What is considered a system call? - operating-system

is using os.mknod(), os.rename(), os.mkdir(), etc. considered a system call?
I'm trying to understand exactly what a system call entails.

A system call is generally considered to be one that is dispatched through the system interrupt vector or an equivalent mechanism (such on Intel processors).

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Why can User call a system call directly?

Before I ask the question, the following is what I know.
The system call is in the kernel area.
The kernel area cannot be used (accessed) directly by the user.
There are two ways to call a system call.
direct call
wrapping function (API) that contains system call
(2. process:
(User Space) wrapping function ->
system call interface ->
(Kernel Space) System call)
So, in 1. case)
How can User use the kernel area directly?
Or I wonder if there's anything I'm mistaken about.
open sns question
internet search
read operating system concepts 10th (page. 64)
The default is that nothing in user-space is able to execute anything in kernel space. How that works depends on the CPU and the OS, but likely involves some kind of "privilege level" that must be matched or exceeded before the CPU will allow software to access the kernel's part of virtual memory.
This default behavior alone would be horribly useless. For an OS to work there must be some way for user-space to transfer control/execution to (at least one) clearly marked and explicitly allowed kernel entry point. This also depends on the OS and CPU.
For example; for "all 80x86" (including all CPUs and CPU modes) an OS can choose between:
a software interrupt (interrupt gate or trap gate)
an exception (e.g. breakpoint exception)
a call gate
a task gate
the sysenter instruction
the syscall instruction
..and most modern operating system choose to use the syscall instruction now.
All of these possibilities share 2 things in common:
a) There is an implied privilege level switch done by the CPU as part of the control transfer
b) The caller is unable to specify the address they're calling. Instead it's set by the kernel (e.g. during the kernel's initialization).

From where is the code for dealing with critical section originated?

While learning the subject of operating systems, Critical Section is a topic which I've come across. To solve this problem, certain methods are provided like semaphores, certain software solutions, etc...etc..etc. But I've a question that from where is the code for implementing these solutions originated? As programmers never are found writing such codes for their program. Suppose I write a simple program executing printf in 'C', I never write any code for critical section problem. And the code is converted into low level instructions and is executed by OS, which behaves as our obedient servant. So, where does code dealing with critical section originate and fit in? Let resources like frame buffer be the critical section.
The OS kernel supplies such inter-thread comms synchronization mechanisms, mutex, semaphore, event, critical section, conditional variables etc. It has to because the kernel needs to block threads that cannot proceed. Many languages provide convenient wrappers around such calls.
Your app accesses them, directly or indirectly, via system calls, ie intrrupts that enter kernel state and ask for such services.
In some cases, a short-term user-space spinlock may get plastered on top, but such code should defer to a system call if the spinner is not quickly satisfied.
In the case of C printf, the relevant library, (stdio usually), will make the calls to lock/unlock the I/O stream, (assuming you have linked in a multithreaded version of the library).

What exactly happens when an OS goes into kernel mode?

I find that neither my textbooks or my googling skills give me a proper answer to this question. I know it depends on the operating system, but on a general note: what happens and why?
My textbook says that a system call causes the OS to go into kernel mode, given that it's not already there. This is needed because the kernel mode is what has control over I/O-devices and other things outside of a specific process' adress space. But if I understand it correctly, a switch to kernel mode does not necessarily mean a process context switch (where you save the current state of the process elsewhere than the CPU so that some other process can run).
Why is this? I was kinda thinking that some "admin"-process was switched in and took care of the system call from the process and sent the result to the process' address space, but I guess I'm wrong. I can't seem to grasp what ACTUALLY is happening in a switch to and from kernel mode and how this affects a process' ability to operate on I/O-devices.
Thanks alot :)
EDIT: bonus question: does a library call necessarily end up in a system call? If no, do you have any examples of library calls that do not end up in system calls? If yes, why do we have library calls?
Historically system calls have been issued with interrupts. Linux used the 0x80 vector and Windows used the 0x2F vector to access system calls and stored the function's index in the eax register. More recently, we started using the SYSENTER and SYSEXIT instructions. User applications run in Ring3 or userspace/usermode. The CPU is very tricky here and switching from kernel mode to user mode requires special care. It actually involves fooling the CPU to think it was from usermode when issuing a special instruction called iret. The only way to get back from usermode to kernelmode is via an interrupt or the already mentioned SYSENTER/EXIT instruction pairs. They both use a special structure called the TaskStateSegment or TSS for short. These allows to the CPU to find where the kernel's stack is, so yes, it essentially requires a task switch.
But what really happens?
When you issue an system call, the CPU looks for the TSS, gets its esp0 value, which is the kernel's stack pointer and places it into esp. The CPU then looks up the interrupt vector's index in another special structure the InterruptDescriptorTable or IDT for short, and finds an address. This address is where the function that handles the system call is. The CPU pushes the flags register, the code segment, the user's stack and the instruction pointer for the next instruction that is after the int instruction. After the systemcall has been serviced, the kernel issues an iret. Then the CPU returns back to usermode and your application continues as normal.
Do all library calls end in system calls?
Well most of them do, but there are some which don't. For example take a look at memcpy and the rest.

Why are there ioctl calls in socket.c?

Trying to understand why there are ioctl calls in socket.c ? I can see a modified kernel that I am using, it has some ioctl calls which load in the required modules when the calls are made.
I was wondering why these calls ended up in socket.c ? Isn't socket kind of not-a-device and ioctls are primarily used for device.
Talking about 2.6.32.0 heavily modified kernel here.
ioctl suffers from its historic name. While originally developed to perform i/o controls on devices, it has a generic enough construct that it may be used for arbitrary service requests to the kernel in context of a file descriptor. A file descriptor is an opaque value (just an int) provided by the kernel that can be associated with anything.
Now if you treat a file descriptor and think of things as files, which most *nix constructs do, open/read/write/close isn't enough. What if you want to label a file (rename)? what if you want to wait for a file to become available (ioctl)? what if you want to terminate everything if a file closes (termios)? all the "meta" operations that don't make sense in the core read/write context are lumped under ioctls; fctls; etc. unless they are so frequently used that they deserve their own system call (e.g. flock(2) functionality in BSD4.2)

System call or function call - performance-wise

In Linux, when you can choose between a system call or a function call to do a task, which option is the better one due to a better performance?
We should note that in most of the cases we do not directly use system call. We use the interface provided by glibc.
http://www.kernel.org/doc/man-pages/online/pages/man2/syscalls.2.html
http://www.gnu.org/software/libc/manual/html_node/System-Calls.html
Now in cases like File Mangement/IPC/ process management etc which are the core resource management activities of the Operating System the only option is system call and not library functions.
In these cases, typically we use Library function which works as a wrapper over a system call. That is say for reading a file, we have many library functions like
fgetc/fgets/fscanf/fread - all should invoke read system call.
So shall we use read system call? or the other library functions?
This should depend on the particular application.If we are using read, then we again need to change the code to run this, on some other operating system where read is not available.
We are losing some flexibilty. It may be useful when we are sure of the platform and we can do some optimisations by using read only or may be the application must use only file descriptors and not file pointer etc.
Now in cases where we need to consider only say user level operations and invoke
no service from operating system , like say copying a string.(strcpy).
In this case definitely we shall not use any system call unnecessarily, if at
all something is there, since it should be an extra overhead due to operating
system intervention, which is not needed in this case.
So I feel choosing between a system call and a library function only occurs for cases where we have a library function built on top of a system call.
(like adding to examples above we can have say malloc which calls system call brk).
Here the choice will depend on the particular type of software, the platform on which it should run, the precise non functional requirements like speed (Though you cannot say with certainty that your code will run faster if you are using brk instead of malloc), portability etc.