ownCloud Unable to Connect to Local Database on Fedora 23 (LEMP stack, selinux permissive)

Question

The Problem

I am having a very strange issue where ownCloud seems unable to access my SQL database, using nginx, mariadb, and php-fpm running on Fedora 23.

When I attempt to access the page, I get an error page that reads "Internal Server Error" without any meaningful output. Looking in the nginx error log, I see this:

PHP message: {"reqId":"b42TI6oHUGKOfGGClEPP","remoteAddr":"REDACTED","app":"core","message":"Exception: {\"Exception\":\"Doctrine\\\\DBAL\\\\DBALException\",\"Message\":\"Failed to connect to the database: An exception occured in driver: SQLSTATE[HY000] [2002] Permission denied\",\"Code\":0,\"Trace\":\"#0 \\\/var\\\/www\\\/owncloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(429): OC\\\\DB\\\\Connection->connect()\\n#1 \\\/var\\\/www\\\/owncloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(389): Doctrine\\\\DBAL\\\\Connection->getDatabasePlatformVersion()\\n#2 \\\/var\\\/www\\\/owncloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(328): Doctrine\\\\DBAL\\\\Connection->detectDatabasePlatform()\\n#3 \\\/var\\\/www\\\/owncloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(621): Doctrine\\\\DBAL\\\\Connection->getDataba

Looking around, it seems the SQLSTATE[HY000] [2002] error is common and has many causes, so I'll just outline what I've already tried:

I can connect to the database using the the same credentials as the ownCloud config from the shell
The MariaDB socket file is accessable by all users, and php.ini is configured to use that socket
I've tried disabling selinux (setting to permissive), going so far to turn it off and reboot completely, and still get the same error
I even tried specifiying 127.0.0.1 as the bind address for MariaDB

Here are some other things of note about my setup:

All services are running on the same machine
Both /var/lib/mysql and /var/www/owncloud were migrated from an Ubuntu 15.10 machine, but I've run restorecon -Rv on both directories and run mysql_upgrade on the database
The machine is a Digital Ocean VPS

Logs

/var/log/nginx/owncloud_error.log

...
PHP message: {"reqId":"UeN9U1jaHrLuCzHUZGIr","remoteAddr":"REDACTED","app":"core","message":"Exception: {\"Exception\":\"Doctrine\\\\DBAL\\\\DBALException\",\"Message\":\"Failed to connect to the database: An exception occured in driver: SQLSTATE[HY000] [2002] Permission denied\",\"Code\":0,\"Trace\":\"#0 \\\/var\\\/www\\\/owncloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(429): OC\\\\DB\\\\Connection->connect()\\n#1 \\\/var\\\/www\\\/owncloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(389): Doctrine\\\\DBAL\\\\Connection->getDatabasePlatformVersion()\\n#2 \\\/var\\\/www\\\/owncloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(328): Doctrine\\\\DBAL\\\\Connection->detectDatabasePlatform()\\n#3 \\\/var\\\/www\\\/owncloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(621): Doctrine\\\\DBAL\\\\Connection->getDataba
2016/05/10 17:11:42 [error] 2175#0: *16 FastCGI sent in stderr: "PHP message: {"reqId":"w8VAqhrnSZX\/5xM1+3C1","remoteAddr":"REDACTED","app":"index","message":"Exception: {\"Exception\":\"Doctrine\\\\DBAL\\\\DBALException\",\"Message\":\"Failed to connect to the database: An exception occured in driver: SQLSTATE[HY000] [2002] Permission denied\",\"Code\":0,\"Trace\":\"#0 \\\/var\\\/www\\\/owncloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(429): OC\\\\DB\\\\Connection->connect()\\n#1 \\\/var\\\/www\\\/owncloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(389): Doctrine\\\\DBAL\\\\Connection->getDatabasePlatformVersion()\\n#2 \\\/var\\\/www\\\/owncloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(328): Doctrine\\\\DBAL\\\\Connection->detectDatabasePlatform()\\n#3 \\\/var\\\/www\\\/owncloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(621): Doctrine\\\\DBAL\\\\Connection->getDatabasePlatform()\\n#4 \\\/var\\\/www\\\/owncloud\\\/lib\\\/priv...
PHP message: {"reqId":"w8VAqhrnSZX\/5xM1+3C1","remoteAddr":"REDACTED","app":"core","message":"Exception: {\"Exception\":\"Doctrine\\\\DBAL\\\\DBALException\",\"Message\":\"Failed to connect to the database: An exception occured in driver: SQLSTATE[HY000] [2002] Permission denied\",\"Code\":0,\"Trace\":\"#0 \\\/var\\\/www\\\/owncloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(429): OC\\\\DB\\\\Connection->connect()\\n#1 \\\/var\\\/www\\\/owncloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(389): Doctrine\\\\DBAL\\\\Connection->getDatabasePlatformVersion()\\n#2 \\\/var\\\/www\\\/owncloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(328): Doctrine\\\\DBAL\\\\Connection->detectDatabasePlatform()\\n#3 \\\/var\\\/www\\\/owncloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(621): Doctrine\\\\DBAL\\\\Connection->getData
2016/05/10 17:11:58 [error] 3308#0: *1 FastCGI sent in stderr: "PHP message: {"reqId":"b42TI6oHUGKOfGGClEPP","remoteAddr":"REDACTED","app":"index","message":"Exception: {\"Exception\":\"Doctrine\\\\DBAL\\\\DBALException\",\"Message\":\"Failed to connect to the database: An exception occured in driver: SQLSTATE[HY000] [2002] Permission denied\",\"Code\":0,\"Trace\":\"#0 \\\/var\\\/www\\\/owncloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(429): OC\\\\DB\\\\Connection->connect()\\n#1 \\\/var\\\/www\\\/owncloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(389): Doctrine\\\\DBAL\\\\Connection->getDatabasePlatformVersion()\\n#2 \\\/var\\\/www\\\/owncloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(328): Doctrine\\\\DBAL\\\\Connection->detectDatabasePlatform()\\n#3 \\\/var\\\/www\\\/owncloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(621): Doctrine\\\\DBAL\\\\Connection->getDatabasePlatform()\\n#4 \\\/var\\\/www\\\/owncloud\\\/lib\\\/priva...
PHP message: {"reqId":"b42TI6oHUGKOfGGClEPP","remoteAddr":"REDACTED","app":"core","message":"Exception: {\"Exception\":\"Doctrine\\\\DBAL\\\\DBALException\",\"Message\":\"Failed to connect to the database: An exception occured in driver: SQLSTATE[HY000] [2002] Permission denied\",\"Code\":0,\"Trace\":\"#0 \\\/var\\\/www\\\/owncloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(429): OC\\\\DB\\\\Connection->connect()\\n#1 \\\/var\\\/www\\\/owncloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(389): Doctrine\\\\DBAL\\\\Connection->getDatabasePlatformVersion()\\n#2 \\\/var\\\/www\\\/owncloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(328): Doctrine\\\\DBAL\\\\Connection->detectDatabasePlatform()\\n#3 \\\/var\\\/www\\\/owncloud\\\/3rdparty\\\/doctrine\\\/dbal\\\/lib\\\/Doctrine\\\/DBAL\\\/Connection.php(621): Doctrine\\\\DBAL\\\\Connection->getDataba

Note: Sorry about the horrible formatting, that's how the log file was.

/var/log/mariadb/mariadb.log

160510 17:16:42 mysqld_safe mysqld from pid file /var/run/mariadb/mariadb.pid ended
160510 17:16:42 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
160510 17:16:42 [Note] /usr/libexec/mysqld (mysqld 10.0.23-MariaDB) starting as process 3637 ...
160510 17:16:42 [Note] InnoDB: Using mutexes to ref count buffer pool pages
160510 17:16:42 [Note] InnoDB: The InnoDB memory heap is disabled
160510 17:16:42 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
160510 17:16:42 [Note] InnoDB: Memory barrier is not used
160510 17:16:42 [Note] InnoDB: Compressed tables use zlib 1.2.8
160510 17:16:42 [Note] InnoDB: Using Linux native AIO
160510 17:16:42 [Note] InnoDB: Using CPU crc32 instructions
160510 17:16:42 [Note] InnoDB: Initializing buffer pool, size = 128.0M
160510 17:16:42 [Note] InnoDB: Completed initialization of buffer pool
160510 17:16:42 [Note] InnoDB: Highest supported file format is Barracuda.
160510 17:16:42 [Note] InnoDB: 128 rollback segment(s) are active.
160510 17:16:42 [Note] InnoDB: Waiting for purge to start
160510 17:16:42 [Note] InnoDB:  Percona XtraDB (http://www.percona.com) 5.6.26-76.0 started; log sequence number 2335654097
160510 17:16:42 [Note] Plugin 'FEEDBACK' is disabled.
160510 17:16:42 [Note] Server socket created on IP: '127.0.0.1'.
160510 17:16:42 [Note] Reading of all Master_info entries succeded
160510 17:16:42 [Note] Added new Master_info '' to hash table
160510 17:16:42 [Note] /usr/libexec/mysqld: ready for connections.
Version: '10.0.23-MariaDB'  socket: '/var/lib/mysql/mysql.sock'  port: 3306  MariaDB Server
160510 17:16:43 [Warning] Access denied for user 'UNKNOWN_MYSQL_USER'@'localhost' (using password: NO)

Note: I've looked into that last warning and apparently it's caused by a startup script checking if the server is running.

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

[10-May-2016 18:01:19] NOTICE: fpm is running, pid 4512
[10-May-2016 18:01:19] NOTICE: ready to handle connections
[10-May-2016 18:01:19] NOTICE: systemd monitor interval set to 10000ms

Note: Not very useful, included for completeness.

Configuration Files

/etc/nginx/nginx.conf

# For more information on configuration, see:
#   * Official English Documentation: http://nginx.org/en/docs/
#   * Official Russian Documentation: http://nginx.org/ru/docs/


user nginx;

worker_processes auto;
error_log /var/log/nginx/error.log;
pid /run/nginx.pid;


events {
    worker_connections 1024;
}

http {
    log_format  main  '$remote_addr - $remote_user [$time_local] "$request" '
                      '$status $body_bytes_sent "$http_referer" '
                      '"$http_user_agent" "$http_x_forwarded_for"';

    access_log  /var/log/nginx/access.log  main;

    sendfile            on;
    tcp_nopush          on;
    tcp_nodelay         on;
    keepalive_timeout   65;
    types_hash_max_size 2048;

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

    # Load modular configuration files from the /etc/nginx/conf.d directory.
    # See http://nginx.org/en/docs/ngx_core_module.html#include
    # for more information.
    include /etc/nginx/conf.d/*.conf;
    include /etc/nginx/hosts.d/*.conf;
}

/etc/nginx/hosts.d/owncloud.conf

upstream php-handler {
    server unix:/run/php-fpm/www.sock;
}

server {
    listen 80;
    listen [::]:80;
    server_name REDACTED;
    return 301 https://$server_name$request_uri;
}

server {
    access_log /var/log/nginx/owncloud_access.log;
    error_log /var/log/nginx/owncloud_error.log;

    listen 443 ssl;
    listen [::]:443 ssl;
    include tls.conf;
    server_name REDACTED;

    ssl_certificate /etc/letsencrypt/live/REDACTED/fullchain.pem;
    ssl_certificate_key /etc/letsencrypt/live/REDACTED/privkey.pem;

    root /var/www/owncloud;

    client_max_body_size 10G;
    fastcgi_buffers 64 4K;

    rewrite ^/caldav(.*)$ /remote.php/caldav$1 redirect;
    rewrite ^/carddav(.*)$ /remote.php/carddav$1 redirect;
    rewrite ^/webdav(.*)$ /remote.php/webdav$1 redirect;

    index index.php;
    error_page 403 /core/templates/403.php;
    error_page 404 /core/templates/404.php;

    location = /robots.txt {
        allow all;
        log_not_found off;
        access_log off;
    }

    location ~ ^/(data|config|\.ht|db_structure\.xml|README) {
        deny all;
    }

    location / {
        rewrite ^/.well-known/carddav /remote.php/carddav/ redirect;
        rewrite ^/.well-known/caldav /remote.php/caldav/ redirect;

        rewrite ^(/core/doc/[^\/]+/)$ $1/index.html;

        try_files $uri $uri/ index.php;
    }

    location ~ ^(.+?\.php)(/.*)?$ {
        try_files $1 = 404;

        include fastcgi_params;
        fastcgi_param SCRIPT_FILENAME $document_root$1;
        fastcgi_param PATH_INFO $2;
        fastcgi_param HTTPS on;
        fastcgi_pass php-handler;
    }

    location ~* ^.+\.(jpg|jpeg|gif|bmp|ico|png|css|js|swf)$ {
        expires 7d;
        access_log off;
    }
}

/etc/php.ini

[PHP]
engine = On
short_open_tag = Off
asp_tags = Off
precision = 14
output_buffering = 4096
zlib.output_compression = Off
implicit_flush = Off
unserialize_callback_func =
serialize_precision = 17
disable_functions =
disable_classes =
zend.enable_gc = On
expose_php = On
max_execution_time = 30
max_input_time = 60
memory_limit = 128M
error_reporting = E_ALL & ~E_DEPRECATED & ~E_STRICT
display_errors = Off
display_startup_errors = Off
log_errors = On
log_errors_max_len = 1024
ignore_repeated_errors = Off
ignore_repeated_source = Off
report_memleaks = On
track_errors = Off
html_errors = On
variables_order = "GPCS"
request_order = "GP"
register_argc_argv = Off
auto_globals_jit = On
post_max_size = 8M
auto_prepend_file =
auto_append_file =
default_mimetype = "text/html"
default_charset = "UTF-8"
doc_root =
user_dir =
enable_dl = Off
file_uploads = On
upload_max_filesize = 2M
max_file_uploads = 20
allow_url_fopen = On
allow_url_include = Off
default_socket_timeout = 60
[CLI Server]
cli_server.color = On
[Date]
[filter]
[iconv]
[intl]
[sqlite]
[sqlite3]
[Pcre]
[Pdo]
[Pdo_mysql]
pdo_mysql.cache_size = 2000
pdo_mysql.default_socket = /var/lib/mysql/mysql.sock
[Phar]
[mail function]
sendmail_path = /usr/sbin/sendmail -t -i
mail.add_x_header = On
[SQL]
sql.safe_mode = Off
[ODBC]
odbc.allow_persistent = On
odbc.check_persistent = On
odbc.max_persistent = -1
odbc.max_links = -1
odbc.defaultlrl = 4096
odbc.defaultbinmode = 1
[Interbase]
ibase.allow_persistent = 1
ibase.max_persistent = -1
ibase.max_links = -1
ibase.timestampformat = "%Y-%m-%d %H:%M:%S"
ibase.dateformat = "%Y-%m-%d"
ibase.timeformat = "%H:%M:%S"
[MySQL]
mysql.allow_local_infile = On
mysql.allow_persistent = On
mysql.cache_size = 2000
mysql.max_persistent = -1
mysql.max_links = -1
mysql.default_port =
mysql.default_socket =
mysql.default_host =
mysql.default_user =
mysql.default_password =
mysql.connect_timeout = 60
mysql.trace_mode = Off
[MySQLi]
mysqli.max_persistent = -1
mysqli.allow_persistent = On
mysqli.max_links = -1
mysqli.cache_size = 2000
mysqli.default_port = 3306
mysqli.default_socket =
mysqli.default_host =
mysqli.default_user =
mysqli.default_pw =
mysqli.reconnect = Off
[mysqlnd]
mysqlnd.collect_statistics = On
mysqlnd.collect_memory_statistics = Off
[OCI8]
[PostgreSQL]
pgsql.allow_persistent = On
pgsql.auto_reset_persistent = Off
pgsql.max_persistent = -1
pgsql.max_links = -1
pgsql.ignore_notice = 0
pgsql.log_notice = 0
[Sybase-CT]
sybct.allow_persistent = On
sybct.max_persistent = -1
sybct.max_links = -1
sybct.min_server_severity = 10
sybct.min_client_severity = 10
[bcmath]
bcmath.scale = 0
[browscap]
[Session]
session.save_handler = files
session.use_strict_mode = 0
session.use_cookies = 1
session.use_only_cookies = 1
session.name = PHPSESSID
session.auto_start = 0
session.cookie_lifetime = 0
session.cookie_path = /
session.cookie_domain =
session.cookie_httponly =
session.serialize_handler = php
session.gc_probability = 1
session.gc_divisor = 1000
session.gc_maxlifetime = 1440
session.referer_check =
session.cache_limiter = nocache
session.cache_expire = 180
session.use_trans_sid = 0
session.hash_function = 0
session.hash_bits_per_character = 5
url_rewriter.tags = "a=href,area=href,frame=src,input=src,form=fakeentry"
[MSSQL]
mssql.allow_persistent = On
mssql.max_persistent = -1
mssql.max_links = -1
mssql.min_error_severity = 10
mssql.min_message_severity = 10
mssql.compatibility_mode = Off
mssql.secure_connection = Off
[Assertion]
[mbstring]
[gd]
[exif]
[Tidy]
tidy.clean_output = Off
[soap]
soap.wsdl_cache_enabled=1
soap.wsdl_cache_dir="/tmp"
soap.wsdl_cache_ttl=86400
soap.wsdl_cache_limit = 5
[sysvshm]
[ldap]
ldap.max_links = -1
[mcrypt]
[dba]
[curl]
[openssl]

Note: Comments removed to massively shrink file.

/etc/php-fpm.conf

include=/etc/php-fpm.d/*.conf
[global]
pid = /run/php-fpm/php-fpm.pid
error_log = /var/log/php-fpm/error.log
daemonize = yes

Note: Comments removed.

/etc/php-fpm.d/www.conf

[www]
user = nginx
group = nginx
listen = /run/php-fpm/www.sock
listen.acl_users = apache,nginx
listen.allowed_clients = 127.0.0.1
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_flag[display_errors] = on
php_admin_value[error_log] = /var/log/php-fpm/www-error.log
php_value[session.save_handler] = files
php_value[session.save_path]    = /var/lib/php/session
php_value[soap.wsdl_cache_dir]  = /var/lib/php/wsdlcache

Note: Comments removed.

/etc/my.cnf

#
# This group is read both both by the client and the server
# use it for options that affect everything
#
[client-server]

#
# This group is read by the server
#
[mysqld]
# Disabling symbolic-links is recommended to prevent assorted security risks
symbolic-links=0

#
# include all files from the config directory
#
!includedir /etc/my.cnf.d

/etc/my.cnf.d/mariadb-server.cnf

#
# These groups are read by MariaDB server.
# Use it for options that only the server (but not clients) should see
#
# See the examples of server my.cnf files in /usr/share/mysql/
#

# this is read by the standalone daemon and embedded servers
[server]

# this is only for the mysqld standalone daemon
# Settings user and group are ignored when systemd is used.
# If you need to run mysqld under a different user or group,
# customize your systemd unit file for mysqld/mariadb according to the
# instructions in http://fedoraproject.org/wiki/Systemd
[mysqld]
datadir=/var/lib/mysql
socket=/var/lib/mysql/mysql.sock
log-error=/var/log/mariadb/mariadb.log
pid-file=/var/run/mariadb/mariadb.pid

log-warnings = 2

bind-address = 127.0.0.1

# this is only for embedded server
[embedded]

# This group is only read by MariaDB servers, not by MySQL.
# If you use the same .cnf file for MySQL and MariaDB,
# you can put MariaDB-only options here
[mariadb]

# This group is only read by MariaDB-10.0 servers.
# If you use the same .cnf file for MariaDB of different versions,
# use this group for options that older servers don't understand
[mariadb-10.0]

It's time to check the permissions on the socket and all of the parent directories. — Michael Hampton, May 11 '16 at 03:14
It appears the permissions on `/var/lib/mysql` were wrong. Sorry for the bother. :/ I probably should have just done an SQL dump, as trying to migrate the origional data directory has been more trouble than it's worth. — MetaNova, May 11 '16 at 04:49

score 0 · Answer 1 · answered May 11 '16 at 04:51

As it turns out, when I copied over /var/lib/mysql from my old system, the permissions weren't corrected, resulting in nginx not having read access to the directory containing the socket file for MariaDB.

The solution was to update the permissions on /var/lib/mysql so nginx had access.

ownCloud Unable to Connect to Local Database on Fedora 23 (LEMP stack, selinux permissive)

The Problem

Logs

Configuration Files

1 Answers1