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

Rust and cuda clang support (#1873)

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 #858 from CEED/jeremy/dump-copy-stuff

Strip redundant/outdated license info duplication

minor - update copyright headers

Merge branch 'master' into valeria/jupyter-notebook-tutorials

Solid Mechanics Example (#474)

libCEED + PETSc Solid Mechanics example

Co-authored-by: Jeremy L Thompson <jeremy.thompson@colorado.edu>
Co-authored-by: Arash Mehraban <arashm81@gmail.com>
Co-au

Solid Mechanics Example (#474)

libCEED + PETSc Solid Mechanics example

Co-authored-by: Jeremy L Thompson <jeremy.thompson@colorado.edu>
Co-authored-by: Arash Mehraban <arashm81@gmail.com>
Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: Valeria Barra <valeriabarra21@gmail.com>


* Solids - initial commit of elasticity example

Co-authored-by: Jeremy L Thompson <jeremy.thompson@colorado.edu>
Co-authored-by: Arash Mehraban <arashm81@gmail.com>

* Solids - add VLA macro

* Solids - fix test for mesh file output string

* Solids - update documentation

Co-authored-by: Jeremy L Thompson <jeremy.thompson@colorado.edu>
Co-authored-by: Arash Mehraban <arashm81@gmail.com>

* Solids - update README

* Solids - update ctx struct and casting for CUDA

* Tests - clean up test conditions for GPU backends

* GPU - fix falbacks identified

* CUDA - whitelist FDM Inverse

* make style

* doc: solids editing/correctness

* Solids - separate FE boilerplate into its own function

* Solids - clean up double includes

* doc: add more complete explanation of hyperelasticity and formulation

* Solids - Use ISGetSize for global number of face sets (had no effect on PETSc bug in MR 2615)

* edited docs for hyperFS

* Improve doc of solids example with some constitent notation and fonts

* HyperSS docs modified

* edited typo

* linearization added

* fixed a typo

* Improved doc

* doc: more writing on hyperelasticity and implementation tradeoffs

* Solids - fix typo

* Solids - compute and store C, Cinv, and S as symmetric

* Solids - use new Newton linearization, but its not converging

* Solids - update BC handling

* Solids - update README with new BC options

* removed old notation

* Solids - whitespace changes only in documentation

* doc: adjust differential notation and derive dP(dF)

* Solids - small documentation flow edits

* Solids - simplify setting BCs

* Solids - Symmetritize e in SS

* Solids - set more reasonable default number of steps for nonlinear

* Solids - fix documentation typo

* Solids - clean up computation of deltaS

* Solids - fix sample runs

* Solids - fix hyperSS jacobian

* Solids - fix hyperSS documentation

* Solids - clean up code for hyperSS

* Solids - add file and function docstrings

* doc: commutative diagram of linearization and stable stress expression

* Solids - update hyperSS documentation with linearization

* doc: further tips on stable computation

* Solids - fix typo with trace in hyperSS

* Solids - intro and hyperSS documentation updates

* Solids - update hyperFS for numerical stability with small E and nearly incompressible

* examples/solids: simpler C = I + 2E

* Solids - more compact/readable E computation

* Solids - minor style consistency change

* Solids - replace log1p with series approximation, log1p is not vectorized in libc

* Solids - refactor common components between hyperFSF and hyperFSdF

* examples/solids: use PETSc dependency flags for incremental rebuild

* examples/solids: extend range of log1p_series via shift/scale

* Solids - add bc_clamp_max option to specify maximum displacement for clamped boundary

* make style

* Solids - update with sample run informantion and spellchecking

* Doc - typo fixes

* Solids - homogonize presentation of command line options

* examples/solids: fix -Wmisleading-indentation

* examples/fluids: PETSc 3.13 compatibility

* examples/solids: use log1p for numerical stability in hyperSS

* doc: copy editing in examples/solids

* Solids - update documentation on running the code

* Solids - convert README to rst and include in documentation

* Solids - clean dependency file

* Solids - use log1p approximation in hyperSS as well

* Solids - update README to explain mms

* Solids - switch range on hyperSS log1p series approximation

* Solids - update README to clarify mandatory options

* Solids - add link to sample meshes

* Solids - simplify listing of mesh options

* Travis - use newer PETSc

* Solids - update sample run to list [.exo file] instead of name of sample mesh

* Solids - update make clean to remove src/*.d

* examples/solids: makefile cleanup

* make style

* doc examples/solids: clean up and explain nondimensionalization

* examples/solids: document algebraic solver

* examples/solids: use CG for Chebyshev eig estimation

* doc: fix references to examples/fluids

* Solids - remove mesh folder

* Solids - drop expicit ExodusII requirement, PETSc supports many types of meshes

* doc: mention PETSc --download-exodusii for Exodus

* doc: fix latexpdf

* Fix \longrightarrow rendering in PDF

* Solids - fix toctree link to README for pdflatex

* Examples and BPs Docs: Homogenize math with dS and dV and other tiny esthetics

* Solids - fix unshifted series for hyperSS log1p

* Improve doc of bpssphere: Add differential for consistency with all other examples and explain domain for clarity

* Solids - include sample mesh image

* Move mesh figure after note and slightly rename inclusion marker

Co-authored-by: Arash Mehraban <arashm81@gmail.com>
Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: valeriabarra <valeriabarra21@gmail.com>

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Multigrid - combine multigrid and petsc example code for reuse

Multigrid - Add multigrid example

Merge pull request #322 from CEED/jeremy/clean-jobserver

Makefile - enable clean in parallel

Makefile - enable clean in parallel

Merge pull request #308 from CEED/jeremy/clean-fix

Makefile: Fix make clean for examples

Makefile: Fix make clean for eamples

Update nek5000 example scripts (#241)

* Update nek5000 examples to use NEKTOOLS_DIR

* Remove +x

* Nek: Fix a bug in generate-boxes.sh script

* Use one script for nek exaamples

* Update m

Update nek5000 example scripts (#241)

* Update nek5000 examples to use NEKTOOLS_DIR

* Remove +x

* Nek: Fix a bug in generate-boxes.sh script

* Use one script for nek exaamples

* Update make-nek-tests.sh

* Update nek-examples.sh

* Change permissions of make-nek-tests.sh

* Update examples Makefile to use new nek script

* Update nek5000 examples build process

* Trying to make travis happy

* Polishing the script

* This should make Travis happy

* Polish nek-examples.sh

* Update examples/Makefile

* Update top-level makefile

* Delete make-nek-tests.sh & update nek-examples.sh

* Update Makefile and examples/Makefile

* Update nek-examples.sh

* Update TESTARGS in bp .usr files

* Update Makefile

* Update .travis.yml

* Update nek-examples.sh

* Add CEED_DIR to tap.sh

* Uncomment OCCA_DIR in Makefile

* Fix make prove and update tap.sh

* Pass NEK5K_DIR and CEED_DIR in prove-all

* Set MPI=0 default for Nek examples/tests

* Nek5K make updates

* Make prove update

* Update make-prove to make all ex except Nek5K in parallel

* Set Nek5K examples to use MPI by default

* Makefile: Improved Nek5k handling

* Makefile: build Nek bps in separate directories

* Nek: rename dir for f77 file length

* debugging

* Nek: use single source

* Makefile: fix Nek mpif.h issue

* Nek: Clean up build proces, improve documentation

* Makefile: enable building single Nek example in parallel with other examples

* Nek: Fix CC/FC and TESTARGS

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Merge pull request #239 from CEED/decorator

Add delegates for specific objects

Nek examples: work around some error messages due to unset env

Explicit time stepping NS solver (#152)

* Squash NS example to single commit

* Update name of NS example and explicitly zero unused outputs

* rename Theta ->theta, deltaTheta -> deltatheta and

Explicit time stepping NS solver (#152)

* Squash NS example to single commit

* Update name of NS example and explicitly zero unused outputs

* rename Theta ->theta, deltaTheta -> deltatheta and make style

* Incorporate Valeria's latest changes

* Fix small bug in Advection header

* Add Valeria's latest updates from ns-working

* Update after Jed's revision

* Improve documentation

* Drop navier-stokes from allexamples

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Add Nek to Travis (#169)

* Add test mode to Nek BP1 and BP3, improve Nek BPs

* Fix OCCA identity rst for multifield, minor NekBP1 fix

* Improve Nek run script

* Add Nek5K to prove-all

*

Add Nek to Travis (#169)

* Add test mode to Nek BP1 and BP3, improve Nek BPs

* Fix OCCA identity rst for multifield, minor NekBP1 fix

* Improve Nek run script

* Add Nek5K to prove-all

* Update travis yml for Nek5K

* Make style

* Adjust Travis yml

* Combine Nek run bash scripts

* Minor Nek script improvements

* Update to Nek 18.0 and reduce number of Nek compiler warnings

* Document required Nek5k version

* Remove stray command

* Remove extra file

* Adapt Nek for CUDA backend

* Fix Nek script string comparison

* Modify Nek script for better exit codes

* typo fix

* Modify the CU function names in nek/bp1.cu and nek/bp3.cu

* .cu file consistency

* Tidy Travis

* Tidy Travis

* Operator fixes

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Merge branch 'master' into evector_support

Merge branch 'nek_example_update' of github:thilinarmtb/libceed [PR #70]

* 'nek_example_update' of github:thilinarmtb/libceed:
Examples: single makefile for all the examples
Nek: Remove a redund

Merge branch 'nek_example_update' of github:thilinarmtb/libceed [PR #70]

* 'nek_example_update' of github:thilinarmtb/libceed:
Examples: single makefile for all the examples
Nek: Remove a redundant echo statement
Nek: Add a Makefile for Nek5000 examples

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Examples: single makefile for all the examples

Several small updates in the Nek scripts and documentations.

With these, I can run all libCEED examples with the /gpu/occa spec on my Linux
box!!

Merge branch 'master' into nek_gpu

Merge branch 'master' into nek5k_updates

Merge branch 'occa-dev' [PR #42]

* occa-dev: (70 commits)
Makefile: explicitly use bash because shell script does not have conforming shebang
make okl-cache: simplify caching call and fix to fin

Merge branch 'occa-dev' [PR #42]

* occa-dev: (70 commits)
Makefile: explicitly use bash because shell script does not have conforming shebang
make okl-cache: simplify caching call and fix to find OCCA executable
Cache OCCA kernels in PETSc examples makefile
[occa] PETSc example with ctx inout, qfdatasize & offsets
[occa] device from ressource, OpenCL TILE size tied to 1
[occa] fixed /ocl/occa
Couple more OKL kernel fixes in example Makefiles
Comment-out the restrict kernels using atomicAdd(double), so we can build the OCCA backends on GPU cards with lower SMs.
[occa] occaPropertiesSet to match new C wrapper API
[occa] dbg macros + ceed argument moved down to occa backend
[occa] Makefile targets comments, occa source debug cleanup
[test] t30 output removed, added V vector 0.0 check
[occa] examples Makefile occa cache
[occa] basis & restrict stat logic to test out of source examples
[occa] pushing backends/occa/*.okl to install prefix/lib/okl and use them if needed
[occa] style
[occa] CeedDebug output when CEED_DEBUG or DBG are non null
[occa] Updated to 1.0 C API
[occa] make style
[occa] cleanup + OCL but tests that use ex1-volume-annulus.okl
...

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Couple more OKL kernel fixes in example Makefiles

[occa] examples Makefile occa cache