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Issue website becoming unavailable when cpu load reaches above 5%

I am using Plesk for many years, never had any problem. recently I have implemented a big database for my website which is based on geonames city data. I have large queries, due to that sometime CPU load reaches above 5% and at that time website becoming unavailable. it is becoming available only after restarting apache and MySQL. I am having a server with E3-1275 v6 CPU and 64gb ram. I have installed Plesk on CentOS 7 and current Plesk version is 17.8.11 but still, I am facing this problem. please help me to resolve this issue. thanks.
 
-------- Storage Engine Statistics --------------------------------------------- --------------------
[--] Status: +ARCHIVE +Aria +BLACKHOLE +CSV +FEDERATED +InnoDB +MEMORY +MRG_MYIS AM +MyISAM +PERFORMANCE_SCHEMA
[--] Data in MyISAM tables: 1.4G (Tables: 17)
[--] Data in InnoDB tables: 278.8M (Tables: 373)
[OK] Total fragmented tables: 0

-------- Analysis Performance Metrics ------------------------------------------ --------------------
[--] innodb_stats_on_metadata: ON
[!!] Stat are updated during querying INFORMATION_SCHEMA.

-------- Security Recommendations ---------------------------------------------- --------------------
[OK] There are no anonymous accounts for any database users
[OK] All database users have passwords assigned
[!!] User 'onlinejy_admin@%' does not specify hostname restrictions.
[--] There are 618 basic passwords in the list.

-------- CVE Security Recommendations ------------------------------------------ --------------------
[!!] CVE-2018-2767(<= 5.5.60) : "Vulnerability in the MySQL Server component of Oracle MySQL (subcomponent: Server: Security: Encryption). Supported versions th at are affected are 5.5.60 and prior
[!!] CVE-2018-3058(<= 5.5.60) : "Vulnerability in the MySQL Server component of Oracle MySQL (subcomponent: MyISAM). Supported versions that are affected are 5. 5.60 and prior
[!!] CVE-2018-3063(<= 5.5.60) : "Vulnerability in the MySQL Server component of Oracle MySQL (subcomponent: Server: Security: Privileges). Supported versions th at are affected are 5.5.60 and prior. Easily exploitable vulnerability allows hi gh privileged attacker with network access via multiple protocols to compromise MySQL Server. Successful attacks of this vulnerability can result in unauthorize d ability to cause a hang or frequently repeatable crash (complete DOS) of MySQL Server. CVSS 3.0 Base Score 4.9 (Availability impacts). CVSS Vector: (CVSS:3.0/ AV:N/AC:L/PR:H/UI:N/S:U/C:N/I:N/A:H)."
[!!] CVE-2018-3066(<= 5.5.60) : "Vulnerability in the MySQL Server component of Oracle MySQL (subcomponent: Server: Options). Supported versions that are affect ed are 5.5.60 and prior
[!!] CVE-2018-3070(<= 5.5.60) : "Vulnerability in the MySQL Server component of Oracle MySQL (subcomponent: Client mysqldump). Supported versions that are affec ted are 5.5.60 and prior
[--] False positive CVE(s) for MySQL and MariaDB 5.5.x can be found.
[--] Check careful each CVE for those particular versions
[!!] 5 CVE(s) found for your MySQL release.

-------- Performance Metrics --------------------------------------------------- --------------------
[--] Up for: 23m 25s (6M q [4K qps], 6K conn, TX: 927M, RX: 401M)
[--] Reads / Writes: 99% / 1%
[--] Binary logging is enabled (GTID MODE: OFF)
[--] Physical Memory : 62.5G
[--] Max MySQL memory : 13.4G
[--] Other process memory: 639.1M
[--] Total buffers: 8.3G global + 24.4M per thread (214 max threads)
[--] P_S Max memory usage: 0B
[--] Galera GCache Max memory usage: 0B
[OK] Maximum reached memory usage: 8.7G (13.85% of installed RAM)
[OK] Maximum possible memory usage: 13.4G (21.39% of installed RAM)
[OK] Overall possible memory usage with other process is compatible with memory available
[OK] Slow queries: 0% (1/6M)
[OK] Highest usage of available connections: 7% (16/214)
[OK] Aborted connections: 0.07% (5/6953)
[!!] name resolution is active : a reverse name resolution is made for each new connection and can reduce performance
[!!] Query cache may be disabled by default due to mutex contention.
[OK] Query cache efficiency: 49.8% (6M cached / 13M selects)
[OK] Query cache prunes per day: 0
[OK] Sorts requiring temporary tables: 0% (0 temp sorts / 246 sorts)
[!!] Joins performed without indexes: 15
[!!] Temporary tables created on disk: 69% (989 on disk / 1K total)
[OK] Thread cache hit rate: 99% (16 created / 6K connections)
[OK] Table cache hit rate: 104% (182 open / 175 opened)
[OK] Open file limit used: 7% (81/1K)
[OK] Table locks acquired immediately: 100% (52K immediate / 52K locks)
[OK] Binlog cache memory access: 100.00% (272 Memory / 272 Total)

-------- Performance schema ---------------------------------------------------- --------------------
[--] Performance schema is disabled.
[--] Memory used by P_S: 0B
[--] Sys schema isn't installed.

-------- ThreadPool Metrics ---------------------------------------------------- --------------------
[--] ThreadPool stat is enabled.
[--] Thread Pool Size: 8 thread(s).
[--] Using default value is good enough for your version (5.5.60-MariaDB)

-------- MyISAM Metrics -------------------------------------------------------- --------------------
[!!] Key buffer used: 18.3% (785M used / 4B cache)
[OK] Key buffer size / total MyISAM indexes: 4.0G/358.4M
[OK] Read Key buffer hit rate: 96.9% (85K cached / 2K reads)

-------- InnoDB Metrics -------------------------------------------------------- --------------------
[--] InnoDB is enabled.
[--] InnoDB Thread Concurrency: 0
[!!] InnoDB File per table is not activated
[!!] InnoDB buffer pool / data size: 128.0M/278.8M
[!!] Ratio InnoDB log file size / InnoDB Buffer pool size (7.8125 %): 5.0M * 2/1 28.0M should be equal 25%
[OK] InnoDB buffer pool instances: 1
[--] InnoDB Buffer Pool Chunk Size not used or defined in your version
[OK] InnoDB Read buffer efficiency: 99.98% (235319173 hits/ 235359788 total)
[OK] InnoDB Write log efficiency: 99.81% (5316127 hits/ 5326136 total)
[OK] InnoDB log waits: 0.00% (0 waits / 10009 writes)

-------- AriaDB Metrics -------------------------------------------------------- --------------------
[--] AriaDB is enabled.
[OK] Aria pagecache size / total Aria indexes: 128.0M/1B
[!!] Aria pagecache hit rate: 21.1% (19 cached / 15 reads)

-------- TokuDB Metrics -------------------------------------------------------- --------------------
[--] TokuDB is disabled.

-------- XtraDB Metrics -------------------------------------------------------- --------------------
[--] XtraDB is disabled.

-------- Galera Metrics -------------------------------------------------------- --------------------
[--] Galera is disabled.

-------- Replication Metrics --------------------------------------------------- --------------------
[--] Galera Synchronous replication: NO
[--] No replication slave(s) for this server.
[--] Binlog format: STATEMENT
[--] XA support enabled: ON
[--] Semi synchronous replication Master: Not Activated
[--] Semi synchronous replication Slave: Not Activated
[--] This is a standalone server

-------- Recommendations ------------------------------------------------------- --------------------
General recommendations:
Control warning line(s) into /var/lib/mysql/onlinejyotish.com.err file
Control error line(s) into /var/lib/mysql/onlinejyotish.com.err file
Restrict Host for user@% to user@SpecificDNSorIp
5 CVE(s) found for your MySQL release. Consider upgrading your version !
MySQL was started within the last 24 hours - recommendations may be inaccura te
Enable the slow query log to troubleshoot bad queries
Configure your accounts with ip or subnets only, then update your configuration with skip-name-resolve=1
Adjust your join queries to always utilize indexes
When making adjustments, make tmp_table_size/max_heap_table_size equal
Reduce your SELECT DISTINCT queries which have no LIMIT clause
Consider installing Sys schema from mysql/mysql-sys
Before changing innodb_log_file_size and/or innodb_log_files_in_group read t his: MySQL :: MySQL 5.7 Reference Manual :: 14.7.2 Changing the Number or Size of InnoDB Redo Log Files
Variables to adjust:
SET innodb_stats_on_metadata = OFF
query_cache_size (=0)
query_cache_type (=0)
join_buffer_size (> 128.0K, or always use indexes with JOINs)
tmp_table_size (> 16M)
max_heap_table_size (> 16M)
innodb_file_per_table=ON
innodb_buffer_pool_size (>= 278.8M) if possible.
innodb_log_file_size should be (=16M) if possible, so InnoDB total log files size equals to 25% of buffer pool size.
 
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