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JS event Loop confuse

I am pretty new to JS event loop, I wonder if anyone could give me a brief walk thru about how js engine run this:
function start(){
setTimeout(function(){
console.log("Timeout")
}, 0)
setImmediate(function(){
console.log("Immediate")
})
process.nextTick(function(){
console.log("next tick")
})
}
The result is :
next tick
Timeout
Immediate
I thought when JS engine runs this,
it parses the script, set Timer, set Immediate, set nextTick queue, then goes into POLL stage, checks if anything queued there(nothing in this case)
Before moving to CHECK stage, it runs nextTick queue, print "next tick".
Moves to CHECK stage, run immediate queue, print "Immediate"
Loops back to TIMER stage, print "Timeout"
My confuse is why setTimeout print out before Immediate?
PS,
After I set Timeout delay from 0 to 3 or more, then the order is:
next tick
Immediate
Timeout
But this still does not explain why previous order JS event loop runs.
I wonder is there anything I missed?

setImmediate queues the function behind whatever I/O, event, callbacks that are already in the event queue. So, in this case setTimeout is already in queue.
I think you should read https://nodejs.org/en/docs/guides/event-loop-timers-and-nexttick/ again. It has answer to all your questions. I am quoting following lines from above mentioned document
setImmediate() vs setTimeout()
setImmediate and setTimeout() are similar, but behave in different ways depending on when they are called.
setImmediate() is designed to execute a script once the current poll phase completes.
setTimeout() schedules a script to be run after a minimum threshold in ms has elapsed.
The order in which the timers are executed will vary depending on the context in which they are called.
Understanding process.nextTick()
process.nextTick() is not technically part of the event loop. Instead, the nextTickQueue will be processed after the current operation completes, regardless of the current phase of the event loop.
Looking back at our diagram, any time you call process.nextTick() in a given phase, all callbacks passed to process.nextTick() will be resolved before the event loop continues. This can create some bad situations because it allows you to "starve" your I/O by making recursive process.nextTick() calls, which prevents the event loop from reaching the poll phase.

How can a script and setTimeout/setInterval work together in NodeJS?

Reading through the NodeJS Event Loop description I wonder how setTimeout and setInterval can actually work.
The page says NodeJS first runs the given script (let REPL alone for now) and then enters the event loop. But what if I call setTimeout in that script and expect it to trigger while the script is still running? Isn't that the normal case actually? According to the description the timer callback will not be triggered before the main script ends, which sounds really weird to me.
For those interested, here's the NodeJS outer even loop (there are actually 2 nested loops): https://github.com/nodejs/node/blob/master/src/node.cc#L4526

let's do this by example
setTimeout(function(){
print('there');
});
print('hi');
this will print hi then there
here's what happen
the script will be proccessed until last line and when ever it finds a timer function
it will add it to a queue which will be handled later at the end of the execution by the queue scheduler
loop queue => [ setTimeout ]
before exit there should be a scheduler, some kind of a loop to check if we
have something in the queue and handle them, then once queue is out of all timers the loop
will exit.
let's suppose we call setTimeout inside setInterval
setInterval(function(){
setTimeout(function(){
print('hi')
}, 500);
}, 1000);
loop queue => [ setInterval ]
after 1000 ms
setInterval will be fired and the inner setTimeout will be added to the queue
loop queue => [ setTimeout, setInterval ]
now we get back to the main loop which will wait for another 500 ms
an fire the inner setTimeout function, then remove it from the queue
because setTimeout should be run once.
loop queue => [ setInterval ]
back to the main loop, we still have items in the queue, so it will wait
another 500 ms and fire again ( 500 + 500 = 1000 ms)
the inner setTimeout function will be added to the queue again
loop queue => [ setTimeout, setInterval ]
back to the main queue agin and again ...
Now this is simply how timers work, they are not meant to handle blocking code, it's
a way to run code at some intervals
setInterval(function(){
// do something long running here
while (1) {}
setTimeout(function(){
print('hi')
}, 500);
}, 1000);
main loop will block here and the inner timeout will not be added to the queue, so this
is a bad idea
nodejs and event loop in general are good with network operations because they don't block when
used with select for example.
setInterval(function(){
// check if socket has something
if (socketHasData( socket )){
processSocketData( socket );
}
// do something else that does not block
// maybe schedule another timer here
print('hello');
}, 1000);
libuv which is the event loop used in nodejs, uses threads to handle some
blocking operations like IO operations, open/read/write files

[EDIT] humm re-reading your initial post, I think I know what bugs you. You mentioned nodejs in your post, implying you might be coding a server.
If you are not really familiar with server side JavaScript and more used to php server for example it might be very confusing indeed.
With a php server, a request creates a new thread that will handle it and when the main script (as you call it) ends, then the thread is killed and nothing else runs on the server (except for the webserver that listens to request, like nginx or apache).
With nodejs, it's different. The main thread is alone and always running. So when a request arrives, callbacks are fired but they are still in that single thread. Said otherwise: the main script never ends (except when you kill it or that your server crashes :) )
Well, that is accurate. Because of the single-threaded nature of JavaScript, if a timer ends while the main thread is busy, the timer's callback will wait.
When you do
setTimeout(callback, 1000)
You are not saying "I want this callback to be called in exactly 1s" but actually "I want this callback to be called in, at least, 1s"
This article by John Resig is an excellent read and goes through the details of the JavaScript's timers https://johnresig.com/blog/how-javascript-timers-work/

But what if I call setTimeout in that script and expect it to trigger while the script is still running?
You don't expect that. You expect your synchronous code run to completion way before the timeout occurs.
If the script is still running, because it's doing something blocking - it hangs - then the timeout callback doesn't get a chance to execute, it will wait. That's exactly why we need to write non-blocking code.
Isn't that the normal case actually?
No. Most of the time no JS is executing, the event loop is idling (while there might be background tasks doing the heavy lifting).

Given that Node is single threaded, it (v8 engine) always executes the current script before moving on to the next one. So when we start a node server with a main script, it loads, parses, compiles and executes that script first, before it runs anything else. Only if the current running script hits an I/O call it gets bumped out to the back of the event loop, giving other scripts or setTimeout callbacks a chance to execute. This is the very nature of JavaScript engine and the reason Node is not considered good for long running, in-memory CPU intensive tasks.
As #atomrc said in his answer, setTimeout and setInterval are just a hint to node to run the callbacks after the timeout period, there are no guarantees.

Javascript internals - clearTimeout just before it fires

Let's say I do this:
var timer = setTimeout(function() {
console.log("will this happen?");
}, 5000);
And then after just less than 5 seconds, another callback (from a network event in NodeJS for example) fires and clears it:
clearTimeout(timer);
Is there any possibility that the callback from the setTimeout call is already in the queue to be executed at this point, and if so will the clearTimeout be in time to stop it?
To clarify, I am talking about a situation where the setTimeout time actually expires and the interpreter starts the process of executing it, but the other callback is currently running so the message is added to the queue. It seems like one of those race condition type things that would be easy to not account for.

Even though Node is single thread, the race condition the question describes is possible.
It can happen because timers are triggered by native code (in lib_uv).
On top of that, Node groups timers with the same timeout value. As a result, if you schedule two timers with the same timeout within the same ms, they will be added to the event queue at once.
But rest assured node internally solves that for you. Quoting code from node 0.12.0:
timer.js > clearTimeout
exports.clearTimeout = function(timer) {
if (timer && (timer[kOnTimeout] || timer._onTimeout)) {
timer[kOnTimeout] = timer._onTimeout = null;
// ...
}
}
On clearing a timeout, Node internally removes the reference to the callback function. So even if the race condition happens, it can do no harm, because those timers will be skipped:
listOnTimeout
if (!first._onTimeout) continue;

Node.js executes in a single thread.
So there cannot be any race conditions and you can reliably cancel the timeout before it triggers.
See also a related discussion (in browsers).
I am talking about a situation where the setTimeout time actually expires and the interpreter starts the process of executing it
Without having looked at Node.js internals, I don't think this is possible. Everything is single-threaded, so the interpreter cannot be "in the process" of doing anything while your code is running.
Your code has to return control before the timeout can be triggered. If you put an infinite loop in your code, the whole system hangs. This is all "cooperative multitasking".

This behavior is defined in the HTML Standard, the fired task starts with:
If the entry for handle in the list of active timers has been cleared, then abort these steps.
Therefore even if the task has been queued already, it'll be aborted.
Whether this applies to Node.js, however, is debatable, as the documentation just states:
The timer functions within Node.js implement a similar API as the timers API provided by Web Browsers but use a different internal implementation that is built around the Node.js Event Loop.

Understanding the Event Loop

I am thinking about it and this is what I came up with:
Let's see this code below:
console.clear();
console.log("a");
setTimeout(function(){console.log("b");},1000);
console.log("c");
setTimeout(function(){console.log("d");},0);
A request comes in, and JS engine starts executing the code above step by step. The first two calls are sync calls. But when it comes to setTimeout method, it becomes an async execution. But JS immediately returns from it and continue executing, which is called Non-Blocking or Async. And it continues working on other etc.
The results of this execution is the following:
a c d b
So basically the second setTimeout got finished first and its callback function gets executed earlier than the first one and that makes sense.
We are talking about single-threaded application here. JS Engine keeps executing this and unless it finishes the first request, it won't go to second one. But the good thing is that it won't wait for blocking operations like setTimeout to resolve so it will be faster because it accepts the new incoming requests.
But my questions arise around the following items:
#1: If we are talking about a single-threaded application, then what mechanism processes setTimeouts while the JS engine accepts more requests and executes them? How does the single thread continue working on other requests? What works on setTimeout while other requests keep coming in and get executed.
#2: If these setTimeout functions get executed behind the scenes while more requests are coming in and being executed, what carries out the async executions behind the scenes? What is this thing that we talk about called the EventLoop?
#3: But shouldn't the whole method be put in the EventLoop so that the whole thing gets executed and the callback method gets called? This is what I understand when talking about callback functions:
function downloadFile(filePath, callback)
{
blah.downloadFile(filePath);
callback();
}
But in this case, how does the JS Engine know if it is an async function so that it can put the callback in the EventLoop? Perhaps something like the async keyword in C# or some sort of an attribute which indicates the method JS Engine will take on is an async method and should be treated accordingly.
#4: But an article says quite contrary to what I was guessing on how things might be working:
The Event Loop is a queue of callback functions. When an async
function executes, the callback function is pushed into the queue. The
JavaScript engine doesn't start processing the event loop until the
code after an async function has executed.
#5: And there is this image here which might be helpful but the first explanation in the image is saying exactly the same thing mentioned in question number 4:
So my question here is to get some clarifications about the items listed above?

1: If we are talking about a single-threaded application, then what processes setTimeouts while JS engine accepts more requests and executes them? Isn't that single thread will continue working on other requests? Then who is going to keep working on setTimeout while other requests keep coming and get executed.
There's only 1 thread in the node process that will actually execute your program's JavaScript. However, within node itself, there are actually several threads handling operation of the event loop mechanism, and this includes a pool of IO threads and a handful of others. The key is the number of these threads does not correspond to the number of concurrent connections being handled like they would in a thread-per-connection concurrency model.
Now about "executing setTimeouts", when you invoke setTimeout, all node does is basically update a data structure of functions to be executed at a time in the future. It basically has a bunch of queues of stuff that needs doing and every "tick" of the event loop it selects one, removes it from the queue, and runs it.
A key thing to understand is that node relies on the OS for most of the heavy lifting. So incoming network requests are actually tracked by the OS itself and when node is ready to handle one it just uses a system call to ask the OS for a network request with data ready to be processed. So much of the IO "work" node does is either "Hey OS, got a network connection with data ready to read?" or "Hey OS, any of my outstanding filesystem calls have data ready?". Based upon its internal algorithm and event loop engine design, node will select one "tick" of JavaScript to execute, run it, then repeat the process all over again. That's what is meant by the event loop. Node is basically at all times determining "what's the next little bit of JavaScript I should run?", then running it. This factors in which IO the OS has completed, and things that have been queued up in JavaScript via calls to setTimeout or process.nextTick.
2: If these setTimeout will get executed behind the scenes while more requests are coming and in and being executed, the thing carry out the async executions behind the scenes is that the one we are talking about EventLoop?
No JavaScript gets executed behind the scenes. All the JavaScript in your program runs front and center, one at a time. What happens behind the scenes is the OS handles IO and node waits for that to be ready and node manages its queue of javascript waiting to execute.
3: How can JS Engine know if it is an async function so that it can put it in the EventLoop?
There is a fixed set of functions in node core that are async because they make system calls and node knows which these are because they have to call the OS or C++. Basically all network and filesystem IO as well as child process interactions will be asynchronous and the ONLY way JavaScript can get node to run something asynchronously is by invoking one of the async functions provided by the node core library. Even if you are using an npm package that defines it's own API, in order to yield the event loop, eventually that npm package's code will call one of node core's async functions and that's when node knows the tick is complete and it can start the event loop algorithm again.
4 The Event Loop is a queue of callback functions. When an async function executes, the callback function is pushed into the queue. The JavaScript engine doesn't start processing the event loop until the code after an async function has executed.
Yes, this is true, but it's misleading. The key thing is the normal pattern is:
//Let's say this code is running in tick 1
fs.readFile("/home/barney/colors.txt", function (error, data) {
//The code inside this callback function will absolutely NOT run in tick 1
//It will run in some tick >= 2
});
//This code will absolutely also run in tick 1
//HOWEVER, typically there's not much else to do here,
//so at some point soon after queueing up some async IO, this tick
//will have nothing useful to do so it will just end because the IO result
//is necessary before anything useful can be done
So yes, you could totally block the event loop by just counting Fibonacci numbers synchronously all in memory all in the same tick, and yes that would totally freeze up your program. It's cooperative concurrency. Every tick of JavaScript must yield the event loop within some reasonable amount of time or the overall architecture fails.

Don't think the host process to be single-threaded, they are not. What is single-threaded is the portion of the host process that execute your javascript code.
Except for background workers, but these complicate the scenario...
So, all your js code run in the same thread, and there's no possibility that you get two different portions of your js code to run concurrently (so, you get not concurrency nigthmare to manage).
The js code that is executing is the last code that the host process picked up from the event loop.
In your code you can basically do two things: run synchronous instructions, and schedule functions to be executed in future, when some events happens.
Here is my mental representation (beware: it's just that, I don't know the browser implementation details!) of your example code:
console.clear(); //exec sync
console.log("a"); //exec sync
setTimeout( //schedule inAWhile to be executed at now +1 s
function inAWhile(){
console.log("b");
},1000);
console.log("c"); //exec sync
setTimeout(
function justNow(){ //schedule justNow to be executed just now
console.log("d");
},0);
While your code is running, another thread in the host process keep track of all system events that are occurring (clicks on UI, files read, networks packets received etc.)
When your code completes, it is removed from the event loop, and the host process return to checking it, to see if there are more code to run. The event loop contains two event handler more: one to be executed now (the justNow function), and another within a second (the inAWhile function).
The host process now try to match all events happened to see if there handlers registered for them.
It found that the event that justNow is waiting for has happened, so it start to run its code. When justNow function exit, it check the event loop another time, searhcing for handlers on events. Supposing that 1 s has passed, it run the inAWhile function, and so on....

The Event Loop has one simple job - to monitor the Call Stack, the Callback Queue and Micro task queue. If the Call Stack is empty, the Event Loop will take the first event from the micro task queue then from the callback queue and will push it to the Call Stack, which effectively runs it. Such an iteration is called a tick in the Event Loop.
As most developers know, that Javascript is single threaded, means two statements in javascript can not be executed in parallel which is correct. Execution happens line by line, which means each javascript statements are synchronous and blocking. But there is a way to run your code asynchronously, if you use setTimeout() function, a Web API given by the browser, which makes sure that your code executes after specified time (in millisecond).
Example:
console.log("Start");
setTimeout(function cbT(){
console.log("Set time out");
},5000);
fetch("http://developerstips.com/").then(function cbF(){
console.log("Call back from developerstips");
});
// Millions of line code
// for example it will take 10000 millisecond to execute
console.log("End");
setTimeout takes a callback function as first parameter, and time in millisecond as second parameter.
After the execution of above statement in browser console it will print
Start
End
Call back from developerstips
Set time out
Note: Your asynchronous code runs after all the synchronous code is done executing.
Understand How the code execution line by line
JS engine execute the 1st line and will print "Start" in console
In the 2nd line it sees the setTimeout function named cbT, and JS engine pushes the cbT function to callBack queue.
After this the pointer will directly jump to line no.7 and there it will see promise and JS engine push the cbF function to microtask queue.
Then it will execute Millions of line code and end it will print "End"
After the main thread end of execution the event loop will first check the micro task queue and then call back queue. In our case it takes cbF function from the micro task queue and pushes it into the call stack then it will pick cbT funcion from the call back queue and push into the call stack.

JavaScript is high-level, single-threaded language, interpreted language. This means that it needs an interpreter which converts the JS code to a machine code. interpreter means engine. V8 engines for chrome and webkit for safari. Every engine contains memory, call stack, event loop, timer, web API, events, etc.
Event loop: microtasks and macrotasks
The event loop concept is very simple. There’s an endless loop, where the JavaScript engine waits for tasks, executes them and then sleeps, waiting for more tasks
Tasks are set – the engine handles them – then waits for more tasks (while sleeping and consuming close to zero CPU). It may happen that a task comes while the engine is busy, then it’s enqueued. The tasks form a queue, so-called “macrotask queue”
Microtasks come solely from our code. They are usually created by promises: an execution of .then/catch/finally handler becomes a microtask. Microtasks are used “under the cover” of await as well, as it’s another form of promise handling. Immediately after every macrotask, the engine executes all tasks from microtask queue, prior to running any other macrotasks or rendering or anything else.

MyFunction() vs window.setTimeout('MyFunction()', 0)?

In javascript, is there any different between these two:
// call MyFunction normal way
MyFunction();
// call MyFunction with setTimeout to 0 //
window.setTimeout('MyFunction()', 0);
The reason I asked was because recently came across the situation where the code only works if I use setTimeout(0) to call the function.
To my understanding, setTimeout(0) is exactly same as calling a function directly because you dont set any delay. But from what I see how it works in the code, setTimeout(0) seems to get executed last.
Can someone clarify exactly how setTimeout(0) really get called in order of the rest of other function call?

setTimeout() always causes the block of JavaScript to be queued for execution. It is a matter of when it will be executed, which is decided by the delay provided.
Calling setTimeout() with a delay of 0, will result in the JavaScript interpreter realizing that it is currently busy (executing the current function), and the interpreter will schedule the script block to be executed once the current call stack is empty (unless there are other script blocks that are also queued up).
It could take a long time for the call stack to become empty, which is why you are seeing a delay in execution. This is primarily due to the single-threaded nature of JavaScript in a single window context.
For the sake of completeness, MyFunction() will immediately execute the function. There will be no queuing involved.
PS: John Resig has some useful notes on how the JavaScript timing mechanism works.
PPS: The reason why your code "seems to work" only when you use setTimeout(fn(),0), is because browsers could update the DOM only when the current call stack is complete. Therefore, the next JavaScript block would recognize the DOM changes, which is quite possible in your case. A setTimeout() callback always creates a new call stack.

I would guess that the timeout only starts when the page is fully loaded, whereas just a plain 'MyFunction()' will execute as soon as it's processed.

The timer will try to execute once your current thread is done. This depends on where you call the window.setTimeout(). If it is in a javascript tag, but not inside a function, then it will be called once the end of the javascript tag is reached. For example:
<html>
<script type="text/javascript">
setTimeout(function(){alert("hello")},0);
var d=Number(new Date())+1000;
while(Number(new Date())<d){
}
alert("hi");
</script>
</html>
If you call the setTimeout inside a function that results from an event occuring, for example onload, then it will wait until the event handler function returns:
<html>
<script type="text/javascript">
document.addEventListener("mousedown",function(){
setTimeout(function(){alert("hello")},0);
var d=Number(new Date())+1000;
while(Number(new Date())<d){
}
alert("hi");
}, true);
</script>
</html>
It is impossible to make one thread in JavaScript wait while another thread is running. Event listeners will wait until the current thread is done before they start running.
The only exception is Web Workers, but they run in a different file, and the only way to communicate between them is using event listeners, so while you can send a message while the other is working, it won't receive that message until it is done, or it manually checks for messages.