Diffusion tamaas f815d803f869

Merge branch 'master' into features/netcdf-mpi
f815d803f869
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Authored by frerot on Jun 16 2021, 02:06.

Description

Merge branch 'master' into features/netcdf-mpi

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Committed

frerot

Jun 16 2021, 02:06

Pushed

frerot

Jun 16 2021, 15:50

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rTAMAASf9a64f324845: [ci] correct verbose flag for twine
rTAMAASb3bc153777cb: tentative parallel implementation of NetCDFDumper

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frerot committed rTAMAASf815d803f869: Merge branch 'master' into features/netcdf-mpi (authored by frerot).Jun 16 2021, 02:06

Merged Changes

This commit merges a very large number of changes. Only the first 50 are shown.

Commit	Author	Details	Committed
f9a64f324845	frerot	[ci] correct verbose flag for twine	Jun 15 2021
fe4baf6011aa	frerot	[ci] only deploying wheels when tests are passing	Jun 15 2021
05b51c6db299	frerot	[ci] activate wheels build on tag	Jun 15 2021
dd5bfe56473c	frerot	[ci] moving wheels step to build	Jun 15 2021
a26e113c41ca	frerot	[ci] setup continuous delivery	Jun 15 2021
96560b231bb5	frerot	[ci] keeping tests logs	Jun 11 2021
79355c2aefe7	frerot	migrated repository to gitlab	Jun 11 2021
e9062e2f90fd	frerot	[ci] fixed wrongly placed post{} + cleanup	Jun 10 2021
1fc7644bad52	frerot	cleaned up license headers	Jun 10 2021
f4302c1266be	frerot	[ci] indentation	Jun 10 2021
e51cb6a111e9	frerot	[ci] removed node	Jun 9 2021
d6be11d5e367	frerot	[ci] moved node in stages	Jun 9 2021
468043414b64	frerot	[ci] trying to use nodes	Jun 9 2021
f3a409f8261b	frerot	[ci] always upload artifacts	Jun 9 2021
ae683ba73eaa	frerot	[ci] changed hbm command names	Jun 9 2021
9fe244aa2311	frerot	[ci] restablished debian image for docker	Jun 9 2021
a53ea126d89c	frerot	[ci] logging and archiving test results	Jun 9 2021
e54b07ea498d	frerot	[ci] added libopenmpi-dev to docker image	Jun 9 2021
abfdd8cd28b0	frerot	stop compile if basic checks are not satisfied	Jun 9 2021
63dab2b443c2	frerot	[ci] trying different technique to save artifacts	Jun 9 2021
dd81cd4ff6c0	frerot	[ci] also saving artifacts in jenkins	Jun 9 2021
ecc1eaeea050	frerot	[ci] correct subcommands names	Jun 9 2021
249346cbbecf	frerot	trying to fix jenkins by fixing dependency resolution order and locales	Jun 9 2021
1ab45bfb8b10	frerot	[doc] using full `numpy` name instead of `np`	Jun 9 2021
e76bb9e66413	frerot	added more docstrings	Jun 9 2021
b4f0f816450c	frerot	using a cuda-enabled docker image	Jun 9 2021
1de4d8b950ca	frerot	added docstrings to some python function bindings	Jun 9 2021
de1480b0e7ae	frerot	compiling tests with cuda	Jun 2 2021
cdc6ac1a08f9	frerot	correctly computing contact area in mpi context	Jun 1 2021
3d1b4c64338f	frerot	corrected includes for cpp tests	May 31 2021
c36392a99574	frerot	re-established sort order for eigenvalues	May 31 2021
fd9661c88813	frerot	removing remnants of fftw's interface	May 29 2021
7faf5c9d3692	frerot	added experimental cuda warning	May 29 2021
0ae1a96db417	frerot	not linking against fftw if cuda is used	May 28 2021
d1dc26e4556a	frerot	reorganized fftw files in their own directory	May 28 2021
4f55fed67f6d	frerot	cosmetic changes to compile command output	May 28 2021
fde6a532b8a1	frerot	Merge branch 'master' into features/cuda	May 28 2021
2baa944ac358	frerot	always compiling mpi_interface.cpp	May 28 2021
0257e3cb2f4e	frerot	making the whole library compile with cuda	May 28 2021
6b9140c22c9b	frerot	fft engine for cuda	May 28 2021
cb90433efaab	frerot	more progress to have tamaas compile with nvcc	May 27 2021
12d9012653a6	frerot	[doc] spacing bullet list items	May 26 2021
5a30f4e328d1	frerot	removing dirty tag in sphinx version string	May 26 2021
7e692627014a	frerot	ensuring uniform surface generator seed accross processes	May 25 2021
0f189d10cd98	frerot	more compatibility with cuda	May 19 2021
31f5a4526a6e	frerot	manually sorting eigenvalues instead of thrust::sort	May 19 2021
c159445c87fb	frerot	using cuda-compatible exchange function instead of std::exchange	May 19 2021
227f8de0a319	frerot	avoiding pointless comparison with 0 warning	May 19 2021
b2df7a0d87de	frerot	__device__, __host__, CUDA_LAMBDA annotations	May 19 2021
c75736b11338	frerot	compatibility changes to cuda in scons	May 19 2021

Changes (265)
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Very Large Commit

This commit is very large. Load each file individually.

		Path
A		.gitattributes
M		.gitlab-ci.yml
M		.gitmodules
M		AUTHORS
M		CHANGELOG.md
P		Dockerfile Deleted after being copied to multiple locations: tests/ci/docker/debian.mpi tests/ci/docker/ubuntu_lts.cuda
M		INFOS.py
M		Jenkinsfile
M		README.md
M		SConstruct
M		doc/SConscript
M		doc/icon.svg
M		doc/sphinx/source/conf.py
M		doc/sphinx/source/contact.rst
M		doc/sphinx/source/index.rst
M		doc/sphinx/source/model.rst
M		doc/sphinx/source/overview.rst
M		doc/sphinx/source/performance.rst
M		doc/sphinx/source/quickstart.rst
M		doc/sphinx/source/rough_surfaces.rst
M		examples/adhesion.py
M		examples/pipe_tools/contact
M		examples/pipe_tools/plot
M		examples/pipe_tools/surface
M		examples/plasticity.py
M		examples/rough_contact.py
M		examples/saturated.py
M		examples/statistics.py
M		examples/stresses.py
M		python/SConscript
M		python/cast.hh
M		python/numpy.hh
M		python/setup.py.in
M		python/tamaas/__init__.py.in
M		python/tamaas/__main__.py
A		python/tamaas/_version.py
M		python/tamaas/compute.py
M		python/tamaas/dumpers/__init__.py
M		python/tamaas/dumpers/_helper.py
M		python/tamaas/nonlinear_solvers/__init__.py
M		python/tamaas_module.cpp
M		python/wrap.hh
M		python/wrap/compute.cpp
M		python/wrap/core.cpp
M		python/wrap/model.cpp
M		python/wrap/model_extensions.hh
M		python/wrap/mpi.cpp
M		python/wrap/percolation.cpp
M		python/wrap/solvers.cpp
M		python/wrap/surface.cpp
M		python/wrap/test_features.cpp
M		site_scons/detect.py
M		site_scons/site_init.py
M		site_scons/site_tools/doxygen.py
M		site_scons/site_tools/nvcc.py
M		site_scons/site_tools/sphinx.py
M		site_scons/site_tools/tamaas.py
M		site_scons/version.py
M		src/SConscript
M		src/core/array.hh
M		src/core/computes.cpp
M		src/core/computes.hh
A	(dir)	src/core/cuda/
P		src/core/cuda/cufft_engine.cpp Copied from src/core/fftw_engine.cpp
P		src/core/cuda/cufft_engine.hh Copied from src/core/fftw_engine.hh
V		src/{core/cuda ← gpu}/unified_allocator.hh
M		src/core/fft_engine.cpp
M		src/core/fft_engine.hh
A	(dir)	src/core/fftw/
V		src/core/{fftw ← }/fftw_allocator.hh
V		src/core/{fftw ← }/fftw_engine.cpp
V		src/core/{fftw ← }/fftw_engine.hh
P		src/core/fftw/interface.hh Copied from src/mpi/mpi_interface.cpp
V		src/core/{fftw/interface_impl.hh ← fftw_interface.hh}
A	(dir)	src/core/fftw/mpi/
V		src/{core/fftw ← }/mpi/fftw_mpi_engine.cpp
V		src/{core/fftw ← }/mpi/fftw_mpi_engine.hh
V		src/{core/fftw/mpi/interface.hh ← mpi/fftw_mpi_interface.hh}
V		src/core/{ → fftw}/fftw_allocator.hh
P		src/core/fftw_engine.cpp Deleted after being copied to multiple locations: src/core/cuda/cufft_engine.cpp src/core/fftw/fftw_engine.cpp
P		src/core/fftw_engine.hh Deleted after being copied to multiple locations: src/core/cuda/cufft_engine.hh src/core/fftw/fftw_engine.hh
V		src/core/{fftw_interface.hh → fftw/interface_impl.hh}
M		src/core/grid.cpp
M		src/core/grid.hh
M		src/core/grid_base.hh
M		src/core/grid_hermitian.cpp
M		src/core/grid_hermitian.hh
M		src/core/grid_tmpl.hh
M		src/core/grid_view.hh
M		src/core/iterator.hh
M		src/core/logger.cpp
M		src/core/logger.hh
M		src/core/loop.cpp
M		src/core/loop.hh
M		src/core/loops/apply.hh
M		src/core/loops/loop_utils.hh
V		src/{core ← mpi}/mpi_interface.cpp
V		src/{core ← mpi}/mpi_interface.hh
V		src/{core ← mpi}/partitioner.hh
M		src/core/ranges.hh
M		src/core/static_types.hh
M		src/core/statistics.cpp
M		src/core/statistics.hh
D		src/core/surface_complex.hh
M		src/core/tamaas.cpp
M		src/core/tamaas.hh
D		src/gpu
D		src/gpu/fftransform_cufft.cpp
D		src/gpu/fftransform_cufft.hh
V		src/{gpu → core/cuda}/unified_allocator.hh
M		src/model/adhesion_functional.cpp
M		src/model/adhesion_functional.hh
M		src/model/be_engine.cpp
M		src/model/be_engine.hh
M		src/model/boussinesq.cpp
M		src/model/boussinesq.hh
M		src/model/boussinesq_helper.hh
M		src/model/elastic_functional.cpp
M		src/model/elastic_functional.hh
M		src/model/elasto_plastic/isotropic_hardening.cpp
M		src/model/elasto_plastic/isotropic_hardening.hh
M		src/model/elasto_plastic/residual.cpp
M		src/model/elasto_plastic/residual.hh
M		src/model/functional.hh
M		src/model/hooke.cpp
M		src/model/hooke.hh
M		src/model/influence.hh
M		src/model/integral_operator.cpp
M		src/model/integral_operator.hh
M		src/model/integration/accumulator.hh
M		src/model/integration/element.cpp
M		src/model/integration/element.hh
M		src/model/integration/integrator.hh
M		src/model/kelvin.cpp
M		src/model/kelvin.hh
M		src/model/kelvin_helper.hh
M		src/model/meta_functional.cpp
M		src/model/meta_functional.hh
M		src/model/mindlin.cpp
M		src/model/mindlin.hh
M		src/model/model.cpp
M		src/model/model.hh
M		src/model/model_dumper.hh
M		src/model/model_factory.cpp
M		src/model/model_factory.hh
M		src/model/model_template.cpp
M		src/model/model_template.hh
M		src/model/model_type.cpp
M		src/model/model_type.hh
M		src/model/volume_potential.cpp
M		src/model/volume_potential.hh
M		src/model/westergaard.cpp
M		src/model/westergaard.hh
D		src/mpi
V		src/{ → core/fftw}/mpi/fftw_mpi_engine.cpp
V		src/{ → core/fftw}/mpi/fftw_mpi_engine.hh
V		src/{mpi/fftw_mpi_interface.hh → core/fftw/mpi/interface.hh}
P		src/mpi/mpi_interface.cpp Deleted after being copied to multiple locations: src/core/fftw/interface.hh src/core/mpi_interface.cpp
V		src/{mpi → core}/mpi_interface.hh
V		src/{mpi → core}/partitioner.hh
M		src/percolation/flood_fill.cpp
M		src/percolation/flood_fill.hh
M		src/solvers/beck_teboulle.cpp
M		src/solvers/beck_teboulle.hh
M		src/solvers/condat.cpp
M		src/solvers/condat.hh
M		src/solvers/contact_solver.cpp
M		src/solvers/contact_solver.hh
M		src/solvers/dfsane_solver.cpp
M		src/solvers/dfsane_solver.hh
M		src/solvers/ep_solver.cpp
M		src/solvers/ep_solver.hh
M		src/solvers/epic.cpp
M		src/solvers/epic.hh
M		src/solvers/kato.cpp
M		src/solvers/kato.hh
M		src/solvers/kato_saturated.cpp
M		src/solvers/kato_saturated.hh
M		src/solvers/polonsky_keer_rey.cpp
M		src/solvers/polonsky_keer_rey.hh
M		src/solvers/polonsky_keer_tan.cpp
M		src/solvers/polonsky_keer_tan.hh
M		src/surface/filter.hh
M		src/surface/isopowerlaw.cpp
M		src/surface/isopowerlaw.hh
M		src/surface/regularized_powerlaw.cpp
M		src/surface/regularized_powerlaw.hh
M		src/surface/surface_generator.cpp
M		src/surface/surface_generator.hh
M		src/surface/surface_generator_filter.cpp
M		src/surface/surface_generator_filter.hh
M		src/surface/surface_generator_random_phase.cpp
M		src/surface/surface_generator_random_phase.hh
M		src/tamaas_info.cpp.in
M		src/tamaas_info.hh
M		tests/SConscript
A		tests/ci/build_wheels.sh
A	(dir)	tests/ci/docker/
P		tests/ci/docker/debian.mpi Copied from Dockerfile
A		tests/ci/docker/manylinux
V		{tests/ci/docker/ubuntu_lts.cuda ← Dockerfile}
M		tests/conftest.py
M		tests/fftfreq.py
M		tests/mpi_routines.py
M		tests/tamaas_gtest_main.cc
M		tests/test.hh
D		tests/test_autocorrelation.py
D		tests/test_bem_grid.py
M		tests/test_boussinesq_surface.py
A		tests/test_cufft.cpp
M		tests/test_dumper.py
M		tests/test_epic.py
V		tests/{test_fft.cpp → test_fftw.cpp}
M		tests/test_fftfreq.cpp
V		tests/{test_fftw.cpp ← test_fft.cpp}
M		tests/test_flood_fill.py
M		tests/test_grid.cpp
M		tests/test_gtest.py
M		tests/test_hertz.py
M		tests/test_hertz_disp.py
M		tests/test_hertz_kato.py
M		tests/test_integral_operators.py
M		tests/test_integration.cpp
M		tests/test_loop.cpp
M		tests/test_memory.py
M		tests/test_model.cpp
M		tests/test_mpi.cpp
M		tests/test_mpi_routines.py
M		tests/test_patch_plasticity.py
M		tests/test_patch_westergaard.py
M		tests/test_rough_surface.cpp
M		tests/test_saturated_pressure.py
M		tests/test_static_types.cpp
M		tests/test_surface.py
M		tests/test_tangential.py
M		tests/test_voigt.py
M		tests/test_westergaard.py
A	(dir)	third-party/expolit/
A		third-party/expolit/.clang-format
A		third-party/expolit/.gitignore
A		third-party/expolit/.gitmodules
A		third-party/expolit/AUTHORS
A		third-party/expolit/Doxyfile
A		third-party/expolit/LICENSE.md
A		third-party/expolit/README.md
A	(dir)	third-party/expolit/benchmarks/
A		third-party/expolit/benchmarks/.gitignore
A		third-party/expolit/benchmarks/SConstruct
A		third-party/expolit/benchmarks/benchmark.cc
A	(dir)	third-party/expolit/benchmarks/site_scons/
A		third-party/expolit/benchmarks/site_scons/detect.py
A	(dir)	third-party/expolit/include/
A	(dir)	third-party/expolit/include/expolit/
A		third-party/expolit/include/expolit/differentiation.hh
A		third-party/expolit/include/expolit/expolit
A		third-party/expolit/include/expolit/exponential.hh
A		third-party/expolit/include/expolit/integration.hh
A		third-party/expolit/include/expolit/litteral.hh
A		third-party/expolit/include/expolit/operations.hh
A		third-party/expolit/include/expolit/polynomial.hh
A		third-party/expolit/include/expolit/types.hh
A	(dir)	third-party/expolit/tests/
A		third-party/expolit/tests/SConstruct
A		third-party/expolit/tests/tests_gtest.cc
A		versioneer.py