nginx makes mysqld die all the time

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nginx makes mysqld die all the time

M. Fioretti
Greetings,

I just migrated to nginx + php-fpm from apache a few websites, on a
centos 6.6 virtual server. The sites are up but... now mysqld (MariaDB,
actually) dies every 10/20 **minutes** with status:

mysqld dead but subsys locked

or

mysqld dead but pid file exists

for reasons not really relevant here I cannot post nginx conf
right away. I **will** do that in a few hours, when I'm back
at my desk. Since the crashes are so frequent, however, any
help to save time is very welcome. Even if it's just request
of other specific info, besides the nginx conf files.

TIA,
Marco

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Re: nginx makes mysqld die all the time

Steve Wilson
Hi,

When I migrated from apache+mod_php to nginx+php-fpm I found I had a few
websites using persistent mysql connections which never closed. I had to
disable this in the php.ini so all the sites fell back to using
non-persistent connections.
I don't know if this will help as it was mysql not maria or other. I
imagine there'll probably be something logged somewhere which needs a
bit of time to find.

On 18/08/2015 14:23, M. Fioretti wrote:

> Greetings,
>
> I just migrated to nginx + php-fpm from apache a few websites, on a
> centos 6.6 virtual server. The sites are up but... now mysqld
> (MariaDB, actually) dies every 10/20 **minutes** with status:
>
> mysqld dead but subsys locked
>
> or
>
> mysqld dead but pid file exists
>
> for reasons not really relevant here I cannot post nginx conf
> right away. I **will** do that in a few hours, when I'm back
> at my desk. Since the crashes are so frequent, however, any
> help to save time is very welcome. Even if it's just request
> of other specific info, besides the nginx conf files.
>
> TIA,
> Marco
>
> _______________________________________________
> nginx mailing list
> [hidden email]
> http://mailman.nginx.org/mailman/listinfo/nginx

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Re: nginx makes mysqld die all the time

M. Fioretti
On 2015-08-18 14:36, Steve Wilson wrote:
> Hi,
>
> When I migrated from apache+mod_php to nginx+php-fpm I found I had a
> few websites using persistent mysql connections which never closed.

Steve, thanks for this tip. This surely was part of the problem, but
not all of it.

Sure enough, when I first noticed this problem, I also found in dmesg
messages like this:

Out of memory: kill process 31066 (mysqld) score 30155 or a child
Killed process 31066 (mysqld)

yesterday, as soon as I was able to ssh again, I turned

mysql.allow_persistent = Off in php.ini (it was On)

and restarted everything. Page load time decreased noticeably AND there
where no more mysql crashes for the rest of the day.
This morning, however, I found mysql died again with the same symptom
(dead but subsystem locked) and a DIFFERENT message in dmesg, that I
had never seen before:

Out of memory: kill process 13812 (php-fpm) score 18223 or a child
Killed process 13812 (php-fpm)

the nginx and php-fpm configuration files are pasted below (I have
several virtual
hosts all configured that way for wordpress, plus one drupal and one
semantic scuttle
site, if it matters). What next? Any help is welcome!

Marco

[root@fima ~]# more /etc/nginx/nginx.conf

user              nginx;
worker_processes  1;

error_log  /var/log/nginx/error.log;
#error_log  /var/log/nginx/error.log  notice;
#error_log  /var/log/nginx/error.log  info;

pid        /var/run/nginx.pid;


events {
     worker_connections  1024;
}

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

     server_names_hash_bucket_size  64;
     server_tokens off;
     access_log  /var/log/nginx/access.log combined  buffer=32k;
     log_format    '$remote_addr - $remote_user [$time_local] $status '
                       '"$request" $body_bytes_sent "$http_referer" '
                       '"$http_user_agent" "$http_x_forwarded_for"';

     sendfile        on;
     #tcp_nopush     on;

     #keepalive_timeout  0;
     keepalive_timeout  65;

     #gzip  on;

     # Load config files from the /etc/nginx/conf.d directory
     # The default server is in conf.d/default.conf
     include /etc/nginx/conf.d/*.conf;

}

and this is configuration for one of the wordpress sites, I only changed
the domain name. The configuration is due to the fact that, for several
reasons out of my control, I **must** run two fully independent
wordpress
installations, but "nested" into each other, that is:

myblog.example.com/   (english blog, by wordpress installed in
$documentroot/myblog)
myblog.example.com/it (italian version, by separate wordpress installed
in $documentroot/myblog_it)

the above worked fine with apache. Can the equivalent config for
nginx be related to the problem I'm seeing? If yes, how, and how to
fix it? And while we are at this: advice on anything else I could
optimize is
also very welcome of course, even if not related to the main problem.


[root@fima ~]# more /etc/nginx/conf.d/stop.conf

server {
        listen       80;
        server_name  myblog.example.com;
        root         /var/www/html/wordpress/;
        include      /etc/nginx/default.d/*.conf;

        # configuration for the italian version, installed
        # in root/myblog_it, but having as url example.com/stop/it

        location ^~ /it/ {
                rewrite ^/it/(.+) /myblog_it/$1 ;
              index             /myblog_it/index.php;
        }

        location /myblog_it/ {
        try_files $uri $uri/ /myblog_it/index.php?args;
                index index.php;
                location ~ \.php$ {
                         fastcgi_pass unix:/tmp/phpfpm.sock;
                         fastcgi_index  index.php;
                         fastcgi_param  SCRIPT_FILENAME  $document_root$fastcgi_script_name;
                         include        fastcgi_params;
                         }
                }

##################################################################
# main blog

         location ^~ / {
                  rewrite ^/(.+) /myblog/$1 ;
                  index          /myblog/index.php;
                 }

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

        location ~ \.php$ {
          fastcgi_pass unix:/tmp/phpfpm.sock;
                  fastcgi_index  index.php;
                  fastcgi_param  SCRIPT_FILENAME  
$document_root/$fastcgi_script_name;
                  include        fastcgi_params;
        }
}


php-fpm configuration:

[root ~]# grep -v '^;' /etc/php-fpm.conf | uniq

include=/etc/php-fpm.d/*.conf

[global]
pid = /var/run/php-fpm/php-fpm.pid

error_log = /var/log/php-fpm/error.log

daemonize = no

emergency_restart_threshold = 10
emergency_restart_interval = 1m
process_control_timeout = 10s

AND ALSO:

[root ~]# grep -v '^;' /etc/php-fpm.d/www.conf | uniq
[www]


listen.allowed_clients = 127.0.0.1

listen = /tmp/phpfpm.sock
listen.owner = nginx
listen.group = nginx
user = nginx
group = nginx

pm = dynamic

pm.max_children = 50

pm.start_servers = 5

pm.min_spare_servers = 5

pm.max_spare_servers = 35





slowlog = /var/log/php-fpm/www-slow.log


php_admin_value[error_log] = /var/log/php-fpm/www-error.log
php_admin_flag[log_errors] = on

php_value[session.save_handler] = files
php_value[session.save_path] = /var/lib/php/session




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Re: nginx makes mysqld die all the time

oscaretu .
Hello.

Perhaphs this can help you about the out of memory: OOM Killer:

https://www.google.com/search?client=ubuntu&channel=fs&q=OOM+Kiler&ie=utf-8&oe=utf-8

Kind regards,

Oscar


On Wed, Aug 19, 2015 at 8:02 AM, M. Fioretti <[hidden email]> wrote:
On 2015-08-18 14:36, Steve Wilson wrote:
Hi,

When I migrated from apache+mod_php to nginx+php-fpm I found I had a
few websites using persistent mysql connections which never closed.

Steve, thanks for this tip. This surely was part of the problem, but
not all of it.

Sure enough, when I first noticed this problem, I also found in dmesg
messages like this:

Out of memory: kill process 31066 (mysqld) score 30155 or a child
Killed process 31066 (mysqld)

yesterday, as soon as I was able to ssh again, I turned

mysql.allow_persistent = Off in php.ini (it was On)

and restarted everything. Page load time decreased noticeably AND there
where no more mysql crashes for the rest of the day.
This morning, however, I found mysql died again with the same symptom
(dead but subsystem locked) and a DIFFERENT message in dmesg, that I
had never seen before:

Out of memory: kill process 13812 (php-fpm) score 18223 or a child
Killed process 13812 (php-fpm)

the nginx and php-fpm configuration files are pasted below (I have several virtual
hosts all configured that way for wordpress, plus one drupal and one semantic scuttle
site, if it matters). What next? Any help is welcome!

Marco

[root@fima ~]# more /etc/nginx/nginx.conf

user              nginx;
worker_processes  1;

error_log  /var/log/nginx/error.log;
#error_log  /var/log/nginx/error.log  notice;
#error_log  /var/log/nginx/error.log  info;

pid        /var/run/nginx.pid;


events {
    worker_connections  1024;
}

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

    server_names_hash_bucket_size  64;
    server_tokens off;
    access_log  /var/log/nginx/access.log combined  buffer=32k;
    log_format    '$remote_addr - $remote_user [$time_local] $status '
                      '"$request" $body_bytes_sent "$http_referer" '
                      '"$http_user_agent" "$http_x_forwarded_for"';

    sendfile        on;
    #tcp_nopush     on;

    #keepalive_timeout  0;
    keepalive_timeout  65;

    #gzip  on;

    # Load config files from the /etc/nginx/conf.d directory
    # The default server is in conf.d/default.conf
    include /etc/nginx/conf.d/*.conf;

}

and this is configuration for one of the wordpress sites, I only changed
the domain name. The configuration is due to the fact that, for several
reasons out of my control, I **must** run two fully independent wordpress
installations, but "nested" into each other, that is:

myblog.example.com/   (english blog, by wordpress installed in $documentroot/myblog)
myblog.example.com/it (italian version, by separate wordpress installed in $documentroot/myblog_it)

the above worked fine with apache. Can the equivalent config for
nginx be related to the problem I'm seeing? If yes, how, and how to
fix it? And while we are at this: advice on anything else I could optimize is
also very welcome of course, even if not related to the main problem.


[root@fima ~]# more /etc/nginx/conf.d/stop.conf

server {
       listen       80;
       server_name  myblog.example.com;
       root         /var/www/html/wordpress/;
       include      /etc/nginx/default.d/*.conf;

       # configuration for the italian version, installed
       # in root/myblog_it, but having as url example.com/stop/it

       location ^~ /it/ {
                rewrite ^/it/(.+) /myblog_it/$1 ;
                index             /myblog_it/index.php;
       }

       location /myblog_it/ {
                try_files $uri $uri/ /myblog_it/index.php?args;
                index index.php;
                location ~ \.php$ {
                         fastcgi_pass unix:/tmp/phpfpm.sock;
                         fastcgi_index  index.php;
                         fastcgi_param  SCRIPT_FILENAME  $document_root$fastcgi_script_name;
                         include        fastcgi_params;
                         }
                }

##################################################################
# main blog

        location ^~ / {
                 rewrite ^/(.+) /myblog/$1 ;
                 index          /myblog/index.php;
                 }

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

        location ~ \.php$ {
                 fastcgi_pass unix:/tmp/phpfpm.sock;
                 fastcgi_index  index.php;
                 fastcgi_param  SCRIPT_FILENAME  $document_root/$fastcgi_script_name;
                 include        fastcgi_params;
                }
}


php-fpm configuration:

[root ~]# grep -v '^;' /etc/php-fpm.conf | uniq

include=/etc/php-fpm.d/*.conf

[global]
pid = /var/run/php-fpm/php-fpm.pid

error_log = /var/log/php-fpm/error.log

daemonize = no

emergency_restart_threshold = 10
emergency_restart_interval = 1m
process_control_timeout = 10s

AND ALSO:

[root ~]# grep -v '^;' /etc/php-fpm.d/www.conf | uniq
[www]


listen.allowed_clients = 127.0.0.1

listen = /tmp/phpfpm.sock
listen.owner = nginx
listen.group = nginx
user = nginx
group = nginx

pm = dynamic

pm.max_children = 50

pm.start_servers = 5

pm.min_spare_servers = 5

pm.max_spare_servers = 35





slowlog = /var/log/php-fpm/www-slow.log


php_admin_value[error_log] = /var/log/php-fpm/www-error.log
php_admin_flag[log_errors] = on

php_value[session.save_handler] = files
php_value[session.save_path] = /var/lib/php/session





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--
Oscar Fernandez Sierra
[hidden email]

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Re: nginx makes mysqld die all the time

M. Fioretti
On 2015-08-19 09:01, oscaretu . wrote:
> Hello.
>
> Perhaphs this can help you about the out of memory: OOM Killer:
>
> https://www.google.com/search?client=ubuntu&channel=fs&q=OOM+Kiler&ie=utf-8&oe=utf-8
> [6]
>
Oscar, and list,

I just looked at the several /var/log/messages files. The last one is
from August 16th.
It contains in equal parts lines like:

kernel: php-fpm invoked oom-killer: gfp_mask=0x201da, order=0,
oom_adj=0...

and "kernel: mysqld invoked oom-killer: ..." etc etc.

Not really useful. I am (re)reading this right now:

http://www.oracle.com/technetwork/articles/servers-storage-dev/oom-killer-1911807.html

but so far it doesn't seem to be really helpful either. I had already
figured out that, for some reason, mysqld and/or php-fpm were consuming
much more memory than would be reasonable. The question is **what**, in
their, or nginx's configuration can make that happen?

As it turned out yesterday, a good part of the problem was, indeed, the
persistent mysqld connections in php.ini. Turning them off made the
situation much better, but not fix it. Today, the question is what else,
exactly, to look for in which logs, and above all if something in the
nginx/
php-fpm configuration I posted in my previous message is the trigger of
this behaviour and must be changed/optimized. Ideas, anybody?

Thanks,
Marco

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Re: nginx makes mysqld die all the time

Steve Wilson
In reply to this post by M. Fioretti
It looks like your machine is running out of memory, again this is
something I think I've dealt with in php-fpm by configuring it to
recycle the child processes so they don't start consuming too much
memory.

Here's my fpm pool config file:

[www]
user = www-data
group = www-data
listen = /var/run/php5-fpm.sock
listen.owner = nginx
listen.group = nginx
listen.mode = 0660
pm = dynamic
pm.max_children = 15
pm.start_servers = 3
pm.min_spare_servers = 2
pm.max_spare_servers = 3
pm.process_idle_timeout = 10s;
pm.max_requests = 10

Do not take this config as-is. I've a group of nginx+php-fpm servers
running for wordpress and drupal (2 each) but your activity may be
considerably higher than what I've got.

The key parts here are the "pm." options so you'll probably want to
investigate each setting and tune to your requirements.

Steve.

On 19/08/2015 07:02, M. Fioretti wrote:

> On 2015-08-18 14:36, Steve Wilson wrote:
>> Hi,
>>
>> When I migrated from apache+mod_php to nginx+php-fpm I found I had a
>> few websites using persistent mysql connections which never closed.
>
> Steve, thanks for this tip. This surely was part of the problem, but
> not all of it.
>
> Sure enough, when I first noticed this problem, I also found in dmesg
> messages like this:
>
> Out of memory: kill process 31066 (mysqld) score 30155 or a child
> Killed process 31066 (mysqld)
>
> yesterday, as soon as I was able to ssh again, I turned
>
> mysql.allow_persistent = Off in php.ini (it was On)
>
> and restarted everything. Page load time decreased noticeably AND there
> where no more mysql crashes for the rest of the day.
> This morning, however, I found mysql died again with the same symptom
> (dead but subsystem locked) and a DIFFERENT message in dmesg, that I
> had never seen before:
>
> Out of memory: kill process 13812 (php-fpm) score 18223 or a child
> Killed process 13812 (php-fpm)
>
> the nginx and php-fpm configuration files are pasted below (I have
> several virtual
> hosts all configured that way for wordpress, plus one drupal and one
> semantic scuttle
> site, if it matters). What next? Any help is welcome!
>
> Marco
>
> [root@fima ~]# more /etc/nginx/nginx.conf
>
> user              nginx;
> worker_processes  1;
>
> error_log  /var/log/nginx/error.log;
> #error_log  /var/log/nginx/error.log  notice;
> #error_log  /var/log/nginx/error.log  info;
>
> pid        /var/run/nginx.pid;
>
>
> events {
>     worker_connections  1024;
> }
>
> http {
>     include       /etc/nginx/mime.types;
>     default_type  application/octet-stream;
>
>     server_names_hash_bucket_size  64;
>     server_tokens off;
>     access_log  /var/log/nginx/access.log combined  buffer=32k;
>     log_format    '$remote_addr - $remote_user [$time_local] $status '
>                       '"$request" $body_bytes_sent "$http_referer" '
>                       '"$http_user_agent" "$http_x_forwarded_for"';
>
>     sendfile        on;
>     #tcp_nopush     on;
>
>     #keepalive_timeout  0;
>     keepalive_timeout  65;
>
>     #gzip  on;
>
>     # Load config files from the /etc/nginx/conf.d directory
>     # The default server is in conf.d/default.conf
>     include /etc/nginx/conf.d/*.conf;
>
> }
>
> and this is configuration for one of the wordpress sites, I only
> changed
> the domain name. The configuration is due to the fact that, for several
> reasons out of my control, I **must** run two fully independent
> wordpress
> installations, but "nested" into each other, that is:
>
> myblog.example.com/   (english blog, by wordpress installed in
> $documentroot/myblog)
> myblog.example.com/it (italian version, by separate wordpress
> installed in $documentroot/myblog_it)
>
> the above worked fine with apache. Can the equivalent config for
> nginx be related to the problem I'm seeing? If yes, how, and how to
> fix it? And while we are at this: advice on anything else I could
> optimize is
> also very welcome of course, even if not related to the main problem.
>
>
> [root@fima ~]# more /etc/nginx/conf.d/stop.conf
>
> server {
>        listen       80;
>        server_name  myblog.example.com;
>        root         /var/www/html/wordpress/;
>        include      /etc/nginx/default.d/*.conf;
>
>        # configuration for the italian version, installed
>        # in root/myblog_it, but having as url example.com/stop/it
>
>        location ^~ /it/ {
>               rewrite ^/it/(.+) /myblog_it/$1 ;
>               index             /myblog_it/index.php;
>        }
>
>        location /myblog_it/ {
>         try_files $uri $uri/ /myblog_it/index.php?args;
> index index.php;
> location ~ \.php$ {
> fastcgi_pass unix:/tmp/phpfpm.sock;
> fastcgi_index  index.php;
> fastcgi_param  SCRIPT_FILENAME  $document_root$fastcgi_script_name;
> include        fastcgi_params;
> }
> }
>
> ##################################################################
> # main blog
>
>         location ^~ / {
>                  rewrite ^/(.+) /myblog/$1 ;
>                  index          /myblog/index.php;
> }
>
> location /myblog/ {
> try_files /$uri /$uri/ /myblog/index.php?args;
>     index                        index.php;
> }
>
> location ~ \.php$ {
>         fastcgi_pass unix:/tmp/phpfpm.sock;
>                  fastcgi_index  index.php;
>                  fastcgi_param  SCRIPT_FILENAME
> $document_root/$fastcgi_script_name;
>                  include        fastcgi_params;
>       }
> }
>
>
> php-fpm configuration:
>
> [root ~]# grep -v '^;' /etc/php-fpm.conf | uniq
>
> include=/etc/php-fpm.d/*.conf
>
> [global]
> pid = /var/run/php-fpm/php-fpm.pid
>
> error_log = /var/log/php-fpm/error.log
>
> daemonize = no
>
> emergency_restart_threshold = 10
> emergency_restart_interval = 1m
> process_control_timeout = 10s
>
> AND ALSO:
>
> [root ~]# grep -v '^;' /etc/php-fpm.d/www.conf | uniq
> [www]
>
>
> listen.allowed_clients = 127.0.0.1
>
> listen = /tmp/phpfpm.sock
> listen.owner = nginx
> listen.group = nginx
> user = nginx
> group = nginx
>
> pm = dynamic
>
> pm.max_children = 50
>
> pm.start_servers = 5
>
> pm.min_spare_servers = 5
>
> pm.max_spare_servers = 35
>
>
>
>
>
> slowlog = /var/log/php-fpm/www-slow.log
>
>
> php_admin_value[error_log] = /var/log/php-fpm/www-error.log
> php_admin_flag[log_errors] = on
>
> php_value[session.save_handler] = files
> php_value[session.save_path] = /var/lib/php/session

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Update on: nginx makes mysqld die all the time

M. Fioretti
In reply to this post by M. Fioretti
On 2015-08-18 15:23, M. Fioretti wrote:
> Greetings,
>
> I just migrated to nginx + php-fpm from apache a few websites, on a
> centos 6.6 virtual server. The sites are up but... now mysqld
> (MariaDB, actually) dies every 10/20 **minutes** with status:

Greetings,
after a few days, I can report that setting:

mysql.allow_persistent = Off

in php.ini, and then tuning some php-fpm parameters as below, fixed
the problem. There surely still is much more that can be optimized
(and comments on the parameters below are welcome!) and I'll ask
about it later, but I haven't seen any more crashes,
and the websites already load quickly.

Thanks to all who helped!!!

Marco

pm = dynamic

pm.max_children = 12

pm.start_servers = 3

pm.min_spare_servers = 2

pm.max_spare_servers = 3

pm.max_requests = 10




















> mysqld dead but subsys locked
>
> or
>
> mysqld dead but pid file exists
>
> for reasons not really relevant here I cannot post nginx conf
> right away. I **will** do that in a few hours, when I'm back
> at my desk. Since the crashes are so frequent, however, any
> help to save time is very welcome. Even if it's just request
> of other specific info, besides the nginx conf files.
>
> TIA,
> Marco
>
> _______________________________________________
> nginx mailing list
> [hidden email]
> http://mailman.nginx.org/mailman/listinfo/nginx

--
http://mfioretti.com

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Re: Update on: nginx makes mysqld die all the time

Steve Wilson
Hi,

On 25/08/2015 08:36, M. Fioretti wrote:

> On 2015-08-18 15:23, M. Fioretti wrote:
>> Greetings,
>>
>> I just migrated to nginx + php-fpm from apache a few websites, on a
>> centos 6.6 virtual server. The sites are up but... now mysqld
>> (MariaDB, actually) dies every 10/20 **minutes** with status:
>
> Greetings,
> after a few days, I can report that setting:
>
> mysql.allow_persistent = Off
>
> in php.ini, and then tuning some php-fpm parameters as below, fixed
> the problem. There surely still is much more that can be optimized
> (and comments on the parameters below are welcome!) and I'll ask
> about it later, but I haven't seen any more crashes,
> and the websites already load quickly.

This is good news, I was actually wondering if you'd sorted it.

> Thanks to all who helped!!!
>
> Marco
>
> pm = dynamic
> pm.max_children = 12
> pm.start_servers = 3
> pm.min_spare_servers = 2
> pm.max_spare_servers = 3
> pm.max_requests = 10

I don't think this is the perfect place to get answers on this, however
my understanding is that this is how it'll work.

php-fpm will manage it's workers dynamically, starting with 3 and being
able to grow to a maximum of 12. To keep resources to a minimum on your
server it will allow for between 2 and 3 of these to be waiting to do
something. If there's more than 3 it'll kill the child, also when each
one has served 10 requests they'll terminate. If there's less than 2
idle children it'll start another until there's a minimum of 2 idle.

The above may not be the optimal configuration for your needs, as
ondemand may be more suited than dynamic or static. I think key factors
are the spec of the server and how busy php is, there may be some way to
monitor the running number of children to fine tune later but may cause
problems if there's a sudden surge in requests.

The php manual has some information on each of these settings at
<http://php.net/manual/en/install.fpm.configuration.php#pm>

Steve.

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