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\page cs_dg_further_reading Further reading
[TOC]
Build and Tool chain
====================
Different parts of the code_saturne tool chain are built with different *programming languages*
and *libraries*.
- *Build system* based on GNU autotools: [autoconf](https://www.gnu.org/software/autoconf),
[automake](https://www.gnu.org/software/automake/),
[libtool](https://www.gnu.org/software/libtool/)
- Requires optional *sh* shell and *m4* macro languages, some *make* file syntax, some
*Python* code.
- *GUI* and scripts (*TUI*): [Python](https://www.python.org/),
[PyQt](https://riverbankcomputing.com/software/pyqt/intro).
- *Preprocessor*: *C* compiler (C99 or above)
- Optional mesh format libraries: *MED*, *CGNS*, *libCCMIO* (see install guide for details).
- *Solver*: *C* and *Fortran* compilers (C11 or above, Fortran 2003 or above.
- Multiple optional external libraries: *MPI*, *PT-SCOTCH*, *MED*, *CGNS*, *Catalyst*,
*CoolProp*, *PETSc*, and others (see install guide for details)
Recommended learning material
=============================
Depending on the part of the code one is working on, further reading and training
may be useful.
For the [Git](https://git-scm.com/) source code management system:
- *pro Git*: https://git-scm.com/book/en/v2
Fortran programming
- Link to various learning resources: https://fortran-lang.org/learn/
- For French readers, the IDRIS courses are recommended: http://www.idris.fr/formations/fortran/
C programming
- Interactive tutorial https://www.learn-c.org/
- MIT OpenCourseWare (OCM): [Practical Programming in C](https://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-087-practical-programming-in-c-january-iap-2010/index.htm)
- Shorter course: [Scientific Programming in C](http://www.courses.physics.helsinki.fi/fys/cprog/)
(see Lectures)
- For French readers, the IDRIS course is recommended: http://www.idris.fr/formations/c/
- *MPI* and *OpenMP* Courses may also be found on the main course material page:
(http://www.idris.fr/formations/supports_de_cours.html
C and Fortran basics
====================
A very brief comparison of equivalent C and Fortran Syntax is provided here,
which may be useful for those already familiar with one or the other.
<table>
<tr><th> <th> C <th> Fortran
<tr><td>
Basic types
<td>
```{.c}
char
_Bool, bool
int
float
double
```
<td>
```{.f90}
character
logical
integer
real
double precision
```
<tr><td>
Basic math functions
<td>
```{.c}
(a)cos (a)sin (a)tan
cosh sinh tanh
exp log
sqrt pow(x, y)
abs fabs
a%b
```
<td>
```{.f90}
(a)dcos (a)dsin (a)dtan
dcosh dsinh dtanh
dexp dlog
sqrt x**y
iabs dabs
mod(a,b)
```
<tr><td>
Logical expressions
<td>
```{.c}
&& || !
< > <= >= == !=
== !=
```
<td>
```{.f90}
.and. .or. .not.
.lt. .gt. .le. .ge. .eq. .ne.
.eqv. .neqv.
```
<tr><td>
Function/subroutine call
<td>
```{.c}
x = f(y);
g(a);
```
<td>
```{.f90}
x = f(y)
call g(a)
```
<tr><td>
Conditional
<td>
```{.c}
if (expr) {
operations;
}
```
<td>
```{.f90}
if (expr) then
operations
end if
```
<tr><td>
Simple loops
<td>
```{.c}
for (i = 0; i < n; i++) {
y /= 2.;
z = x + i + y*5.;
}
```
<td>
```{.f90}
do i = 0, n
y = y/2.d0
z = x + i + y*5.d0
end do
```
<tr><td>
Complex loops
<td>
```{.c}
while (expr) {
operations
}
```
<td>
```{.f90}
do while (expr)
operations
end do
```
<tr><td>
Loop control
<td>
```{.c}
for (i = 0; i < n; i++) {
if (ignore_condition)
continue;
else if (exit_loop_condition)
break;
}
```
<td>
```{.f90}
do i = 0, n
if (ignore_condition)
cycle;
else if (exit_loop_condition)
exit;
end do
```
<tr><td>
Variable declaration and initialization
<td>
```{.c}
int i, j,
k = 0, l = 1;
double a = 1.;
```
<td>
```{.f90}
integer :: i, j, &
k = 0, l = 1
double precision :: a = 1.d0
```
<tr><td>
Array declaration and initialization
<td>
```{.c}
int tab[2][3] = {{1, 2, 3},
{4, 5, 6}};
printf("%d", tab[1][0]); // 4
```
<td>
```{.f90}
integer, dimension(3,2) :: tab
data / 1, 2, 3, 4, 5, 6 /
write(*,*) tab(2, 1) ! 2
```
</table>
An important difference to be aware of between C and Fortran is that when
calling functions, C passes arguments by copy (so changing argument
values in C has not effect unless that argument is a pointer or array
(see following sections), while in Fortran, variables are passed by
reference, allowing their modification directly.
C language
==========
C variable declarations
-----------------------
A variable may be initialized upon its declaration:
```{.c}
double a[4] = {1, 2, 3, 4};
double b[] = {1, 2, 3, 4};
double matrix[3][4] = {{1., 0., 0., 0.},
{0., 1., 0., 0.},
{0., 0., 1., 0.}};
static int call_id = 0; /* static C equivalent
to Fortran save */
const double pi = 4.*atan(1.), e = exp(1);
```
\Remark
In Fortran, initialization with declaration implies *save* attribute, so
the following are equivalent:
```{.f90}
integer :: i = 4
integer, save :: i = 4
```
C Types and Structures
----------------------
C allows defining additional types, as well as structures.
- `typedef double cs_real_t` defines a `cs_real_t` type
identical to `double`
- `typedef cs_real_t cs_real_3_t` defines a `cs_real_3_t` type
identical to an array of 3 `cs_real_t` types
- indirectly equivalent to an array of 3 `double` types
- code_saturne makes use of this to define additional types (see especially
\ref cs_defs.h and [integer type descriptions](@ref sec_prg_lang_integer_types)
- the `_t` postfix is a convention, which is recognized
by some text editors (such as Emacs) for syntax coloring.
Pointers and arrays
-------------------
Understanding pointers is essential in C
- In any language, variables are stored in memory.
- C allows access not only to a variable's value, but to its memory location
(based on its memory model; this is usually a logical, not physical address)
- A *pointer* is a variable referencing another variable's memory location.
- In C, some operations cannot be done without handling pointers.
- For a given type, prefixing `*` to the variable's declaration
declares it as a pointer to a variable of that type
- For a pointer, prefixing `*` to the pointer's name *dereferences* a pointer
(that is accesses the value pointed to)
- Prefixing `&` to a variable obtains a reference (pointer) to that variable.
A simple example is best:
```{.c}
double x;
double a = 1.0, b = 2.0; // variables
double *p = NULL;
p = &a; // p points to a
x = *p; // x now has a's value
p = &b; // p points to b
*p = 12; // b's value is now 12.
```
Note that pointers in other languages (especially Fortran) are often more
restrictive, or include additional metadata.
- Pointers in C are simply a memory address.
- Associated type information (used for pointer arithmetic and checks) is defined
in the source code and managed by the compiler, _not stored in the pointer_
(i.e. no runtime introspection)
### C Pointers and arrays
- Array syntax may be used with pointers.
- Pointer "arithmetic" is based on the pointer's type (unless `void`).
- A single (but important) difference between pointers and arrays:
- An array declaration implies local memory allocation, a pointer does not.
- This is reflected by the different behavior of the `sizeof`
- In addition to the following example, check the tutorial at:
https://boredzo.org/pointers/
```{.c}
double x;
double a[3] = {1.0, 2.0, 3.0};
double *p = a; // p points to beginning of a
x = *p; // same as a[0]
x = p[0]; // same as a[0]
x = p[2]; // same as a[2]
p[1] *= 2; // a[1] *= 2
p++; // point to next value
x = *p; // same as a[1]
```
### Remarks on pointers
Character strings do not have a dedicated type in C:
- Strings are simply arrays or pointers to characters.
- Strings end when a character with code 0 (`\0`) is encountered
Pointers may be _cast_ from one type to another. For example:
```{.c}
int a[3][3] = {{11, 12, 13},
{21, 22, 23},
{31, 32, 33}};
int *p = (int *)a;
const int *q = (const int *)a;
```
C structures
------------
We will refer to other sources to detail usage of structures in code_saturne,
focusing here on specific aspects.
- Some structures are defined directly in a header (`.h`) file
```{.c}
typedef struct {
int n; /* number of elements */
double *val; /* list of element values */
} cs_simple_struct_t;
```
- Such structures may be used normally, with full access to members from any
file including the header
- Other structures are defined in in a source (`.c`) file
```{.c}
typedef struct _cs_opaque_t {
int n; /* number of elements */
double *val; /* list of element values */
};
```
with a matching entry in a header (`.h`) file
```{.c}
typedef struct _cs_opaque_t cs_opaque_t;
```
- Such structures may be used normally inside the source file, but their members
are _hidden_ from within other files.
- This allows protecting structure members, ensuring they are only accessed from
within the associated module
- If the file is large and needs to be split, we place the definition in a
separate header file, accessed only from a restricted set of files
(see for example `src/base/cs_matrix*.h`).
Using opaque structures has advantages:
- It conveys the information to most users that they can use the structure without
worrying about its internals
- Structure internals can be modified without breaking compatibility (changing
access functions
It also has some disadvantages:
- Access is more cumbersome, requiring functions.
- Due to function call overheads, many calls to simple functions in a loop are
more costly than direct access, or than a function which loops internally
C storage class specifiers
--------------------------
A variable declaration can be combined with a \emph{storage class specifier}.
- `static` indicates the variable is "permanent":
- Its values are saved from one call to the next, like *save* in Fortran
- `extern` indicates we reference a variable, but its memory location is not
defined here; for example:
- `int option = 2;` in a _single_ (owning) `.c` file.
- `extern int option;` in a `.h` or other `.c` file.
This ensures the variable is accessible from multiple files, but defined in
a single location.
- For global variables, avoids conflicts (bugs) due to multiple copies
- `auto` is the default, so no point in specifying it.
- `register` recommends to keep an often-used variable in a _register_
- Very fast, very small memory; the compiler does what it can / wants
- `volatile` indicates the variable may be modified by concurrent thread
- Reload from memory, not from cache.
### C const attribute
A variable declaration may specify one or more `const` attributes.
- A `const` attribute indicates the function may not modify this variable
- For a pointer, be careful where `const` is placed:
```{.c}
const double a[]; /* cannot modify
content of a */
const double *b; /* same with b */
double *const c; /* can not modify pointer
to c, but can modify
content pointed to */
const double *const c; /* can modify neither pointer
nor content */
```
### C const attribute
- As variables are passed by copy, some constructs are not very useful.
- For example, `inline int f(const int *const t)` and
`inline int f(const int *t)` are equivalent from the caller's side.
- Only in the function body, the first syntax indicates we cannot locally modify
the pointer to `t`.
- Compilers allow mixing the first syntax in the body with one or the other in
the prototype.
- Proof if needed that for the caller, it is all the same.
- From a readability standpoint, we prefer the second syntax, as it is
less cluttered.
- There may still be relics of the first syntax in code_saturne, especially
in `src/gui`; choose more recent code examples, such as \ref cs_field.c;
- It is strongly recommended to use `const` as much as possible
- It is more or less equivalent to `intent(in)` in Fortran, and can allow
detecting unintentional variable modifications at compile time.
### C restrict attribute
A variable declaration may also be qualified with a `restrict` attribute.
- The `restrict` attribute indicates that no other pointer refers to the same content.
- For example, with `int f(double *restrict a, double *restrict b)`, we tell
the compiler that arrays a and b do not overlap.
- Allows a better optimization, possibly vectorisation.
- Most performance differences between C and Fortran are due to aliasing
(forbidden in Fortran, assumed by default in C).
- C _strict aliasing_ rules: between different types
`double` and `int` for example, aliasing is _automatically_ forbidden.
- This is useful only to help optimization of costly loops
- If we forget to use this, we may lose some performance
- If we incorrectly declare a variable `restrict`, we may have
_undefined_ behavior...
- In Fortran, passing the same array (or overlapping arrays) twice as
function arguments may also lead to similar behavior...
### C functions
Like most programming languages, C allows grouping statements in functions.
- A function definition is composed of a _header_ and a _body_.
- The _header_ describes the return type, the function name, and
function arguments. if no value is returned or the function has no arguments,
`void` is used to indicate this.
- A function body contains the actual instructions of the function
- The following example function returns the dot product of 2 arrays
```{.c}
double f(int n, double x[], double y[])
{
int i;
double r = 0;
for (i = 0; i < n; i++)
r = r + x[i]*y[i];
return r;
}
```
- Modern C strongly recommends functions be described by a _prototype_
(i.e. interface), declared before defining or calling functions.
- C++ requires this absolutely.
- A function prototype resembles its header, ended by a semicolon (`;`).
- For the previous example, the matching prototype is:
```{.c}
double f(int n, double x[], double y[]);
```
- Only parameter types are required to match in the definition and prototype,
so compilers will not complain if names are different
- But the code maintainers _will_ !
- And the documentation generator will emit warnings
Prototypes are usually grouped in `header` files, inserted locally using the
`#include` preprocessor directive.
- If the `static` qualifier is prefixed to a function
declaration, that function is defined locally only
- In this case, prototypes are not necessary (functions referenced by others
must appear first).
- Functions with the same name may be used in different files with no risk.
- Using `static inline`, the function body is copied at each call
- Avoids call overhead for short functions, leads to larger code.
- `inline` without `static` is tricky: see a more complete C course, or avoid it.
- In code_saturne, some simple computation functions are defined as
`static inline`;
- Their definition appear in header (`.h`) files in this case
- See for example \ref cs_math.h.
- In code_saturne, many low-level functions are defined as `static`
- When they are only needed locally, this avoids cluttering the
Doxygen documentation with low-level functions
- This also allows using shorter names, without worrying about
`cs_<module>_` "namespace" issues.
- As per static (i.e. file-local) global variables, we simply prefix the names
of those functions with an underscore: `_`
- As those functions do not require prototypes, they are defined at the beginning
of the file; if function `b` calls function `a`, then `a` must be
defined first.
- If such functions may become useful elsewhere, it is best to make
them non-static (i.e. global), move them in the file, and add a prototype
rather than to adopt a copy-paste programming style...
- A function is called by providing its name and arguments
```{.c}
r = f(3, x, y); // returns r
g(x); // returns no value
s = h(); // takes no argument
```
- A function returning a value is equivalent to a Fortran _function_, and a
function returning void to a Fortran _subroutine_.
- In C, functions <span style="color:red">pass arguments by value</span>.
- Item array contents, or values referenced by pointers may be modified normally
- Non-pointer (or array) arguments are copied, so the original is
unchanged in the calling code
- In Fortran, functions and subroutines
<span style="color:red">pass arguments by reference</span>.
- Unless otherwise specified
(using for example `integer, value :: n`)
- Values modified in the function are still after its return.
Example of call by value semantics:
```{.c}
/* callee function */
void f(double x, double y[2]) {
x = x/2;
y[1] = x;
}
/* caller function */
void g(void) {
double x = 10, y[] = {1., 2.}; /* initialization */
f(x, y); /* call to f */
/* now x = 10, y[] = {1., 5.} */
...
}
```
### C function pointers
Generic functions may be called using _function pointers_
- Don't be intimidated by the name
- Some users don't even realize they are using function pointers.
- In practical terms, function pointers allow passing a function as an argument
to a function
- To illustrate this, let us look at the examples in \ref cs_post.h and in
\ref cs_user_postprocess.c.
- ... not so hard, is it now ?
Memory management
-----------------
Explicit memory allocation operations return pointers
- Using the `malloc`, `realloc`, and `free` functions or similar
- In code_saturne, the \ref BFT_MALLOC, \ref BFT_REALLOC, and \ref BFT_FREE
functions add type and result checking and instrumentation.
- Explicit allocation as described above is usually done on a memory area called the
[heap](https://en.wikipedia.org/wiki/Memory_management#HEAP), which is a large,
usually extensible memory area.
- If memory is allocated but never freed, memory "leaks" then possibly runs out
- Use [Valgrind](https://www.valgrind.org), the GCC and Clang
[AddressSanitizer](https://github.com/google/sanitizers/wiki/AddressSanitizer)
tools, or `export CS_MEM_LOG=mem_log` in your environment to check for this.
- Automatic allocation of variables and fixed-size arrays is done on a smaller
memory area called the [stack](https://en.wikipedia.org/wiki/Stack_(abstract_data_type))
- Does not incurr any overhead (fast).
- Automatically freed when variable goes out of scope.
- Overwrites on the stack may crash even your debugger...
- they also may crash _Valgrind_, but can be detected with the
_AddressSanitizer_ tools.
C Preprocessing
---------------
Before the C compilation proper, a first stage replaces character sequences based
on several rules.
- It is called the _preprocessor_
- Directives start with `#`
- `#include`, `#if`, `#ifdef`, `#ifndef`, `#define`,
- Allows defining _macros_
- Using a common coding convention, we write them in capitals.
```{.c}
#define CS_MIN(a,b) ((a) < (b) ? (a) : (b))
```
- No need for `;` at the end of the line (or statement).
- Do not define macros if another solution is possible
- Avoid arguments with side effects; for example,
`CS_MIN(f(x),g(x))` calls either `f(x)` or `g(x)` twice...
- Some macros are predefined; to know them, the solution is compiler
dependent. With *gcc*, the following command is
useful: `gcc -dM -E - < /dev/null`
- One of the main uses of the preprocessor is conditional compilation
```{.c}
#if defined (HAVE_MPI)
...
#endif
```
- To disable code containing comments, nothing beats:
```{.c}
#if 0
...
#endif
```
- This avoids comment nesting issues, and some editors such as _vim_
even colorize the block as a comment.
### C Preprocessor macros in code_saturne
- code_saturne defines several preprocessor macros, among which the following:
- \ref CS_ABS(a): absolute value of a
- \ref CS_MAX(a, b): maximum of a and b
- \ref CS_MIN(a, b): minimum of a and b
- \ref CS_F_(fname): access to field structure of field with
canonical name `name`.
- Note: the C language also defines `double fmax(double x, double y)` and
`double fmaxf(float x, float y)`;
- They do not have multiple macro argument evaluation side effects
- They are applicable only to `double` or `float` values, though automatic
type casting in C allows use of either (with a different precision).
- Applying them to integers would lead to non-natural rounding and
overflow behavior.
### Preprocessors in various programming languages
Preprocessors do not exist in all "modern" languages, are often decried by purists,
but are very useful in C and C++ for optional library support.
- in Python, not missed, as we can use `try...import` sequences
- Almost all Fortran compilers allow for the use of the C preprocessor, or a slightly
adapted version of it (`fpp`)
- The Fortran 95 standard suggested (as an optional appendix) a conditional
compilation mechanism, named coco (conditional compilation)
- Very few compilers support it
- As always, before trying to follow a standard, check how well it is supported
- In this specific case, a tool less powerful the the C preprocessor was invented,
15 or so years later; it is not surprising it failed
- coco was recently retired from the latest Fortran standards, so it can be
safely forgotten.
C variable and function scoping
-------------------------------
Compared to Fortran, variables may have a local scope:
```{.c}
int f(int n, double x[]) {
int i;
i = 6;
{
int i, j; /* i masks previous definition */
for (i = 0, j = 1; i < n; i++, j+= rand())
x[i] += j;
}
/* i = 6 again */
{
int j; /* the previous definition is unknown here ! */
for (j = 0; j < n; j++)
x[j] += 1.;
}
}
```
### Advantages and precautions:
- Avoid multiple definitions of a variable on different levels
- Check for compiler warnings: *definition shadows previous definition*
- Local definitions may improve readability.
- Local definitions ensure variables are _local_ (and thus automatically private)
in OpenMP sections.
Since the C99 standard, variables may be defined in a
function body, or even in a control structure:
```{.c}
int f(int n, double x[]) {
int i;
i = 6;
for (int j = 0; j < n; j++)
x[j] += 1.;
for (int j = 0; j < n; j++)
x[j] += 1.;
printf("value of j: %d\n", j); /* error, j not
defined here */
}
```
The C scoping rules also allow definition of global variables.
- Declaring a variable in a source file outside a function makes it _global_
- It is recommended to add an initialization to the declaration when
possible, which is safer and simple than requiring additional initialization
functions
- Adding the `static` qualifier makes that variable accessible only from the
file in which it is declared.
- Another similar variable in another file would be completely independent.
- If global visibility is desired, the definition should be unique,
and the variable defined using the the `extern` qualifier.
- An `extern const` qualifier may be used to make the variable read only.
- Useful for pointers to structures, allowing safe reading of structure
members, but modification only though a specific function (see
the handling of \ref cs_glob_time_step in `src/base/cs_glob_time_step.c`
`src/base/cs_glob_time_step.h` for example).
### Main global variables in code_saturne
- In code_saturne, we try to minimize the use of global variables, but a few
are used, as placing them in a structure would be cumbersome for C/Fortran
interoperability.
```{.c}
(int) cs_glob_n_ranks // cs_defs.h
(int) cs_glob_rank_id // cs_defs.h
(cs_matrix_t} cs_glob_matrix_default // cs_matrix.h
(cs_matrix_structure_t} cs_glob_matrix_default_struct
(cs_mesh_t) cs_glob_mesh // cs_mesh.h
(cs_mesh_quantities_t) cs_glob_mesh_quantities // ...
(cs_time_step_t) cs_glob_time_step // cs_time_step.h
(cs_field_pointer_val_t) cs_glob_field_pointers // ...
```
C Undefined behavior
--------------------
Some ambiguous constructions lead to what is called _unspecified behavior_.
- The compiler is free to do whatever it wants in such cases.
- different compilers may exhibit different behaviors
- <span style="color:red">Avoid at all costs</span>, but in general,
there is nothing to worry about as long as the code's conventions
are followed.
- Example: incorrect character string usage
```{.c}
char *p = "Code_Saturne"; // forbidden in C++11,
// obsolete in C++98/C++03
p[0] = 'C'; // undefined behavior due to above
// (but works with most compilers)
```
- Correct character string usage
```{.c}
char p[] = "Code_Saturne"; // array, not just pointer
p[0] = 'C'; // OK
```
- Example: division by zero
```{.c}
int x = 1;
return x/0; // undefined behavior
```
- Example: out of bounds array access
- this detected by _Address Sanitizer_, but not by _Valgrind_:
as `arr` is declared as a local array, it is instanciated on the _stack_,
not the _heap_.
```{.c}
int arr[4] = {0, 1, 2, 3};
int j = arr[5]; // stack buffer overflow
```
- Example: out of scope return value
```{.c}
*double badarray(void) {
double t[] = {0, 1, 2};
return t; // memory location freed on return
}
```
- Example: undefined (or not always defined) return value
- Very easy to avoid, as current compilers emit a warning.
- You check compiler warnings, of course ?
```{.c}
int
f(int x)
{
if (x < 1) {
return -x;
}
} /* undefined behavior if x >= 1 */
```
- Example: incrementation before/after use (note 84) C11 standard?
```{.c}
printf("%d %d\n",
++n, pow(2, n)); /* is n incremented
before or after
calling power ? */
i = ++i + 1;
a[i++] = i; /* is i incremented before or
after assignment ?*/
/* The constructs below are safe: */
i = i + 1;
a[i] = i;
a[i++] = j;
```
- _Rule of thumb_: to be safe, avoid incrementation operators on an index
which appears multiple times in an expression.
C Pragmas
---------
Another type of element may start with a `#`, but is not related to the
preprocessor: `pragmas`
- `#pragma omp ...` for optional thread/task parallelism using the _OpenMP_ model
- `#pragma disjoint(<variable list)` for directives specific to optimizations
using the IBM XL compilers (at least in older versions); in most cases,
the `restrict` keyword is a more portable alternative
- `#pragma GCC ...` for directives specific to GCC
The most frequent pragmas in code_saturne are related to _OpenMP_ parallelism
- They are used only if this programming model is activated
In a general manner, a `pragma` not known to a given compiler is ignored
C Decorators
------------
In a few rare places, we use _decorators_
- In the following example, the `__attribute__` decorator is used to specify
that the function behaves like `printf` regarding its arguments, so as to
benefit from compiler argument checking
```{.c}
#if defined(__GNUC__)
int
bft_printf(const char *const format,
...)
__attribute__((format(printf, 1, 2)));
#else
int
bft_printf(const char *const format,
...);
#endif
```
Various decorators exist, but we do not use them much in code_saturne,
as they are _not portable_.
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