LCOV - minor updates

CPU - Use work vectors for AssembleLinearQF

change dim/ncomp ordering for CPU ref non-tensor gradient basis evaluation

Assemble Linear QFunction (#306)

* Operator - add interface for AssembleLinearQF

* Operator - Refactor Ref/Blocked/Opt basis apply

* Operator - Add AssembleLinearQF impl for Ref/Blocked/Opt, n

Assemble Linear QFunction (#306)

* Operator - add interface for AssembleLinearQF

* Operator - Refactor Ref/Blocked/Opt basis apply

* Operator - Add AssembleLinearQF impl for Ref/Blocked/Opt, not impl message for OCCA/CUDA

* AssembleQF - Add grad test and clean up code

* CPU - Add operator eval mode error, remove opt inlineing

* Operator - clarify QF assemble documentation, style updates

* Interface - style and consistency updates

* Tests - add more complex assembled qfunction test

* Tests - add fortran test for assemble linear qfunction

* Tests - Update t53* tests for new Fortran source macro

* Merge - small fixes

* Operator - convert to backend creating assembled qdata vector

* Operator - zero qvecs before using in assembly of qf

* Operator - expand assemble QF documentation

* CPU - minor fix in AssembleLineaorQF to prevent uninitalized memory

* Tests - fix wording in t531, t532

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MAGMA - drop unused dtensor_contract

MAGMA - style updates and switch for basis

Magma dev optimizations (#111)

* makefile changes

* update magma backend

* magma qfunctions updated to new interface

* in the magmabackend we manage where pointers are - if on CPU, on some

Magma dev optimizations (#111)

* makefile changes

* update magma backend

* magma qfunctions updated to new interface

* in the magmabackend we manage where pointers are - if on CPU, on some cases we still need and may call the CPU code

* update the reflect changes in the API

* update the reflect changes in the API

* add the q functions for ex1.c

* Switch to CeedIntPow

* Fix merge errors

* Clean up Magma operator loops

* Move zeroing lvec

* fix bug in the rebase and add some qfunctions. This passes the tests now

* adding new files, changing -O to -O3

* new faster way of checking CPU vs. GPU pointers

* core magma device functions for basis apply

* new kernels for basis apply

* use the new magma_isdevptr function

* minor cleanup

* new headers and defs

* calling the new magma functions for basis apply

* undo O3, and change default magma directory

* use static

* use static

* modify the generator to add before __global__

* remove unnecessary header

* silence some warnings

* Makefile: restore NVCC and NVCCFLAGS to match master

* first pass as updating new Magma work, untested

* Use CUDA backend to dispatch

* Device memory for MAGMA

* Add copyright messages and tidy

* WIP: starting fresh on magma-dev-rebae. Add magma_is_devptr

* WIP: starting fresh on magma-dev-rebae. Fix build issue

* WIP: starting fresh on magma-dev-rebae. Fix build issue

* WIP: starting fresh on magma-dev-rebae. Fix build issue

* WIP: starting fresh on magma-dev-rebae. Fix this include

* WIP: starting fresh on magma-dev-rebae. Fix build issue.

* WIP: starting fresh on magma-dev-rebase. Mostly fixing compilation errors

* WIP: starting fresh on magma-dev-rebase. Disbale magma-basis for now

* WIP: starting fresh on magma-dev-rebase. Edit the required magma src files

* move CeedVector_Magma functions from magma-dev branch

* add includes

* fix build errors

* disable magma vector logic for now

* Remove reference in CeedDelegate

* add RestoreArray calls to CeedBasisApply_Magma

* add basis for magma

* magma batched operator

* Change batch calls to match Q-vector ordering

* minor cleanup of unused variable

* update magma portion of Makefile

* remove magma vectors

* remove unused contract variable

* change extern to CEED_INTERN

* merge in updates from master branch

* MAGMA - add lcov markers

* remove stray example script

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Merge pull request #360 from CEED/jed/config-flags

Jed/config flags and string processing

Clean up string processing code smells; -Wstringop-truncation

This pattern is detected by gcc-9 at high optimization:

warning: ‘strncpy’ output truncated before terminating nul copying as many byte

Clean up string processing code smells; -Wstringop-truncation

This pattern is detected by gcc-9 at high optimization:

warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
87 | strncpy(source_copy, source, strlen(source));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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XSMM - Minor style cleanup

XSMM - drop unused tensor contract fallback when C != 1

Codecov Exceptions (#356)

* Tests - Add lcov exceptions to t304-f/t305-f

* Backends - add lcov exceptions for error messages intentionally not tested

* Interface - add lcov exceptions for erro

Codecov Exceptions (#356)

* Tests - Add lcov exceptions to t304-f/t305-f

* Backends - add lcov exceptions for error messages intentionally not tested

* Interface - add lcov exceptions for error messages intentionally not tested

* Tests - additional lcov exceptions

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Improved performance of cuda-gen backend (#341)

Thanks-to: Tim Warburton
Some of these optimizations are the results of the knowledge and experience gathered by Tim Warburton and his team in libPar

Improved performance of cuda-gen backend (#341)

Thanks-to: Tim Warburton
Some of these optimizations are the results of the knowledge and experience gathered by Tim Warburton and his team in libParanumal and then ported to libCEED.

* Add colocated gradient in 3D.

* Treat the qFunction by slice in 3d to avoid using too many registers.

* Minor fix

* Minor fix.

* Minor fix

* Compute the colocated gradient slice by slice.

* Add synchthreads after initialization of the matrices.

* Remove code print.

* Add a critical #pragma unroll

* Fix typo on "collocated".

* Remove dead code.

* Use ColloGrad3d functions.

* Fix cuda-gen backend when collocated gradient is not available.

* make style

* make style

* Add some comments.

* Replace int by CeedInt.

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QFunction Create by Name (#311)

This PR adds a QFunction gallery to libCEED with 1D, 2D, and 3D mass and Poisson operators.

Closes issue #37, issue #340

* Add QFunction gallery, rename focca

QFunction Create by Name (#311)

This PR adds a QFunction gallery to libCEED with 1D, 2D, and 3D mass and Poisson operators.

Closes issue #37, issue #340

* Add QFunction gallery, rename focca

* Gallery - add initial QFunctions

* Add a test for using the QF gallery

* Modify ex1 to use gallery

* Add multiple test configs to tap

* Move output to test directory

* Update junit

* Add OCCA galley exception

* Add ex2

* Update ex2 for dim->ncompx

* Gallery - modify to work for CUDA as is

* Update Documentation

* Gallery - typo fix

* Gallery - convention change, postappend qfunction family variant

* Gallery - update template with new name checking convention

* Gallery - condense diff3DBuild QFunction

* Gallery - rename diff -> poisson

* Gallery - clarify poisson3DBuild comment

* Gallery - use Pragma SIMD, store Qdata in Voigt convention

* Examples - Convert BP3-6 to Voigt convention

* Examples - add cl option to switch between header and gallery qfs in CEED examples

* Examples - clean up construction of QF name

* Gallery - Switch to PascalCase for gallery names

* Doc - fix function type page

* Interface - Make sure strncpy result is null terminated

* Gallery - Update Poisson 2/3D Apply to new QF body

* make style

* make style - fix worst style problems

* make style - add gallery to make style

* Doc - update documentation errors and inconsistencies

* Examples - test ex1 ex2 with and without gallary

* Examples - reduce testing of ex1/ex2 without gallery, clean up non-gallery qfunctions

* MFEM - revert another make style mistake

* Manual make style updates

* Doc - update function documentation page

* Style updates, document test numbering conventions

* doc: resolve ambiguous image location warning, allow more Dot nodes

* Tests - style and cast cleanup

* Tests - fix README indentation

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Add CeedPragmaOMP to bps (#338)


* Convert petsc BP3&4 to loops

* Update petsc/bp4.h looping

* Switch to CeedPragmaSIMD and make examples/petsc/bp3.h consistent with bp4.h

Remove CeedPragm

Add CeedPragmaOMP to bps (#338)


* Convert petsc BP3&4 to loops

* Update petsc/bp4.h looping

* Switch to CeedPragmaSIMD and make examples/petsc/bp3.h consistent with bp4.h

Remove CeedPragmaOMP directive in Nek example and update documentation

* Remove restric qualifier in petsc/bp3.h and update documentation

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CUDA - Rename SyncState -> CeedCudaSyncState

Single Source QFunction (#304)

Introduce a new macro CEED_QFUNCTION that allows to define qFunctions in a single source code independently of the targeted backend.

Thanks-to: Jeremy Thompson
Tha

Single Source QFunction (#304)

Introduce a new macro CEED_QFUNCTION that allows to define qFunctions in a single source code independently of the targeted backend.

Thanks-to: Jeremy Thompson
Thanks-to: Jed Brown
This work is the result of a fruitful discussion between Jed Brown, Jeremy Thompson and Yohann Dudouit. Jeremy Thompson also implemented important features in this commit and was very active and helpful all along the progress of this work.

[NEWS] Breaking change: QFunctionField parameter 'ncomp' changed to 'size'. This change requires setting the previous value of 'ncomp' to 'ncomp*dim' when adding a QFunctionField with eval mode 'CEED_EVAL_GRAD'.

* First steps toward cuda-gen backend!

* Closer to real code generation.

* Generated code should be ready for nvrtc.

* The code generation skeleton is ready.

* Hack with the qfunction to make the operator kernel compile.

* Some tweaks in the makefile + Input fields structure change.

* Remove using cout.

* 1d interp and grad device functions.

* 1d readDofs, readQuads, writeDofs, writeQuads.

* Remove dead code.

* readDofs, readQuads, writeDofs, writeQuads for 2d and 3d

* 2d interp and grad

* 3d interp and grad

* - weight functions for 1d,2d,3d
- link the indices to the kernel
- link the fields to the kernel
- link the basis to the kernel

* Add the qFunction reader + inlining

* Add qf files for the tests.

* Add qf file for ceed/ex1

* Add qf file for mfem/bp1

* All tests pass.

* Add qFunction for mfem/bp3, petsc/bp1, and petsc/bp3.

* mfem/bp1 passes + remove dead code

* Fix a bug in n_quads_out for writeQuads

* mfem/bp3 passes.

* All tests all examples pass.

* Temporary tweaks for mfem benchmarking

* Add Context management.

* Modify .qf files to take into account the context.

* Enable optimizations.

* First set of optimization for 2D and 3D.

* double pointer format for the qFunction.

* Change the .qf files to have the same code as the C functions.

* Make previous Cuda backends use .qf files.

* Add a return value to qFunctions.

* Make cpu backends use .qf files.

* Minor: clean commented code.

* Add guarded math.h for petsc examples.

* Remove previous nek qf files.

* Remove .cu files.

* Remove .qf files.

* Remove dead code in the tests.

* make style

* Make style fix.

* more make style fixes.

* CEED_QFUNCTION - improve macro for CPU filenames

* Add CEED_QFUNCTION macro to navierstokes.c

* Fix PETSc gitignore

* Change default NS problemtype to density_current (#307) in navierstokes.c

* Fix petsc bp1.h

* Real Fix for petsc bp1.h...

* fix

* README - Add /gpu/cuda/gen

* PETSc - Update dmplex example to use *_loc

* cuda/reg - fix typo

* Revert a couple of small changes

* Fix a bug in mfem bp3 similar to the previous bug in petsc bp3.

* Make PETSc qfunctions look closer to master, and minor style for debugging.

* More uniformity changes

* Fix a strange CUDA_OUT_OF_RESSOURCE bug.

* NS - fix fname variables

* Use a different convention for qFunction ncomp.

* update cuda-gen backend and bpsdmplex.

* PETSc - style update

* update mfem bp1 and bp3.

* Interface - Use size instead of ncomp for QFunction fields

* update ceed example and tests.

* Tests - Update ncomp to size

* CPU Backends - Update ncomp to size

* CPU Backends - style

* Nek - Update ncomp to size

* Opt - fix style

* CUDA - update ncomp to size

* Doc - Update API documentation for QFunction \ncomp->size

* OCCA - Patch QFunction ncomp -> size, work but revamp will be better

* OCCA - assert dim>0 for clang-tidy

* CUDA - Change GetNumComp to GetSize

* Basis - Shift check for dim > 0 to interface

* Doc update

* Update NS field size

* NS - Fix problem options

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Ref - fix indentation

Ref - remove dead code from basis collo grad

Add Grad w/collo Interp mode to CPU backends (#290)

* Add Grad w/collo Interp mode to CPU backends

* Ref - Update dofs to nodes in basis documentation

* Ref - use memcpy for collo interp

Make style

Rename NDoF to NNodes and style updates

Documentation Typo Fixes (#321)

* Basis - fix typo in doc

* Ceed - fix typo in doc

* Operator - fix typo in doc

* QFunction - fix typo in doc

* Ceed.h - fix typos in doc

* Ref - fix t

Documentation Typo Fixes (#321)

* Basis - fix typo in doc

* Ceed - fix typo in doc

* Operator - fix typo in doc

* QFunction - fix typo in doc

* Ceed.h - fix typos in doc

* Ref - fix typos in doc

* Blocked - fix typos in doc

* READMEs - typo fixes

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Merge pull request #310 from CEED/yohann/fix-atomicAdd

Fix atomicAdd in cuda-gen backend

Fix a bug in the description of vectorial bps in petsc (#309)

Also fix a bug introduced in cuda-gen backend to overcome the bug in the bps.