We Keep Coding

When event looping is blocking the application from I/O actions?

I just read an article about the event loop in JavaScript.
I found two contradictive phrases and I would be glad if someone could clarify.
A downside of this model is that if a message takes too long to
complete, the web application is unable to process user interactions
like click or scroll. The browser mitigates this with the "a script is
taking too long to run" dialog
A very interesting property of the event loop model is that
JavaScript, unlike a lot of other languages, never blocks. Handling
I/O is typically performed via events and callbacks, so when the
application is waiting for an IndexedDB query to return or an XHR
request to return, it can still process other things like user input
So, when is the first one true and when is the second one true?

"A very interesting property of the event loop model is that
JavaScript, unlike a lot of other languages, never blocks.
This is misleading. Without clever programming, JavaScript would always block the UI thread, because runtime logic always blocks the UI, by design. At a smooth sixty frames a second, that means your application logic must always cooperatively yield control (or simply complete execution) within about 16 milliseconds, otherwise your UI will freeze or stutter.
Because of this, most JavaScript APIs that might take a long time (eg. network requests) are designed in such a way to use techniques (eg callbacks, promises) to circumvent this problem, so that they do not block the event loop, avoiding the UI becoming unresponsive.
Put another way: host environments (eg a Web browser or a Node.js runtime instance) are specifically designed to enable the use of an event-based programming model (originally inspired by programming environments like Hypercard on the Mac) whereby the host environment can be asked to perform a long-running task (eg run a timer), without blocking the main thread of execution, and for your program to be notified later, via an "event" when the long-running task is complete, enabling your program to pick-up where it left-off.

Both are correct, even though I agree it is somewhat wrongly expressed.
So by points:
It's true that if a synchronous task takes too long to complete, the event loop "gets stuck" there and then all other queued tasks can't run till it finishes.
Here it is talking about asynchronous tasks so even though an HTTP request, an I/O request or whatever that is async takes too long to process, all the synchronous tasks can keep doing their job, like processing user input

There are two types of code inside Javascript
Synchronous (it's like going one by one).
Asynchronous (it's like skipping for the future)
Synchronous code
You want to find the prime number from 1 to 10000000 with synchronous code you will write a function and that function will perform the calculation and finds out the prime number in the given range but what will happen with synchronous code. The javascript engine is not able to do any task until that task gets finished.
Asynchronous Code
If you wrap the same code inside a callback or more friendly with the SetTimeout method the javascript put that function inside the event queue and perform the other operation when a certain time came the timeout method fires callback certainly when there is nothing inside the call stack, it will ask event loop to pass the first thing which is inside the event queue. So this more about finding an idle time to perform the heavy operation.
Use javascript workers to perform heavy mathematics tasks not
SetTimeout because eventually, it will block the engine when the
function is inside the call stack.

Chrome profiler - Why do functions sometimes stop for a little time?

Here is a picture of my web execution captured by Chrome Performance Devtools:
I notice that functions will be stopped many times during execution, when my web functions are stopped Chrome executes some RegExp operations (as shown in the picture). I don't understand what this is, and why it happens. Please help explain, thanks.
Update: here is a function which is also executed in the same manner:

What you describe
The way you describe the problem it sounds like you think the JavaScript virtual machine is putting the functions on hold (stopping them) while they are executing (i.e. before they return) to do something else and then resumes the functions.
The image you are showing does not suggest that at all to me.
What I'm seeing
The VM executes:
callback, which calls
some function whose name is hidden by a tooltip, which calls:
fireWith, which calls:
fire, which calls:
etc...
Then the deepest function returns, and the one that called it returns, and so on and so forth until fire returns, fireWith returns, the function whose name we cannot read returns, and callback returns.
Then the VM runs a RegExp function, and it calls a function named callback again, and the whole thing starts anew. In other words, the second column with callback and the rest is a new invocation of the functions. The functions are not "stop[ping] for a little time": they are called multiple times.
I see this all the time in libraries that respond to events. They typically will loop over event handlers to call them. Given a complex enough library, there'a fair amount of glue code that may sit between the loop that calls the handlers and your custom code so there's a lot of repetitive calls that show up in profiling.

How can stringByEvaluatingJavaScriptFromString be re-entrant?

I'm building a hybrid native/HTML5 app on iOS. As part of the native/HTML5 bridge, I'm executing some JavaScript code via stringByEvaluatingJavaScriptFromString.
I make sure to call this function from the main dispatch queue on the native side. Most of the time, the effect on the JavaScript side is that the invoked JavaScript code is called directly from the top level (of the JavaScript stack), even if multiple calls to stringByEvaluatingJavaScriptFromString occur in close proximity.
Occasionally, however, I see evidence that a call to stringByEvaluatingJavaScriptFromString occurs during the middle of method execution - that is, a method called by e.g. an event handler doesn't return before the method called by stringByEvaluatingJavaScriptFromString starts to execute.
Given that JavaScript is single-threaded, how is this possible?

This question has been plaguing me for months, and I finally have proof of the answer.
While iOS generally executes stringByEvaluatingJavaScriptFromString calls at the top of the JavaScript stack, there are certain system calls that appear to "yield" to pending evaluations. The one I have specifically identified is XmlHttpRequest.send(): if there happen to be pending evaluations at the time send() is called, send() will block until those evaluations are executed. There may be others as well.
If this behavior is undesirable, you can avoid the re-entrancy of code by wrapping the function invoked by stringByEvaluatingJavaScriptFromString in setTimeout(..., 0). See this question for background information on why such calls can be useful.
Edit: Though it occurs to me after writing this that it's a bit strange that xhr.send() will execute any pending evaluations, but won't execute pending timeouts. I'll have to do some more experiments...
Edit 2: Experiments indicate that xhr.send() does not in fact execute pending timeouts. The inconsistency is a bit odd, but there you have it.

When is JavaScript synchronous?

I have been under the impression for that JavaScript was always asynchronous. However, I have learned that there are situations where it is not (ie DOM manipulations). Is there a good reference anywhere about when it will be synchronous and when it will be asynchronous? Does jQuery affect this at all?

JavaScript is always synchronous and single-threaded. If you're executing a JavaScript block of code on a page then no other JavaScript on that page will currently be executed.
JavaScript is only asynchronous in the sense that it can make, for example, Ajax calls. The Ajax call will stop executing and other code will be able to execute until the call returns (successfully or otherwise), at which point the callback will run synchronously. No other code will be running at this point. It won't interrupt any other code that's currently running.
JavaScript timers operate with this same kind of callback.
Describing JavaScript as asynchronous is perhaps misleading. It's more accurate to say that JavaScript is synchronous and single-threaded with various callback mechanisms.
jQuery has an option on Ajax calls to make them synchronously (with the async: false option). Beginners might be tempted to use this incorrectly because it allows a more traditional programming model that one might be more used to. The reason it's problematic is that this option will block all JavaScript on the page until it finishes, including all event handlers and timers.

JavaScript is single threaded and has a synchronous execution model. Single threaded means that one command is being executed at a time. Synchronous means one at a time i.e. one line of code is being executed at time in order the code appears. So in JavaScript one thing is happening at a time.
Execution Context
The JavaScript engine interacts with other engines in the browser.
In the JavaScript execution stack there is global context at the bottom and then when we invoke functions the JavaScript engine creates new execution contexts for respective functions. When the called function exits its execution context is popped from the stack, and then next execution context is popped and so on...
For example
function abc()
{
console.log('abc');
}
function xyz()
{
abc()
console.log('xyz');
}
var one = 1;
xyz();
In the above code a global execution context will be created and in this context var one will be stored and its value will be 1... when the xyz() invocation is called then a new execution context will be created and if we had defined any variable in xyz function those variables would be stored in the execution context of xyz(). In the xyz function we invoke abc() and then the abc() execution context is created and put on the execution stack... Now when abc() finishes its context is popped from stack, then the xyz() context is popped from stack and then global context will be popped...
Now about asynchronous callbacks; asynchronous means more than one at a time.
Just like the execution stack there is the Event Queue. When we want to be notified about some event in the JavaScript engine we can listen to that event, and that event is placed on the queue. For example an Ajax request event, or HTTP request event.
Whenever the execution stack is empty, like shown in above code example, the JavaScript engine periodically looks at the event queue and sees if there is any event to be notified about. For example in the queue there were two events, an ajax request and a HTTP request. It also looks to see if there is a function which needs to be run on that event trigger... So the JavaScript engine is notified about the event and knows the respective function to execute on that event... So the JavaScript engine invokes the handler function, in the example case, e.g. AjaxHandler() will be invoked and like always when a function is invoked its execution context is placed on the execution context and now the function execution finishes and the event ajax request is also removed from the event queue... When AjaxHandler() finishes the execution stack is empty so the engine again looks at the event queue and runs the event handler function of HTTP request which was next in queue. It is important to remember that the event queue is processed only when execution stack is empty.
For example see the code below explaining the execution stack and event queue handling by Javascript engine.
function waitfunction() {
var a = 5000 + new Date().getTime();
while (new Date() < a){}
console.log('waitfunction() context will be popped after this line');
}
function clickHandler() {
console.log('click event handler...');
}
document.addEventListener('click', clickHandler);
waitfunction(); //a new context for this function is created and placed on the execution stack
console.log('global context will be popped after this line');
And
<html>
<head>
</head>
<body>
<script src="program.js"></script>
</body>
</html>
Now run the webpage and click on the page, and see the output on console. The output will be
waitfunction() context will be popped after this line
global context will be emptied after this line
click event handler...
The JavaScript engine is running the code synchronously as explained in the execution context portion, the browser is asynchronously putting things in event queue. So the functions which take a very long time to complete can interrupt event handling. Things happening in a browser like events are handled this way by JavaScript, if there is a listener supposed to run, the engine will run it when the execution stack is empty. And events are processed in the order they happen, so the asynchronous part is about what is happening outside the engine i.e. what should the engine do when those outside events happen.
So JavaScript is always synchronous.

JavaScript is single-threaded, and all the time you work on a normal synchronous code-flow execution.
Good examples of the asynchronous behavior that JavaScript can have are events (user interaction, Ajax request results, etc) and timers, basically actions that might happen at any time.
I would recommend you to give a look to the following article:
How JavaScript Timers Work
That article will help you to understand the single-threaded nature of JavaScript and how timers work internally and how asynchronous JavaScript execution works.

To someone who really understands how JS works this question might seem off, however most people who use JS do not have such a deep level of insight (and don't necessarily need it) and to them this is a fairly confusing point, I will try to answer from that perspective.
JS is synchronous in the way its code is executed. each line only runs after the line before it has completed and if that line calls a function after that is complete etc...
The main point of confusion arises from the fact that your browser is able to tell JS to execute more code at anytime (similar to how you can execute more JS code on a page from the console). As an example JS has Callback functions who's purpose is to allow JS to BEHAVE asynchronously so further parts of JS can run while waiting for a JS function that has been executed (I.E. a GET call) to return back an answer, JS will continue to run until the browser has an answer at that point the event loop (browser) will execute the JS code that calls the callback function.
Since the event loop (browser) can input more JS to be executed at any point in that sense JS is asynchronous (the primary things that will cause a browser to input JS code are timeouts, callbacks and events)
I hope this is clear enough to be helpful to somebody.

Definition
The term "asynchronous" can be used in slightly different meanings, resulting in seemingly conflicting answers here, while they are actually not. Wikipedia on Asynchrony has this definition:
Asynchrony, in computer programming, refers to the occurrence of events independent of the main program flow and ways to deal with such events. These may be "outside" events such as the arrival of signals, or actions instigated by a program that take place concurrently with program execution, without the program blocking to wait for results.
non-JavaScript code can queue such "outside" events to some of JavaScript's event queues. But that is as far as it goes.
No Preemption
There is no external interruption of running JavaScript code in order to execute some other JavaScript code in your script. Pieces of JavaScript are executed one after the other, and the order is determined by the order of events in each event queue, and the priority of those queues.
For instance, you can be absolutely sure that no other JavaScript (in the same script) will ever execute while the following piece of code is executing:
let a = [1, 4, 15, 7, 2];
let sum = 0;
for (let i = 0; i < a.length; i++) {
sum += a[i];
}
In other words, there is no preemption in JavaScript. Whatever may be in the event queues, the processing of those events will have to wait until such piece of code has ran to completion. The EcmaScript specification says in section 8.4 Jobs and Jobs Queues:
Execution of a Job can be initiated only when there is no running execution context and the execution context stack is empty.
Examples of Asynchrony
As others have already written, there are several situations where asynchrony comes into play in JavaScript, and it always involves an event queue, which can only result in JavaScript execution when there is no other JavaScript code executing:
setTimeout(): the agent (e.g. browser) will put an event in an event queue when the timeout has expired. The monitoring of the time and the placing of the event in the queue happens by non-JavaScript code, and so you could imagine this happens in parallel with the potential execution of some JavaScript code. But the callback provided to setTimeout can only execute when the currently executing JavaScript code has ran to completion and the appropriate event queue is being read.
fetch(): the agent will use OS functions to perform an HTTP request and monitor for any incoming response. Again, this non-JavaScript task may run in parallel with some JavaScript code that is still executing. But the promise resolution procedure, that will resolve the promise returned by fetch(), can only execute when the currently executing JavaScript has ran to completion.
requestAnimationFrame(): the browser's rendering engine (non-JavaScript) will place an event in the JavaScript queue when it is ready to perform a paint operation. When JavaScript event is processed the callback function is executed.
queueMicrotask(): immediately places an event in the microtask queue. The callback will be executed when the call stack is empty and that event is consumed.
There are many more examples, but all these functions are provided by the host environment, not by core EcmaScript. With core EcmaScript you can synchronously place an event in a Promise Job Queue with Promise.resolve().
Language Constructs
EcmaScript provides several language constructs to support the asynchrony pattern, such as yield, async, await. But let there be no mistake: no JavaScript code will be interrupted by an external event. The "interruption" that yield and await seem to provide is just a controlled, predefined way of returning from a function call and restoring its execution context later on, either by JS code (in the case of yield), or the event queue (in the case of await).
DOM event handling
When JavaScript code accesses the DOM API, this may in some cases make the DOM API trigger one or more synchronous notifications. And if your code has an event handler listening to that, it will be called.
This may come across as pre-emptive concurrency, but it is not: it is the JavaScript code that initiates the API call, and thus controls that the API can do some stuff, but this is just like a function call: once your event handler(s) return(s), the DOM API will eventually also return, and the original JavaScript code will continue after the API call it made.
In other cases the DOM API will just dispatch an event in the appropriate event queue, and JavaScript will pick it up once the call stack has been emptied.
See synchronous and asynchronous events

"I have been under the impression for that JavaScript was always
asynchronous"
You can use JavaScript in a synchronous way, or an asynchronous way. In fact JavaScript has really good asynchronous support. For example I might have code that requires a database request. I can then run other code, not dependent on that request, while I wait for that request to complete. This asynchronous coding is supported with promises, async/await, etc. But if you don't need a nice way to handle long waits then just use JS synchronously.
What do we mean by 'asynchronous'. Well it does not mean multi-threaded, but rather describes a non-dependent relationship. Check out this image from this popular answer:
A-Start ------------------------------------------ A-End
| B-Start -----------------------------------------|--- B-End
| | C-Start ------------------- C-End | |
| | | | | |
V V V V V V
1 thread->|<-A-|<--B---|<-C-|-A-|-C-|--A--|-B-|--C-->|---A---->|--B-->|
We see that a single threaded application can have async behavior. The work in function A is not dependent on function B completing, and so while function A began before function B, function A is able to complete at a later time and on the same thread.
So, just because JavaScript executes one command at a time, on a single thread, it does not then follow that JavaScript can only be used as a synchronous language.
"Is there a good reference anywhere about when it will be synchronous and when it will be asynchronous"
I'm wondering if this is the heart of your question. I take it that you mean how do you know if some code you are calling is async or sync. That is, will the rest of your code run off and do something while you wait for some result? Your first check should be the documentation for whichever library you are using. Node methods, for example, have clear names like readFileSync. If the documentation is no good there is a lot of help here on SO. EG:
How to know if a function is async?

Are Mutexes needed in javascript?

I have seen this link: Implementing Mutual Exclusion in JavaScript.
On the other hand, I have read that there are no threads in javascript, but what exactly does that mean?
When events occur, where in the code can they interrupt?
And if there are no threads in JS, do I need to use mutexes in JS or not?
Specifically, I am wondering about the effects of using functions called by setTimeout() and XmlHttpRequest's onreadystatechange on globally accessible variables.

Javascript is defined as a reentrant language which means there is no threading exposed to the user, there may be threads in the implementation. Functions like setTimeout() and asynchronous callbacks need to wait for the script engine to sleep before they're able to run.
That means that everything that happens in an event must be finished before the next event will be processed.
That being said, you may need a mutex if your code does something where it expects a value not to change between when the asynchronous event was fired and when the callback was called.
For example if you have a data structure where you click one button and it sends an XmlHttpRequest which calls a callback the changes the data structure in a destructive way, and you have another button that changes the same data structure directly, between when the event was fired and when the call back was executed the user could have clicked and updated the data structure before the callback which could then lose the value.
While you could create a race condition like that it's very easy to prevent that in your code since each function will be atomic. It would be a lot of work and take some odd coding patterns to create the race condition in fact.

The answers to this question are a bit outdated though correct at the time they were given. And still correct if looking at a client-side javascript application that does NOT use webworkers.
Articles on web-workers:
multithreading in javascript using webworkers
Mozilla on webworkers
This clearly shows that javascript via web-workers has multithreading capabilities. As concerning to the question are mutexes needed in javascript? I am unsure of this. But this stackoverflow post seems relevant:
Mutual Exclusion for N Asynchronous Threads

Yes, mutexes can be required in Javascript when accessing resources that are shared between tabs/windows, like localStorage.
For example, if a user has two tabs open, simple code like the following is unsafe:
function appendToList(item) {
var list = localStorage["myKey"];
if (list) {
list += "," + item;
}
else {
list = item;
}
localStorage["myKey"] = list;
}
Between the time that the localStorage item is 'got' and 'set', another tab could have modified the value. It's generally unlikely, but possible - you'd need to judge for yourself the likelihood and risk associated with any contention in your particular circumstances.
See the following articles for a more detail:
Wait, Don't Touch That: Mutual Exclusion Locks & JavaScript - Medium Engineering
JavaScript concurrency and locking the HTML5 localStorage - Benjamin Dumke-von der Eh, Stackoverflow

As #william points out,
you may need a mutex if your code does something where it expects a
value not to change between when the asynchronous event was fired and
when the callback was called.
This can be generalised further - if your code does something where it expects exclusive control of a resource until an asynchronous request resolves, you may need a mutex.
A simple example is where you have a button that fires an ajax call to create a record in the back end. You might need a bit of code to protect you from trigger happy users clicking away and thereby creating multiple records. there are a number of approaches to this problem (e.g. disable the button, enable on ajax success). You could also use a simple lock:
var save_lock = false;
$('#save_button').click(function(){
if(!save_lock){
//lock
save_lock=true;
$.ajax({
success:function()
//unlock
save_lock = false;
}
});
}
}
I'm not sure if that's the best approach and I would be interested to see how others handle mutual exclusion in javascript, but as far as i'm aware that's a simple mutex and it is handy.

JavaScript is single threaded... though Chrome may be a new beast (I think it is also single threaded, but each tab has it's own JavaScript thread... I haven't looked into it in detail, so don't quote me there).
However, one thing you DO need to worry about is how your JavaScript will handle multiple ajax requests coming back in not the same order you send them. So, all you really need to worry about is make sure your ajax calls are handled in a way that they won't step on eachother's feet if the results come back in a different order than you sent them.
This goes for timeouts too...
When JavaScript grows multithreading, then maybe worry about mutexes and the like....

JavaScript, the language, can be as multithreaded as you want, but browser embeddings of the javascript engine only runs one callback (onload, onfocus, <script>, etc...) at a time (per tab, presumably). William's suggestion of using a Mutex for changes between registering and receiving a callback should not be taken too literally because of this, as you wouldn't want to block in the intervening callback since the callback that will unlock it will be blocked behind the current callback! (Wow, English sucks for talking about threading.) In this case, you probably want to do something along the lines of redispatching the current event if a flag is set, either literally or with the likes of setTimeout().
If you are using a different embedding of JS, and that executes multiple threads at once, it can get a bit more dicey, but due to the way JS can use callbacks so easily and locks objects on property access explicit locking is not nearly as necessary. However, I would be surprised if an embedding designed for general code (eg, game scripting) that used multi threading didn't also give some explicit locking primitives as well.
Sorry for the wall of text!

Events are signaled, but JavaScript execution is still single-threaded.
My understanding is that when event is signaled the engine stops what it is executing at the moment to run event handler. After the handler is finished, script execution is resumed. If event handler changed some shared variables then resumed code will see these changes appearing "out of the blue".
If you want to "protect" shared data, simple boolean flag should be sufficient.