 2010-2020, 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.
|
||||
|
||||
set(AMGX_EXAMPLES_SRCS)
|
||||
list(APPEND AMGX_EXAMPLES_SRCS
|
||||
ex1.cpp
|
||||
)
|
||||
|
||||
if (MFEM_USE_MPI)
|
||||
list(APPEND AMGX_EXAMPLES_SRCS
|
||||
ex1p.cpp
|
||||
)
|
||||
endif()
|
||||
|
||||
set(AMGX_JSON_FILES amg_pcg.json multi_gs.json precon.json)
|
||||
|
||||
# Include the source directory where mfem.hpp and mfem-performance.hpp are.
|
||||
include_directories(BEFORE ${PROJECT_BINARY_DIR})
|
||||
|
||||
# Add targets to copy *.json files from the source directory
|
||||
foreach(JSON_FILE ${AMGX_JSON_FILES})
|
||||
add_custom_command(OUTPUT ${JSON_FILE}
|
||||
COMMAND ${CMAKE_COMMAND} -E copy_if_different
|
||||
${CMAKE_CURRENT_SOURCE_DIR}/${JSON_FILE} ${JSON_FILE}
|
||||
COMMENT "copy ${JSON_FILE}")
|
||||
endforeach()
|
||||
add_custom_target(copy_amgx_json_files DEPENDS ${AMGX_JSON_FILES}
|
||||
COMMENT "Copying AMGX example json files ...")
|
||||
|
||||
# Add "test_amgx" target, see below.
|
||||
add_custom_target(test_amgx
|
||||
${CMAKE_CTEST_COMMAND} -R amgx USES_TERMINAL)
|
||||
|
||||
# Add one executable per cpp file, adding "amgx_" as prefix. Sets
|
||||
# "copy_amgx_json_files" as a prerequisite for the given examples. Also, sets
|
||||
# "test_amgx" as a target that depends on the given examples.
|
||||
set(PFX amgx_)
|
||||
add_mfem_examples(AMGX_EXAMPLES_SRCS ${PFX} copy_amgx_json_files test_amgx)
|
||||
|
||||
# Testing.
|
||||
# The AMGX tests can be run separately using the target "test_amgx"
|
||||
# which builds the examples and runs:
|
||||
# ctest -R amgx
|
||||
|
||||
# Command line options for the tests.
|
||||
# Example 1/1p:
|
||||
set(EX1_TEST_OPTS)
|
||||
set(EX1P_TEST_OPTS)
|
||||
|
||||
# Add the tests: one test per source file.
|
||||
foreach(SRC_FILE ${AMGX_EXAMPLES_SRCS})
|
||||
get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
|
||||
string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
|
||||
string(TOUPPER ${TEST_NAME} UP_TEST_NAME)
|
||||
set(TEST_NAME ${PFX}${TEST_NAME})
|
||||
|
||||
set(THIS_TEST_OPTIONS "-no-vis")
|
||||
list(APPEND THIS_TEST_OPTIONS ${${UP_TEST_NAME}_TEST_OPTS})
|
||||
# message(STATUS "Test ${TEST_NAME} options: ${THIS_TEST_OPTIONS}")
|
||||
|
||||
if (NOT (${TEST_NAME} MATCHES ".*p$"))
|
||||
add_test(NAME ${TEST_NAME}_ser
|
||||
COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
|
||||
else()
|
||||
add_test(NAME ${TEST_NAME}_np=${MFEM_MPI_NP}
|
||||
COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
|
||||
${MPIEXEC_PREFLAGS}
|
||||
$<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
|
||||
${MPIEXEC_POSTFLAGS})
|
||||
endif()
|
||||
endforeach()
|
||||
@@ -0,0 +1,18 @@
|
||||
Finite Element Discretization Library
|
||||
__
|
||||
_ __ ___ / _| ___ _ __ ___
|
||||
| '_ ` _ \ | |_ / _ \| '_ ` _ \
|
||||
| | | | | || _|| __/| | | | | |
|
||||
|_| |_| |_||_| \___||_| |_| |_|
|
||||
|
||||
https://mfem.org
|
||||
|
||||
This directory contains modifications of the example codes that illustrate the
|
||||
use of MFEM features based on NVIDIA's multigrid library AmgX.
|
||||
|
||||
To build these examples, make sure that MFEM is configured with the option
|
||||
"MFEM_USE_AMGX = YES", see the top-level INSTALL file for details (version
|
||||
2.1 of AmgX is recommended, though older versions may work too.
|
||||
|
||||
We recommend comparing the original example codes with the corresponding files
|
||||
in the current directory.
|
||||