Readme update

Readability changes

Merge pull request #205 from CEED/example-readme-rename

Rename BPdescription.md to README.md

Rename BPdescription.md to README.md

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 pull request #203 from CEED/intel-f-fix

Intel Fortran Fix

Switch tests to .f90 extension

Edit t200-f

Merge pull request #202 from CEED/XSMM-fix

Fix LIBXSMM capitalization

Fix LIBXSMM capitalization

Merge pull request #201 from CEED/makefile-varname-fix

In Makefile: replace '-' with '_' in a variable name.

In Makefile: replace '-' with '_' in a variable name.

Benchmarking (#187)

* Add make benchmarks

* Various tweaks related to the benchmarks.

* In Makefile:
* target 'all' now builds the library, all tests and examples
* the old 'all' target is n

Benchmarking (#187)

* Add make benchmarks

* Various tweaks related to the benchmarks.

* In Makefile:
* target 'all' now builds the library, all tests and examples
* the old 'all' target is now called 'par'
* the target 'examples' will build also the MFEM and PETSc examples if
the respective library is available.

In the benchmarks/ directory:
* remove 'config.sh'
* cleanup unused stuff from 'benchmark.sh'.

* Fix postprocess scripts, convert to Python 3

* Small update in README.md

* Set benchmark cg its max, update gitignore

* Minor makefile fix

* In Makefile, add 'par' to the list of phony targets.

* In benchmarks/postprocess-table.py, sort the table by backend first.

* Small update in examples/petsc/Makefile - add a comment that
PETSC_ARCH can be undefined/empty, e.g. when using PETSc installed
through Spack.

* In Makefile, update the benchmarking targets:
* add separate targets for individual tests: `bench-petsc-bp1`,
`bench-petsc-bp3`, etc
* `make benchmarks` runs all defined benchmarks.

Update README.md to reflect the above changes.

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Slight adjustment in the BSD license text to help GH recognize it.

Merge pull request #186 from CEED/libxsmm

Initial libXSMM Backend

Switch libXSMM serial basis apply to Nek style

Switch to latest libXSMM vs release

Initial libXSMM backend

Cuda backend (#175)

Thanks-to: Steven Roberts
- for achieving most of the initial work, the code was well designed, clean, and pleasantly written.
Thanks-to: Jeremy Thompson
- for his constant

Cuda backend (#175)

Thanks-to: Steven Roberts
- for achieving most of the initial work, the code was well designed, clean, and pleasantly written.
Thanks-to: Jeremy Thompson
- for his constant support, exceptional patience, and the numerous relevant suggestions.

* Start cuda branch

* Start cuda branch

* Cuda backend works correctly for example 1

* More reliable operator destroy

* Fix cuda registration

* Makefile now works for cuda backend

* Start qfunction parallelization

* Remove extra cuda flags

* Cuda backend uses vector api instead of directly accessing internals

* Fix header from find and replace mistake

* Cuda qfunction callback working properly

* Cuda uses same integer pow function as other backends

* Use nvcc if available to support Cuda backend

* Remove extra memcpys from getting and restoring arrays

* MFEM examples work for cuda backend

* Optimized basis kernels to better utilize shared memory

* More kernel optimization

* Active/passive updates

* Make cuda kernels static to minimize external functions

* Fix cuda qfunction kernel loop condition

* Switch to NVRTC for cuda backend

* Add nelem argument to cuda basis apply

* First commit for the libParanumal backend

* Adds a function skeleton for the ceed-libparanumal-opearator.c

* Adds OperatorDestroy and OperatorSetupFields to the libParanumal backend.

* Adds some guidelines for the implementation of the backend.

* Partially implement OperatorSetup for libparanumal.

- The core of the OperatorSetup is written
- Adds a spec field to CeedQFunction_private

* Adds the CeedQFunctionCreateInteriorFromGallery.

- The gallery only contains a skeleton for "elliptic" for the moment.
- Comment some code unecessary for the moment.

* Change the default fields for elliptic.

* Add setters, remove impl header from CPU, OCCA backends

* Add global NUM_BACKEND, fix qf user pointer getter

* Improve operator field frees

* Update MAGMA backend

* Use Occa Vectors in the libParanumal backend.

* Typo Fix

* Vector inputs for BasisApply and QFApply; CPU backends, OCCA, and tests converted

* Implements the new version of CeedQFunctionApply_Cuda.

* Update the Cuda backend to PR174.

* Bug fix in Cuda backend.

- Replace sprintf by snprintf
- More careful use of the macro 'va_arg'

* Vector inputs for BasisApply and QFApply; CPU backends, OCCA, and tests converted

* Update MAGMA backend to vector inputs

* Modify restriction create in the cuda backend to handle memory correctly.

* Modify restriction destroy and apply of the cuda backend.

* Corrects a few typos in the cuda backend.

* Replace a CeedFree by a cudaFree...

* CeedVectorRestoreArrayRead was syncing unnecessarly data.

* CeedVectorRestoreArrayRead was syncing unnecessarly data.

* [FIX] Adds CeedVectorRestoreArray in the restriction of the cuda backend.

* Adds an error check.

* Handles indice==NULL for identity restriction.

* Adds an CeedElemRestrictionCreateBlocked_Cuda that errors.

* Adds VectorRestor in BasisApply.

* Attempt to make SetValue function.

* Adds the memState variable inside the CeedVectorCuda and uses it.

* Fix a bug that was passing the pointer instead of the address of
the pointer to CeedFree......

* Some cleaning.

* Fix a logic error in VectorGetArray.

- Now allocates an array whatever the memState is

* Fix: Basis apply checks if emode!=CEED_EVAL_WEIGHT before getting u array.

* Cleaning for PR to libCEED repo.

* Uses Setters instead of direct struct access.

* Use Getters instead of direct structure access.

* minor forgot to get ierr in after calling some functions.

* Forget to add the SetValue function in Cuda Vector...

* minor: Works even better if we give the right function to SetValue

* Fix: Set the right function for RestrictionBlocked...

* Replace some CeedChk with CeedChk_Cu

* Fix: Replace 'vec' by its length 'length'.

* Adds some CeedChk.

* Fix the Cuda_context_destroyed bug

* Adds error checking to cudaMemcpyH2D but not to D2H since it errors...

* Use Occa file approach to read Cuda QFunctions.

* Fix a few bugs

* Test a new approach to pass the qFunction fields.

* Remove typo in t400.cu and remove debugging printf.

* Append the Cuda Fields struct at the beginning of each qFunction .cu file.

* Add qFunctions for t500, t501 and t502.

* Correct cu functions for t502.

* Memcpy the ctx on the device at each Apply call.

* Checks errors in VectorSync.

* Modifies a bit the memState logic.

* Adds a Cuda implementation of Operator instead of using Ref.

* Remove some unnecessary GetArray in OperatorApply.

* Does a trick for CEED_EVAL_NONE output.

* Fix a bug in CEED_EVAL_WEIGHT.

* Applies the QFunction to all elements, not only the first one...

* A debugging commit.

* Fix: CEED_EVAL_WEIGHT use nelem in BasisApply_Cuda.

* Rewritten weight kernel.

* All C tests pass.

* Cleaning for PR.

* Remove unneeded commented code.

* Remove commented code.

* Remove the check on the pointer in RestoreArray.

* Fix a CeedFree bug.

* Fix the edata memory leak.

* Fix misuse of CeedFree.

* Allocate device memory if there is a magic context appearing due to Fortran.

* make style

* Adds cu files for petsc/bp1 mfem/bp1 and ceed/ex1.

* Remove a warning.

* Remove switch case fall-thourgh to remove warnings.

* Remive some bugs, make other bugs show up.

* Implement the Identity Restriction.

* Size correctly the restriction.

* Modify GPU restriction kernels instead of making dummy identity.

* Add cudaFree(0) before compiling to initialize the context (?!)

* Rewritten weight kernel.

* Fix typo in weight kernel.

* Fix typo in weight kernel.

* Add bp1.cu and bp3.cu for the petsc examples.

* Rewritten interp kernel for Cuda backend.

The interp kernel was not writting data in the layout that the
QFunction is expecting.

* Rewritten grad kernel for Cuda backend.

- Small fix on the interp kernel.
- The grad kernel was not writting data in the layout that the
QFunction is expecting.

* Fix the logic in interp kernel.

* Fix the shared memory size.

* Modify grad kernel to take into account the libCEED data layout.

* Add a cuda file for mfem/bp3.

* Add synchronisation to mfem bp1 and bp3.

* Fix the grad and weight kernel to have the correct data layout.

* Forgotten cu files for Fortran.

* Corrects some typos in the Cuda file for petsc/bp1.

* Add Cuda files for the new t401 test.

* Update the logic on the transfer of the qFunction ctx.

* Write petsc/bp1 in C++ instead of C.

* Minor fix: typo

* Add synchronization to petsc/bp1+bp3.

* Removes the sync on rho in petsc/bp1+bp3.

* Integrate Jeremy Thompson's remarks to the PR.

* Use CeedError instead of exit(1).

* Removes -lstdc++ and adds Ceed in front of DeviceSetValue function.

* Removes synchronization on 'u' in the Apply.

* minor

* make style

* Use the new context interface.

* Minor

* Minor.

* Minor.

* Make style using align-pointer=name

* Minor: some cleaning

* CeedQFunctionUser: write documentation

* Make NVCC compatible with new OPT compiler options

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Merge pull request #192 from CEED/azure-pipelines

Set up CI with Azure Pipelines

Merge pull request #182 from CEED/avx

AVX Backend

avx vectorized backend

Edge cases for AVX BasisApply

Priority adjustment to match libXSMM branch

Remove scalar/simd mix for Intel

Check for CC AVX support

AVX: proposed doc and makefile detectio

avx vectorized backend

Edge cases for AVX BasisApply

Priority adjustment to match libXSMM branch

Remove scalar/simd mix for Intel

Check for CC AVX support

AVX: proposed doc and makefile detection update

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Set up CI with Azure Pipelines

Merge pull request #189 from CEED/fortran-tests-fform, close issue #84

Use -ffree-form for Fortran test suite

Set Fortran test file width to 80