MySQL server has gone away

[cscd98]

running setup from CLI or Web.

OSX, PHP 7.0.1, (Percona) mysqld --version
mysqld Ver 5.6.25-73.1 for osx10.11 on x86_64 (Homebrew)

Starting Magento installation:
File permissions check...
[Progress: 1 / 465]
Enabling Maintenance Mode...
[Progress: 2 / 465]
Installing deployment configuration...
[Progress: 3 / 465]
Cleaning up database...
Cleaning up database `magento2_default`
[Progress: 4 / 465]
Installing database schema:
Schema creation/updates:
Module 'Magento_Store':
Installing schema.. 
[Progress: 5 / 465]
Module 'Magento_Directory':
Installing schema.. 
[Progress: 6 / 465]
Module 'Magento_Theme':
Installing schema.. 
[Progress: 7 / 465]
Module 'Magento_Eav':
Installing schema.. 
[Progress: 8 / 465]
Module 'Magento_AdvancedPricingImportExport':
[Progress: 9 / 465]
Module 'Magento_Backend':
[Progress: 10 / 465]
Module 'Magento_Amqp':
[Progress: 11 / 465]
Module 'Magento_Authorization':
Installing schema.. 
[Progress: 12 / 465]
Module 'Magento_Customer':
Installing schema.. Upgrading schema.. 
[Progress: 13 / 465]
Module 'Magento_AdminNotification':
Installing schema.. 
[Progress: 14 / 465]
Module 'Magento_Backup':
[Progress: 15 / 465]
Module 'Magento_Indexer':
Installing schema.. 
[Progress: 16 / 465]
Module 'Magento_Rule':
[Progress: 17 / 465]
Module 'Magento_Cms':
Installing schema.. 
[Progress: 18 / 465]
Module 'Magento_Catalog':
Installing schema.. Upgrading schema.. 
[Progress: 19 / 465]
Module 'Magento_BundleImportExport':
[Progress: 20 / 465]
Module 'Magento_CacheInvalidate':
[Progress: 21 / 465]
Module 'Magento_Payment':
[Progress: 22 / 465]
Module 'Magento_AdvancedCatalog':
[Progress: 23 / 465]
Module 'Magento_MediaStorage':
[Progress: 24 / 465]
Module 'Magento_CatalogImportExport':
[Progress: 25 / 465]
Module 'Magento_Quote':
Installing schema.. Upgrading schema.. 
[Progress: 26 / 465]
Module 'Magento_Search':
Installing schema.. Upgrading schema.. 
[Progress: 27 / 465]
Module 'Magento_SalesSequence':
Installing schema.. 
[Progress: 28 / 465]
Module 'Magento_Msrp':
[Progress: 29 / 465]
Module 'Magento_Sales':
Installing schema.. 
[Progress: 30 / 465]
Module 'Magento_CatalogUrlRewrite':
Installing schema.. 
[Progress: 31 / 465]
Module 'Magento_Widget':
Installing schema.. 
[Progress: 32 / 465]
Module 'Magento_CatalogInventory':
Installing schema.. 
[Progress: 33 / 465]
Module 'Magento_CheckoutAgreements':
Installing schema.. Upgrading schema.. 
[Progress: 34 / 465]
Module 'Magento_AdvancedCheckout':
[Progress: 35 / 465]
Module 'Magento_CmsUrlRewrite':
[Progress: 36 / 465]
Module 'Magento_Config':
Installing schema.. 
[Progress: 37 / 465]
Module 'Magento_ConfigurableImportExport':
[Progress: 38 / 465]
Module 'Magento_Checkout':
[Progress: 39 / 465]
Module 'Magento_Contact':
[Progress: 40 / 465]
Module 'Magento_Cookie':
[Progress: 41 / 465]
Module 'Magento_Cron':
Installing schema.. 
[Progress: 42 / 465]
Module 'Magento_CurrencySymbol':
[Progress: 43 / 465]
Module 'Magento_CustomAttributeManagement':
[Progress: 44 / 465]
Module 'Magento_Captcha':
Installing schema.. 
[Progress: 45 / 465]
Module 'Magento_CustomerBalance':
Installing schema.. 
[Progress: 46 / 465]
Module 'Magento_CatalogRule':
Installing schema.. 
[Progress: 47 / 465]
Module 'Magento_CustomerFinance':
[Progress: 48 / 465]
Module 'Magento_CustomerImportExport':
[Progress: 49 / 465]
Module 'Magento_SalesRule':
Installing schema.. 
[Progress: 50 / 465]
Module 'Magento_Cybersource':
[Progress: 51 / 465]
Module 'Magento_Deploy':
[Progress: 52 / 465]
Module 'Magento_Developer':
[Progress: 53 / 465]
Module 'Magento_Dhl':
[Progress: 54 / 465]
Module 'Magento_AdvancedSearch':
Installing schema.. 
[Progress: 55 / 465]
Module 'Magento_Downloadable':
Installing schema.. 
[Progress: 56 / 465]
Module 'Magento_ImportExport':
Installing schema.. Upgrading schema.. 
[Progress: 57 / 465]
Module 'Magento_User':
Installing schema.. Upgrading schema.. 
[Progress: 58 / 465]
Module 'Magento_Email':
Installing schema.. 
[Progress: 59 / 465]
Module 'Magento_EncryptionKey':
[Progress: 60 / 465]
Module 'Magento_Enterprise':
[Progress: 61 / 465]
Module 'Magento_Eway':
[Progress: 62 / 465]
Module 'Magento_Fedex':
[Progress: 63 / 465]
Module 'Magento_GiftCard':
Installing schema.. 
[Progress: 64 / 465]
Module 'Magento_GiftCardAccount':
Installing schema.. 
[Progress: 65 / 465]
Module 'Magento_GiftCardImportExport':
[Progress: 66 / 465]
Module 'Magento_GiftMessage':
Installing schema.. 
[Progress: 67 / 465]
Module 'Magento_Wishlist':
Installing schema.. 
[Progress: 68 / 465]
Module 'Magento_GiftWrapping':
Installing schema.. 
[Progress: 69 / 465]
Module 'Magento_GoogleAdwords':
[Progress: 70 / 465]
Module 'Magento_GoogleAnalytics':
[Progress: 71 / 465]
Module 'Magento_GoogleOptimizer':
Installing schema.. 
[Progress: 72 / 465]
Module 'Magento_PageCache':
[Progress: 73 / 465]
Module 'Magento_GroupedImportExport':
[Progress: 74 / 465]
Module 'Magento_GroupedProduct':
[Progress: 75 / 465]
Module 'Magento_DownloadableImportExport':
[Progress: 76 / 465]
Module 'Magento_CustomerCustomAttributes':
Installing schema.. 
[Progress: 77 / 465]
Module 'Magento_Integration':
Installing schema.. 
[Progress: 78 / 465]
Module 'Magento_Reports':
Installing schema.. 
[Progress: 79 / 465]
Module 'Magento_LayeredNavigation':
[Progress: 80 / 465]
Module 'Magento_Logging':
Installing schema.. 
[Progress: 81 / 465]
Module 'Magento_Marketplace':
[Progress: 82 / 465]
Module 'Magento_CatalogEvent':
Installing schema.. 
[Progress: 83 / 465]
Module 'Magento_MessageQueue':
[Progress: 84 / 465]
Module 'Magento_ConfigurableProduct':
Installing schema.. 
[Progress: 85 / 465]
Module 'Magento_MultipleWishlist':
Installing schema.. 
[Progress: 86 / 465]
Module 'Magento_Multishipping':
[Progress: 87 / 465]
Module 'Magento_MysqlMq':
Installing schema.. 
[Progress: 88 / 465]
Module 'Magento_NewRelicReporting':
Installing schema.. 
[Progress: 89 / 465]
Module 'Magento_Newsletter':
Installing schema.. 
[Progress: 90 / 465]
Module 'Magento_OfflinePayments':
[Progress: 91 / 465]
Module 'Magento_OfflineShipping':
Installing schema.. 
[Progress: 92 / 465]
Module 'Magento_VersionsCms':
Installing schema.. 
[Progress: 93 / 465]
Module 'Magento_Authorizenet':
[Progress: 94 / 465]
Module 'Magento_Paypal':
Installing schema.. 
[Progress: 95 / 465]
Module 'Magento_Persistent':
Installing schema.. 
[Progress: 96 / 465]
Module 'Magento_PersistentHistory':
[Progress: 97 / 465]
Module 'Magento_Bundle':
Installing schema.. Upgrading schema.. 
[Progress: 98 / 465]
Module 'Magento_ProductAlert':
Installing schema.. 
[Progress: 99 / 465]
Module 'Magento_ProductVideo':
Installing schema.. 
[Progress: 100 / 465]
Module 'Magento_PromotionPermissions':
[Progress: 101 / 465]
Module 'Magento_CatalogSearch':
Installing schema.. 
[Progress: 102 / 465]
Module 'Magento_Reminder':
Installing schema.. 
[Progress: 103 / 465]
Module 'Magento_WebsiteRestriction':
[Progress: 104 / 465]
Module 'Magento_RequireJs':
[Progress: 105 / 465]
Module 'Magento_ResourceConnections':
[Progress: 106 / 465]
Module 'Magento_Review':
Installing schema.. 
[Progress: 107 / 465]
Module 'Magento_Reward':
Installing schema.. 
[Progress: 108 / 465]
Module 'Magento_Rma':
Installing schema.. 
[Progress: 109 / 465]
Module 'Magento_Rss':
[Progress: 110 / 465]
Module 'Magento_CustomerSegment':
Installing schema.. 
[Progress: 111 / 465]
Module 'Magento_Banner':
Installing schema.. 
[Progress: 112 / 465]
Module 'Magento_SalesArchive':
[Progress: 113 / 465]
Module 'Magento_TargetRule':
Installing schema.. 
[Progress: 114 / 465]
Module 'Magento_Braintree':
[Progress: 115 / 465]
Module 'Magento_SampleData':
[Progress: 116 / 465]
Module 'Magento_ScalableCheckout':
[Progress: 117 / 465]
Module 'Magento_ScalableInventory':
Installing schema.. 
[Progress: 118 / 465]
Module 'Magento_ScalableOms':
[Progress: 119 / 465]
Module 'Magento_ScheduledImportExport':
Installing schema.. 
[Progress: 120 / 465]
Module 'Magento_CatalogPermissions':
Installing schema.. 
[Progress: 121 / 465]
Module 'Magento_SendFriend':
Installing schema.. 
[Progress: 122 / 465]
Module 'Magento_Ui':
Installing schema.. 
[Progress: 123 / 465]
Module 'Magento_Sitemap':
Installing schema.. 
[Progress: 124 / 465]
Module 'Magento_Solr':
[Progress: 125 / 465]
Module 'Magento_CatalogRuleConfigurable':
[Progress: 126 / 465]
Module 'Magento_Support':
Installing schema.. 
[Progress: 127 / 465]
Module 'Magento_Swagger':
[Progress: 128 / 465]
Module 'Magento_Swatches':
Installing schema.. 
[Progress: 129 / 465]
Module 'Magento_GoogleTagManager':
Installing schema.. 
[Progress: 130 / 465]
Module 'Magento_Tax':
Installing schema.. 
[Progress: 131 / 465]
Module 'Magento_TaxImportExport':
[Progress: 132 / 465]
Module 'Magento_PricePermissions':
[Progress: 133 / 465]
Module 'Magento_Translation':
Installing schema.. 
[Progress: 134 / 465]
Module 'Magento_Shipping':
[Progress: 135 / 465]
Module 'Magento_Ups':
[Progress: 136 / 465]
Module 'Magento_UrlRewrite':
Installing schema.. 
[Progress: 137 / 465]
Module 'Magento_AdminGws':
Installing schema.. 
[Progress: 138 / 465]
Module 'Magento_Usps':
[Progress: 139 / 465]
Module 'Magento_Variable':
Installing schema.. 
[Progress: 140 / 465]
Module 'Magento_Version':
[Progress: 141 / 465]
Module 'Magento_BannerCustomerSegment':
Installing schema.. 
[Progress: 142 / 465]
Module 'Magento_VisualMerchandiser':
Installing schema.. 
[Progress: 143 / 465]
Module 'Magento_Webapi':
[Progress: 144 / 465]
Module 'Magento_Invitation':
Installing schema.. 
[Progress: 145 / 465]
Module 'Magento_Weee':
Installing schema.. 
[Progress: 146 / 465]
Module 'Magento_CatalogWidget':
[Progress: 147 / 465]
Module 'Magento_GiftRegistry':
Installing schema.. 
[Progress: 148 / 465]
Module 'Magento_Worldpay':
[Progress: 149 / 465]
Module 'Mirasvit_Core':
Installing schema.. 
[Progress: 150 / 465]
Module 'Mirasvit_Misspell':
Installing schema.. 
[Progress: 151 / 465]
Module 'Mirasvit_Search':
Installing schema.. 
[Progress: 152 / 465]
Module 'Mirasvit_SearchAutocomplete':
[Progress: 153 / 465]
Module 'Mirasvit_SearchMysql':
[Progress: 154 / 465]
Module 'Mirasvit_SearchSphinx':
[Progress: 155 / 465]
Schema post-updates:
Module 'Magento_Store':
[Progress: 156 / 465]
Module 'Magento_Directory':
[Progress: 157 / 465]
Module 'Magento_Theme':
[Progress: 158 / 465]
Module 'Magento_Eav':
[Progress: 159 / 465]
Module 'Magento_AdvancedPricingImportExport':
[Progress: 160 / 465]
Module 'Magento_Backend':
[Progress: 161 / 465]
Module 'Magento_Amqp':
[Progress: 162 / 465]
Module 'Magento_Authorization':
[Progress: 163 / 465]
Module 'Magento_Customer':
[Progress: 164 / 465]
Module 'Magento_AdminNotification':
[Progress: 165 / 465]
Module 'Magento_Backup':
[Progress: 166 / 465]
Module 'Magento_Indexer':
Running recurring.. PHP Notice:  PDO::__construct(): send of 127 bytes failed with errno=32 Broken pipe in /Users/ccarnell/Sites/xx/vendor/magento/zendframework1/library/Zend/Db/Adapter/Pdo/Abstract.php on line 128

Notice: PDO::__construct(): send of 127 bytes failed with errno=32 Broken pipe in /Users/ccarnell/Sites/xxvendor/magento/zendframework1/library/Zend/Db/Adapter/Pdo/Abstract.php on line 128



  [Zend_Db_Adapter_Exception]                        
  SQLSTATE[HY000] [2006] MySQL server has gone away

[cscd98]

closed by max_allowed_packet=100M

[cscd98]

Seems to have come back again

[markshust]

MySQL gone away is typically an out-of-memory error. How much RAM do you have devoted to MySQL and the machine you are installing on?

[cscd98]

@markoshust I have 16GB of RAM on my macbook.

This is my /etc/my.cnf:

[mysqld]
max_allowed_packet=512M # default is 4194304
connect_timeout=60 # default 10

sql_mode=NO_ENGINE_SUBSTITUTION,STRICT_TRANS_TABLES 

[cscd98]

@markoshust

http://bugs.mysql.com/bug.php?id=79125

[vrann]

The following link provides solution which solved issue for me:
http://stackoverflow.com/questions/17813630/mysql-5-6-headaches-on-mac-osx

innodb_file_per_table = OFF
table_open_cache = 250

Please use it on development environment only.

[cscd98]

@vrann Seems to have fixed it for me, thanks!

[cscd98]

In case anyone finds this again..

# check open file limit
sysctl kern.maxfiles

# edit sysctl
sudo vim /etc/sysctl.conf

# add these two lines
kern.maxfiles=10485760
kern.maxfilesperproc=1048576

# reboot
sudo reboot

# check new file limit
sysctl kern.maxfiles

Better solution without turning off innodb_file_per_table. Works on OSX Sierra

You have to create a file at /Library/LaunchDaemons/limit.maxfiles.plist (owner: root:wheel, mode: 0644):

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN"
        "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
  <dict>
    <key>Label</key>
    <string>limit.maxfiles</string>
    <key>ProgramArguments</key>
    <array>
      <string>launchctl</string>
      <string>limit</string>
      <string>maxfiles</string>
      <string>262144</string>
      <string>524288</string>
    </array>
    <key>RunAtLoad</key>
    <true/>
    <key>ServiceIPC</key>
    <false/>
  </dict>
</plist>

My ulimit is now:

core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
file size               (blocks, -f) unlimited
max locked memory       (kbytes, -l) unlimited
max memory size         (kbytes, -m) unlimited
open files                      (-n) 262144
pipe size            (512 bytes, -p) 1
stack size              (kbytes, -s) 8192
cpu time               (seconds, -t) unlimited
max user processes              (-u) 709
virtual memory          (kbytes, -v) unlimited