[SOLVED] ERROR! MariaDB server process #{pid} is not running

MariaDB 10.1.41 run on Mojave MacOS MacBook.

When I take it up by mysql.server start Everything is ok, PID file is created, process is running, connections are allowed, no errors in log, everything works ok.

But when I want to shut it down with mysql.server stop, I get notice: ERROR! MariaDB server process #28071 is not running! (number 28071 is a example process id at the moment of writing this question).

Still nothing in log, the process is still active (in top / ps, etc), but PID file is gone

I can kill it by kill -15, but thats not the way.

It was working ok, and it stops after I recovered machine from backup (returned from Apple repair service with cleaned hard drive).

my.cnf

[client]

# password       = your_password
port = 3306

socket = "/tmp/mysql.sock"

[mysqld]

#default-time-zone=+00:00
default_time_zone="Europe/Warsaw"

port = 3306
socket = "/tmp/mysql.sock"
tmpdir = "/tmp"
datadir = "/Users/epacha/Work/mysql"

pid-file = /var/run/mysqld/mysqld.pid
pid_file = /var/run/mysqld/mysqld.pid

# enable-named-pipe
key_buffer_size = 32M
max_allowed_packet = 32M
sort_buffer_size = 512K
net_buffer_length = 8K
read_buffer_size = 256K
read_rnd_buffer_size = 512K
myisam_sort_buffer_size = 8M
log_error = "/Users/epacha/Work/logs/mysql_error.log"

#innodb_force_recovery = 1

# Change here for bind listening
# bind-address="127.0.0.1"
# bind-address = ::1          # for ipv6

# Where do all the plugins live
#plugin_dir = "/Users/epacha/Work/mysql/lib/plugin/"

#skip-networking
#skip-federated

#log-bin=mysql-bin

server-id = 1

#master-host     =   <hostname>
#master-user     =   <username>
#master-password =   <password>
#master-port     =  <port>

#log-bin=mysql-bin

# Point the following paths to different dedicated disks
#log-update = /path-to-dedicated-directory/hostname

# Uncomment the following if you are using BDB tables
#bdb_cache_size = 4M
#bdb_max_lock = 10000

# Comment the following if you are using InnoDB tables
#skip-innodb
#innodb_data_home_dir = "/Users/epacha/Work/mysql"
#innodb_log_group_home_dir = "/Users/epacha/Work/mysql"

innodb_data_home_dir = "/Users/epacha/Work/mysql"
#innodb_log_group_home_dir = "/Users/epacha/Work/mysql"
innodb_data_file_path = ibdata1:10M:autoextend

#innodb_log_arch_dir = "/Users/epacha/Work/mysql"
## You can set .._buffer_pool_size up to 50 - 80 %
## of RAM but beware of setting memory usage too high

innodb_buffer_pool_size = 512MB

# DEPRECATED innodb_additional_mem_pool_size = 32MB

# ? innodb_empty_free_list_algorithm = 32M

## Set .._log_file_size to 25 % of buffer pool size
innodb_log_file_size = 128MB
innodb_log_buffer_size = 128MB
innodb_flush_log_at_trx_commit = 1
innodb_lock_wait_timeout = 50

## UTF 8 Settings
#init-connect=\'SET NAMES utf8\'

collation_server=utf8_unicode_ci
character_set_server=utf8

#skip-character-set-client-handshake
#character_sets-dir="/Users/epacha/Work/mysql/charsets"

[mysqldump]
quick
max_allowed_packet = 128M

[mysql]
no-auto-rehash
#safe-updates

[isamchk]
key_buffer_size = 32M
sort_buffer_size = 32M
read_buffer = 2M
write_buffer = 2M

[myisamchk]
key_buffer_size = 20M
sort_buffer_size = 20M
read_buffer = 2M
write_buffer = 2M

[mysqlhotcopy]
interactive-timeout

mysql_error.log

190902 17:48:40 mysqld_safe Starting mysqld daemon with databases from /Users/epacha/Work/mysql
2019-09-02 17:48:40 4582905280 [Note] /usr/local/Cellar/mariadb@10.1/10.1.41/bin/mysqld (mysqld 10.1.41-MariaDB) starting as process 28702 ...
2019-09-02 17:48:40 4582905280 [Warning] Setting lower_case_table_names=2 because file system for /Users/epacha/Work/mysql/ is case insensitive
2019-09-02 17:48:40 4582905280 [Note] InnoDB: Using mutexes to ref count buffer pool pages
2019-09-02 17:48:40 4582905280 [Note] InnoDB: The InnoDB memory heap is disabled
2019-09-02 17:48:40 4582905280 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2019-09-02 17:48:40 4582905280 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
2019-09-02 17:48:40 4582905280 [Note] InnoDB: Compressed tables use zlib 1.2.11
2019-09-02 17:48:40 4582905280 [Note] InnoDB: Using SSE crc32 instructions
2019-09-02 17:48:40 4582905280 [Note] InnoDB: Initializing buffer pool, size = 512.0M
2019-09-02 17:48:40 4582905280 [Note] InnoDB: Completed initialization of buffer pool
2019-09-02 17:48:40 4582905280 [Note] InnoDB: Highest supported file format is Barracuda.
2019-09-02 17:48:40 4582905280 [Note] InnoDB: 128 rollback segment(s) are active.
2019-09-02 17:48:40 4582905280 [Note] InnoDB: Waiting for purge to start
2019-09-02 17:48:40 4582905280 [Note] InnoDB:  Percona XtraDB (http://www.percona.com) 5.6.44-86.0 started; log sequence number 15092793366
2019-09-02 17:48:40 123145520132096 [Note] InnoDB: Dumping buffer pool(s) not yet started
2019-09-02 17:48:40 4582905280 [Note] Plugin 'FEEDBACK' is disabled.
2019-09-02 17:48:40 4582905280 [Note] Server socket created on IP: '::'.
2019-09-02 17:48:40 4582905280 [Note] /usr/local/Cellar/mariadb@10.1/10.1.41/bin/mysqld: ready for connections.
Version: '10.1.41-MariaDB'  socket: '/tmp/mysql.sock'  port: 3306  Homebrew