Basic Object Design and Implementation — PETSc 3.16.5 documentation

# Basic Object Design and Implementation

PETSc is designed by using strong data encapsulation. Hence, any collection of data (for instance, a sparse matrix) is stored in a way that is completely private from the application code. The application code can manipulate the data only through a well-defined interface, since it does not “know” how the data is stored internally.

## Introduction

PETSc is designed around several classes including `Vec` (vectors) and `Mat` (matrices, both dense and sparse). Each class is implemented by using a C `struct` that contains the data and function pointers for operations on the data (much like virtual functions in C++ classes). Each class consists of three parts:

A (small) common part shared by all PETSc classes (for example, both `KSP` and `PC` have this same header).

Another common part shared by all PETSc implementations of the class (for example, both `KSPGMRES` and `KSPCG` have this common subheader).

A private part used by only one particular implementation written in PETSc.

For example, all matrix (`Mat`) classes share a function table of operations that may be performed on the matrix; all PETSc matrix implementations share some additional data fields, including matrix parallel layout, while a particular matrix implementation in PETSc (say compressed sparse row) has its own data fields for storing the actual matrix values and sparsity pattern. This will be explained in more detail in the following sections. New class implementations must use the PETSc common part.

We will use `<class>_<implementation>` to denote the actual source code and data structures used for a particular implementation of an object that has the `<class>` interface.

## Organization of the Source Code

Each class has the following organization.

Its own, application-public, include file `include/petsc<class>.h`.

Its own directory, `src/<class>` or `src/<package>/<class>`.

A data structure defined in the file `include/petsc/private/<class>impl.h`. This data structure is shared by all the different PETSc implementations of the class. For example, for matrices it is shared by dense, sparse, parallel, and sequential formats.

An abstract interface that defines the application-callable functions for the class. These are defined in the directory `src/<class>/interface`. This is how polymorphism is supported with code that implements the abstract interface to the operations on the object. Essentially, these routines do some error checking of arguments and logging of profiling information and then call the function appropriate for the particular implementation of the object. The name of the abstract function is `<class>Operation`, for instance, `MatMult()` or `PCCreate(`), while the name of a particular implementation is `<class>Operation_<implementation>`, for instance, `MatMult_SeqAIJ()` or `PCCreate_ILU()`. These naming conventions are used to simplify code maintenance (also see Section [sec:stylenames]).

One or more actual implementations of the class (for example, sparse uniprocessor and parallel matrices implemented with the AIJ storage format). These are each in a subdirectory of `src/<class>/impls`. Except in rare circumstances, data structures defined here should not be referenced from outside this directory.

Each type of object (for instance, a vector) is defined in its own public include file, by `typedef _p_<class>* <class>`; (for example, `typedef _p_Vec* Vec;`). This organization allows the compiler to perform type checking on all subroutine calls while at the same time completely removing the details of the implementation of `_p_<class>` from the application code. This capability is extremely important because it allows the library internals to be changed without altering or recompiling the application code.

## Common Object Header

All PETSc/PETSc objects have the following common header structures defined in include/petsc/private/petscimpl.h:

    typedef struct {
      PetscErrorCode (*getcomm)(PetscObject,MPI_Comm*);
      PetscErrorCode (*view)(PetscObject,Viewer);
      PetscErrorCode (*destroy)(PetscObject);
      PetscErrorCode (*query)(PetscObject,const char*,PetscObject*);
      PetscErrorCode (*compose)(PetscObject,const char*,PetscObject);
      PetscErrorCode (*composefunction)(PetscObject,const char*,void(*)(void));
      PetscErrorCode (*queryfunction)(PetscObject,const char*,void (**)(void));
    } PetscOps;

    struct _p_<class> {
      PetscClassId     classid;
      PetscOps         *bops;
      <class>Ops       *ops;
      MPI_Comm         comm;
      PetscLogDouble   flops,time,mem;
      int              id;
      int              refct;
      int              tag;
      DLList           qlist;
      OList            olist;
      char             *type_name;
      PetscObject      parent;
      char             *name;
      char             *prefix;
      void             *cpp;
      void             **fortran_func_pointers;
      ..........
      CLASS-SPECIFIC DATASTRUCTURES
    };

Here `<class>ops` is a function table (like the `PetscOps` above) that contains the function pointers for the operations specific to that class. For example, the PETSc vector class object operations in include/petsc/private/vecimpl.h include the following.

    typedef struct _VecOps* VecOps;
    struct _VecOps {
      PetscErrorCode (*duplicate)(Vec,Vec*); /* get single vector */
      PetscErrorCode (*duplicatevecs)(Vec,PetscInt,Vec**); /* get array of vectors */
      PetscErrorCode (*destroyvecs)(PetscInt,Vec[]); /* free array of vectors */
      PetscErrorCode (*dot)(Vec,Vec,PetscScalar*); /* z = x^H * y */
      PetscErrorCode (*mdot)(Vec,PetscInt,const Vec[],PetscScalar*); /* z[j] = x dot y[j] */
      PetscErrorCode (*norm)(Vec,NormType,PetscReal*); /* z = sqrt(x^H * x) */
      PetscErrorCode (*tdot)(Vec,Vec,PetscScalar*); /* x'*y */
      PetscErrorCode (*mtdot)(Vec,PetscInt,const Vec[],PetscScalar*);/* z[j] = x dot y[j] */
      PetscErrorCode (*scale)(Vec,PetscScalar);  /* x = alpha * x   */
      PetscErrorCode (*copy)(Vec,Vec); /* y = x */
      PetscErrorCode (*set)(Vec,PetscScalar); /* y = alpha  */
      PetscErrorCode (*swap)(Vec,Vec); /* exchange x and y */
      PetscErrorCode (*axpy)(Vec,PetscScalar,Vec); /* y = y + alpha * x */
      PetscErrorCode (*axpby)(Vec,PetscScalar,PetscScalar,Vec); /* y = alpha * x + beta * y*/
      PetscErrorCode (*maxpy)(Vec,PetscInt,const PetscScalar*,Vec*); /* y = y + alpha[j] x[j] */
      ... (AND SO ON) ...
    };

    struct _p_Vec {
      PetscClassId           classid;
      PetscOps               *bops;
      VecOps                 *ops;
      MPI_Comm               comm;
      PetscLogDouble         flops,time,mem;
      int                    id;
      int                    refct;
      int                    tag;
      DLList                 qlist;
      OList                  olist;
      char                   *type_name;
      PetscObject            parent;
      char                   *name;
      char                   *prefix;
      void                   **fortran_func_pointers;
      void                   *data;     /* implementation-specific data */
      PetscLayout            map;
      ISLocalToGlobalMapping mapping;   /* mapping used in VecSetValuesLocal() */
    };

Each PETSc object begins with a `PetscClassId`, which is used for error checking. Each different class of objects has its value for `classid`; these are used to distinguish between classes. When a new class is created you need to call

    PetscClassIdRegister(const char *classname,PetscClassId *classid);

For example,

    PetscClassIdRegister("index set",&IS_CLASSID);

you can verify that an object is valid of a particular class with `PetscValidHeaderSpecific`, for example,

    PetscValidHeaderSpecific(x,VEC_CLASSID,1);

The third argument to this macro indicates the position in the calling sequence of the function the object was passed in. This is to generate more complete error messages.

To check for an object of any type, use

    PetscValidHeader(x,1);

## Common Object Functions

Several routines are provided for manipulating data within the header. These include the specific functions in the PETSc common function table. The function pointers are not called directly; rather you should call `PetscObjectFunctionName()`, where `FunctionName` is one of the functions listed below with the first letter of each word capitalized.

`getcomm(PetscObject,MPI_Comm*)` obtains the MPI communicator associated with this object.

`view(PetscObject,PetscViewer)` allows you to store or visualize the data inside an object. If the Viewer is NULL, then it should cause the object to print information on the object to textttstdout.

`destroy(PetscObject)` causes the reference count of the object to be decreased by one or the object to be destroyed and all memory used by the object to be freed when the reference count drops to zero. If the object has any other objects composed with it, they are each sent a `destroy()`; that is, the `destroy()` function is called on them also.

`compose(PetscObject,const char *name,PetscObject)` associates the second object with the first object and increases the reference count of the second object. If an object with the same name was previously composed, that object is dereferenced and replaced with the new object. If the second object is NULL and an object with the same name has already been composed, that object is dereferenced (the `destroy()` function is called on it, and that object is removed from the first object). This is a way to remove, by name, an object that was previously composed.

`query(PetscObject,const char *name,PetscObject*)` retrieves an object that was previously composed with the first object via `PetscObjectCompose()`. It retrieves a NULL if no object with that name was previously composed.

`composefunction(PetscObject,const char *name,void *func)` associates a function pointer with an object. If the object already had a composed function with the same name, the old one is replaced. If `func` is `NULL`, the existing function is removed from the object. The string `name` is the character string name of the function.

For example, `fname` may be `PCCreate_LU`.

`queryfunction(PetscObject,const char *name,void **func)` retrieves a function pointer that was associated with the object via `PetscObjectComposeFunction()`. If dynamic libraries are used, the function is loaded into memory at this time (if it has not been previously loaded), not when the `composefunction()` routine was called.

Since the object composition allows one to compose PETSc objects only with PETSc objects rather than any arbitrary pointer, PETSc provides the convenience object `PetscContainer`, created with the routine `PetscContainerCreate(MPI_Comm,PetscContainer*)`, to allow wrapping any kind of data into a PETSc object that can then be composed with a PETSc object.

## Object Function Implementation

This section discusses how PETSc implements the `compose()`, `query()`, `composefunction()`, and `queryfunction()` functions for its object implementations. Other PETSc-compatible class implementations are free to manage these functions in any manner; but unless there is a specific reason, they should use the PETSc defaults so that the library writer does not have to “reinvent the wheel.”

### Compose and Query Objects

In src/sys/objects/olist.c, PETSc defines a C `struct`

    typedef struct _PetscObjectList* PetscObjectList;
    struct _PetscObjectList {
        char             name[128];
        PetscObject      obj;
        PetscObjectList  next;
    };

from which linked lists of composed objects may be constructed. The routines to manipulate these elementary objects are

    int PetscObjectListAdd(PetscObjectList *fl,const char *name,PetscObject obj);
    int PetscObjectListDestroy(PetscObjectList *fl);
    int PetscObjectListFind(PetscObjectList fl,const char *name,PetscObject *obj)
    int PetscObjectListDuplicate(PetscObjectList fl,PetscObjectList *nl);

The function `PetscObjectListAdd()` will create the initial PetscObjectList if the argument `fl` points to a NULL.

The PETSc object `compose()` and `query()` functions are as follows (defined in src/sys/objects/inherit.c).

    PetscErrorCode PetscObjectCompose_Petsc(PetscObject obj,const char *name,PetscObject ptr)
    {
      PetscErrorCode ierr;

      PetscFunctionBegin;
      PetscObjectListAdd(&obj->olist,name,ptr);
      PetscFunctionReturn(0);
    }

    PetscErrorCode PetscObjectQuery_Petsc(PetscObject obj,const char *name,PetscObject *ptr)
    {
      PetscErrorCode ierr;

      PetscFunctionBegin;
      PetscObjectListFind(obj->olist,name,ptr);
      PetscFunctionReturn(0);
    }

### Compose and Query Functions

PETSc allows you to compose functions by specifying a name and function pointer. In src/sys/dll/reg.c, PETSc defines the following linked list structure.

    struct _n_PetscFunctionList {
      void              (*routine)(void);    /* the routine */
      char              *name;               /* string to identify routine */
      PetscFunctionList next;                /* next pointer */
      PetscFunctionList next_list;           /* used to maintain list of all lists for freeing */
    };

Each PETSc object contains a `PetscFunctionList` object. The `composefunction()` and `queryfunction()` are given by the following.

    PetscErrorCode PetscObjectComposeFunction_Petsc(PetscObject obj,const char *name,void *ptr)
    {
      PetscErrorCode ierr;

      PetscFunctionBegin;
      PetscFunctionListAdd(&obj->qlist,name,fname,ptr);
      PetscFunctionReturn(0);
    }

    PetscErrorCode PetscObjectQueryFunction_Petsc(PetscObject obj,const char *name,void (**ptr)(void))
    {
      PetscErrorCode ierr;

      PetscFunctionBegin;
      PetscFunctionListFind(obj->qlist,name,ptr);
      PetscFunctionReturn(0);
    }

In addition to using the `PetscFunctionList` mechanism to compose functions into PETSc objects, it is also used to allow registration of new class implementations; for example, new preconditioners.

### Simple PETSc Objects

Some simple PETSc objects do not need `PETSCHEADER` and the associated functionality. These objects are internally named as `_n_<class>` as opposed to `_p_<class>`, for example, `_n_PetscTable` vs `_p_Vec`.

## PETSc Packages

The PETSc source code is divided into the following library-level packages: `sys`, `Vec`, `Mat`, `DM`, `KSP`, `SNES`, `TS`, `TAO`. Each of these has a directory under the `src` directory in the PETSc tree and, optionally, can be compiled into separate libraries. Each package defines one or more classes; for example, the `KSP` package defines the `KSP` and `PC` classes, as well as several utility classes. In addition, each library-level package may contain several class-level packages associated with individual classes in the library-level package. In general, most “important” classes in PETSc have their own class level package. Each package provides a registration function `XXXInitializePackage()`, for example `KSPInitializePackage()`, which registers all the classes and events for that package. Each package also registers a finalization routine, `XXXFinalizePackage()`, that releases all the resources used in registering the package, using `PetscRegisterFinalize()`. The registration for each package is performed “on demand” the first time a class in the package is utilized. This is handled, for example, with code such as

    PetscErrorCode  VecCreate(MPI_Comm comm, Vec *vec)
    {
      Vec            v;

      PetscFunctionBegin;
      PetscValidPointer(vec,2);
      *vec = NULL;
      VecInitializePackage();
      ...

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