Full jit compiled operator: cuda-gen backend (#275)

* First steps toward cuda-gen backend!

* Closer to real code generation.

* Generated code should be ready for nvrtc.

* The code generatio

Full jit compiled operator: cuda-gen backend (#275)

* 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.

* Makefile tweaks and destructor code.

* make style.

* Add -MP flag.

* Fix linking issues with the tests.

* Update .qf files for the tests.

* Add .qf files for nek5000 examples.

* Use shared memory for B and G matrices.

* Fix bug introduced in previous commit.

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Merge pull request #300 from CEED/jeremy/doc-fix

README: Update corectness for examples

README: Update corectness for examples

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 #298 from CEED/jeremy/ref-priority-fix

Fix ref backend priorities

Merge pull request #297 from CEED/jeremy/209-f-fix

Fix typo in t209-f

backends: fix ref backend priorities

tests: fix typo in t209-f

Merge pull request #296 from CEED/jed/fix-error-reduction

examples/petsc: fix max reduction type and address

examples/petsc: fix max reduction type and address

Merge branch 'valeria/fix-ns-derivatives' [PR #292]

* valeria/fix-ns-derivatives:
examples/navier-stokes: formatting cleanup
navier-stokes: use du[3][3] to clean up indexing
Fix derivatives or

Merge branch 'valeria/fix-ns-derivatives' [PR #292]

* valeria/fix-ns-derivatives:
examples/navier-stokes: formatting cleanup
navier-stokes: use du[3][3] to clean up indexing
Fix derivatives order in du

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examples/navier-stokes: formatting cleanup

[Jed] Commit revised to leave derivatives intact.

Merge pull request #295 from CEED/cpu_priority_fix

BugFix - Resource strcmp in LIBXSMM backends

Update CPU backends to give default for /cpu/self/***

Fix resource strcmp in xsmm backends

Merge pull request #291 from CEED/rstr-mult

Add ElemRestrGetMultiplicity and Tests

Add ElemRestrGetMult and tests

Merge pull request #289 from CEED/cuda-occa-copy-vals

Update CUDA/OCCA CEED_COPY_VALUES logic

Update CUDA/OCCA CEED_COPY_VALUES logic

Merge branch 'yohann/cuda-restr-opt' [PR #269]

* yohann/cuda-restr-opt:
Remove dead or unnecessary code.
Remove dead code. Cuda-reg restriction optimization.
Optimization of 3D kernels for cud

Merge branch 'yohann/cuda-restr-opt' [PR #269]

* yohann/cuda-restr-opt:
Remove dead or unnecessary code.
Remove dead code. Cuda-reg restriction optimization.
Optimization of 3D kernels for cuda-shared backend.
Optimization of 1D kernels for cuda-shared backend.
Optimization of 2D kernels for cuda-shared backend.
Minor bug fix
Optimization of weight kernel and dynamic allocation of shared memory.
Optimization of cuda-reg restriction.
Start the optimization of the Cuda restriction operator.

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navier-stokes: use du[3][3] to clean up indexing

Reported-by: Leila Ghaffari <Leila.Ghaffari@colorado.edu>

Fix derivatives order in du

Merge branch 'master' into yohann/cuda-restr-opt

Conflicts:
backends/cuda-reg/ceed-cuda-reg-restriction.c
backends/cuda-shared/ceed-cuda-shared-basis.c

Merge pull request #284 from CEED/jed/blas-lib

Makefile: MKL link flags for non-Intel compilers

Makefile: MKL link flags for non-Intel compilers

One can always run

make BLAS_LIB=-mkl

when using the Intel compiler, but it's typically important for us to
link the sequential version and we'd

Makefile: MKL link flags for non-Intel compilers

One can always run

make BLAS_LIB=-mkl

when using the Intel compiler, but it's typically important for us to
link the sequential version and we'd like a system that works with
non-Intel compilers, where the incantation is so hard to remember that
Intel made a web app:

https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/

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