Node.js Server Timeout Problems (EC2 + Express + PM2) - node.js

I'm relatively new to running production node.js apps and I've recently been having problems with my server timing out.
Basically after a certain amount of usage & time my node.js app stops responding to requests. I don't even see routes being fired on my console anymore - it's like the whole thing just comes to a halt and the HTTP calls from my client (iPhone running AFNetworking) don't reach the server anymore. But if I restart my node.js app server everything starts working again, until things inevitable stop again. The app never crashes, it just stops responding to requests.
I'm not getting any errors, and I've made sure to handle and log all DB connection errors so I'm not sure where to start. I thought it might have something to do with memory leaks so I installed node-memwatch and set up a listener for memory leaks but that doesn't get called before my server stops responding to requests.
Any clue as to what might be happening and how I can solve this problem?
Here's my stack:
Node.js on AWS EC2 Micro Instance (using Express 4.0 + PM2)
Database on AWS RDS volume running MySQL (using node-mysql)
Sessions stored w/ Redis on same EC2 instance as the node.js app
Clients are iPhones accessing the server via AFNetworking
Once again no errors are firing with any of the modules mentioned above.

First of all you need to be a bit more specific about timeouts.
TCP timeouts: TCP divides a message into packets which are sent one by one. The receiver needs to acknowledge having received the packet. If the receiver does not acknowledge having received the package within certain period of time, a TCP retransmission occurs, which is sending the same packet again. If this happens a couple of more times, the sender gives up and kills the connection.
HTTP timeout: An HTTP client like a browser, or your server while acting as a client (e.g: sending requests to other HTTP servers), can set an arbitrary timeout. If a response is not received within that period of time, it will disconnect and call it a timeout.
Now, there are many, many possible causes for this... from more trivial to less trivial:
Wrong Content-Length calculation: If you send a request with a Content-Length: 20 header, that means "I am going to send you 20 bytes". If you send 19, the other end will wait for the remaining 1. If that takes too long... timeout.
Not enough infrastructure: Maybe you should assign more machines to your application. If (total load / # of CPU cores) is over 1, or your memory usage is high, your system may be over capacity. However keep reading...
Silent exception: An error was thrown but not logged anywhere. The request never finished processing, leading to the next item.
Resource leaks: Every request needs to be handled to completion. If you don't do this, the connection will remain open. In addition, the IncomingMesage object (aka: usually called req in express code) will remain referenced by other objects (e.g: express itself). Each one of those objects can use a lot of memory.
Node event loop starvation: I will get to that at the end.
For memory leaks, the symptoms would be:
the node process would be using an increasing amount of memory.
To make things worse, if available memory is low and your server is misconfigured to use swapping, Linux will start moving memory to disk (swapping), which is very I/O and CPU intensive. Servers should not have swapping enabled.
cat /proc/sys/vm/swappiness
will return you the level of swappiness configured in your system (goes from 0 to 100). You can modify it in a persistent way via /etc/sysctl.conf (requires restart) or in a volatile way using: sysctl vm.swappiness=10
Once you've established you have a memory leak, you need to get a core dump and download it for analysis. A way to do that can be found in this other Stackoverflow response: Tools to analyze core dump from Node.js
For connection leaks (you leaked a connection by not handling a request to completion), you would be having an increasing number of established connections to your server. You can check your established connections with netstat -a -p tcp | grep ESTABLISHED | wc -l can be used to count established connections.
Now, the event loop starvation is the worst problem. If you have short lived code node works very well. But if you do CPU intensive stuff and have a function that keeps the CPU busy for an excessive amount of time... like 50 ms (50 ms of solid, blocking, synchronous CPU time, not asynchronous code taking 50 ms), operations being handled by the event loop such as processing HTTP requests start falling behind and eventually timing out.
The way to find a CPU bottleneck is using a performance profiler. nodegrind/qcachegrind are my preferred profiling tools but others prefer flamegraphs and such. However it can be hard to run a profiler in production. Just take a development server and slam it with requests. aka: a load test. There are many tools for this.
Finally, another way to debug the problem is:
env NODE_DEBUG=tls,net node <...arguments for your app>
node has optional debug statements that are enabled through the NODE_DEBUG environment variable. Setting NODE_DEBUG to tls,net will make node emit debugging information for the tls and net modules... so basically everything being sent or received. If there's a timeout you will see where it's coming from.
Source: Experience of maintaining large deployments of node services for years.

Related

Except from memory and CPU leaks, what will be reasons for Node.js server might go went down?

I have a Node.js (Express.js) server for my React.js website as BFF. I use Node.js for SSR, proxying some request and cache some pages in Redis. In last time I found that my server time to time went down. I suggest an uptime is about 2 days. After restart, all ok, then response time growth from hour to hour. I have resource monitoring at this server, and I see that server don't have problems with RAM or CPU. It used about 30% of RAM and 20% of CPU.
I regret to say it's a big production site and I can't make minimal reproducible example, cause i don't know where is reason of these error :(
Except are memory and CPU leaks, what will be reasons for Node.js server might go went down?
I need at least direction to search.
UPDATE1:
"went down" - its when kubernetes kills container due 3 failed life checks (GET request to a root / of website)
My site don't use any BD connection but call lots of 3rd party API's. About 6 API requests due one GET/ request from browser
UPDATE2:
Thx. To your answers, guys.
To understand what happend inside my GET/ request, i'm add open-telemetry into my server. In longtime and timeout GET/ requests i saw long API requests with very big tcp.connect and tls.connect.
I think it happens due lack of connections or something about that. I think Mostafa Nazari is right.
I create patch and apply them within the next couple of days, and then will say if problem gone
I solve problem.
It really was lack of connections. I add reusing node-fetch connection due keepAlive and a lot of cache for saving connections. And its works.
Thanks for all your answers. They all right, but most helpful thing was added open-telemetry to my server to understand what exactly happens inside request.
For other people with these problems, I'm strongly recommended as first step, add telemetry to your project.
https://opentelemetry.io/
PS: i can't mark two replies as answer. Joe have most detailed and Mostafa Nazari most relevant to my problem. They both may be "best answers".
Tnx for help, guys.
Gradual growth of response time suggest some kind of leak.
If CPU and memory consumption is excluded, another potentially limiting resources include:
File descriptors - when your server forgets to close files. Monitor for number of files in /proc//fd/* to confirm this. See what those files are, find which code misbehaves.
Directory listing - even temporary directory holding a lot of files will take some time to scan, and if your application is not removing some temporary files and lists them - you will be in trouble quickly.
Zombie processes - just monitor total number of processes on the server.
Firewall rules (some docker network magic may in theory cause this on host system) - monitor length of output of "iptables -L" or "iptables-save" or equivalent on modern kernels. Rare condition.
Memory fragmentation - this may happen in languages with garbage collection, but often leaves traces with something like "Can not allocate memory" in logs. Rare condition, hard to fix. Export some health metrics and make your k8s restart your pod preemptively.
Application bugs/implementation problems. This really depends on internal logic - what is going on inside the app. There may be some data structure that gets filled in with data as time goes by in some tricky way, becoming O(N) instead of O(1). Really hard to trace down, unless you have managed to reproduce the condition in lab/test environment.
API calls from frontend shift to shorter, but more CPU-hungry ones. Monitor distribution of API call types over time.
Here are some of the many possibilities of why your server may go down:
Memory leaks The server may eventually fail if a Node.js application is leaking memory, as you stated in your post above. This may occur if the application keeps adding new objects to the memory without appropriately cleaning up.
Unhandled exceptions The server may crash if an exception is thrown in the application code and is not caught. To avoid this from happening, ensure that all exceptions are handled properly.
Third-party libraries If the application uses any third-party libraries, the server may experience problems as a result. Before using them, consider examining their resource usage, versions, or updates.
Network Connection The server's network connection may have issues if the server is sending a lot of queries to third-party APIs or if the connection is unstable. Verify that the server is handling connections, timeouts, and retries appropriately.
Connection to the Database Even though your server doesn't use any BD connections, it's a good idea to look for any stale connections to databases that could be problematic.
High Volumes of Traffic The server may experience performance issues if it is receiving a lot of traffic. Make sure the server is set up appropriately to handle a lot of traffic, making use of load balancing, caching, and other speed enhancement methods. Cloudflare is always a good option ;)
Concurrent Requests Performance problems may arise if the server is managing a lot of concurrent requests. Check to see if the server is set up correctly to handle several requests at once, using tools like a connection pool, a thread pool, or other concurrency management strategies.
(Credit goes to my System Analysis and Design course slides)
With any incoming/outgoing web requests, 2 File Descriptors will be acquired. as there is a limit on number of FDs, OS does not let new Socket to be opened, this situation cause "Timeout Error" on clients. you can easily check number of open FDs by sudo ls -la /proc/_PID_/fd/ | tail -n +4 | wc -l where _PID_ is nodejs PID, if this value is rising, you have connection leak issue.
I guess you need to do the following to prevent Connection Leak:
make sure you are closing outgoing API call Http Connection (it depends on how you are opening them, some libraries manage this and you just need to config them)
cache your outgoing API call (if it is possible) to reduce API call
for your outgoing API call, use Connection pool, this would manage number of open HttpConnection, reuse already-opened connection and ...
review your code, so that you can serve a request faster than now (for example make your API call more parallel instead of await or nested call). anything you do to make your response faster, is good for preventing this situation
I solve problem. It really was lack of connections. I add reusing node-fetch connection due keepAlive and a lot of cache for saving connections. And its works.
Thanks for all your answers. They all right, but most helpful thing was added open-telemetry to my server to understand what exactly happens inside request.
For other people with these problems, I'm strongly recommended as first step, add telemetry to your project.
https://opentelemetry.io/

AppEngine nodejs app sporadically sends 502s and restarts

We have a nodejs app that gets successfully deployed to a standard environment. Something happens after about two hours (or sooner depending on traffic): our downstream clients start receiving a bunch of 502 responses and then the service stabilizes. We think this has been happening for at least a few months.
When investigating the cause of the 502s, I see that:
There are no unhandled exception/promise rejection logs to indicate that the node app has crashed
I console.log when receiving SIGTERM and that, too, does not appear in the logs
The logs of the nginx sidecar include the following:
2020/06/16 23:11:11 [error] 35#35: *1149 recv() failed (104: Connection reset by peer) while reading response header from upstream, client: 169.254.1.1, server: _, request: "POST /api/redacted HTTP/1.1", upstream: "http://127.0.0.1:8081/api/redacted", host: "redacted.appspot.com""
I'm assuming that the 502s are coming from nginx because the upstream has disappeared. Are there other explanations I should explore?
If GAE is replacing my app containers intentionally, shouldn't that process prevent these types of 502s?
Should I expect something other than SIGTERM to be sent by the environment when the application/container is getting replaced?
Update #1 (2020-06-22)
I investigated and found evidence that we might be exceeding memory quota so I changed our instance_class from F1 to F2. As I write this our instances are sitting at ~200M of memory usage (F2s have 512M available). Additionally, I use the --max-old-space-size switch to set nodes memory usage to 496M.
The 502s are still happening.
I suspect that the 502s are happening as a result of the autoscaler terminating instances. Our app never receives SIGTERM (even during deployments). That means I can't close http keepalive connections gracefully and might explain why nginx raises Connection reset by peer.
Update #2 (2020-06-24)
Our service is just standard REST type stuff, no heavy loops.
I'll post another update with some memory graphs but I don't see any spikes. Perhaps a small memory leak.
Here's our app.yaml:
service: redacted
runtime: nodejs12
instance_class: F2
handlers:
- url: /.*
secure: always
redirect_http_response_code: 301
script: auto
We had a very similar problem with our Node.js app deployed on App Engine Flexible.
In our case, we ultimately determined that we had memory pressure that was causing the Node.js garbage collector to sometimes delay the processing of a request for hundreds of milliseconds (sometimes more). This caused our health check URLs to sporadically timeout, prompting GAE to remove the instance from the active pool.
Because we typically had just two instances handling the steady traffic, removing one instance quickly overloaded the remaining instance, and it would soon suffer the same fate.
We were surprised to find that it could take two minutes or longer before App Engine assigned traffic to a newly-created instance. Between the time our original instances were declared unhealthy, and when new instance(s) were online, 502s would be returned (presumably by GAE's nginx) to the client.
We were able to stabilize the environment simply by adding:
automatic_scaling:
min_num_instances: 4
To our app.yaml. Because two instances were generally sufficient for the traffic, ensuring we always had four running apparently kept our memory usage low enough to prevent the GC from stalling request handling, and even if it did, we had enough excess capacity to handle one instance being removed.
The scaling settings for GAE standard are slightly different.
In retrospect, we could see that our latency/response times would get a little "jittery" before the real problems started. Most responses had typical response times ~30ms, but increasingly we would see outlier requests in the x00ms range. You may want to check your request logs to see if you see something similar.
New Relic's Node.js VM data was helpful in detecting that garbage collection was taking an increasing amount of time.
Usually, 502 messages are errors on nginx side, as you have mentioned. The detailed logs related to this errors are not surfaced to Cloud Logging, yet.
According to your behavior, it seems a workload, so we can relate this case to an issue with running out of resources.
There are somethings that are well worth to take a look:
Check your metrics. The memory and CPU usage should be under healthy limits.
Check whether your scaling metrics are being enough to your workload.
Is there a chance to share these metrics near to the restart event?
Also, i t would be goo if you share your resources and scaling in the app.yaml.

Weird Tomcat outage, possibly related to maxConnections

In my company we experienced a serious problem today: our production server went down. Most people accessing our software via a browser were unable to get a connection, however people who had already been using the software were able to continue using it. Even our hot standby server was unable to communicate with the production server, which it does using HTTP, not even going out to the broader internet. The whole time the server was accessible via ping and ssh, and in fact was quite underloaded - it's normally running at 5% CPU load and it was even lower at this time. We do almost no disk i/o.
A few days after the problem started we have a new variation: port 443 (HTTPS) is responding but port 80 stopped responding. The server load is very low. Immediately after restarting tomcat, port 80 started responding again.
We're using tomcat7, with maxThreads="200", and using maxConnections=10000. We serve all data out of main memory, so each HTTP request completes very quickly, but we have a large number of users doing very simple interactions (this is high school subject selection). But it seems very unlikely we would have 10,000 users all with their browser open on our page at the same time.
My question has several parts:
Is it likely that the "maxConnections" parameter is the cause of our woes?
Is there any reason not to set "maxConnections" to a ridiculously high value e.g. 100,000? (i.e. what's the cost of doing so?)
Does tomcat output a warning message anywhere once it hits the "maxConnections" message? (We didn't notice anything).
Is it possible there's an OS limit we're hitting? We're using CentOS 6.4 (Linux) and "ulimit -f" says "unlimited". (Do firewalls understand the concept of Tcp/Ip connections? Could there be a limit elsewhere?)
What happens when tomcat hits the "maxConnections" limit? Does it try to close down some inactive connections? If not, why not? I don't like the idea that our server can be held to ransom by people having their browsers on it, sending the keep-alive's to keep the connection open.
But the main question is, "How do we fix our server?"
More info as requested by Stefan and Sharpy:
Our clients communicate directly with this server
TCP connections were in some cases immediately refused and in other cases timed out
The problem is evident even connecting my browser to the server within the network, or with the hot standby server - also in the same network - unable to do database replication messages which normally happens over HTTP
IPTables - yes, IPTables6 - I don't think so. Anyway, there's nothing between my browser and the server when I test after noticing the problem.
More info:
It really looked like we had solved the problem when we realised we were using the default Tomcat7 setting of BIO, which has one thread per connection, and we had maxThreads=200. In fact 'netstat -an' showed about 297 connections, which matches 200 + queue of 100. So we changed this to NIO and restarted tomcat. Unfortunately the same problem occurred the following day. It's possible we misconfigured the server.xml.
The server.xml and extract from catalina.out is available here:
https://www.dropbox.com/sh/sxgd0fbzyvuldy7/AACZWoBKXNKfXjsSmkgkVgW_a?dl=0
More info:
I did a load test. I'm able to create 500 connections from my development laptop, and do an HTTP GET 3 times on each, without any problem. Unless my load test is invalid (the Java class is also in the above link).
It's hard to tell for sure without hands-on debugging but one of the first things I would check would be the file descriptor limit (that's ulimit -n). TCP connections consume file descriptors, and depending on which implementation is in use, nio connections that do polling using SelectableChannel may eat several file descriptors per open socket.
To check if this is the cause:
Find Tomcat PIDs using ps
Check the ulimit the process runs with: cat /proc/<PID>/limits | fgrep 'open files'
Check how many descriptors are actually in use: ls /proc/<PID>/fd | wc -l
If the number of used descriptors is significantly lower than the limit, something else is the cause of your problem. But if it is equal or very close to the limit, it's this limit which is causing issues. In this case you should increase the limit in /etc/security/limits.conf for the user with whose account Tomcat is running and restart the process from a newly opened shell, check using /proc/<PID>/limits if the new limit is actually used, and see if Tomcat's behavior is improved.
While I don't have a direct answer to solve your problem, I'd like to offer my methods to find what's wrong.
Intuitively there are 3 assumptions:
If your clients hold their connections and never release, it is quite possible your server hits the max connection limit even there is no communications.
The non-responding state can also be reached via various ways such as bugs in the server-side code.
The hardware conditions should not be ignored.
To locate the cause of this problem, you'd better try to replay the scenario in a testing environment. Perform more comprehensive tests and record more detailed logs, including but not limited:
Unit tests, esp. logic blocks using transactions, threading and synchronizations.
Stress-oriented tests. Try to simulate all the user behaviors you can come up with and their combinations and test them in a massive batch mode. (ref)
More specified Logging. Trace client behaviors and analysis what happened exactly before the server stopped responding.
Replace a server machine and see if it will still happen.
The short answer:
Use the NIO connector instead of the default BIO connector
Set "maxConnections" to something suitable e.g. 10,000
Encourage users to use HTTPS so that intermediate proxy servers can't turn 100 page requests into 100 tcp connections.
Check for threads hanging due to deadlock problems, e.g. with a stack dump (kill -3)
(If applicable and if you're not already doing this, write your client app to use the one connection for multiple page requests).
The long answer:
We were using the BIO connector instead of NIO connector. The difference between the two is that BIO is "one thread per connection" and NIO is "one thread can service many connections". So increasing "maxConnections" was irrelevant if we didn't also increase "maxThreads", which we didn't, because we didn't understand the BIO/NIO difference.
To change it to NIO, put this in the element in server.xml:
protocol="org.apache.coyote.http11.Http11NioProtocol"
From what I've read, there's no benefit to using BIO so I don't know why it's the default. We were only using it because it was the default and we assumed the default settings were reasonable and we didn't want to become experts in tomcat tuning to the extent that we now have.
HOWEVER: Even after making this change, we had a similar occurrence: on the same day, HTTPS became unresponsive even while HTTP was working, and then a little later the opposite occurred. Which was a bit depressing. We checked in 'catalina.out' that in fact the NIO connector was being used, and it was. So we began a long period of analysing 'netstat' and wireshark. We noticed some periods of high spikes in the number of connections - in one case up to 900 connections when the baseline was around 70. These spikes occurred when we synchronised our databases between the main production server and the "appliances" we install at each customer site (schools). The more we did the synchronisation, the more we caused outages, which caused us to do even more synchronisations in a downward spiral.
What seems to be happening is that the NSW Education Department proxy server splits our database synchronisation traffic into multiple connections so that 1000 page requests become 1000 connections, and furthermore they are not closed properly until the TCP 4 minute timeout. The proxy server was only able to do this because we were using HTTP. The reason they do this is presumably load balancing - they thought by splitting the page requests across their 4 servers, they'd get better load balancing. When we switched to HTTPS, they are unable to do this and are forced to use just one connection. So that particular problem is eliminated - we no longer see a burst in the number of connections.
People have suggested increasing "maxThreads". In fact this would have improved things but this is not the 'proper' solution - we had the default of 200, but at any given time, hardly any of these were doing anything, in fact hardly any of these were even allocated to page requests.
I think you need to debug the application using Apache JMeter for number of connection and use Jconsole or Zabbix to look for heap space or thread dump for tomcat server.
Nio Connector of Apache tomcat can have maximum connections of 10000 but I don't think thats a good idea to provide that much connection to one instance of tomcat better way to do this is to run multiple instance of tomcat.
In my view best way for Production server: To Run Apache http server in front and point your tomcat instance to that http server using AJP connector.
Hope this helps.
Are you absolutely sure you're not hitting the maxThreads limit? Have you tried changing it?
These days browsers limit simultaneous connections to a max of 4 per hostname/ip, so if you have 50 simultaneous browsers, you could easily hit that limit. Although hopefully your webapp responds quickly enough to handle this. Long polling has become popular these days (until websockets are more prevalent), so you may have 200 long polls.
Another cause could be if you use HTTP[S] for app-to-app communication (that is, no browser involved). Sometimes app writers are sloppy and create new connections for performing multiple tasks in parallel, causing TCP and HTTP overhead. Double check that you are not getting an inflood of requests. Log files can usually help you on this, or you can use wireshark to count the number of HTTP requests or HTTP[S] connections. If possible, modify your API to handle multiple API calls in one HTTP request.
Related to the last one, if you have many HTTP/1.1 requests going across one connection, and intermediate proxy may be splitting them into multiple connections for load balancing purposes. Sounds crazy I know, but I've seen it happen.
Lastly, some crawl bots ignore the crawl delay set in robots.txt. Again, log files and/or wireshark can help you determine this.
Overall, run more experiments with more changes. maxThreads, https, etc. before jumping to conclusions with maxConnections.

Node js avoid pyramid of doom and memory increases at the same time

I am writing a socket.io based server and I'm trying to avoid the pyramid of doom and to keep the memory low.
I wrote this client - http://jsfiddle.net/QUDXU/1/ which i run with node client-cluster 1000. So 1000 connections that are making continuous requests.
For the server side a tried 3 different solutions which i tested. The results in terms of RAM used by the server, after i let everything run for an hour are:
Simple callbacks - http://jsfiddle.net/DcWmJ/ - 112MB
Q module - http://jsfiddle.net/hhsja/1/ - 850MB and increasing
Async module - http://jsfiddle.net/SgemT/ - 1.2GB and increasing
The server and clients are on different machines. (Softlayer cloud instances). Node 0.10.12 and Socket.io 0.9.16
Why is this happening? How can I keep the memory low and use some kind of library which allows to keep the code readable?
Option 1. You can use the cluster module and gracefully kill your workers from time to time (make sure you disconnect() first). You can check process.memoryUsage().rss > 130000000 in the master and kill the workers when they exceed 130MB, for example :)
Option 2. NodeJS has the habit of using memory and rarely doing rigorous cleanups. As V8 reaches the maximum memory limit, GC calls are more aggressive. So you could lower the maximum memory a node process can take up by running node --max-stack-size <amount>. I do this when running node on embedded devices (often with less than 64 MB of ram available).
Option 3. If you really want to keep the memory low, use weak references where it is possible (anywhere except in long-running calls) https://github.com/TooTallNate/node-weak . This way, the objects will get garbage collected sooner. Extensive tests to make sure everything works are needed, though. GL if u use this one :) https://github.com/TooTallNate/node-weak
It seems like the problem was on the client script, not on the server one. I ran 1000 processes, each of them emitting messages to the server at every second. I think the server was getting very busy resolving all of those requests and thus using all of that memory. I rewrote the client side like this, spawning a number of processes proportional to the number of processors, each of them connecting multiple times like this:
client = io.connect(selectedEnvironment, { 'force new connection': true, 'reconnect': false });
Notice the 'force new connection' flag that allows to connect multiple clients using the same instance of socket.io-client.
The part that solved my problem was actually how the requests were made: any client would make another request after a second from receiving the acknowledge of the previous request, not at every second.
Connecting 1000 clients is making my server using ~100MB RSS. I also used async on the server script which seems very elegant and easier to understand than Q.
The bad part is that I've been running the server for about 2-3 days and the memory rised at 250MB RSS. This, I don't know why.

Linux TCP weirdly unresponsive when under heavy load

I'm trying to get an HTTP server I'm writing on to behave well when under heavy load, but I'm getting some weird behavior that I cannot quite understand.
My testing consists of using ab (the Apache benchmark program) over the loopback interface at a concurrency level of 1000 (ab -n 50000 -c 1000 http://localhost:8080/apa), while straceing the server process. Strace both slows processing down well enough for the problem to be readily reproducible and allows me to debug the server internals post completion to some extent. I also capture the network traffic with tcpdump while the test is running.
What happens is that ab stops running a while into the test, complaining that a connection returned ECONNRESET, which I find a bit weird. I could easily buy into a connection timing out since the server might simply not have the bandwidth to process them all, but shouldn't that reasonably return ETIMEDOUT or even ECONNREFUSED if not all connections can be accepted?
I used Wireshark to extract the packets constituting the first connection to return ECONNRESET, and its brief packet list looks like this:
(The entire tcpdump file of this connection is available here.)
As you can see from this dump, the connection is accepted (after a few SYN retransmissions), and then the request is retransmitted a few times, and then the server resets the connection. I'm wondering, what could cause this to happen? Normally, Linux' TCP implementation ACKs data before the reading process even chooses to receive it so long as their is space in the TCP window, so why doesn't it do that here? Are there some kind of shared buffers that are running out? Most importantly, why is the kernel responding with a RST packet all of a sudden instead of simply waiting and letting the client re-transmit further?
For the record, the strace of the process indicates that it never even accepts a connection from the port in this connection (port 56946), so this seems to be something Linux does on its own. It is also worth noting that the server works perfectly well as long as ab's concurrency level is low enough (it works perfectly well up to about 100, and then starts failing intermittently somewhere between 100-500), and that its request throughput is rather constant regardless of the concurrency level (it processes somewhere between 6000-7000 requests per second as long as it isn't being straced). I have not found any particular correlation between the frequency of the problem occurring and my backlog setting to listen() (I'm currently using 128, but I've tried up to 1024 without it seeming to make a difference).
In case it matters, I'm running Linux 3.2.0 on this AMD64 box.
The backlog queue filled up: hence the SYN retransmissions.
Then a slot became available: hence the SYN/ACK.
Then the GET was sent, followed by four retransmissions, which I can't account for.
Then the server gave up and reset the connection.
I suspect you have a concurrency or throughput problem in your server which is preventing you from accepting connections rapidly enough. You should have a thread that is dedicated to doing nothing else but calling accept() and either starting another thread to handle the accepted socket or else queueing a job to handle it to a thread pool. I would then speculate that Linux resets connections on connections which are in the backlog queue and which are receiving I/O retries, but that's only a guess.

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