Merge pull request #1881 from CEED/SirAlienTheGreat/rust-qfunctions

Rust and cuda clang support (#1873)

clang - keep temp files from overwriting each other

Rust and cuda clang support (#1873)

* Switch compiler to clang (not portable)

* test add_num

* compile with llvm tools

* not working linking

* not fixed

* Update ex1-volume.h

* update

* remov

Rust and cuda clang support (#1873)

* Switch compiler to clang (not portable)

* test add_num

* compile with llvm tools

* not working linking

* not fixed

* Update ex1-volume.h

* update

* remove global path

* changes

* changes 2

* crate works

* basic gpu rust compilation

* still not working

* rust source roots basic support

* nvrtc/clang selection

* cleanup

* update example (not working)

* add rust example

* fix merge issue

* delete temp files

* cleanup

* rust qfunc 2d array (needs doc)

* cleanup

* more cleanup

* downgrade back to c++11

* format

* final draft cleanup

* formatting + CUDA_CLANG -> GPU_CLANG

* Update cuda CEED_QFUNCTION_RUST

* fix python

* fix python and format

* format fr

* update comment

* fix python fr

* Apply error suggestions from code review

* update errors to libceed format

* Apply suggestions from code review

* add optimization flag

* remove line breaks

* Apply suggestions from code review

* avoid python in macro better

* add rust example

* format

* Apply suggestions from code review

* move rust example to own directory

* Simplify python exclusion logic

* re-fix python

* Update python/build_ceed_cffi.py

* change names and simplify makefile

* Revert "change names and simplify makefile"

This reverts commit 96e762f9f5d50d8ed9d3673e7fda850dfc390abe.

* Apply Jeremy's diff

* Simplify CeedCallSystem

* use rust-install llvm tools

* add gitignores

* update paths

* example absolute path

* fix comments

* apply partial diff

* add newline

* add makefile

* Update examples/rust-qfunctions/Makefile

* update makefile

---------

Co-authored-by: Allen MacFarland <alma4974@noether>

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Merge pull request #1880 from CEED/zach/update-gitignore

Add .venv to gitignore

Add .venv to gitignore

Merge pull request #1752 from CEED/zach/update-gitignore

Add common profiling outputs to .gitignore

clean up duplicates

Add common profiling outputs to .gitignore

Merge pull request #1531 from CEED/jrwrigh/gitignore_test_dir

chore: Add tests/test_dir to .gitignore

chore: Add tests/test_dir to .gitignore

This directory is created by the fluids smartsim regression test. If the
test is successful, then the directory is deleted. If it is not, this is
left over, f

chore: Add tests/test_dir to .gitignore

This directory is created by the fluids smartsim regression test. If the
test is successful, then the directory is deleted. If it is not, this is
left over, for debugging purposes.

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Merge pull request #1529 from CEED/jrwrigh/fix_multiplicity_training

fluids: Fix SmartSim training multiplicity, add GetInverseMultiplicity

fluids: Test zbox in SmartSim test

This tests whether the output training data handles multiplicity
correctly. And also is the first fluids test with zbox.

Merge pull request #1448 from CEED/jed/doc-update-backends-diagram

doc: update libCEEDBackends.svg

doc: update libCEEDBackends.svg

* include .tex source for future updates
* latex .gitignore

DMSwarm Example with Interpolation and Projection (#1284)

* petsc - initial DMSwarm example

* swarm - links and runs

* swarm - fixed default box dims

* swarm - clearer error messages

* s

DMSwarm Example with Interpolation and Projection (#1284)

* petsc - initial DMSwarm example

* swarm - links and runs

* swarm - fixed default box dims

* swarm - clearer error messages

* swarm - clearer background mesh setup requirements

* swarm - Tensor bad :(

* Fix inequality direction for verification

* swarm - add viewing command

* swarm - DMSwarmPICField_coor

* swarm - DMSwarmGetCellDM

* swarm - dm_plex_hash_location true

* fix coordinate ordering

* "working" two-way projection

* libceed mostly correct, off by a permutation or something

* add tolerance parameter and make test succeed

* Use DMProjectFunction to support high-order bases

* minor clarity change

* prefer PetscPrintf over printf

* consistency

* minor - make uniform vs sin distributed points cl option

* fix VLA declaration

* minor reorganizing

* swarm value check in separate fn

* minor reorg and rename

* style

* separate interpolate logic into its own fns

* consistency

* fix error message

* woops, use field name arg

* improve indexing, switch to uniform for test

* fix multiple comp

* drop unused function

* draft documentation

* style

* Update PETSc style documentation

Co-authored-by: Zach Atkins <zach.atkins@colorado.edu>

* Update examples/petsc/dmswarm.c

* add create/destroy for ceed ctx object

* use libCEED rstr

* add P2C/C2P utils

* minor simplifications

* add projection swarm to mesh

* minor

* update gitignore

* add gauss point locations, lumped comparison

* simplify uniform/gauss coords logic

* fix segfault

* drop comparison - can replicate with CL options

* add polynomial target option

* minor tidying

* revert accidental change

* lumped test

* update tolerance option description

Co-authored-by: Zach Atkins <zach.atkins@colorado.edu>

* add points_per_cell option

* Fix siliness by Jeremy

Co-authored-by: Zach Atkins <zach.atkins@colorado.edu>

* fix scoping and logic

* style

* discontinuous sphere target

* add cellwise random swarm

---------

Co-authored-by: Zach Atkins <zach.atkins@colorado.edu>

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Vortex shedding / flow past cylinder (#1082)

* add vortex shedding problem

* add file for the Qfunctions

* add yaml file

* update problem setup

* update IC qfunc

* update problem set

Vortex shedding / flow past cylinder (#1082)

* add vortex shedding problem

* add file for the Qfunctions

* add yaml file

* update problem setup

* update IC qfunc

* update problem setup

* update initial condition

* update yaml file

* add mesh file

* add vortexshedding to navierstokes.h

* register vortexshedding to cloptions.c

* update configuration/yaml file

* fix Min function

* examples/fluids: fix boundary condition labels for cylinder

$PhysicalNames
6
2 1 "inlet"
2 2 "outlet"
2 3 "top"
2 4 "bottom"
2 5 "cylinderwalls"
2 6 "frontandback"
$EndPhysicalNames

* update QFunctions in navierstokes.c

* update data and BC structs in navierstokes.h

* update vortexshedding.c

* update states

* update IC in vortexshedding.h

* add freestream BC to cloptions

* updates in setuplibceed.c

* include freestream BC in example

* cleanup duplicate variable names

* rename variables as freestream

* clean-up some warning messages

* clean up example

* add cylinder.geo

* label physical volume

* examples/fluids: fix cylinder mesh and add vortexshedding defaults

* update gravity vector

* examples/fluids: match domain to Shakib, get vortex street

* update to quadratic mesh

* clean up yaml file

* delete vortexshedding.c and vortexshedding.h

* remove vortexshedding from register

* update yaml file

* examples/fluids: Newtonian "still" initial condition

Reinstate outflow boundaries that were previously removed so that
existing tests can pass.

* examples/fluids: freestream inherits reference state

Fix freestream context reference counting bug.

* examples/fluids: avoid designated initializer in kernel code (breaks CUDA)

* add Shakib91 to references

* remove cylinder.geo and cylinder.msh

* wip:add documentation for vortex shedding

* update path to cylinder.msh

* add subdirectory for meshes

* parameterize cylinder.geo

* some fixes in cylinder.geo

* Fix cylinder.geo file

* examples/fluids: fix up mesh parametrization

Fix cylinder size (the function is Sqrt, not sqrt) and parametrize
resolution and aspect.

* examples/fluids: fix build after broken merge from main

* update Shakib1991 in references

* wip:docs for vortex shedding

* remove TODO comment

* reformulate docs

* fix docs

* delete cylinder.msh file

* work on documentation

* add vortex runtime options

* examples/fluids: update vortex shedding docs and mesh

Co-authored-by: Jed Brown <jed@jedbrown.org>

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Merge pull request #1124 from CEED/jed/release-0.11

Release 0.11

gitignore: cgns and webm

Rust - add examples (#683)

* Rust - initial version of ex1

Example - move closure

Co-authored-by: Jed Brown <jed@jedbrown.org>

typo fix

Co-authored-by: Jed Brown <jed@jedbrown.org>

mi

Rust - add examples (#683)

* Rust - initial version of ex1

Example - move closure

Co-authored-by: Jed Brown <jed@jedbrown.org>

typo fix

Co-authored-by: Jed Brown <jed@jedbrown.org>

minor tidying

order -> degree

drop operator applicaiton messages

* rust: make top-level workspace and use libceed from path

This allows a single "cargo test" from the top level.

* rust: add version-sync (to help us remember when we publish a crate)

* examples - consistency update

* Rust - add Cargo.lock to top level gitignore

* rust - refactor example to add tests

* Rust - test and style from workspace

* Rust - update year in header

* Rust - add error values to Error, switch to String

* Rust - add input validation in check

* Rust - format volume output in example

* Rust - update example help output

* Rust - example tests rename to simplify

* Rust - split example 1 into 3 parts

* rust: std::sync::Once for CeedRegisterAll()

* Promote CeedRegisterAll() and CeedQFunctionRegisterAll() to User
* Guard calls to CeedInit() to avoid races in parallel testing

* Examples - update rust example to new builder syntax

* Examples - add rust ex2

* Rust - add CEED_STRIDES_BACKEND

* Examples - drop unused restriction in ceed ex2

* Rust - minor documentation update

* Rust - adopt convention of 'dimension-like' values all using usize; reduces casting

* Actions - add Rust code coverage

* Rust - fix usize conversion

* Rust - update casting between i32(C interface) and usize(Rust interface)

* Actions - include Rust doctests

* Actions - Rust doctest coverange only avaliable in nightly

* Rust - drop explict typing of values passed to C get* functions

* Rust - modify version numbers tests, cargo-tarpaulin and cargo have different calling paths in tests

* cargo fmt

* Examples - add separate Rust example quiet mode

* Actions - rustfmt not always avaliable on nightly

* Rust - simplify version tests

* Actions - add a few notes

* CodeCov - try adding gallery to 'fixes'

* CodeCov - drop some codecov noise in examples

* Examples - test all combinations in ex1/ex2

* Rust - test 3d examples without quiet flag

* Actions - use gcc-10 for compatibility in gcov reports

* Examples - test gallery in 1/2/3d in Rust ex

* Gitlab - also report gcov version

* JUnit - adjust indentation

* Gitlab - make it easier to find complier info in logs

* Tests - fix minor styling strangeness in t002

* Actions - only upload rust coverage

* Actions - exclude non-rust files from rust coverage

* Cov - exclude weak symbols code, not useful cov info

* Examples - clean up options creation for tests in Rust examples

* Examples - simplify tolerance for testing Rust examples

* cargo fmt

* Examples - another match

* Examples - common Rust example code in shared local crate

Co-authored-by: Jed Brown <jed@jedbrown.org>

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Merge pull request #674 from CEED/jed/static-link

static link

gitignore: output formats and .cache for clangd

Merge branch 'main' into yohann/fix-cuda-gen

OCCA Backend Update (#305)

* [Docs] Update docs for new OCCA backend

* [Fortran] CeedVectorRestoreArray fix

* [Test] Updates t002-ceed test to support query params

* [Make] Adds tidy for cp

OCCA Backend Update (#305)

* [Docs] Update docs for new OCCA backend

* [Fortran] CeedVectorRestoreArray fix

* [Test] Updates t002-ceed test to support query params

* [Make] Adds tidy for cpp files

* [OCCA] Updates OCCA backend

* PR feedback: Update StrideType naming

* PR feedback: Fixed USER_STRIDES vs BACKEND_STRIDES usage

* [OCCA] Add comments to code generation

* [CI] Removes commit from OCCA build

* PR Feedback: Update README

* PR Feedback: Removed compiler warnings

* Fix restriction function changes

* occa: track AssembleLinear -> LinearAssemble

* [OCCA][Vector] Adds takeArray method

* [OCCA][Restriction] Fixes restriction strides

* [OCCA][Operator] Adds point block diagonal registration

* [OCCA][Operator] Fixes

* OCCA - update debug color for visability

* Travis - fix extra fi

* OCCA - adjust kernel, multi component derivatives are expected as [dim][comp][q]

* OCCA - adjust basis kernel args in operator kernel to agree with expected [dim][comp][q] ordeing

* OCCA - fix uninitalized memory in grad transpose 3d kernel

* OCCA - fix Elayout description

* OCCA - fix bad dimensions in basis kernel

* OCCA - fix TakeArray to sync before returning array pointer

* MFEM - print error when test fails

* OCCA - fix 2d grad kernels

* OCCA - flag digonal of composite operators unsupported

* OCCA - fix restoreArray logic

* OCCA - minor cleanup with GPU

* Travis - add 'make info' where able for debugging

* OCCA - explictily test OpenCL mode

* OCCA - drop restrict for ElemRestriction kernels, OpenCL doesn't like it

* OCCA - explicitly test cuda and hip versions of OCCA backend

* OCCA - explicitly test OpenMP mode in OCCA

* Tests - modify check for VLA support for OCCA to catch all OCCA modes

* WIP - test possible OCCA fix for PowerPC

* OCCA - separate CPU modes for testing as well

* Readme - update list of OCCA backend modes

* Makefile - fix unterminated addprefix

* OCCA - enable direct access to OCCA Serial mode

* OCCA - add comments to registration

* Makefile - remove extra )

* OCCA - remove pass by reference C++ syntax for OpenCL compatability

* OCCA - drop use of @restrict for OpenCL

* OCCA - remove OpenCL mode, not fully supported in OCCA (see OCCA issue #166)

* OCCA - fixing rebase issues

* OCCA - Fix implementation of QFunctionContext

* OCCA - move GetContextSize so ierr check actually works

* Travis - use libOCCA instead of jeremylt/occa

* Junit - update OCCA test skip list

* Make - simplify OCCA check for enabled modes

Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: Jeremy L. Thompson <jeremy.thompson@colorado.edu>

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Merge pull request #538 from CEED/jed/petsc-3.14-gcc-10

Jed/petsc 3.14 gcc 10

gitignore: .prove and Python cache