MYSQL Select query stuck at “Sending data”

I have an select query with about 1M records, I'm working on Magento 1.9 database.

    SELECT IF(sup_ap.is_percent = 1, TRUNCATE(mt.value + (mt.value * sup_ap.pricing_value / 100), 4),
          mt.value + SUM(sup_ap.pricing_value)) AS `value`,
       75                                       AS `attribute_id`,
       `supl`.`product_id`                      AS `entity_id`,
       `cs`.`store_id`
FROM `catalog_product_entity_decimal` AS `mt`
         LEFT JOIN `catalog_product_super_attribute` AS `sup_a` ON mt.entity_id = product_id
         INNER JOIN `catalog_product_super_attribute_pricing` AS `sup_ap`
                    ON sup_ap.product_super_attribute_id = sup_a.product_super_attribute_id
         INNER JOIN `catalog_product_super_link` AS `supl` ON mt.entity_id = supl.parent_id
         INNER JOIN `catalog_product_entity_int` AS `pint`
                    ON pint.entity_id = supl.product_id and pint.attribute_id = sup_a.attribute_id and
                       pint.value = sup_ap.value_index
         INNER JOIN `core_store` AS `cs` ON cs.website_id = sup_ap.website_id
WHERE (mt.entity_id in (select product_id from catalog_product_super_attribute))
  AND (mt.attribute_id = '75')
GROUP BY `entity_id`, `cs`.`store_id`
LIMIT 500

My Explain:

+------+-------------+---------------------------------+--------+----------------------------------------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------+---------+------------------------------------+------+----------------------------------------------+
| id   | select_type | table                           | type   | possible_keys                                                                                                                                                  | key                                                            | key_len | ref                                | rows | Extra                                        |
+------+-------------+---------------------------------+--------+----------------------------------------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------+---------+------------------------------------+------+----------------------------------------------+
|    1 | PRIMARY     | cs                              | index  | IDX_CORE_STORE_WEBSITE_ID                                                                                                                                      | IDX_CORE_STORE_WEBSITE_ID                                      | 2       | NULL                               |    7 | Using index; Using temporary; Using filesort |
|    1 | PRIMARY     | sup_ap                          | ref    | UNQ_CAT_PRD_SPR_ATTR_PRICING_PRD_SPR_ATTR_ID_VAL_IDX_WS_ID,IDX_CAT_PRD_SPR_ATTR_PRICING_PRD_SPR_ATTR_ID,IDX_CATALOG_PRODUCT_SUPER_ATTRIBUTE_PRICING_WEBSITE_ID | IDX_CATALOG_PRODUCT_SUPER_ATTRIBUTE_PRICING_WEBSITE_ID         | 2       | cs.website_id                      |   11 |                                              |
|    1 | PRIMARY     | sup_a                           | eq_ref | PRIMARY,UNQ_CATALOG_PRODUCT_SUPER_ATTRIBUTE_PRODUCT_ID_ATTRIBUTE_ID,IDX_CATALOG_PRODUCT_SUPER_ATTRIBUTE_PRODUCT_ID                                             | PRIMARY                                                        | 4       | sup_ap.product_super_attribute_id  |    1 |                                              |
|    1 | PRIMARY     | mt                              | ref    | UNQ_CAT_PRD_ENTT_DEC_ENTT_ID_ATTR_ID_STORE_ID,IDX_CATALOG_PRODUCT_ENTITY_DECIMAL_ENTITY_ID,IDX_CATALOG_PRODUCT_ENTITY_DECIMAL_ATTRIBUTE_ID                     | UNQ_CAT_PRD_ENTT_DEC_ENTT_ID_ATTR_ID_STORE_ID                  | 6       | sup_a.product_id,const             |    1 |                                              |
|    1 | PRIMARY     | catalog_product_super_attribute | ref    | UNQ_CATALOG_PRODUCT_SUPER_ATTRIBUTE_PRODUCT_ID_ATTRIBUTE_ID,IDX_CATALOG_PRODUCT_SUPER_ATTRIBUTE_PRODUCT_ID                                                     | UNQ_CATALOG_PRODUCT_SUPER_ATTRIBUTE_PRODUCT_ID_ATTRIBUTE_ID    | 4       | sup_a.product_id                   |    1 | Using index; FirstMatch(mt)                  |
|    1 | PRIMARY     | supl                            | ref    | UNQ_CATALOG_PRODUCT_SUPER_LINK_PRODUCT_ID_PARENT_ID,IDX_CATALOG_PRODUCT_SUPER_LINK_PARENT_ID,IDX_CATALOG_PRODUCT_SUPER_LINK_PRODUCT_ID                         | IDX_CATALOG_PRODUCT_SUPER_LINK_PARENT_ID                       | 4       | sup_a.product_id                   |    4 |                                              |
|    1 | PRIMARY     | pint                            | ref    | UNQ_CATALOG_PRODUCT_ENTITY_INT_ENTITY_ID_ATTRIBUTE_ID_STORE_ID,IDX_CATALOG_PRODUCT_ENTITY_INT_ATTRIBUTE_ID,IDX_CATALOG_PRODUCT_ENTITY_INT_ENTITY_ID            | UNQ_CATALOG_PRODUCT_ENTITY_INT_ENTITY_ID_ATTRIBUTE_ID_STORE_ID | 6       | supl.product_id,sup_a.attribute_id |    1 | Using where                                  |
+------+-------------+---------------------------------+--------+----------------------------------------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------+---------+------------------------------------+------+----------------------------------------------+

I have no experience about optimize the select query with stuck at sending data, I tried update the select query to this:

SELECT IF(sup_ap.is_percent = 1, TRUNCATE(mt.value + (mt.value * sup_ap.pricing_value / 100), 4),
          mt.value + SUM(sup_ap.pricing_value)) AS `value`,
       75                                       AS `attribute_id`,
       `supl`.`product_id`                      AS `entity_id`,
       `cs`.`store_id`
FROM (select entity_id, `value` from `catalog_product_entity_decimal` where attribute_id = '75') AS `mt`
         LEFT JOIN `catalog_product_super_attribute` AS `sup_a` ON mt.entity_id = product_id
         INNER JOIN `catalog_product_super_attribute_pricing` AS `sup_ap`
                    ON sup_ap.product_super_attribute_id = sup_a.product_super_attribute_id
         INNER JOIN `catalog_product_super_link` AS `supl` ON mt.entity_id = supl.parent_id
         INNER JOIN `catalog_product_entity_int` AS `pint`
                    ON pint.entity_id = supl.product_id and pint.attribute_id = sup_a.attribute_id and
                       pint.value = sup_ap.value_index
         INNER JOIN `core_store` AS `cs` ON cs.website_id = sup_ap.website_id
WHERE (sup_a.product_id is not null)
GROUP BY `entity_id`, `cs`.`store_id`
LIMIT 500;

New Explain:

+------+-------------+--------------------------------+--------+----------------------------------------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------+---------+------------------------------------+------+----------------------------------------------+
| id   | select_type | table                          | type   | possible_keys                                                                                                                                                  | key                                                            | key_len | ref                                | rows | Extra                                        |
+------+-------------+--------------------------------+--------+----------------------------------------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------+---------+------------------------------------+------+----------------------------------------------+
|    1 | SIMPLE      | cs                             | index  | IDX_CORE_STORE_WEBSITE_ID                                                                                                                                      | IDX_CORE_STORE_WEBSITE_ID                                      | 2       | NULL                               |    7 | Using index; Using temporary; Using filesort |
|    1 | SIMPLE      | sup_ap                         | ref    | UNQ_CAT_PRD_SPR_ATTR_PRICING_PRD_SPR_ATTR_ID_VAL_IDX_WS_ID,IDX_CAT_PRD_SPR_ATTR_PRICING_PRD_SPR_ATTR_ID,IDX_CATALOG_PRODUCT_SUPER_ATTRIBUTE_PRICING_WEBSITE_ID | IDX_CATALOG_PRODUCT_SUPER_ATTRIBUTE_PRICING_WEBSITE_ID         | 2       | cs.website_id                      |   11 |                                              |
|    1 | SIMPLE      | sup_a                          | eq_ref | PRIMARY,UNQ_CATALOG_PRODUCT_SUPER_ATTRIBUTE_PRODUCT_ID_ATTRIBUTE_ID,IDX_CATALOG_PRODUCT_SUPER_ATTRIBUTE_PRODUCT_ID                                             | PRIMARY                                                        | 4       | sup_ap.product_super_attribute_id  |    1 | Using where                                  |
|    1 | SIMPLE      | catalog_product_entity_decimal | ref    | UNQ_CAT_PRD_ENTT_DEC_ENTT_ID_ATTR_ID_STORE_ID,IDX_CATALOG_PRODUCT_ENTITY_DECIMAL_ENTITY_ID,IDX_CATALOG_PRODUCT_ENTITY_DECIMAL_ATTRIBUTE_ID                     | UNQ_CAT_PRD_ENTT_DEC_ENTT_ID_ATTR_ID_STORE_ID                  | 6       | sup_a.product_id,const             |    1 |                                              |
|    1 | SIMPLE      | supl                           | ref    | UNQ_CATALOG_PRODUCT_SUPER_LINK_PRODUCT_ID_PARENT_ID,IDX_CATALOG_PRODUCT_SUPER_LINK_PARENT_ID,IDX_CATALOG_PRODUCT_SUPER_LINK_PRODUCT_ID                         | IDX_CATALOG_PRODUCT_SUPER_LINK_PARENT_ID                       | 4       | sup_a.product_id                   |    4 |                                              |
|    1 | SIMPLE      | pint                           | ref    | UNQ_CATALOG_PRODUCT_ENTITY_INT_ENTITY_ID_ATTRIBUTE_ID_STORE_ID,IDX_CATALOG_PRODUCT_ENTITY_INT_ATTRIBUTE_ID,IDX_CATALOG_PRODUCT_ENTITY_INT_ENTITY_ID            | UNQ_CATALOG_PRODUCT_ENTITY_INT_ENTITY_ID_ATTRIBUTE_ID_STORE_ID | 6       | supl.product_id,sup_a.attribute_id |    1 | Using where                                  |
+------+-------------+--------------------------------+--------+----------------------------------------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------+---------+------------------------------------+------+----------------------------------------------+

Update 1: Table Structors

1: catalog_product_entity_decimal;

CREATE TABLE `catalog_product_entity_decimal` (
  `value_id` int(11) NOT NULL AUTO_INCREMENT COMMENT 'Value ID',
  `entity_type_id` smallint(5) unsigned NOT NULL COMMENT 'Entity Type ID',
  `attribute_id` smallint(5) unsigned NOT NULL COMMENT 'Attribute ID',
  `store_id` smallint(5) unsigned NOT NULL COMMENT 'Store ID',
  `entity_id` int(10) unsigned NOT NULL COMMENT 'Entity ID',
  `value` decimal(12,4) DEFAULT NULL COMMENT 'Value',
  PRIMARY KEY (`value_id`),
  UNIQUE KEY `UNQ_CAT_PRD_ENTT_DEC_ENTT_ID_ATTR_ID_STORE_ID` (`entity_id`,`attribute_id`,`store_id`),
  KEY `IDX_CATALOG_PRODUCT_ENTITY_DECIMAL_STORE_ID` (`store_id`),
  KEY `IDX_CATALOG_PRODUCT_ENTITY_DECIMAL_ENTITY_ID` (`entity_id`),
  KEY `IDX_CATALOG_PRODUCT_ENTITY_DECIMAL_ATTRIBUTE_ID` (`attribute_id`),
  CONSTRAINT `FK_CATALOG_PRODUCT_ENTITY_DECIMAL_STORE_ID_CORE_STORE_STORE_ID` FOREIGN KEY (`store_id`) REFERENCES `core_store` (`store_id`) ON DELETE CASCADE ON UPDATE CASCADE,
  CONSTRAINT `FK_CAT_PRD_ENTT_DEC_ATTR_ID_EAV_ATTR_ATTR_ID` FOREIGN KEY (`attribute_id`) REFERENCES `eav_attribute` (`attribute_id`) ON DELETE CASCADE ON UPDATE CASCADE,
  CONSTRAINT `FK_CAT_PRD_ENTT_DEC_ENTT_ID_CAT_PRD_ENTT_ENTT_ID` FOREIGN KEY (`entity_id`) REFERENCES `catalog_product_entity` (`entity_id`) ON DELETE CASCADE ON UPDATE CASCADE
) ENGINE=InnoDB AUTO_INCREMENT=28087876 DEFAULT CHARSET=utf8 COMMENT='Catalog Product Decimal Attribute Backend Table'

2: catalog_product_super_attribute_pricing

CREATE TABLE `catalog_product_super_attribute_pricing` (
  `value_id` int(10) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Value ID',
  `product_super_attribute_id` int(10) unsigned NOT NULL DEFAULT '0' COMMENT 'Product Super Attribute ID',
  `value_index` varchar(255) NOT NULL COMMENT 'Value Index',
  `is_percent` smallint(5) unsigned DEFAULT '0' COMMENT 'Is Percent',
  `pricing_value` decimal(12,4) DEFAULT NULL COMMENT 'Pricing Value',
  `website_id` smallint(5) unsigned NOT NULL DEFAULT '0' COMMENT 'Website ID',
  PRIMARY KEY (`value_id`),
  UNIQUE KEY `UNQ_CAT_PRD_SPR_ATTR_PRICING_PRD_SPR_ATTR_ID_VAL_IDX_WS_ID` (`product_super_attribute_id`,`value_index`,`website_id`),
  KEY `IDX_CAT_PRD_SPR_ATTR_PRICING_PRD_SPR_ATTR_ID` (`product_super_attribute_id`),
  KEY `IDX_CATALOG_PRODUCT_SUPER_ATTRIBUTE_PRICING_WEBSITE_ID` (`website_id`),
  CONSTRAINT `FK_CAT_PRD_SPR_ATTR_PRICING_WS_ID_CORE_WS_WS_ID` FOREIGN KEY (`website_id`) REFERENCES `core_website` (`website_id`) ON DELETE CASCADE ON UPDATE CASCADE,
  CONSTRAINT `FK_CDE8813117106CFAA3AD209358F66332` FOREIGN KEY (`product_super_attribute_id`) REFERENCES `catalog_product_super_attribute` (`product_super_attribute_id`) ON DELETE CASCADE ON UPDATE CASCADE
) ENGINE=InnoDB AUTO_INCREMENT=150 DEFAULT CHARSET=utf8 COMMENT='Catalog Product Super Attribute Pricing Table'

3: catalog_product_super_link

CREATE TABLE `catalog_product_super_link` (
  `link_id` int(10) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Link ID',
  `product_id` int(10) unsigned NOT NULL DEFAULT '0' COMMENT 'Product ID',
  `parent_id` int(10) unsigned NOT NULL DEFAULT '0' COMMENT 'Parent ID',
  PRIMARY KEY (`link_id`),
  UNIQUE KEY `UNQ_CATALOG_PRODUCT_SUPER_LINK_PRODUCT_ID_PARENT_ID` (`product_id`,`parent_id`),
  KEY `IDX_CATALOG_PRODUCT_SUPER_LINK_PARENT_ID` (`parent_id`),
  KEY `IDX_CATALOG_PRODUCT_SUPER_LINK_PRODUCT_ID` (`product_id`),
  CONSTRAINT `FK_CAT_PRD_SPR_LNK_PARENT_ID_CAT_PRD_ENTT_ENTT_ID` FOREIGN KEY (`parent_id`) REFERENCES `catalog_product_entity` (`entity_id`) ON DELETE CASCADE ON UPDATE CASCADE,
  CONSTRAINT `FK_CAT_PRD_SPR_LNK_PRD_ID_CAT_PRD_ENTT_ENTT_ID` FOREIGN KEY (`product_id`) REFERENCES `catalog_product_entity` (`entity_id`) ON DELETE CASCADE ON UPDATE CASCADE
) ENGINE=InnoDB AUTO_INCREMENT=1200 DEFAULT CHARSET=utf8 COMMENT='Catalog Product Super Link Table'

4: catalog_product_entity_int

CREATE TABLE `catalog_product_entity_int` (
  `value_id` int(11) NOT NULL AUTO_INCREMENT COMMENT 'Value ID',
  `entity_type_id` int(10) unsigned NOT NULL COMMENT 'Entity Type ID',
  `attribute_id` smallint(5) unsigned NOT NULL COMMENT 'Attribute ID',
  `store_id` smallint(5) unsigned NOT NULL COMMENT 'Store ID',
  `entity_id` int(10) unsigned NOT NULL COMMENT 'Entity ID',
  `value` int(11) DEFAULT NULL COMMENT 'Value',
  PRIMARY KEY (`value_id`),
  UNIQUE KEY `UNQ_CATALOG_PRODUCT_ENTITY_INT_ENTITY_ID_ATTRIBUTE_ID_STORE_ID` (`entity_id`,`attribute_id`,`store_id`),
  KEY `IDX_CATALOG_PRODUCT_ENTITY_INT_ATTRIBUTE_ID` (`attribute_id`),
  KEY `IDX_CATALOG_PRODUCT_ENTITY_INT_STORE_ID` (`store_id`),
  KEY `IDX_CATALOG_PRODUCT_ENTITY_INT_ENTITY_ID` (`entity_id`),
  CONSTRAINT `FK_CATALOG_PRODUCT_ENTITY_INT_STORE_ID_CORE_STORE_STORE_ID` FOREIGN KEY (`store_id`) REFERENCES `core_store` (`store_id`) ON DELETE CASCADE ON UPDATE CASCADE,
  CONSTRAINT `FK_CAT_PRD_ENTT_INT_ATTR_ID_EAV_ATTR_ATTR_ID` FOREIGN KEY (`attribute_id`) REFERENCES `eav_attribute` (`attribute_id`) ON DELETE CASCADE ON UPDATE CASCADE,
  CONSTRAINT `FK_CAT_PRD_ENTT_INT_ENTT_ID_CAT_PRD_ENTT_ENTT_ID` FOREIGN KEY (`entity_id`) REFERENCES `catalog_product_entity` (`entity_id`) ON DELETE CASCADE ON UPDATE CASCADE
) ENGINE=InnoDB AUTO_INCREMENT=36351339 DEFAULT CHARSET=utf8 COMMENT='Catalog Product Integer Attribute Backend Table'

5: core_store

CREATE TABLE `core_store` (
  `store_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Store Id',
  `code` varchar(32) DEFAULT NULL COMMENT 'Code',
  `website_id` smallint(5) unsigned NOT NULL DEFAULT '0' COMMENT 'Website Id',
  `group_id` smallint(5) unsigned NOT NULL DEFAULT '0' COMMENT 'Group Id',
  `name` varchar(255) NOT NULL COMMENT 'Store Name',
  `sort_order` smallint(5) unsigned NOT NULL DEFAULT '0' COMMENT 'Store Sort Order',
  `is_active` smallint(5) unsigned NOT NULL DEFAULT '0' COMMENT 'Store Activity',
  PRIMARY KEY (`store_id`),
  UNIQUE KEY `UNQ_CORE_STORE_CODE` (`code`),
  KEY `IDX_CORE_STORE_WEBSITE_ID` (`website_id`),
  KEY `IDX_CORE_STORE_IS_ACTIVE_SORT_ORDER` (`is_active`,`sort_order`),
  KEY `IDX_CORE_STORE_GROUP_ID` (`group_id`),
  CONSTRAINT `FK_CORE_STORE_GROUP_ID_CORE_STORE_GROUP_GROUP_ID` FOREIGN KEY (`group_id`) REFERENCES `core_store_group` (`group_id`) ON DELETE CASCADE ON UPDATE CASCADE,
  CONSTRAINT `FK_CORE_STORE_WEBSITE_ID_CORE_WEBSITE_WEBSITE_ID` FOREIGN KEY (`website_id`) REFERENCES `core_website` (`website_id`) ON DELETE CASCADE ON UPDATE CASCADE
) ENGINE=InnoDB AUTO_INCREMENT=3 DEFAULT CHARSET=utf8 COMMENT='Stores'

Extremely grateful that you could take a moment to consider keep an eye on the issue above.

Update 2

I find out the problem that I have a join condition with 2 two columns has difference type.

pint.value = sup_ap.value_index