Mysql – Why might a query not run until after I restart the MySQL server

Why might MySQL not execute a query? Why might it freeze? It simply sits there and does nothing. Show processlist gives a result of "sending data" for as many hours as it takes for me to give up and restart MySQL after which the query runs in a fraction of a second. The log yields no errors. Explain shows the joining tables and the keys they are matched on.

act and cls are indexed primary on L_ID and normal s_ID

MySQL freezes when attempting to run a query unless I restart MySQL before running it. I hope someone here might be able to give me an idea as to why or better still what to do about it.

I have a local host running XAMPP and a query that crunches data locally that looks like this:

INSERT INTO table
SELECT
    act.P_ID,
    act.L_ID,
    act.L_Price,
    act.A,
    act.C,
    round(((count(*) / sum(1/(cls.S_Price / cls.Sq))* act.Sq)+avg(cls.S_Price))/2) AS abc,
    STDDEV((cls.S_Price / cls.Sq))/avg((cls.S_Price / cls.Sq)) AS std_dev, 
    count(*) as `samp`,
    GROUP_CONCAT(DISTINCT cls.L_ID) as comps,
    @datenow as `Timestamp`,
    '1' AS B_score
FROM
    act_table AS act
JOIN cls_table AS cls ON cls.S_ID = act.S_ID
AND cls.R = "val"
AND cls.S = "val"
AND cls.Sq BETWEEN act.Sq *.2 AND act.Sq * 1.8
AND cls.YB BETWEEN act.YB - 10 AND act.Year_Built + 12
AND cls.pv = act.pv
AND cls.PP = act.PP
AND cls.Bd = act.Bd
AND cls.th = act.th
AND cls.C_D > now()-interval 3 month
AND act.s_ID !=""
GROUP BY
    act.P_ID
HAVING `samp` > 1
AND std_dev <= .1;

I can run it one time. If I need to run it again I have to restart the MySQL server in XAMPP. The cls table has around 40,000 records and act has around 7,000. After restarting MySQL it executes in 0.674s.

I run the query from Navicat, a graphical database management software.

SHOW ENGINE InnoDB STATUS

Gives a result of:

=====================================
2016-01-20 07:49:30 2aa0 INNODB MONITOR OUTPUT
=====================================
Per second averages calculated from the last 25 seconds
-----------------
BACKGROUND THREAD
-----------------
srv_master_thread loops: 1893 srv_active, 0 srv_shutdown, 225772 srv_idle
srv_master_thread log flush and writes: 227665
----------
SEMAPHORES
----------
OS WAIT ARRAY INFO: reservation count 52114
OS WAIT ARRAY INFO: signal count 95463
Mutex spin waits 264459, rounds 1248653, OS waits 21862
RW-shared spins 93765, rounds 1229580, OS waits 21549
RW-excl spins 93314, rounds 612670, OS waits 7456
Spin rounds per wait: 4.72 mutex, 13.11 RW-shared, 6.57 RW-excl
------------
TRANSACTIONS
------------
Trx id counter 15954141
Purge done for trx's n:o < 15954137 undo n:o < 0 state: running but idle
History list length 588
LIST OF TRANSACTIONS FOR EACH SESSION:
---TRANSACTION 0, not started
MySQL thread id 163, OS thread handle 0x2aa0, query id 7705288 optimus-PC 10.10.102.114 jemima init
SHOW ENGINE InnoDB STATUS
---TRANSACTION 15954140, ACTIVE 5 sec fetching rows
mysql tables in use 6, locked 6
392 lock struct(s), heap size 27512, 27219 row lock(s)
MySQL thread id 161, OS thread handle 0x2ef4, query id 7705282 optimus-PC 10.10.102.114 jemima Sending data
INSERT INTO table
SELECT
    act.P_ID,
    act.L_ID,
    act.L_Price,
    act.A,
    act.C,
    round(((count(*) / sum(1/(cls.S_Price / cls.Sq))* act.Sq)+avg(cls.S_Price))/2) AS abc,
    STDDEV((cls.S_Price / cls.Sq))/avg((cls.S_Price / cls.Sq)) AS std_dev, 
    count(*) as `samp`,
    GROUP_CONCAT(DISTINCT cls.L_ID) as comps,
    @datenow as `Timestamp`,
    '1' AS B_score
FROM
    act_table AS act
JOIN cls_table AS cls ON cls.S_ID = act.S_ID
AND cls.R = "val"
AND cls.S = "val"
AND cls.Sq BETWEEN act.Sq *.2 AND act.Sq * 1.8
AND cls.YB BETWEEN act.YB - 10 AND act.Year_Built + 12
AND cls.pv = act.pv
AND cls.PP = act.PP
AND cls.Bd = act.Bd
AND cls.th = act.th
AND cls.C_D > now()-interval 3 month
AND act.s_ID !=""
GROUP BY
    act.P_ID
HAVING `samp` > 1
AND std_dev <= .1;
--------
FILE I/O
--------
I/O thread 0 state: wait Windows aio (insert buffer thread)
I/O thread 1 state: wait Windows aio (log thread)
I/O thread 2 state: wait Windows aio (read thread)
I/O thread 3 state: wait Windows aio (read thread)
I/O thread 4 state: wait Windows aio (read thread)
I/O thread 5 state: wait Windows aio (read thread)
I/O thread 6 state: wait Windows aio (write thread)
I/O thread 7 state: wait Windows aio (write thread)
I/O thread 8 state: wait Windows aio (write thread)
I/O thread 9 state: wait Windows aio (write thread)
Pending normal aio reads: 0 [0, 0, 0, 0] , aio writes: 0 [0, 0, 0, 0] ,
 ibuf aio reads: 0, log i/o's: 0, sync i/o's: 0
Pending flushes (fsync) log: 0; buffer pool: 0
2810151 OS file reads, 733114 OS file writes, 63302 OS fsyncs
54.08 reads/s, 16384 avg bytes/read, 13.32 writes/s, 1.76 fsyncs/s
-------------------------------------
INSERT BUFFER AND ADAPTIVE HASH INDEX
-------------------------------------
Ibuf: size 1, free list len 7149, seg size 7151, 7251 merges
merged operations:
 insert 122683, delete mark 1668046, delete 28597
discarded operations:
 insert 0, delete mark 0, delete 0
Hash table size 2212699, node heap has 881 buffer(s)
309907.24 hash searches/s, 5169.03 non-hash searches/s
---
LOG
---
Log sequence number 3963944279169
Log flushed up to   3963944279169
Pages flushed up to 3963944279169
Last checkpoint at  3963944279169
0 pending log writes, 0 pending chkp writes
21912 log i/o's done, 0.68 log i/o's/second
----------------------
BUFFER POOL AND MEMORY
----------------------
Total memory allocated 544210944; in additional pool allocated 0
Dictionary memory allocated 1038260
Buffer pool size   32768
Free buffers       1024
Database pages     30862
Old database pages 11372
Modified db pages  0
Pending reads 0
Pending writes: LRU 0, flush list 0, single page 0
Pages made young 1155251, not young 48421006
32.20 youngs/s, 7462.94 non-youngs/s
Pages read 2798392, created 408832, written 667825
54.08 reads/s, 0.64 creates/s, 12.20 writes/s
Buffer pool hit rate 1000 / 1000, young-making rate 0 / 1000 not 7 / 1000
Pages read ahead 33.28/s, evicted without access 0.00/s, Random read ahead 0.00/s
LRU len: 30862, unzip_LRU len: 0
I/O sum[746]:cur[0], unzip sum[0]:cur[0]
--------------
ROW OPERATIONS
--------------
0 queries inside InnoDB, 0 queries in queue
0 read views open inside InnoDB
Main thread id 3936, state: sleeping
Number of rows inserted 4309763, updated 8216503, deleted 12560, read 4268362560
42.60 inserts/s, 0.00 updates/s, 0.00 deletes/s, 321801.25 reads/s
----------------------------
END OF INNODB MONITOR OUTPUT
============================