Nginx Domains Permission related doubt and issues

Please fill in any relevant information that applies to you:

• CentOS Version: i.e. CentOS 6 64bit /
  
• Centmin Mod Version Installed: 123.09beta01
• Nginx Version Installed: i.e. 1.13.5
• PHP Version Installed: i.e. 5.6.30
  
• MariaDB MySQL Version Installed: 10.1.21
• When was last time updated Centmin Mod code base ? : Today
  
• Persistent Config:
  
  Code:

  LETSENCRYPT_DETECT='y'
  SECOND_IP=xxx.xxx.xxx.xxx
  

I have actually few doubts, I plan to move some IP based vhosts from cpanel to this server.
1. My first doubt / issue is : What should be owner / permission for public files ie.
files residing at : /home/nginx/domains/mydomain.com/public

I synced files from old server to this one, generally I use chown to fix permission issue but there I am not sure what should be permission as now I am receiving "Permission Denied" error although files are there.

2. Second doubt / issue is again related to permission, I created ftp user during vhost created from Option #2 , however, after login, I get error if I try to get inside "public" directory, but can access rest ..

---

Any insight ?

 

Thanks, I figured out that its nginx, then fixed the permissions and issue is resolved.
Now problem I have related to db migration which I have not really mentioned earlier. I have around 15-16 db on cpanel server with 11 users for mysql, now things is that I want to keep old password, old username in order to avoid touching code.

In past I have done several dump and restore but only for single database at a time, this time I did

Code (Text):

mysqldump -uroot --all-databases > dump.sql

and then restored it to new centminmod server, my assumption is that it should also restore all users , privileges along with database.
After restoration, I can see all users are created
(SELECT user FROM mysql.user; )

But on website, they are not able to connect. However, database restoration completed without error.

Can you advice that my assumption about complete restoration along with users and permission is incorrect for mysql ?

 

Thanks for detailed answers. I did mess it up as I also copied mysql system data assuming it will create copy.
In my cpanel it was mysql 5.5 while here its 10.1 mariadb.

As you suggested, have nuked the database and did mysql_install_db --user=mysql to reinitialize data directory.

So essentially there is on one liner to do the mysql transfer. I will keep posted as I try things out.

 

Well, I did fresh import without system database and then separate import for users and their privileges , now I am stuck with weird issue that I can access database from command line but not from PHP.

ie. if I do this :

Code (Text):

mysql -usomeuser -p 

After providing its password, I can enter, further
show databases;show grants is also showing proper data.

But from php I am receiving "permission denied : 2002" .

Any advice ?

 

Yes, I did.

Code (Text):

MariaDB [(none)]> FLUSH PRIVILEGES;
Query OK, 0 rows affected (0.00 sec)

And did restart

Code (Text):

# mysqlrestart
Shutting down MySQL... SUCCESS!
Starting MySQL.171008 22:23:15 mysqld_safe Logging to '/var/lib/mysql/mob-ugi-ds-da.r2itservices.com.err'.
171008 22:23:15 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
 SUCCESS!

I have verified almost all users manually, each can login with its password and has desired grant.

This is now driving me nuts .

From mysql docs , error 2002 means there is no mysql running or script is not able to find one. I checked through default socket, and I suppose its working as expected. Or is there any error in my.cnf (its default as of now).

Code (Text):

# mysqladmin --protocol=SOCKET --socket=/var/lib/mysql/mysql.sock version
mysqladmin  Ver 9.1 Distrib 10.1.28-MariaDB, for Linux on x86_64
Copyright (c) 2000, 2017, Oracle, MariaDB Corporation Ab and others.

Server version          10.1.28-MariaDB
Protocol version        10
Connection              Localhost via UNIX socket
UNIX socket             /var/lib/mysql/mysql.sock
Uptime:                 7 min 55 sec

Threads: 1  Questions: 981  Slow queries: 0  Opens: 652  Flush tables: 1  Open tables: 509  Queries per second avg: 2.065

Any advice ?

 

These are custom php app, running fine on other cpanel server with same code.
I also did "mysql_upgrade" but no effect.

Have also tried restart, even had rebooted the server. Further, since zend_opcache is enabled, after each code change, have to restart php-fpm.

App is connecting to localhost.

Here is grant for one such user :

Code (Text):

Grants for bud_cu@localhost
GRANT USAGE ON *.* TO 'bud_cu'@'localhost' IDENTIFIED BY PASSWORD '*C40C784HHH4E7946TYR27DCE7A1948E1053935'
GRANT SELECT, INSERT, UPDATE, DELETE, CREATE ON `bud_db3`.* TO 'bud_cu'@'localhost'

I am looking forward to see how centminmod performs as compared to cpanel stack but this sql user stuff has already eaten 2 days, pretty annoying. I have gut feeling that is something rather small which is being overlooked.. ..

 

I doubt it because if there was such database related issue then would have not been able to access from the CLI.

Do you think there is some library missing in my install because cli essentially means that I am using mysql-client to make interaction but can't do same using php .

And as per your suggestion, created new user, given it grant over existing db, but same error.

I am out of ideas ..

 

php 5.6.31,
There is no error related to php besides error_reporting(E_ALL);

I have tried using mysql_ as well mysqli_ , both same issue.
Here is output you asked :

Code (Text):

# php -m
[PHP Modules]
bcmath
bz2
calendar
Core
ctype
curl
date
dom
enchant
ereg
exif
filter
ftp
gd
geoip
gettext
gmp
hash
iconv
igbinary
imagick
imap
intl
json
ldap
libxml
mailparse
mbstring
mcrypt
memcache
memcached
mhash
mysql
mysqli
mysqlnd
openssl
pcntl
pcre
PDO
pdo_mysql
pdo_sqlite
Phar
posix
pspell
readline
redis
Reflection
session
shmop
SimpleXML
snmp
soap
sockets
SPL
sqlite3
standard
sysvmsg
sysvsem
sysvshm
tidy
tokenizer
xml
xmlreader
xmlrpc
xmlwriter
xsl
Zend OPcache
zip
zlib

[Zend Modules]
Zend OPcache

Also, I created a new database, populated some test data, added a new user with full privileges but same issue. With my limited knowledge, my conclusion is that php extension is not able to find connection to mysql server / mariadb server at all. In other words, it can not see mysql server running .

 

No, no PHP/WEB app is working.

Just permission denied, even in log files

Also, just to rule out :

Code (Text):

# sestatus
SELinux status:                 disabled

Further, I installed phpmyadmin using your installer, Addon phpmyadmin.sh - CentminMod.com LEMP Nginx web stack for CentOS

Even its not able to connect with errors:

Code (Text):

#2002 - Permission denied — The server is not responding (or the local server's socket is not correctly configured).

 mysqli_real_connect(): (HY000/2002): Permission denied

 

As said, left it as it is .

Its content:

Code (Text):

# cat /etc/my.cnf
[client]
socket=/var/lib/mysql/mysql.sock

[mysql]
max_allowed_packet = 128M

[mysqld]
ignore_db_dirs=cmsetiofiotest
local-infile=0
ignore_db_dirs=lost+found
character-set-server=utf8
datadir=/var/lib/mysql
socket=/var/lib/mysql/mysql.sock

#bind-address=127.0.0.1
# optimized my.cnf for MariaDB 5.5.x
# by eva2000
# vbtechsupport.com

tmpdir=/home/mysqltmp

innodb=ON
#skip-federated
##skip-pbxt
##skip-pbxt_statistics
#skip-archive
#skip-name-resolve
#old_passwords
back_log = 512
max_connections = 750
key_buffer_size = 384M
myisam_sort_buffer_size = 256M
myisam_max_sort_file_size = 2048M
join_buffer_size = 256K
read_buffer_size = 256K
sort_buffer_size = 512K
table_definition_cache = 8192
table_open_cache = 8192
thread_cache_size = 256
wait_timeout = 1800
connect_timeout = 10
tmp_table_size = 512M
max_heap_table_size = 512M
max_allowed_packet = 128M
#max_seeks_for_key = 4294967295
#group_concat_max_len = 1024
max_length_for_sort_data = 1024
net_buffer_length = 16384
max_connect_errors = 100000
concurrent_insert = 2
read_rnd_buffer_size = 512K
bulk_insert_buffer_size = 8M
# query_cache boost for MariaDB >10.1.2+
# https://community.centminmod.com/posts/30811/
query_cache_limit = 1024K
query_cache_size = 128M
query_cache_type = 1
query_cache_min_res_unit = 2K
query_prealloc_size = 262144
query_alloc_block_size = 65536
transaction_alloc_block_size = 8192
transaction_prealloc_size = 4096
default-storage-engine = InnoDB

log_warnings=1
slow_query_log=0
long_query_time=1
slow_query_log_file=/var/lib/mysql/slowq.log
#log-error=/var/log/mysqld.log

# innodb settings
innodb_large_prefix=1
innodb_purge_threads = 4
innodb_file_format = Barracuda
innodb_file_per_table = 1
innodb_open_files = 1000
innodb_data_file_path= ibdata1:10M:autoextend
innodb_buffer_pool_size = 1024M

## https://mariadb.com/kb/en/mariadb/xtradbinnodb-server-system-variables/#innodb_buffer_pool_instances
innodb_buffer_pool_instances=1

innodb_log_files_in_group = 2
innodb_log_file_size = 384M
innodb_log_buffer_size = 8M
innodb_flush_log_at_trx_commit = 2
#innodb_thread_concurrency = 20
innodb_lock_wait_timeout=50
innodb_flush_method = O_DIRECT
innodb_support_xa=1

# 200 * # DISKS
innodb_io_capacity = 2900
innodb_io_capacity_max = 5800
innodb_read_io_threads = 4
innodb_write_io_threads = 4
innodb_flush_neighbors = 0

# mariadb settings
[mariadb]
#thread-handling = pool-of-threads
#thread-pool-size= 20
#mysql --port=3307 --protocol=tcp
#extra-port=3307
#extra-max-connections=1

userstat = 0
key_cache_segments = 1
aria_group_commit = none
aria_group_commit_interval = 0
aria_log_file_size = 768M
aria_log_purge_type = immediate
aria_pagecache_buffer_size = 768M
aria_sort_buffer_size = 192M

[mariadb-5.5]
innodb_file_format = Barracuda
innodb_file_per_table = 1

#ignore_db_dirs=
query_cache_strip_comments=0

innodb_read_ahead = linear
innodb_adaptive_flushing_method = estimate
innodb_flush_neighbor_pages = 1
innodb_stats_update_need_lock = 0
innodb_log_block_size = 512

log_slow_filter =admin,filesort,filesort_on_disk,full_join,full_scan,query_cache,query_cache_miss,tmp_table,tmp_table_on_disk

[mysqld_safe]
socket=/var/lib/mysql/mysql.sock
#log-error=/var/log/mysqld.log
#nice = -5
open-files-limit = 8192

[mysqldump]
quick
max_allowed_packet = 128M

[myisamchk]
tmpdir=/home/mysqltmp
key_buffer = 384M
sort_buffer = 64M
read_buffer = 64M
write_buffer = 64M

[mysqlhotcopy]
interactive-timeout

[mariadb-10.0]
innodb_file_format = Barracuda
innodb_file_per_table = 1

# 2 variables needed to switch from XtraDB to InnoDB plugins
#plugin-load=ha_innodb
#ignore_builtin_innodb

## MariaDB 10 only save and restore buffer pool pages
## warm up InnoDB buffer pool on server restarts
#innodb_buffer_pool_dump_at_shutdown=1
#innodb_buffer_pool_load_at_startup=1
innodb_buffer_pool_populate=0
## Disabled settings
performance_schema=OFF
innodb_stats_on_metadata=OFF
innodb_sort_buffer_size=2M
innodb_online_alter_log_max_size=128M
query_cache_strip_comments=0
log_slow_filter =admin,filesort,filesort_on_disk,full_join,full_scan,query_cache,query_cache_miss,tmp_table,tmp_table_on_disk

[mariadb-10.1]
innodb_file_format = Barracuda
innodb_file_per_table = 1

## wsrep specific
# wsrep_on=OFF
# wsrep_provider
# wsrep_cluster_address
# binlog_format=ROW
# default_storage_engine=InnoDB
# innodb_autoinc_lock_mode=2
# innodb_doublewrite=1
# query_cache_size=0

# 2 variables needed to switch from XtraDB to InnoDB plugins
#plugin-load=ha_innodb
#ignore_builtin_innodb

## MariaDB 10 only save and restore buffer pool pages
## warm up InnoDB buffer pool on server restarts
#innodb_buffer_pool_dump_at_shutdown=1
#innodb_buffer_pool_load_at_startup=1
innodb_buffer_pool_populate=0
## Disabled settings
performance_schema=OFF
innodb_stats_on_metadata=OFF
innodb_sort_buffer_size=2M
innodb_online_alter_log_max_size=128M
query_cache_strip_comments=0
log_slow_filter =admin,filesort,filesort_on_disk,full_join,full_scan,query_cache,query_cache_miss,tmp_table,tmp_table_on_disk

# Defragmenting unused space on InnoDB tablespace
innodb_defragment=1
innodb_defragment_n_pages=7
innodb_defragment_stats_accuracy=0
innodb_defragment_fill_factor_n_recs=20
innodb_defragment_fill_factor=0.9
innodb_defragment_frequency=40