A new I/O file format

Thoughts on a rather generic AMR I/O file format and library

(That would be useful for the Einstein Toolkit and related projects) This is related to the motivation for ticket 1033

General Thoughts

Uses

• generic file I/O, i.e. exporting/importing data
• checkpointing, recovery
• visualization
• post-processing
• long-term archival

Necessary Properties

• needs to be based on HDF5, or an equivalent portrable, widely-supported file format
• needs to support efficient parallel I/O (including quick discovery of file contents, quick reading of individual datasets)
• needs to be portable
• should be useful for similar projects, e.g. Enzo
• must support unigrid, AMR, multi-block, DGFE, staggered grids
• must be usable from C, C++, Fortran, Python, Mathematica
• should be implemented in a portable stand-alone library that can easily be used in various projects
• must remain accessible without such a library

Ideas

We introduce various concepts that abstract various properties. Data are described in terms of these concepts instead of using ad-hoc descriptions for datasets.

It seems useful that each concept has abstract properties and several concrete realizations.

Concepts:

• project (consisting of simulations)
• manifold (consisting of discretizations)
• coordinate systems (various types)
• tangent spaces (what is the connection to a coordinate system?)
• tensors (described via bases) (should bases be related to tangent spaces?)
• generic variable types (such as "floating"), implemented via concrete types (such as float32, float64)
• fields, as defined by the user

Names should be illustrative only and don't matter; only the connection between these concepts are relevant.

Prototype, written in a C++ style

// Note: Unless noted otherwise, all pointers are non-null

// When translating to HDF5:
// - structs become objects, usually groups
// - simple struct fields (int, string) become attributes of the group
// - pointers become links inside the group
// - sets containing non-pointers become objects inside the group
// - sets containing pointers become links inside a subgroup of the group
// - vectors of simple types (int, string) become attributes
// - other vectors become objects inside a subgroup the group, sorted
//   alphabetically

// Tensor types

struct TensorType {
  int dimension;
  int rank;
  set<TensorComponent> storedcomponents;
  bool invariant() const {
    return dimension >= 0 && rank >= 0 &&
           storedcomponent.size() < pow(tensortype.dimension, tensortype.rank);
  }
};
set<TensorType> tensortypes;

struct TensorComponent {
  TensorType &tensortype;
  // We use objects to denote most concepts, but we make an exception
  // for tensor component indices and tangent space basis vectors,
  // which we number consecutively starting from zero. This simplifies
  // the representation, and it introduces a canonical order (e.g. x,
  // y, z) among the tangent space directions that people are
  // expecting.
  int storedcomponent;
  vector<int> indexvalues;
  bool invariant() const {
    bool inv = storedcomponent >= 0 &&
               storedcomponent < tensortype.storedcomponents.size() &&
               indexvalues.size() == tensortype->rank;
    for (int iv : indexvalues)
      inv &= iv >= 0 && iv < tensortype->dimension;
    return inv;
  }
};

TensorType Scalar3D{"Scalar3D", 3, 0, {TensorComponent{Scalar3D, {}}}};

TensorType Vector3D{"Vector3D",
                    3,
                    1,
                    {TensorComponent{Vector3D, {0}},
                     TensorComponent{Vector3D, {1}},
                     TensorComponent{Vector3D, {2}}}};

TensorType SymmetricTensor3D{"SymmetricTensor3D",
                             3,
                             2,
                             {TensorComponent{SymmetricTensor3D, {0, 0}},
                              TensorComponent{SymmetricTensor3D, {0, 1}},
                              TensorComponent{SymmetricTensor3D, {0, 2}},
                              TensorComponent{SymmetricTensor3D, {1, 0}},
                              TensorComponent{SymmetricTensor3D, {1, 1}},
                              TensorComponent{SymmetricTensor3D, {2, 2}}}};

// High-level continuum concepts

struct Manifold {
  int dimension;
  set<Discretization> discretizations;
  set<Field *> fields;
  bool invariant() const { return dimension >= 0; }
};
set<Manifold> manifolds;

struct TangentSpace {
  int dimension;
  set<Basis> bases;
  set<Field *> fields;
  bool invariant() const { return dimension >= 0; }
};
set<TangentSpace> tangentspaces;

struct Field {
  Manifold *manifold;
  TangentSpace *tangentspace;
  TensorType *tensortype;
  set<DiscreteField> discretefields;
  bool invariant() const {
    return tangentspace->dimension == tensortype->dimension;
  }
};
set<Field> Fields;

// Manifold discretizations

struct Discretization {
  Manifold &manifold;
  set<DiscretizationBlock> discretizationblocks;
  bool invariant() const { return true; }
};

struct DiscretizationBlock {
  // Discretization of a certain region, represented by contiguous data
  Discretization &discretization;
  // bounding box? in terms of coordinates?
  // connectivity? neighbouring blocks?
  // overlaps?
  bool invariant() const { return true; }
};

// Tangent space bases

struct Basis {
  TangentSpace &tangentspace;
  vector<BasisVector> basisvectors;
  set<CoordinateBasis *> coordinatebases;
  bool invariant() const {
    return basisvectors.size() == tangentspace->dimension;
  }
};

struct BasisVector {
  Basis &basis;
  // Since a BasisVector denotes essentially only an integer, we
  // should be able to replace it by an integer. Not sure this is
  // worthwhile. This essentially only gives names to directions; could use
  // vector<string> in TangentSpace for this instead.
  int direction;
  set<CoordinateBasisElement *> coordinatebasiselements;
  bool invariant() const {
    return direction >= 0 && direction < basis->basisvectors.size() &&
           basis->basisvectors[direction] == this;
  }
};

// Discrete fields

struct DiscreteField {
  Field &field;
  Discretization *discretization;
  Basis *basis;
  set<DiscreteFieldBlock> discretefieldblocks;
  bool invariant() const {
    return field->manifold == discretization->manifold &&
           field->tangentspace == basis->tangentspace;
  }
};

struct DiscreteFieldBlock {
  // Discrete field on a particular region (discretization block)
  DiscreteField &discretefield;
  DiscretizationBlock *discretizationblock;
  set<DiscreteFieldBlockData> discretefieldblockdata;
  bool invariant() const { return true; }
};

struct DiscreteFieldBlockData {
  // Tensor component for a discrete field on a particular region
  DiscreteFieldBlock &discretefieldblock;
  TensorComponent *tensorcomponent;
  hid_t hdf5_dataset;
  bool invariant() const {
    return discretefieldblock.discretefield->field->tensortype ==
           tensorcomponent->tensortype;
  }
};

// Coordinates

struct CoordinateSystem {
  Manifold *manifold;
  vector<CoordinateField> coordinatefields;
  set<CoordinateBasis *> coordinatebases;
  bool invariant() const { return true; }
};
set<Coordinate> coordinates;

struct CoordinateField {
  CoordinateSystem &coordinatesystem;
  int direction;
  Field *field;
  bool invariant() const {
    return direction >= 0 &&
           direction < coordinatesystem->coordinatefields.size() &&
           coordinatesystem->coordinatefields[direction] == this;
  }
};

struct CoordinateBasis {
  CoordinateSystem *coordinatesystem;
  Basis *basis;
  vector<CoordinateBasisElement> coordinatebasiselements;
};

struct CoordinateBasisElement {
  CoordinateBasis &coordinatebasis;
  CoordinateField *coordinatefield;
  BasisVector *basisvector;
  bool invariant() const {
    return coordinatefield->direction == basisvector->direction;
  }
};