Matlab error compiling C files with mex - c

i'm trying to compile a program for image deblurring.
I try to run
mex apply_blur_kernel_mex.c
where the file apply_blur_kernel_mex.c have the following code
#include <mex.h>
#include <stdlib.h>
#include <math.h>
#include <matrix.h>
#include "ow_homography.h"
...
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
...
compute_homography_matrix(Ksharp, &theta_list[k*3], invKblurry, H);
...
}
The problem is in the function compute_homography_matrix that is in another file ow_homography.h
#ifndef OW_HOMOGRAPHY_H
#define OW_HOMOGRAPHY_H
#include "ow_mat3.h"
INLINE void compute_homography_matrix(const double *Ksharp, const double *theta, const double *invKblurry, double *H) {
double R[9];
/* Compute homography */
cp3(invKblurry,H);
rot3(theta[0],theta[1],theta[2],R);
mmip3(R,H);
mmip3(Ksharp,H);
}
This last operations (cp3, rot3...) are in another file ow_mat3.h that contains all the operations for the program.
So when i try to call
mex apply_blur_kernel_mex.c
i have the following problem:
Error using mex
Undefined symbols for architecture x86_64:
"_compute_homography_matrix", referenced from:
mexFunction in apply_blur_kernel_mex.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
Any suggestions to solve this problem?
Thank you all.

http://clang.llvm.org/compatibility.html#inline
C compatibility C99 inline functions
By default, Clang builds C code in GNU C11 mode, so it uses standard
C99 semantics for the inline keyword. These semantics are different
from those in GNU C89 mode, which is the default mode in versions of
GCC prior to 5.0. For example, consider the following code:
inline int add(int i, int j) { return i + j; }
int main() { int i = add(4, 5); return i; }
In C99, inline means that a function's definition is provided only for
inlining, and that there is another definition (without inline)
somewhere else in the program. That means that this program is
incomplete, because if add isn't inlined (for example, when compiling
without optimization), then main will have an unresolved reference to
that other definition. Therefore we'll get a (correct) link-time error
like this:
Undefined symbols: "_add", referenced from:
_main in cc-y1jXIr.o
By contrast, GNU C89 mode (used by default in older versions of GCC)
is the C89 standard plus a lot of extensions. C89 doesn't have an
inline keyword, but GCC recognizes it as an extension and just treats
it as a hint to the optimizer.
There are several ways to fix this problem:
1) Change add to a static inline function. This is usually the right solution if only one translation unit needs to use the function.
static inline functions are always resolved within the translation
unit, so you won't have to add a non-inline definition of the function
elsewhere in your program.
2) Remove the inline keyword from this definition of add. The inline keyword is not required for a function to be inlined, nor does it
guarantee that it will be. Some compilers ignore it completely. Clang
treats it as a mild suggestion from the programmer.
3) Provide an external (non-inline) definition of add somewhere else in your program. The two definitions must be equivalent!
4)Compile in the GNU C89 dialect by adding -std=gnu89 to the set of Clang options. This option is only recommended if the program source
cannot be changed or if the program also relies on additional
C89-specific behavior that cannot be changed.
All of this only applies to C code; the meaning of inline in C++ is
very different from its meaning in either GNU89 or C99.

Related

Why does global variable definition in C header file work? [duplicate]

This question already has answers here:
What happens if I define the same variable in each of two .c files without using "extern"?
(3 answers)
Closed 2 years ago.
From what I saw across many many stackoverflow questions among other places, the way to define globals is to define them in exactly one .c file, then declare it as an extern in a header file which then gets included in the required .c files.
However, today I saw in a codebase global variable definition in the header file and I got into arguing, but he insisted it will work. Now, I had no idea why, so I created a small project to test it out real quick:
a.c
#include <stdio.h>
#include "a.h"
int main()
{
p1.x = 5;
p1.x = 4;
com = 6;
change();
printf("p1 = %d, %d\ncom = %d\n", p1.x, p1.y, com);
return 0;
}
b.c
#include "a.h"
void change(void)
{
p1.x = 7;
p1.y = 9;
com = 1;
}
a.h
typedef struct coord{
int x;
int y;
} coord;
coord p1;
int com;
void change(void);
Makefile
all:
gcc -c a.c -o a.o
gcc -c b.c -o b.o
gcc a.o b.o -o run.out
clean:
rm a.o b.o run.out
Output
p1 = 7, 9
com = 1
How is this working? Is this an artifact of the way I've set up the test? Is it that newer gcc has managed to catch this condition? Or is my interpretation of the whole thing completely wrong? Please help...
This relies on so called "common symbols" which are an extension to standard C's notion of tentative definitions (https://port70.net/~nsz/c/c11/n1570.html#6.9.2p2), except most UNIX linkers make it work across translation units too (and many even with shared dynamic libaries)
AFAIK, the feature has existed since pretty much forever and it had something to do with fortran compatibility/similarity.
It works by the compiler placing giving uninitialized (tentative) globals a special "common" category (shown in the nm utility as "C", which stands for "common").
Example of data symbol categories:
#!/bin/sh -eu
(
cat <<EOF
int common_symbol; //C
int zero_init_symbol = 0; //B
int data_init_symbol = 4; //D
const int const_symbol = 4; //R
EOF
) | gcc -xc - -c -o data_symbol_types.o
nm data_symbol_types.o
Output:
0000000000000004 C common_symbol
0000000000000000 R const_symbol
0000000000000000 D data_init_symbol
0000000000000000 B zero_init_symbol
Whenever a linker sees multiple redefinitions for a particular symbol, it usually generates linkers errors.
But when those redefinitions are in the common category, the linker will merge them into one.
Also, if there are N-1 common definitions for a particular symbol and one non-tentative definition (in the R,D, or B category), then all the definitions are merged into the one nontentative definition and also no error is generated.
In other cases you get symbol redefinition errors.
Although common symbols are widely supported, they aren't technically standard C and relying on them is theoretically undefined behavior (even though in practice it often works).
clang and tinycc, as far as I've noticed, do not generate common symbols (there you should get a redefinition error). On gcc, common symbol generation can be disabled with -fno-common.
(Ian Lance Taylor's serios on linkers has more info on common symbols and it also mentions how linkers even allow merging differently sized common symbols, using the largest size for the final object: https://www.airs.com/blog/archives/42 . I believe this weird trick was once used by libc's to some effect)
That program should not compile (well it should compile, but you'll have double definition errors in your linking phase) due to how the variables are defined in your header file.
A header file informs the compiler about external environment it normally cannog guess by itself, as external variables defined in other modules.
As your question deals with this, I'll try to explain the correct way to define a global variable in one module, and how to inform the compiler about it in other modules.
Let's say you have a module A.c with some variable defined in it:
A.c
int I_am_a_global_variable; /* you can even initialize it */
well, normally to make the compiler know when compiling other modules that you have that variable defined elsewhere, you need to say something like (the trick is in the extern keyword used to say that it is not defined here):
B.c
extern int I_am_a_global_variable; /* you cannot initialize it, as it is defined elsewhere */
As this is a property of the module A.c, we can write a A.h file, stating that somewhere else in the program, there's a variable named I_am_a_global_variable of type int, in order to be able to access it.
A.h
extern int I_am_a_global_variable; /* as above, you cannot initialize the variable here */
and, instead of declaring it in B.c, we can include the file A.h in B.c to ensure that the variable is declared as the author of B.c wanted to.
So now B.c is:
B.c
#include "A.h"
void some_function() {
/* ... */
I_am_a_global_variable = /* some complicated expression */;
}
this ensures that if the author of B.c decides to change the type or the declaration of the variable, he can do changing the file A.h and all the files that #include it should be recompiled (you can do this in the Makefile for example)
A.c
#include "A.h" /* extern int I_am_a_global_variable; */
int I_am_a_global_variable = 27;
In order to prevent errors, it is good that A.c also #includes the file A.h, so the declaration
extern int I_am_a_global_variable; /* as above, you cannot initialize the variable here */
and the final definition (that is included in A.c):
int I_am_a_global_variable = 23; /* I have initialized it to a non-default value to show how to do it */
are consistent between them (consider the author changes the type of I_am_a_global_variable to double and forgets to change the declaration in A.h, the compiler will complaint about non-matching declaration and definition, when compiling A.c (which now includes A.h).
Why I say that you will have double definition errors when linking?
Well, if you compile several modules with the statement (result of #includeing the file A.h in several modules) with the statement:
#include "A.h" /* this has an extern int I_am_a_global_variable; that informs the
* compiler that the variable is defined elsewhere, but see below */
int I_am_a_global_variable; /* here is _elsewhere_ :) */
then all those modules will have a global variable I_m_a_global_variable, initialized to 0, because the compiler defined it in every module (you don't say that the variable is defined elsewhere, you are stating it to declare and define it in this compilation unit) and when you link all the modules together you'll end with several definitions of a variable with the same name at several places, and the references from other modules using this variable will don't know which one is to be used.
The compiler doesn't know anything of other compilations for an application when it is compiling module A, so you need some means to tell it what is happening around. The same as you use function prototypes to indicate it that there's a function somewhere that takes some number of arguments of types A, B, C, etc. and returns a value of type Z, you need to tell it that there's a variable defined elsewhere that has type X, so all the accesses you do to it in this module will be compiled correctly.

Inline function with assert creates an undefined reference? [duplicate]

This question already has answers here:
Is "inline" without "static" or "extern" ever useful in C99?
(3 answers)
What does extern inline do?
(7 answers)
Closed 2 years ago.
divide.h
#pragma once
#include <assert.h>
inline int divide(int a, int b)
{
assert(b != 0);
return a / b;
}
main.c
#include <divide.h>
int main(void)
{
divide(10, 2);
return 0;
}
I am unable to compile the following solely because of the assert. If I remove the assert, everything works fine.
$ gcc --version
gcc (GCC) 8.1.0
$ gcc main.c
main.c:(.text+0xf): undefined reference to `divide'
$ gcc main.c -O3 # Compilation with optimization works as asserts are removed.
When placing the defintion of divide inside a .c file, everything works fine. However, shouldn't the following also work since the function is declared as inline?
The C99 standard says this about inline functions in 6.7.4 "Function specifiers":
An inline definition provides an alternative to an external definition, which a translator may use to implement any call to the function in the same translation unit. It is unspecified whether a call to the function uses the inline definition or the external definition.
So an implementation can choose to not inline a function call in which case there needs to be an external definition of the function. I'd guess that since the assert is a debugging tool, GCC doesn't want to inline functions that have active asserts to aid in debugging.

How to compile C code with C headers and CUDA code?

I have a main code wich uses some libraries and I been compiling it like this:
gcc importedCFile1.c importedCFile2.c mainCode.c -O3 -lm -Wall -o maincode -lrt
Now I have added CUDA code in mainCode and changed its extension to .cu... So, how can I compile the whole thing?
I tried:
nvcc importedCFile1.c importedCFile2.c mainCode.cu -o maincode
but I got a lot of "undefined reference" to my functions in the imported C files.
To include my C files I am using:
extern "C" {
#include "importedCFile1.h"
#include "importedCFile2.h"
}
And ´importedCFile1.c´ is using some functions and variables declared in ´importedCFile2.c´ and ´mainCode.cu´. Like this:
extern int **se; // Variables from mainCode
extern int *n;
extern int numNodes;
extern int *getVector(int n); // Function from mainCode
extern int iRand(int high); // Function from importedCFile2
This functions are the cause of the undefined references. What should I do?
Also, how do I add the flags I need for the C code, such as -lrt, O3, lm and Wall??
EDIT: You can find a reduced example of the problem here:
https://github.com/mvnarvaezt/cuda/tree/master/minimalExample
If you compile the mainCode.c and importedCFile.c with gcc it works fine. If you compile mainCode.cu and importedCFile.c with nvcc you will get an undefined reference to anExample() (the function in importedCFile.c).
And you comment the header importing importedCFile.c and the call to anExampled() function it would work find.
Your problem is that the C code in importedFile.c is trying to call back C++ functions in mainCode.cu.
In order to be callable from C, C++ functions must have C linkage. Declare getVector() as
extern "C" int *getVector(int n) {
in mainCode.cu, and your example will compile fine.

Gcc uses sqrt without including math.h

Anyone knows why this c program compiles and uses the sqrt of math.h?
this would output 2.236068
main.c
#include <stdio.h>
#include "math_utils.h"
int main(void){
printf("%f\n", sqrt(5));
return 0;
}
math_utils.h
#ifndef MATH_UTILS_Hs
#define MATH_UTILS_Hs
double sqrt(double number){
return number + 5;
}
#endif // MATH_UTILS_Hs
I am currently using mingw GCC on windows
gcc performs an optimization where it expects standard library functions to behave like the standard says to turn calls into the C standard library into more efficient machine code. For example, it's likely that gcc emits a single fsqrt instruction for your sqrt() call, never calling your custom sqrt() at all.
You can turn off this behaviour by supplying -fno-builtin to turn this optimization off for all recognized functions or by supplying -fno-builtin-function to turn off this optimization for function only. For example, -fno-builtin-sqrt would make gcc honour your non-standard sqrt().

Detect -nostdlib or just detect whether stdlib is available or not

I have a homework assignment that requires us to open, read and write to file using system calls rather than standard libraries. To debug it, I want to use std libraries when test-compiling the project. I did this:
#ifdef HOME
//Home debug prinf function
#include <stdio.h>
#else
//Dummy prinf function
int printf(const char* ff, ...) {
return 0;
}
#endif
And I compile it like this: gcc -DHOME -m32 -static -O2 -o main.exe main.c
Problem is that I with -nostdlib argument, the standard entry point is void _start but without the argument, the entry point is int main(const char** args). You'd probably do this:
//Normal entry point
int main(const char** args) {
_start();
}
//-nostdlib entry point
void _start() {
//actual code
}
In that case, this is what you get when you compile without -nostdlib:
/tmp/ccZmQ4cB.o: In function `_start':
main.c:(.text+0x20): multiple definition of `_start'
/usr/lib/gcc/i486-linux-gnu/4.7/../../../i386-linux-gnu/crt1.o:(.text+0x0): first defined here
Therefore I need to detect whether stdlib is included and do not define _start in that case.
The low-level entry point is always _start for your system. With -nostdlib, its definition is omitted from linking so you have to provide one. Without -nostdlib, you must not attempt to define it; even if this didn't get a link error from duplicate definition, it would horribly break the startup of the standard library runtime.
Instead, try doing it the other way around:
int main() {
/* your code here */
}
#ifdef NOSTDLIB_BUILD /* you need to define this with -D */
void _start() {
main();
}
#endif
You could optionally add fake arguments to main. It's impossible to get the real ones from a _start written in C though. You'd need to write _start in asm for that.
Note that -nostdlib is a linker option, not compile-time, so there's no way to automatically determine at compile-time that that -nostdlib is going to be used. Instead just make your own macro and pass it on the command line as -DNOSTDLIB_BUILD or similar.

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