How can you flush a write using a file descriptor?

I think what you are looking for may be

int fsync(int fd);

or

int fdatasync(int fd);

fsync will flush the file from kernel buffer to the disk. fdatasync will also do except for the meta data.

You have two choices:

1. Use fileno() to obtain the file descriptor associated with the stdio stream pointer

2. Don't use <stdio.h> at all, that way you don't need to worry about flush either - all writes will go to the device immediately, and for character devices the write() call won't even return until the lower-level IO has completed (in theory).

For device-level IO I'd say it's pretty unusual to use stdio. I'd strongly recommend using the lower-level open(), read() and write() functions instead (based on your later reply):

int fd = open("/dev/i2c", O_RDWR);ioctl(fd, IOCTL_COMMAND, args);write(fd, buf, length);

fflush() only flushes the buffering added by the stdio fopen() layer, as managed by the FILE * object. The underlying file itself, as seen by the kernel, is not buffered at this level. This means that writes that bypass the FILE * layer, using fileno() and a raw write(), are also not buffered in a way that fflush() would flush.

As others have pointed out, try not mixing the two. If you need to use "raw" I/O functions such as ioctl(), then open() the file yourself directly, without using fopen<() and friends from stdio.