Upstream time using Nginx, Thin / Rails when reading response header from upstream

I am running Nginx to send requests to two thin servers. The site works about 90% of the time and then from time to time it just stops responding and I get errors like this

2014/11/28 21:40:05 [error] 21516#0: *1458 upstream timed out (110: Connection timed out) while reading response header from upstream, client: X.X.X.X, server: www...com, request: "HEAD / HTTP/1.1", upstream: "http://127.0.0.1:5001/", host: "www.example.com", referrer: "http://www.example.com/"

      

        
        
        
      

    

I have searched the internet for solutions, but unfortunately most of them involve this issue when it happens all the time. In this case, it usually means that Thin just doesn't work. In my case, my site is up most of the time. I can ping thin servers. Although I haven't tried pinging them until the site is responding. This can give me a deeper understanding of the problem.

Here is my nginx.conf and the sites available

user www-data;
worker_processes 2;
pid /var/run/nginx.pid;
events {
  worker_connections 768;
  multi_accept on;
}
http {

  sendfile on;
  tcp_nopush on;
  tcp_nodelay on;
  keepalive_timeout 70;
  types_hash_max_size 2048;

  include /etc/nginx/mime.types;
  default_type application/octet-stream;
  client_max_body_size 100M;

  access_log /var/log/nginx/access.log;
  error_log /var/log/nginx/error.log;

  gzip on;
  gzip_disable "msie6";

  gzip_static on;

  gzip_comp_level 6;

  gzip_types text/plain text/css application/json application/x-javascript text/xml application/xml application/xml+rss text/javascript application/octet-stream;

  ssl_session_cache shared:SSL:10m;
  ssl_session_timeout 10m;

  include /etc/nginx/conf.d/*.conf;
  include /etc/nginx/sites-enabled/*;
}

      

        
        
        
      

    

And support sites / default

map $http_upgrade $connection_upgrade {
 default Upgrade;
 ''      close;
}
upstream example {
  server 127.0.0.1:5000;
  server 127.0.0.1:5001;
}
upstream websocket {
  server 127.0.0.1:5001;
}
server {
  listen 80;
  listen 443 ssl;
  keepalive_timeout 70;
  root /data/example/;
  index index.html index.htm;
  server_name www.example.com;
  ssl_certificate     <PATH>;
  ssl_certificate_key <PATH>;

  location ~ ^/assets/ {
    include /etc/nginx/block.list;
    expires 1d; 
    add_header Cache-Control public;
    add_header ETag ""; 
    proxy_set_header  X-Real-IP  $remote_addr;
    proxy_set_header  X-Forwarded-For $proxy_add_x_forwarded_for;
    proxy_set_header  X-Forwarded-Proto $scheme;
    proxy_set_header Host $http_host;
    proxy_redirect off;
    proxy_pass http://example;
  }

  location /websocket {
    include /etc/nginx/block.list;
    proxy_set_header  X-Real-IP  $remote_addr;
    proxy_set_header  X-Forwarded-For $proxy_add_x_forwarded_for;
    proxy_set_header  X-Forwarded-Proto $scheme;
    proxy_set_header Host $http_host;
    proxy_redirect off;

    proxy_http_version 1.1;
    proxy_set_header Upgrade $http_upgrade;
    proxy_set_header Connection $connection_upgrade;
    proxy_pass http://websocket;
  }

  location / {
    include /etc/nginx/block.list;
    proxy_set_header  X-Real-IP  $remote_addr;
    proxy_set_header  X-Forwarded-For $proxy_add_x_forwarded_for;
    proxy_set_header  X-Forwarded-Proto $scheme;
    proxy_set_header Host $http_host;
    proxy_redirect off;

    proxy_pass http://example;
  }
}

      

        
        
        
      

    

The last thing I did was remove some instructions if

in the config file. I'm not sure if this was doing anything. The problem hasn't happened since then, but I don't think it was long enough.

EDIT: The problem came back. I'll go back to the square.

if (-f $request_filename/index.html) {
   rewrite (.*) $1/index.html break;
}
if (-f $request_filename.html) {
    rewrite (.*) $1.html break;
}
set $flags ""; 
if (!-f $request_filename) {
    set $flags "${flags}R";
}
if ($flags = "R") {
    proxy_pass http://example;
    break;
}