MySQL advice and investigation - mysql

Question

Intro:
I have a Debian 8 VPS with SSD and 512MB RAM (1024MB Burst) and use it only with MySQL. I have turned off all unnecessary services and gave every resources on db and system. I have 5 workstations only. The ping and network are stable.
The main problem is that if I do 10 consecutive queries like this:
(SELECT IFNULL(SUM(Qtty), 0) FROM operations
WHERE blablabla
FROM (goods LEFT JOIN store ON goods.ID = store.GdID)
WHERE Deleted <> -1
GROUP BY goods.ID;
Randomly 5-6 of them are executed for 2s, but the rest for 8s or more! I see no reason for this behavior. When i activate slow_query_log, it have just the same query, nothing else.
My InnoDB data is 98MB is there any reason to give more RAM to innodb_buffer_pool_size or 128 is enough?
innodb_log_file_size must be 25% - 50%, which size would be better for me?
tmp dir is tmpfs, so if tmp_table_size is placed there, is there any reason to give it more RAM or is enough to use 1M for example?
table_open_cache - I have about 200 tables, is there any reason to make it 20000 for example, as the mysqltuner advises me?
Can i tuning something else?
my.cnf
skip-external-locking
skip-name-resolve
performance_schema = OFF
thread_stack = 192K
thread_cache_size = 10 #this is managed globally and is equal to max_connections
max_connections = 10
max_connect_errors = 10
connect_timeout = 20
wait_timeout = 20
interactive_timeout = 20
sql_mode = TRADITIONAL
default_storage_engine = InnoDB
innodb_buffer_pool_instances = 1
innodb_buffer_pool_size = 250M
innodb_log_file_size = 100M
innodb_strict_mode = ON
innodb_flush_method = O_DIRECT
innodb_flush_neighbors = 0
innodb_read_io_threads = 4
innodb_write_io_threads = 4
innodb_io_capacity = 2000
innodb_io_capacity_max = 3000
key_buffer = 128K
delay_key_write = ON
tmp_table_size = 10M # 32M = 53% temp
max_heap_table_size = 10M
query_cache_type = 0
query_cache_size = 0
table_open_cache = 5000
table_definition_cache = 3000

Answer 1

Suggestions to consider for your my.cnf [mysqld] section
max_connections=20 # from 10 to affect thread_cache_size
. because 8 threads used by MySQL + 5 concurrent = 13 and you will have a few extra, please
tmp_table_size=16M # from 10M to reduce 41% temp tables created on disk
max_heap_table_size=16M # from 10M should always be = tmp_table_size
innodb_read_io_threads=64 # from 4 to let the ponies run
innodb_write_io_threads=64 # from 4 to push on through
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Answer 2

Again thanks for the detailed answer and sorry for the delay. Unfortunately, I travel often without internet and contact by Skype is almost impossible.
I noticed something that can help: often, when running even very small queries, the server responds with "ERROR 2006 (HY000): MySQL server has gone away". If i repeat the operation - everything is fine. The problem is on the server, not in db?
The db is about 100MB, so i increase and max_allowed_packet to 512MB, innodb io_threads to 64. I tried with increased net_read_timeout, net_write_timeout, wait_timeout and interactive_timeout to 28800 and there is an improvement.
This is my timeouts now, does it make sense to change something?
connect_timeout 120
delayed_insert_timeout 300
innodb_flush_log_at_timeout 1
innodb_lock_wait_timeout 50
innodb_rollback_on_timeout OFF
interactive_timeout 28800
lock_wait_timeout 31536000
net_read_timeout 30
net_write_timeout 60
slave_net_timeout 3600
thread_pool_idle_timeout 60
wait_timeout 28800