dup2 + fcntl

C'est sûrement dû au CLOSE-ON-EXEC. Je ne pense pas que tu puisses le manipuler directement en utilisant des FILE *, mais avec des file descriptor ça devrait marcher, comme dans ce bout de code :

#include <stdio.h>
#include <fcntl.h>
#include <unistd.h>
int main(int ac, char **av)
{
 int input, output;
 const char * modem = "/dev/ttyMODEM";
 const char * argv[4];
 input = open(modem, O_RDONLY);
 if (input < 0) {
	fprintf(stderr, "Can't open <%s> for reading: %m\n", modem);
	return 1;
 }
 output = open(modem, O_WRONLY);
 if (output < 0) {
	fprintf(stderr, "Can't open <%s> for writing: %m\n", modem);
	return 1;
 }
 if (fcntl(input, F_SETFD, 0) < 0) {
	fprintf(stderr, "Failed to clear close-on-exec flag in input: %m\n");
	return 1;
 }
 if (fcntl(output, F_SETFD, 0) < 0) {
	fprintf(stderr, "Failed to clear close-on-exec flag in output: %m\n");
	return 1;
 }
 if (dup2(input, STDIN_FILENO) < 0) {
	fprintf(stderr, "Cant set input: %m\n");
	return 1;
 }
 if (dup2(output, STDOUT_FILENO) < 0) {
	fprintf(stderr, "Cant set output: %m\n");
	return 1;
 }
 close(input);
 close(output);
 argv[0] = "/usr/sbin/chat";
 argv[1] = "-v";
 argv[2] = "-f";
 argv[3] = NULL;
 if (execv(argv[0], argv) < 0) {
	fprintf(stderr, "Failed to execv(%s, %s, %s): %m\n", argv[0], argv[1], argv[2]);
	return 1;
 }
 return 0;
}