Mysql Nginx:无法访问服务器或当活动连接数超过100时响应速度非常慢

我已经在我的VPS上安装了Ubuntu14.04、nginx、mariadb和hhvm，以便运行Laravel应用程序。但是，当活动连接超过100个时，用户无法始终访问我们的服务器（或者他们需要等待很长时间）。我可以知道是什么原因导致这件事吗？这是我的VPS的日志和配置

cpu信息：

  processor       : 0
  vendor_id       : GenuineIntel
  cpu family      : 6
  model           : 45
  model name      : Intel(R) Xeon(R) CPU E5-2620 0 @ 2.00GHz
  stepping        : 7
  cpu MHz         : 1500.138
  cache size      : 15360 KB
  physical id     : 0
  siblings        : 12
  core id         : 0
  cpu cores       : 6
  apicid          : 0
  initial apicid  : 0
  fpu             : yes
  fpu_exception   : yes
  cpuid level     : 13
  wp              : yes

内存：

顶部：

iotop：

nginx状态：

Active connections: 112
server accepts handled requests
269927 269927 368061
Reading: 0 Writing: 2 Waiting: 110 

nginx配置：

user www-data;
worker_processes 6;
pid /run/nginx.pid;

events {
worker_connections 4096;
use epoll;
multi_accept on;
}

worker_rlimit_nofile 10000;

http {
##
# Basic Settings
##

client_max_body_size 110m;
client_body_buffer_size 10K;
client_header_timeout 12;
client_body_timeout 12;
send_timeout 12;
sendfile on;

proxy_buffer_size 128k;
proxy_buffers 4 256k;
proxy_busy_buffers_size 256k;

tcp_nopush on;
tcp_nodelay on;

keepalive_timeout 12;
types_hash_max_size 2048;
server_tokens off;
reset_timedout_connection on;

limit_conn_zone $binary_remote_addr zone=addr:5m;

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

ssl_protocols TLSv1 TLSv1.1 TLSv1.2; # Dropping SSLv3, ref: POODLE
ssl_prefer_server_ciphers on;

##
# Logging Settings
##

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

##
# Gzip Settings
##

gzip on;
gzip_disable "msie6";
gzip_proxied expired no-cache no-store private auth;
gzip_min_length 10240;
gzip_comp_level 4;
gzip_types text/plain text/css application/json application/javascript text/xml application/xml application/xml+rss text/javascript;

##
# Cache Configs
##

open_file_cache max=100000 inactive=20s;
open_file_cache_valid 30s;
open_file_cache_min_uses 5;
open_file_cache_errors on;

##
# Virtual Host Configs
##

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

服务器配置：

  server {
     server_name www.xxx.com;
     return 301 $scheme://xxx.com$request_uri;
  }

  server {
    listen 80;

    ##
    # Static File Caching
    ##

    location ~* .(jpg|jpeg|png|gif|ico)$ {
            expires 365d;
    }

    root /xxx/xxx.com/public;

    index index.php index.html index.htm index.nginx-debian.html;

    server_name xxx.com;

    access_log off;
    error_log /var/log/nginx/xxx-error.log error;

    charset utf-8;

    location / {
        try_files $uri $uri/ /index.php?$query_string;
    }

    include hhvm-with-fallback.conf;

    # pass the PHP scripts to FastCGI server listening on 127.0.0.1:9000
    #
    location @fallback {     
        try_files $uri =404;     
        fastcgi_split_path_info ^(.+\.php)(/.+)$;     
        include fastcgi_params;     
        fastcgi_index index.php;     
        fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;     
        fastcgi_param SERVER_NAME $host;     
        fastcgi_pass unix:/var/run/php5-fpm.sock; 
    }

    # deny access to .htaccess files, if Apache's document root
    # concurs with nginx's one
    #
    location ~ /\.ht {
        deny all;
    }

  }

mysql配置：

[client]
port        = 3306
socket      = /var/run/mysqld/mysqld.sock

[mysqld_safe]
socket      = /var/run/mysqld/mysqld.sock
nice        = 0

[mysqld]
#
# * Basic Settings
#
user        = mysql
pid-file    = /var/run/mysqld/mysqld.pid
socket      = /var/run/mysqld/mysqld.sock
port        = 3306
basedir     = /usr
datadir     = /var/lib/mysql
tmpdir      = /tmp
lc_messages_dir = /usr/share/mysql
lc_messages = en_US
skip-external-locking

bind-address        = 127.0.0.1
#
# * Fine Tuning
#
max_connections     = 500
connect_timeout     = 5
wait_timeout        = 600
max_allowed_packet  = 16M
thread_cache_size       = 128
sort_buffer_size    = 4M
bulk_insert_buffer_size = 16M
tmp_table_size      = 32M
max_heap_table_size = 32M
#
# * MyISAM
#
# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched. On error, make copy and try a repair.
myisam_recover          = BACKUP
key_buffer_size     = 128M
#open-files-limit   = 2000
table_open_cache    = 400
myisam_sort_buffer_size = 512M
concurrent_insert   = 2
read_buffer_size    = 2M
read_rnd_buffer_size    = 1M
#
# * Query Cache Configuration
#
# Cache only tiny result sets, so we can fit more in the query cache.
query_cache_limit       = 128K
query_cache_size        = 64M
# for more write intensive setups, set to DEMAND or OFF
#query_cache_type       = DEMAND

#general_log_file        = /var/log/mysql/mysql.log
#general_log             = 1

log_warnings        = 2
#
# Enable the slow query log to see queries with especially long duration
#slow_query_log[={0|1}]
slow_query_log_file = /var/log/mysql/mariadb-slow.log
long_query_time = 10
#log_slow_rate_limit    = 1000
log_slow_verbosity  = query_plan

log_bin         = /var/log/mysql/mariadb-bin
log_bin_index       = /var/log/mysql/mariadb-bin.index

#sync_binlog        = 1
expire_logs_days    = 10
max_binlog_size         = 100M

default_storage_engine  = InnoDB
#innodb_log_file_size   = 50M
innodb_buffer_pool_size = 256M
innodb_log_buffer_size  = 8M
innodb_file_per_table   = 1
innodb_open_files   = 400
innodb_io_capacity  = 400
innodb_flush_method = O_DIRECT

[mysqldump]
quick
quote-names
max_allowed_packet  = 16M

[mysql]
#no-auto-rehash # faster start of mysql but no tab completition

[isamchk]
key_buffer      = 16M

hhvm php.ini

  ; php options
  session.save_handler = files
  session.save_path = /var/lib/php5
  session.gc_maxlifetime = 1440

  ; hhvm specific 
  hhvm.log.level = Warning
  hhvm.log.always_log_unhandled_exceptions = true
  hhvm.log.runtime_error_reporting_level = 8191
  hhvm.mysql.typed_results = false

hhvm server.ini

      ; php options

      pid = /var/run/hhvm/pid

      ; hhvm specific 

      hhvm.server.port = 9000
      hhvm.server.type = fastcgi
      hhvm.server.default_document = index.php
      hhvm.log.use_log_file = true
      hhvm.log.file = /var/log/hhvm/error.log
      hhvm.repo.central.path = /var/run/hhvm/hhvm.hhbc

“显示完整进程列表；”结果

---

显示nginx的服务器配置和phpconfig@AlexeyTen谢谢你的评论。我已经显示了php和nginx服务器配置。您没有显示nginx的服务器配置。除了nginx配置（您还没有完整提供）之外，如果在问题发生时看到MySql的“show full processlist”查询的结果也会很好。我特别感兴趣的是是否有任何“卡住”的查询——执行时间超过5秒的查询。查询执行时间通常显示在第6列。@IvanTsirulev这是“显示完整的进程列表”结果

      ; php options

      pid = /var/run/hhvm/pid

      ; hhvm specific 

      hhvm.server.port = 9000
      hhvm.server.type = fastcgi
      hhvm.server.default_document = index.php
      hhvm.log.use_log_file = true
      hhvm.log.file = /var/log/hhvm/error.log
      hhvm.repo.central.path = /var/run/hhvm/hhvm.hhbc

  +--------+------+-----------+---------------+---------+------+-------+-----------------------+----------+
  | Id     | User | Host      | db            | Command | Time | State | Info                  | Progress |
  +--------+------+-----------+---------------+---------+------+-------+-----------------------+----------+
  | 126338 | root | localhost | NULL          | Query   |    0 | init  | show full processlist |    0.000 |
  | 127981 | root | localhost | pa_db | Sleep   |    5 |       | NULL                  |    0.000 |
  +--------+------+-----------+---------------+---------+------+-------+-----------------------+----------+