Refine PETSc DMPlex BPs

This currently only views shape, but could some day learn to view
values. Adding to public interface because it's a useful tool for
debugging user code.

Initial work on PETSc DMPlex BPs

Nek: create bps qf files

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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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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examples/petsc: fix max reduction type and address

examples/navier-stokes: formatting cleanup

[Jed] Commit revised to leave derivatives intact.

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

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

Fix derivatives order in du

Convert BP5 BP6 to GLL

Update qextra to reflect BP paper

Improve petsc-bps benchmark output (#266)

* Improve petsc-bps benchmark output

Mesh Order -> Number of 1D Basis Nodes

* Update postprocess-base.py for new output

* Fix line break in plot ti

Improve petsc-bps benchmark output (#266)

* Improve petsc-bps benchmark output

Mesh Order -> Number of 1D Basis Nodes

* Update postprocess-base.py for new output

* Fix line break in plot title and pdf file name

* Shorten plot title

* Fix legend polynomial order p

* Update postprocessing scripts to use Pandas

* Benchmarks: plot title, tasks->ranks

* Update title with latex \times symbol and icrease font size in title, legend, and axes

* Postprocess script title, num_proc_node instead of num_proc

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Merge pull request #267 from CEED/valeria/Makefile-include

Add -include directive to Makefile

Minor documentation fix in examples/README.md

Typo: Error -> Error3

Add PETSc BP2, BP4, BP5, BP6 (#243)

* Add PETSc BP2, BP4, BP5, BP6

* Documentation update

* Update make benchmark

* Minor changes

* Add PETSc bpData structure

* Update make benchmarks

Add PETSc BP2, BP4, BP5, BP6 (#243)

* Add PETSc BP2, BP4, BP5, BP6

* Documentation update

* Update make benchmark

* Minor changes

* Add PETSc bpData structure

* Update make benchmarks

* Benchmark - use default qextra

* Documentation fix

* Clean up PETSc bps.c, add benchmarking first run

* Drop -ksp_max_it from benchmarkscript

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Merge pull request #239 from CEED/decorator

Add delegates for specific objects

Merge pull request #240 from valeriabarra/rescaled-ns-example

Rescaled ns example

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

Merge pull request #177 from CEED/t106-vec

Adds a Vector unit test using CEED_MEM_DEVICE.

Some tidying

Rescale time-stepper options with units of time

Rename field name Total Energy -> EnergyDensity

Add PetscObjectSetName to set solution's vec name