PETSc Style and Usage Guide — PETSc 3.14.5 documentation

petsc-3.14.5 2021-03-03
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# PETSc Style and Usage Guide

The PETSc team uses certain conventions to make the source code consistent and hence easier to maintain. We will interchangeably use the terminology subclass, implementation, or type 1 to refer to a concrete realization of an abstract base class. For example, `KSPGMRES` is a type for the base class `KSP`.

## Names

Consistency of names for variables, functions, and so on is extremely important. We use several conventions

1. All function names and enum types consist of acronyms or words, each of which is capitalized, for example, `KSPSolve()` and `MatGetOrdering()`.

2. All enum elements and macro variables are named with all capital letters. When they consist of several complete words, there is an underscore between each word. For example, `MATFINALASSEMBLY`.

3. Functions that are private to PETSc (not callable by the application code) either

   - have an appended `_Private` (for example, `StashValues_Private`) or

   - have an appended `_Subtype` (for example, `MatMultSeq_AIJ`).

   In addition, functions that are not intended for use outside of a particular file are declared `static`. Also see item on symbol visibility in Usage of PETSc Functions and Macros.

4. Function names in structures (for example, `_matops`) are the same as the base application function name without the object prefix and are in small letters. For example, `MatMultTranspose()` has a structure name of `multtranspose`.

5. Names of implementations of class functions should begin with the function name, an underscore, and the name of the implementation, for example, `KSPSolve_GMRES()`.

6. Each application-usable function begins with the name of the class object, followed by any subclass name, for example, `ISInvertPermutation()`, `MatMult()`, or `KSPGMRESSetRestart()`.

7. Functions that PETSc provides as defaults for user-providable functions end with `Default` (for example, `KSPMonitorDefault()` or `PetscSignalHandlerDefault()`).

8. Options database keys are lower case, have an underscore between words, and match the function name associated with the option without the word “set” or “get”, for example, `-ksp_gmres_restart`.

9. Specific `XXXType` values (for example, `MATSEQAIJ`) do not have an underscore in them unless they refer to another package that uses an underscore, for example, `MATSOLVERSUPERLU_DIST`.

## Coding Conventions and Style

Within the PETSc source code, we adhere to the following guidelines so that the code is uniform and easily maintained.

### C Formatting

1. No tabs are allowed in any of the source code.

2. All PETSc function bodies are indented two characters.

3. Each additional level of loops, `if` statements, and so on is indented two more characters.

4. Wrapping lines should be avoided whenever possible.

5. Source code lines do not have a hard length limit; generally, we like them less than 150 characters wide.

6. The local variable declarations should be aligned. For example, use the style

       PetscScalar a;
       PetscInt    i,j;

   instead of

       PetscScalar a;
       PetscInt i,j; /* Incorrect */

7. Assignment and comparison operations, for example, `x = 22.0` or `x < 22.0`, should have single spaces around the operator. This convention is true even when assignments are given directly in a line that declares the variable, such as `PetscReal r = 22.3`. The exception is when these symbols are used in a `for` loop; then, there should be no spaces, for example, `for (i=0; i<m; i++)`. Comparisons in `while()` constructs should have the spaces.

8. When declaring variables there should be no space between multiple variables, for example, `PetscReal a,b,c`, not `PetscReal a, b, c`.

9. The prototypes for functions should not include the names of the variables; for example, write

       PETSC_EXTERN PetscErrorCode MyFunction(PetscInt);

   not

       PETSC_EXTERN PetscErrorCode MyFunction(PetscInt myvalue); /* Incorrect */

10. All local variables of a particular type (for example, `PetscInt`) should be listed on the same line if possible; otherwise, they should be listed on adjacent lines.

11. Equal signs should be aligned in regions where possible.

12. There must be a single blank line between the local variable declarations and the body of the function.

13. Indentation for `if` statements must be done as follows.

        if ( ) {
          ....
        } else {
          ....
        }

14. Never have

        if ( )
          a single indented line /* Incorrect */

    or

        for ( )
          a single indented line /* Incorrect */

    Instead, use either

        if ( ) a single statement

    or

        if ( ) {
          a single indented line
        }

    Note that error checking is a separate statement, so the following is incorrect

        if ( ) ierr = XXX();CHKERRQ(ierr); /* Incorrect */

    and instead you should use

        if ( ) {
          ierr = XXX();CHKERRQ(ierr);
        }

15. Always have a space between `if` or `for` and the following `()`.

16. The open brace should be on the same line as the `if ( )` test, `for ( )`, and so forth, not on its own line, for example,

        } else {

    instead of

        }
        else { /* Incorrect */

    See the next item for an exception. The closing brace should always be on its own line.

17. In function declarations, the opening brace should be on the next line, not on the same line as the function name and arguments. This is an exception to the previous item.

18. Do not leave sections of commented-out code in the source files.

19. Use classic block comments (`/* Comment */`) for multi-line comments and for all comments in headers. Single-line comments in source files (not headers) may use the C99/C++ style (`// Comment`). The rationale is that it must be possible for users to build applications using strict `-std=c89` even though PETSc (since v3.14) uses select C99 features internally.

20. All variables must be declared at the beginning of the code block (C89 style), never mixed in with code. When variables are only used in a limited scope, it is encouraged to declare them in that scope. For example:

        if (cond) {
          PetscScalar *tmp;

          ierr = PetscMalloc1(10,&tmp);CHKERRQ(ierr);
          // use tmp
          ierr = PetscFree(tmp);CHKERRQ(ierr);
        }

    It is also permissible to use `for` loop declarations:

        for (PetscInt i=0; i<n; i++) {
          // loop body
        }

21. Do not include a space after a `(` or before a `)`. Do not write

        ierr = PetscMalloc1( 10,&a );CHKERRQ(ierr); /* Incorrect */

    but instead write

        ierr = PetscMalloc1(10,&a);CHKERRQ(ierr);

22. Do not use a space after the `)` in a cast or between the type and the `*` in a cast.

23. Do not include a space before or after a comma in lists. That is, do not write

        ierr = func(a, 22.0);CHKERRQ(ierr); /* Incorrect */

    but instead write

        ierr = func(a,22.0);CHKERRQ(ierr);

### C Usage

1. Array and pointer arguments where the array values are not changed should be labeled as `const` arguments.

2. Scalar values passed to functions should never be labeled as `const`.

3. Subroutines that would normally have a `void**` argument to return a pointer to some data should actually be prototyped as `void*`. This prevents the caller from having to put a `(void**)` cast in each function call. See, for example, `DMDAVecGetArray()`.

4. Do not use the `register` directive.

5. Do not use `if (rank == 0)` or `if (v == NULL)` or `if (flg == PETSC_TRUE)` or `if (flg == PETSC_FALSE)`. Instead, use `if (!rank)` or `if (!v)` or `if (flg)` or `if (!flg)`.

6. Do not use `#ifdef` or `#ifndef`. Rather, use `#if defined(...` or `#if !defined(...`. Better, use `PetscDefined()` (see below).

7. Never use system random number generators such as `rand()` in PETSc code or examples because these can produce different results on different systems thus making portability testing difficult. Instead use `PetscRandom` which produces the exact same results regardless of system it is used on.

8. Variadic macros may be used in PETSc source files, but must work with MSVC and must not be required in public headers (which must be usable with strict `-std=c89`). Most compilers have conforming implementations of the C99/C++11 rules for `__VA_ARGS__`, but MSVC’s implementation is not conforming and may need workarounds. See `PetscDefined()` for an example of how to work around MSVC’s limitations to write a macro that is usable in both.

9. Do not use language features that are not in the intersection of C99, C++11, and MSVC. Examples of such features include designated initializers and variable-length arrays. Note that variable-length arrays (including VLA-pointers) are not supported in C++ and were made optional in C11 and that designated initializers are not in C++.

### Usage of PETSc Functions and Macros

1. Public PETSc include files, `petsc*.h`, should not reference private PETSc `petsc/private/*impl.h` include files.

2. Public and private PETSc include files cannot reference include files located in the PETSc source tree.

3. When possible, use `PetscDefined()` instead of preprocessor conditionals. For example use:

       if (PetscDefined(USE_DEBUG)) { ... }

   instead of:

       #if defined(PETSC_USE_DEBUG)
         ...
       #endif

   The former usage allows syntax and type checking in all configurations of PETSc, where as the latter needs to be compiled with and without debugging just to confirm that it compiles.

4. The first line of the executable statements in functions must be `PetscFunctionBegin;`

5. Use `PetscFunctionReturn(returnvalue)`, not `return(returnvalue);`

6. Never put a function call in a `return` statement; do not write

       PetscFunctionReturn( somefunction(...) ); /* Incorrect */

7. Do not put a blank line immediately after `PetscFunctionBegin;` or a blank line immediately before `PetscFunctionReturn(0);`.

8. Do not use `sqrt()`, `pow()`, `sin()`, and so on directly in PETSc C/C++ source code or examples (usage is fine in Fortran source code). Rather, use `PetscSqrtScalar()`, `PetscSqrtReal()`, and so on, depending on the context. See `petscmath.h` for expressions to use.

9. Do not include `assert.h` in PETSc source code. Do not use `assert()`, it doesn’t play well in the parallel MPI world.

10. The macros `SETERRQ()` and `CHKERRQ()` should be on the same line as the routine to be checked unless doing so violates the 150 character-width-rule. Try to make error messages short but informative.

11. Do not include a space before `CHKXXX()`. That is, do not write

        ierr = PetscMalloc1(10,&a); CHKERRQ(ierr); /* Incorrect */

    but instead write

        ierr = PetscMalloc1(10,&a);CHKERRQ(ierr);

12. Except in code that may be called before PETSc is fully initialized, always use `PetscMallocN()` (for example, `PetscMalloc1()`), `PetscCallocN()`, `PetscNew()`, and `PetscFree()`, not `malloc()` and `free()`.

13. MPI routines and macros that are not part of the 1.0 or 1.1 standard should not be used in PETSc without appropriate `./configure` checks and `#if defined()` checks. Code should also be provided that works if the MPI feature is not available, for example,

        #if defined(PETSC_HAVE_MPI_IN_PLACE)
          ierr = MPI_Allgatherv(MPI_IN_PLACE,0,MPI_DATATYPE_NULL,lens,
                                recvcounts,displs,MPIU_INT,comm);CHKERRQ(ierr);
        #else
          ierr = MPI_Allgatherv(lens,sendcount,MPIU_INT,lens,recvcounts,
                                displs,MPIU_INT,comm);CHKERRQ(ierr);
        #endif

14. Do not introduce PETSc routines that provide essentially the same functionality as an available MPI routine. For example, do not write a routine `PetscGlobalSum()` that takes a scalar value and performs an `MPI_Allreduce()` on it. Instead, use the MPI routine `MPI_Allreduce()` directly in the code.

15. Never use a local variable counter such as `PetscInt flops = 0;` to accumulate flops and then call `PetscLogFlops();` always just call `PetscLogFlops()` directly when needed.

16. Library functions should be declared `PETSC_INTERN` if they are intended to be visible only within a single PETSc shared library. They should be declared `PETSC_EXTERN` if intended to be visible across shared libraries. Note that PETSc can be configured to build a separate shared library for each top-level class (`Mat`, `Vec`, `KSP`, and so on) and that plugin implementations of these classes can be included as separate shared libraries; thus, private functions may need to be marked `PETSC_EXTERN`. For example,

    - `MatStashCreatePrivate` is marked `PETSC_INTERN` as it is used across compilation units, but only within the `Mat` package;

    - all functions, such as `KSPCreate()`, included in the public headers (`include/petsc*.h`) should be marked `PETSC_EXTERN`;

17. Before removing or renaming an API function, type, or enumerator, `PETSC_DEPRECATED_XXX()` should be used in the relevant header file to indicate the new, correct usage and the version number where the deprecation will first appear. For example,

        typedef NewType OldType PETSC_DEPRECATED_TYPEDEF("Use NewType (since version 3.9)");
        PETSC_DEPRECATED_FUNCTION("Use NewFunction() (since version 3.9)") PetscErrorCode OldFunction();
        #define OLD_ENUMERATOR_DEPRECATED  OLD_ENUMERATOR PETSC_DEPRECATED_ENUM("Use NEW_ENUMERATOR (since version 3.9)")
        typedef enum {
          OLD_ENUMERATOR_DEPRECATED = 3,
          NEW_ENUMERATOR = 3
        } MyEnum;

    The old function or type, with the deprecation warning, should remain for at least one major release. The function or type’s manual page should be updated (see Manual Page Format).

18. Before removing or renaming an options database key, `PetscOptionsDeprecated()` should be used for at least one major release.

19. The format strings in PETSc ASCII output routines, such as `PetscPrintf`, take a for all PETSc variables of type `PetscInt`, not a .

20. All arguments of type `PetscReal` to PETSc ASCII output routines, such as `PetscPrintf`, must be cast to `double`, for example,

        PetscPrintf(PETSC_COMM_WORLD,"Norm %g\n",(double)norm);

## Formatted Comments

PETSc uses formatted comments and the Sowing packages [Gro95b] [Gro95a] to generate documentation (manual pages) and the Fortran interfaces. Documentation for Sowing and the formatting may be found at http://wgropp.cs.illinois.edu/projects/software/sowing/; in particular, see the documentation for `doctext`.

- `/*@`
  a formatted comment of a function that will be used for both
  documentation and a Fortran interface.
- `/*@C`
  a formatted comment of a function that will be used only for
  documentation, not to generate a Fortran interface. In general, such
  labeled C functions should have a custom Fortran interface provided.
  Functions that take `char*` or function pointer arguments must have
  the `C` symbol and a custom Fortran interface provided.
- `/*E`
  a formatted comment of an enum used for documentation only. Note
  that each of these needs to be listed in
  `lib/petsc/conf/bfort-petsc.txt` as a native and defined in the
  corresponding `include/petsc/finclude/petscxxx.h` Fortran include
  file and the values set as parameters in the file
  `src/SECTION/f90-mod/petscSUBSECTION.h`, for example,
  `src/vec/f90-mod/petscis.h`.
- `/*S`
  a formatted comment for a data type such as `KSP`. Note that each
  of these needs to be listed in `lib/petsc/conf/bfort-petsc.txt` as
  a `nativeptr`.
- `/*MC`
  a formatted comment of a CPP macro or enum value for documentation.

The Fortran interface files supplied by the user go into the two directories `ftn-custom` and `f90-custom`, while those generated by Sowing go into `ftn-auto`.

### Manual Page Format

Each function, typedef, class, macro, enum, and so on in the public API should include the following data, correctly formatted (see codes section) to generate complete manual pages and Fortran interfaces with Sowing. All entries below should be separated by blank lines. Except where noted, add a newline after the section headings.

1. The item’s name, followed by a dash and brief (one-sentence) description.

2. If documenting a function implemented with a preprocessor macro (e.g., `PetscOptionsBegin()`), an explicit `Synopsis:` section noting the required header and the function signature.

3. If documenting a function, a description of the function’s “collectivity” (whether all ranks in an MPI communicator need to participate). Unless otherwise noted, it’s assumed that this collectivity is with respect to the MPI communicator associated with the first argument.

   - `Not Collective` if the function need not be called on all MPI ranks

   - `Collective [on XXX]` if the function is a collective operation (with respect to the MPI communicator associated with argument `XXX`)

   - `Logically Collective [on XXX][; YYY must contain common value]` if the function is collective but does not require any actual synchronization (e.g. setting class parameters uniformly). Any argument YYY which must have the same value on all ranks of the MPI communicator should be noted here.

4. If documenting a function with input parameters, a list of input parameter descriptions in an `Input Parameters:` section.

5. If documenting a function with output parameters, a list of output parameter descriptions in an `Output Parameters:` section.

6. If documenting a function that interacts with the options database, a list of options database keys in an `Options Database Keys:` section.

7. (Optional) a `Notes:` section containing in-depth discussion, technical caveats, special cases, and so on. If it is ambiguous whether returned pointers/objects need to be freed/destroyed by the user or not, this information should be mentioned here.

8. (If applicable) a `Fortran Notes:` section detailing any relevant differences in calling or using the item from Fortran.

9. `Level:` (no newline) followed by `beginner`, `intermediate`, `advanced`, `developer`, or `deprecated`.

10. `.seealso:` (no newline), followed by a list of related manual pages. These manual pages should usually also point back to this manual page in their `seealso:` sections.

1

  Type also refers to the string name of the subclass.

## References

Gro95a

  W Gropp. Users manual for doctext: producing documentation from source code. Technical Report ANL/MCS-TM-206, Argonne National Laboratory, 1995.

Gro95b

  W Gropp. Users manual for bfort: producing Fortran interfaces to C source code. Technical Report ANL/MCS-TM-208, Argonne National Laboratory, 1995.