php - MYSQL query performs very slow

Question

I have developed a user bulk upload module. There are 2 situations, when I do a bulk upload of 20 000 records when database has zero records. Its taking about 5 hours. But when the database already has about 30 000 records the upload is very very slow. It takes about 11 hours to upload 20 000 records. I am just reading a CSV file via fgetcsv method.

if (($handle = fopen($filePath, "r")) !== FALSE) {
            while (($peopleData = fgetcsv($handle, 10240, ",")) !== FALSE) {
                if (count($peopleData) == $fieldsCount) {

//inside i check if user already exist (firstName & lastName & DOB)
//if not, i check if email exist. if exist, update the records.
//other wise insert a new record.
}}}

Below are the queries that run. (I am using Yii framework)

SELECT * 
FROM `AdvanceBulkInsert` `t` 
WHERE renameSource='24851_bulk_people_2016-02-25_LE CARVALHO 1.zip.csv' 
LIMIT 1

SELECT cf.*, ctyp.typeName, cfv.id as customId, cfv.customFieldId, 
       cfv.relatedId, cfv.fieldValue, cfv.createdAt 
FROM `CustomField` `cf` 
    INNER JOIN CustomType ctyp on ctyp.id = cf.customTypeId 
    LEFT OUTER JOIN CustomValue cfv on cf.id = cfv.customFieldId 
                and relatedId = 0 
    LEFT JOIN CustomFieldSubArea cfsa on cfsa.customFieldId = cf.id 
WHERE ((relatedTable = 'people' and enabled = '1') 
  AND (onCreate = '1')) 
  AND (cfsa.subarea='peoplebulkinsert') 
ORDER BY cf.sortOrder, cf.label

SELECT * 
FROM `User` `t` 
WHERE `t`.`firstName`='Franck' 
  AND `t`.`lastName`='ALLEGAERT ' 
  AND `t`.`dateOfBirth`='1971-07-29' 
  AND (userType NOT IN ("1")) 
LIMIT 1

If exist update the user:

UPDATE `User` SET `id`='51394', `address1`='49 GRANDE RUE', 
                  `mobile`='', `name`=NULL, `firstName`='Franck', 
                  `lastName`='ALLEGAERT ', `username`=NULL, 
                  `password`=NULL, `email`=NULL, `gender`=0, 
                  `zip`='60310', `countryCode`='DZ', 
                  `joinedDate`='2016-02-23 10:44:18', 
                  `signUpDate`='0000-00-00 00:00:00', 
                  `supporterDate`='2016-02-25 13:26:37', `userType`=3, 
                  `signup`=0, `isSysUser`=0, `dateOfBirth`='1971-07-29', 
                  `reqruiteCount`=0, `keywords`='70,71,72,73,74,75', 
                  `delStatus`=0, `city`='AMY', `isUnsubEmail`=0, 
                  `isManual`=1, `isSignupConfirmed`=0, `profImage`=NULL, 
                  `totalDonations`=NULL, `isMcContact`=NULL, 
                  `emailStatus`=NULL, `notes`=NULL, 
                  `addressInvalidatedAt`=NULL, 
                  `createdAt`='2016-02-23 10:44:18', 
                  `updatedAt`='2016-02-25 13:26:37', `longLat`=NULL 
WHERE `User`.`id`='51394'

If user don't exist, insert new record.

Table engine type is MYISAM. Only the email column has a index.

How can I optimize this to reduce the processing time?

Query 2, took 0.4701 seconds which means for 30 000 records it will take 14103 sec, which is about 235 minutes. approx 6 hours.

Update

CREATE TABLE IF NOT EXISTS `User` (
  `id` bigint(20) NOT NULL,
  `address1` text COLLATE utf8_unicode_ci,
  `mobile` varchar(15) COLLATE utf8_unicode_ci DEFAULT NULL,
  `name` varchar(45) COLLATE utf8_unicode_ci DEFAULT NULL,
  `firstName` varchar(64) COLLATE utf8_unicode_ci DEFAULT NULL,
  `lastName` varchar(64) COLLATE utf8_unicode_ci DEFAULT NULL,
  `username` varchar(20) COLLATE utf8_unicode_ci DEFAULT NULL,
  `password` varchar(45) COLLATE utf8_unicode_ci DEFAULT NULL,
  `email` varchar(45) COLLATE utf8_unicode_ci DEFAULT NULL,
  `gender` tinyint(2) NOT NULL DEFAULT '0' COMMENT '1 - female, 2-male, 0 - unknown',
  `zip` varchar(15) COLLATE utf8_unicode_ci DEFAULT NULL,
  `countryCode` varchar(3) COLLATE utf8_unicode_ci DEFAULT NULL,
  `joinedDate` datetime DEFAULT NULL,
  `signUpDate` datetime NOT NULL COMMENT 'User signed up date',
  `supporterDate` datetime NOT NULL COMMENT 'Date which user get supporter',
  `userType` tinyint(2) NOT NULL,
  `signup` tinyint(2) NOT NULL DEFAULT '0' COMMENT 'whether user followed signup process 1 - signup, 0 - not signup',
  `isSysUser` tinyint(1) NOT NULL DEFAULT '0' COMMENT '1 - system user, 0 - not a system user',
  `dateOfBirth` date DEFAULT NULL COMMENT 'User date of birth',
  `reqruiteCount` int(11) DEFAULT '0' COMMENT 'User count that he has reqruited',
  `keywords` text COLLATE utf8_unicode_ci COMMENT 'Kewords',
  `delStatus` tinyint(2) NOT NULL DEFAULT '0' COMMENT '0 - active, 1 - deleted',
  `city` varchar(50) COLLATE utf8_unicode_ci DEFAULT NULL,
  `isUnsubEmail` tinyint(1) NOT NULL DEFAULT '0' COMMENT '0 - ok, 1 - Unsubscribed form email',
  `isManual` tinyint(1) NOT NULL DEFAULT '0' COMMENT '0 - ok, 1 - Manualy add',
  `longLat` varchar(45) COLLATE utf8_unicode_ci DEFAULT NULL COMMENT 'Longitude and Latitude',
  `isSignupConfirmed` tinyint(4) NOT NULL DEFAULT '0' COMMENT 'Whether user has confirmed signup ',
  `profImage` tinytext COLLATE utf8_unicode_ci COMMENT 'Profile image name or URL',
  `totalDonations` float DEFAULT NULL COMMENT 'Total donations made by the user',
  `isMcContact` tinyint(1) DEFAULT NULL COMMENT '1 - Mailchimp contact',
  `emailStatus` tinyint(2) DEFAULT NULL COMMENT '1-bounced, 2-blocked',
  `notes` text COLLATE utf8_unicode_ci,
  `addressInvalidatedAt` datetime DEFAULT NULL,
  `createdAt` datetime NOT NULL,
  `updatedAt` datetime DEFAULT NULL
) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;

CREATE TABLE IF NOT EXISTS `AdvanceBulkInsert` (
  `id` int(11) NOT NULL,
  `source` varchar(256) NOT NULL,
  `renameSource` varchar(256) DEFAULT NULL,
  `countryCode` varchar(3) NOT NULL,
  `userType` tinyint(2) NOT NULL,
  `size` varchar(128) NOT NULL,
  `errors` varchar(512) NOT NULL,
  `status` char(1) NOT NULL COMMENT '1:Queued, 2:In Progress, 3:Error, 4:Finished, 5:Cancel',
  `createdAt` datetime NOT NULL,
  `createdBy` int(11) NOT NULL
) ENGINE=MyISAM DEFAULT CHARSET=latin1;

CREATE TABLE IF NOT EXISTS `CustomField` (
  `id` int(11) NOT NULL,
  `customTypeId` int(11) NOT NULL,
  `fieldName` varchar(64) COLLATE utf8_unicode_ci DEFAULT NULL,
  `relatedTable` varchar(64) COLLATE utf8_unicode_ci DEFAULT NULL,
  `defaultValue` text COLLATE utf8_unicode_ci,
  `sortOrder` int(11) NOT NULL DEFAULT '0',
  `enabled` char(1) COLLATE utf8_unicode_ci DEFAULT '1',
  `listItemTag` char(1) COLLATE utf8_unicode_ci DEFAULT NULL,
  `required` char(1) COLLATE utf8_unicode_ci DEFAULT '0',
  `onCreate` char(1) COLLATE utf8_unicode_ci DEFAULT '1',
  `onEdit` char(1) COLLATE utf8_unicode_ci DEFAULT '1',
  `onView` char(1) COLLATE utf8_unicode_ci DEFAULT '1',
  `listValues` text COLLATE utf8_unicode_ci,
  `label` varchar(64) COLLATE utf8_unicode_ci DEFAULT NULL,
  `htmlOptions` text COLLATE utf8_unicode_ci
) ENGINE=MyISAM AUTO_INCREMENT=12 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;

CREATE TABLE IF NOT EXISTS `CustomFieldSubArea` (
  `id` int(11) NOT NULL,
  `customFieldId` int(11) NOT NULL,
  `subarea` varchar(256) COLLATE utf8_unicode_ci NOT NULL
) ENGINE=MyISAM AUTO_INCREMENT=43 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;

CREATE TABLE IF NOT EXISTS `CustomValue` (
  `id` int(11) NOT NULL,
  `customFieldId` int(11) NOT NULL,
  `relatedId` int(11) NOT NULL,
  `fieldValue` text COLLATE utf8_unicode_ci,
  `createdAt` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP
) ENGINE=MyISAM AUTO_INCREMENT=86866 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;

Entire PHP Code is here http://pastie.org/10737962

Update 2

Explain output of the Query

Answer 1

Indexes are your friend.

UPDATE User ... WHERE id = ... -- Desperately needs an index on ID, probably PRIMARY KEY.

Similarly for renameSource.

SELECT * 
FROM `User` `t` 
WHERE `t`.`firstName`='Franck' 
  AND `t`.`lastName`='ALLEGAERT ' 
  AND `t`.`dateOfBirth`='1971-07-29' 
  AND (userType NOT IN ("1")) 
LIMIT 1;

Needs INDEX(firstName, lastName, dateOfBirth); the fields can be in any order (in this case).

Look at each query to see what it needs, then add that INDEX to the table. Read my Cookbook on building indexes.