=========================================================
General
=========================================================

- Make representations code take Gimpl
- Simplify the HMCand remove modules
- Lattice_arith - are the mult, mac etc.. still needed after ET engine?
- Lattice_rng
- Lattice_transfer.h
- accelerate A2Autils -- off critical path for HMC

=========================================================
GPU branch code item work list
=========================================================

* sum_cpu promote to double during summation for increased precisoin.
* Introduce sumD & ReduceD 
* GPU sum is probably better currently.

* Accelerate the cshift & benchmark

* 0) Single GPU
- 128 bit integer table load in GPU code.
  - ImprovedStaggered accelerate & measure perf
  - Gianluca's changes to Cayley into gpu-port
  - Mobius kernel fusion.                     -- Gianluca?
  - Lebesque order reintroduction. StencilView should have pointer to it
  - Lebesgue reorder in all kernels

* 3) Comms/NVlink
- OpenMP tasks to run comms threads. Experiment with it 
- Remove explicit openMP in staggered. 
- Single parallel region around both the Kernel call and the comms.
- Fix the halo exchange SIMT loop
- Stencil gather ??
- SIMD dirs in stencil

* 4) ET enhancements
- eval -> scalar ops in ET engine
- coalescedRead, coalescedWrite in expressions.

* 5) Misc
- Conserved current clean up.
- multLinkProp eliminate

8) Merge develop and test HMC

9) Gamma tables on GPU; check this. Appear to work, but no idea why. Are these done on CPU?

10) Audit
-     pragma once uniformly
-     Audit NAMESPACE CHANGES
-     Audit changes

-----
Gianluca's changes
- Performance impact of construct in aligned allocator???
---------

- merge2 where is it used. Audit routines, comment out and check compile.

-----------------------------
DONE:
-----------------------------
=============================================================================================
AUDIT ContractWWVV with respect to develop    -- DONE
- GPU accelerate EOFA                                                  -- DONE
- LinalgUtils  ssp loop not offloaded                                  -- DONE
- coalescedRead <- threadIdx.x                                         -- DONE
- Stencil.h : Thread loops in exchange code. Need to offload these     -- DONE ; pending debug
- Mobius/Domain EOFA cache header implementaiotn has thread_loop       -- DONE ; pending test
- Differentiate non-temporal coalescedWrite from temporal              -- DONE

- Clean up PRAGMAS, and SIMT_loop                                      -- DONE
  thread_loop interface revisit.
  _foreach
  _for

- Staggered kernels -> GPU coalesced loop, loop in kernels -- DONE
- Staggered kernels inline for GPU -- DONE

-- Common source GPU and CPU generic kernels???                  ---- DONE
--   - Uniform coding between GPU kernels and CPU kernels attempt  ---- DONE, got faster !

-- Figure what to do about "multLinkGpu" etc.. in FermionOperatorImpl. -- DONE
-- Gparity is the awkward one                                          -- DONE
-- Solve non-Gparity first.                                            -- DONE
-- Simplify the operator IMPL support                                  -- DONE
-- 
--
-- Investigate why slower than september     --- DONE
--
-- Single GPU simd target (VGPU) --- DONE
--
-- Reread WilsonKernels and check diffs -- DONE
--

- AVX512 still broken, lebesgue order missing ?

* Gianluca merger
  - Cayley coefficients -> GPU retention or prefetch
  - Make GPU offload reductions deterministic -- Gianluca merge
  - Lattice_reduction - remnant thread_loops must offload. Audit thread_loop in main code for non-accelerated code  
  - Inner product compare to Summit inner product optimisation
  - CayleyFermion5D.cc - flop count line 166 odd. Shouldn't depend on arch
  -                    - Review Vector use
  - CayleyFermion5D.h  - DperpGPU unify coding style

- Committed my modifications
- Accelerate non-dslash elements of Mobius; check accelerator_loop uniformly used in fermion operators
   - Merged Gianluca modifications
- Verify HMC one flavour ratio
- GPU offload reductions: using thrust::reduce?
- Deprecate JSON.
- pugixml difficult.
- Eigen problematic.
- Audit HMC timestep / traj length size
- GPU offload reductions; thrust initial ; inclusive_scan vs reduce?
- Pragmas.h - prune and remove strong_inline (?)
- GPU offload reductions; thrust initial ; inclusive_scan vs reduce?
- Remove old parallel_for macros, fix errors
- - Need (1) omp parallel for     <-- thread_loop
- -      (2) omp for
- -      (3) omp for collapse(n)
- -      (4) omp parallel for collapse(n)
- - Only (1) has a natural mirror in accelerator_loop
- - Nested loop macros get cumbersome made a generic interface for N deep
- - Don't like thread_region and thread_loop_in_region
- - Could replace with 

    thread_nested(1, 
      for {

      }
    );
    thread_nested(2,
      for (){
        for (){

	}
      }
    );

    and same "in_region".


-----------------------------
Physics item work list:
-----------------------------

2)- Consistent linear solver flop count/rate -- PARTIAL, time but no flop/s yet
4)- Multigrid Wilson and DWF, compare to other Multigrid implementations
5)- HDCR resume

-----------------------------


Nov 2018

1)- BG/Q port and check ; Andrew says ok.
3)- Physical propagator interface  -- DONE

DONE
a) namespaces & indentation
 GRID_BEGIN_NAMESPACE();
 GRID_END_NAMESPACE();
-- delete QCD namespace

b) GPU branch
- start branch
- Increase Macro use in core library support; prepare for change
- Audit volume of "device" code
- Virtual function audit
- Start port once Nvidia box is up
- Cut down volume of code for first port? How?

----------------------------
Recent DONE 
-- RNG I/O in ILDG/SciDAC (minor) 
-- Precision conversion and sort out localConvert      <-- partial/easy
-- Conserved currents (Andrew)
-- Split grid
-- Christoph's local basis expansion Lanczos
-- MultiRHS with spread out extra dim -- Go through filesystem with SciDAC I/O ; <-- DONE ; bmark cori
-- Lanczos Remove DenseVector, DenseMatrix; Use Eigen instead. <-- DONE
-- GaugeFix into central location                      <-- DONE
-- Scidac and Ildg metadata handling                   <-- DONE
-- Binary I/O MPI2 IO                                  <-- DONE
-- Binary I/O speed up & x-strips                      <-- DONE
-- Cut down the exterior overhead                      <-- DONE
-- Interior legs from SHM comms                        <-- DONE
-- Half-precision comms                                <-- DONE
-- Merge high precision reduction into develop         <-- DONE
-- BlockCG, BCGrQ                                      <-- DONE
-- multiRHS DWF; benchmark on Cori/BNL for comms elimination <-- DONE
   -- slice* linalg routines for multiRHS, BlockCG    

-----
* Forces; the UdSdU  term in gauge force term is half of what I think it should
  be. This is a consequence of taking ONLY the first term in:

  dSg/dt = dU/dt dSdU + dUdag/dt dSdUdag

  in the fermion force.

  Now, S_mom = - tr Pmu Pmu      ; Pmu anti-herm

                                  .
       d Smom/dt = - 2.0 tr Pmu Pmu   = - dSg/dt = - tr Pmu [Umu dSdUmu + UmuDag dSdUmuDag]

           .
       => Pmu =  Umu dSdUmu

       Where the norm is half expected.

  This means we must double the force in the Test_xxx_force routines, and is the origin of the factor of two.
  This 2x is applied by hand in the fermion routines and in the Test_rect_force routine.

* Support different boundary conditions (finite temp, chem. potential ... )

- Sign of force term.

- Reversibility test.

- Rename "Ta" as too unclear

- Lanczos

- Audit oIndex usage for cb behaviour

- Prepare multigrid for HMC. - Alternate setup schemes.

- Support for ILDG --- ugly, not done

- Flavour matrices?

- FFTnD ?

- Gparity; hand opt use template specialisation elegance to enable the optimised paths ?

- Gparity force term; Gparity (R)HMC.

- Mobius implementation clean up to rmove #if 0 stale code sequences

- CG -- profile carefully, kernel fusion, whole CG performance measurements.

================================================================
* Hacks and bug fixes to clean up and Audits
================================================================

*  Extract/merge/set cleanup ; too many variants; rationalise and call simpler ones

*  Rewrite core tensor arithmetic support to be more systematic
 =  Use #define repetitive sequences to minimise code, decrease line count by thousands possible,
    with more robust and maintainable implementation.

*  Ensure we ET as much as possible; move unop functions into ET framework.
   - tests with expression args to all functions

* FIXME audit

* const audit

Insert/Extract
* Replace vset with a call to merge.; 
* care in Gmerge,Gextract over vset .
* extract / merge extra implementation removal      
* Optimise the extract/merge SIMD routines; Azusa??
 - I have collated into single location at least.
 - Need to use _mm_*insert/extract routines.

* Thread scaling tests Xeon, XeonPhi

Not sure of status of this -- reverify. Things are working nicely now though.

* Make the Tensor types and Complex etc... play more nicely.

  - TensorRemove is a hack, come up with a long term rationalised approach to Complex vs. Scalar<Scalar<Scalar<Complex > > >
    QDP forces use of "toDouble" to get back to non tensor scalar. This role is presently taken TensorRemove, but I
    want to introduce a syntax that does not require this.

  - Reductions that contract indices on a site should always demote the tensor structure.
    norm2(), innerProduct.

  - Result of Sum(), SliceSum // spatial sums
              trace, traceIndex etc.. do not.

  - problem arises because "trace" returns Lattice<TComplex> moving everything down to Scalar,
    and then Sum and SliceSum to not remove the Scalars. This would be fixed if we 
    template specialize the scalar scalar scalar sum and SliceSum,  on the basis of being
    pure scalar.

======================================================================
======================================================================
======================================================================
======================================================================
RECENT
---------------

  - Support different fermion representations? -- DONE
  - contained entirely within the integrator presently
  - Clean up HMC                                                             -- DONE
  - LorentzScalar<GaugeField> gets Gauge link type (cleaner).                -- DONE
  - Simplified the integrators a bit.                                        -- DONE
  - Multi-timescale looks broken and operating on single timescale for now.  -- DONE
  - pass GaugeField as template param.                        -- DONE
  - Reunitarise                                               -- DONE
  - Force Gradient                                            -- DONE
  - Prefer "RefreshInternal" or such like to "init" in naming -- DONE
  - Parallel io improvements                                  -- DONE
  - Plaquette and link trace checks into nersc reader from the Grid_nersc_io.cc test. -- DONE


DONE:


- MultiArray -- MultiRHS done
- ConjugateGradientMultiShift -- DONE
- MCR                         -- DONE
- Remez -- Mike or Boost?     -- DONE
- Proto (ET)                  -- DONE
- uBlas                       -- DONE ; Eigen
- Potentially Useful Boost libraries -- DONE ; Eigen
- Aligned allocator; memory pool -- DONE
- Multiprecision              -- DONE
- Serialization               -- DONE
- Regex -- Not needed
- Tokenize -- Why?

- Random number state save restore -- DONE
- Rectangle gauge actions. -- DONE
  Iwasaki,
  Symanzik,
  ... etc...
Done: Cayley, Partial , ContFrac force terms.

DONE
- PseudoFermions
=> generalise to non-const EE ; likely defer (??) (NOT DONE)
Done:
  - TwoFlavour
  - TwoFlavourEvenOdd        
  - TwoFlavourRatio
  - TwoFlavourRatioEvenOdd

Done:
  - OneFlavourRationalEvenOdd
  - OneFlavourRationalRatioEvenOdd
  - OneFlavourRationalRatio

Done
=> Test DWF HMC
   - Fix a threading bug that has been introduced and prevents HMC running hybrid OMP mode

Done:
- RNG filling from sparser grid, lower dim grid.


DONE
  - MacroMagic -> virtual reader class.

*** Expression template engine: -- DONE

[   -- Norm2(expression) problem: introduce norm2 unary op, or Introduce conversion automatic from expression to Lattice<vobj>
* Strong test for norm2, conj and all primitive types. -- tests/Grid_simd.cc is almost there
* Implement where within expression template scheme.
* Check for missing functionality                    - partially audited against QDP++ layout

   // Unary functions
   // cos,sin, tan, acos, asin, cosh, acosh, tanh, sinh, // Scalar<vReal> only arg
   // exp, log, sqrt, fabs
   // transposeColor, transposeSpin,
   // adjColor, adjSpin,
   // copyMask.
   // localMaxAbs
   // Fourier transform equivalent.]


* CovariantShift support                             -----Use a class to store gauge field? (parallel transport?)

-- coherent framework for implementing actions and their forces.
Actions 

DONE
* Fermion
  - Wilson
  - Clover
  - DomainWall
  - Mobius
  - z-Mobius


Algorithms (lots of reuse/port from BFM)
* LinearOperator
* LinearSolver
* Polynomial 
* Eigen
* CG
* Pcg
* Adef2
* DeflCG
* fPcg
* MCR
* HDCG
* HMC, 
* Heatbath
* Integrators, leapfrog, omelyan, force gradient etc...
* etc..

Done
* Pauli, SU subgroup, etc.. 

* su3 exponentiation & log etc.. [Jamie's code?]

======================================================================================================
FUNCTIONALITY: it pleases me to keep track of things I have done (keeps me arguably sane)
======================================================================================================

* Link smearing/boundary conds; Policy class based implementation ; framework more in place -- DONE
* Command line args for geometry, simd, etc. layout. Is it necessary to have -- DONE
  user pass these? Is this a QCD specific?

* Stencil -- DONE
* Test infrastructure -- DONE
* Fourspin, two spin project --- DONE
* Dirac Gamma/Dirac structures ---- DONE
* Conditional execution, where etc...                -----DONE, simple test
* Integer relational support                         -----DONE
* Coordinate information, integers etc...            -----DONE
* Integer type padding/union to vector.              -----DONE 
* LatticeCoordinate[mu]                              -----DONE
* expose traceIndex, peekIndex, transposeIndex etc at the Lattice Level -- DONE
* TraceColor, TraceSpin.                             ----- DONE (traceIndex<1>,traceIndex<2>, transposeIndex<1>,transposeIndex<2>)
                                                     ----- Implement mapping between traceColour and traceSpin and traceIndex<1/2>.
* How to do U[mu] ... lorentz part of type structure or not. more like chroma if not. -- DONE

* Twospin/Fourspin/Gamma/Proj/Recon                  ----- DONE
* norm2l is a hack. figure out syntax error and make this norm2 c.f. tests/Grid_gamma.cc -- DONE

* subdirs lib, tests ??                              ----- DONE
  - lib/math        
  - lib/cartesian
  - lib/cshift
  - lib/stencil
  - lib/communicator
  - lib/algorithms
  - lib/qcd
  - lib/io/   -- GridLog, GridIn, GridErr, GridDebug, GridMessage
  - lib/qcd/actions
  - lib/qcd/measurements

* Subset support, slice sums etc...                  -----DONE
  sliceSum(orthog)
  sum
  innerProduct
  norm2

* Subgrid Transferral                                -----DONE
  subBlock (coarseLattice,fineLattice)
  projectBlockBasis  
  promoteBlockBasis

* random number generation                           ----- DONE

* Broadcast, reduction tests. innerProduct, localInnerProduct --- DONE

* I/O support
* NERSC Lattice loading, plaquette test             ------- DONE single node 

* Controling std::cout                              ------- DONE

* Had to hack assignment to 1.0 in the tests/Grid_gamma test -- DONE
* Reduce implemention is poor ; need threaded reductions; OMP isn't able to do it for generic objects. -- DONE
* Bug in RNG with complex numbers ; only filling real values; need helper function -- DONE
* Conformable test in Cshift routines. -- none needed ; there is only one 
* Conformable testing in expression templates -- DONE (recursive)

* Bug in SeedFixedIntegers gave same output on each site. -- DONE
  Implement and use lattice IO to verify this.            -- cout for lattice types DONE