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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Merge pull request #373 from CEED/jeremy/op-refcount-fields

Add refcounts for Operator field components

Operator - add refcounts for Operator field components

Merge pull request #371 from CEED/jeremy/magma-basis-switch

Minor MAGMA Updates

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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Improve ceed-elemrestriction interface doc (#370)

* Improve ceed-elemrestriction interface doc

Merge pull request #369 from CEED/jeremy/t412-fix

QFunction - Fix identity qfunction field size

QFunction - Fix identity qfunction field size

Merge pull request #366 from CEED/jeremy/petsc-3.12

Travis - Update to PETSc 3.12.0

Travis - Update to PETSc 3.12.0

Merge pull request #365 from CEED/jeremy/mpi-ierr

PETSc - Fix MPI_Allreduce warning w/ierr check

PETSc - Fix MPI_Allreduce warning w/ierr check

PETSc - add MPI_Reduce and PetscBarrier for benchmarking (#364)

* PETSc - add MPI_Reduce and PetscBarrier for benchmarking

* Update examples/petsc/bps.c

Co-Authored-By: Jed Brown <jed@jedbrown

PETSc - add MPI_Reduce and PetscBarrier for benchmarking (#364)

* PETSc - add MPI_Reduce and PetscBarrier for benchmarking

* Update examples/petsc/bps.c

Co-Authored-By: Jed Brown <jed@jedbrown.org>

* Update examples/petsc/bps.c

Co-Authored-By: Jed Brown <jed@jedbrown.org>

* Update examples/petsc/bpsdmplex.c

Co-Authored-By: Jed Brown <jed@jedbrown.org>

* Update examples/petsc/bpsdmplex.c

Co-Authored-By: Jed Brown <jed@jedbrown.org>

* Navier Stokes - revert stray commit

* PETSc - Use MPI_Allreduce

* PETSc - Use MPI_Allreduce for final time as well

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Remove PetscRoundReal because not supported anymore (#363)

Merge pull request #362 from CEED/jeremy/whitespace-revert

Revert 1d5e3c8

README - revert 1d5e3c8, whitespace needed for proper indentation on GitHub

Merge pull request #361 from CEED/jeremy/typo

Style - minor typo fix

Another very minor style fix

Style - minor typo fix

libCEED-0.5

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

Jed/config flags and string processing

Merge pull request #359 from CEED/jeremy/more-tests

Expand Test Suite