Encountered error in Mysql::initcache

So I was having some strange issues with a table on staging database for a site. This table is innodb and despite the fact that I've never had to run optimize table on an innodb table I decided to give it a go. Of course 3 hours later when it was still not finished I decided to kill the process and thats when everything started going wrong. Since then phpMyAdmin will not work on the account and neither will the mysql databases tab. I tried manually deleting the table files from the database folder but that did not work, probably made it worse. I disabled the tweak settings for "Use INFORMATION_SCHEMA to acquire MySQL disk usage [?]" I have also even tried using the cpanel api to delete and re-create the database to no avail. This is only bugged out on this one account. The message I get when trying to view the mysql databases tab is: 58675 And here is the log output when that happens:


[2019-05-15 10:03:14 -0500] warn [cpmysql] [30483] TIME 1557932594 UID 0 clobbered stale lock file "/var/cpanel/databases/humboldt.json.lock" (NAME "/usr/local/cpanel/bin/admin/Cpanel/cpmysql", UID 0) written by PID 29305 at 1557932542 at /usr/local/cpanel/Cpanel/SafeFile.pm line 940,  line 1.
        Cpanel::SafeFile::_lock_wait("/var/cpanel/databases/humboldt.json") called at /usr/local/cpanel/Cpanel/SafeFile.pm line 360
        Cpanel::SafeFile::_safelock("/var/cpanel/databases/humboldt.json") called at /usr/local/cpanel/Cpanel/SafeFile.pm line 563
        Cpanel::SafeFile::_safe_open(undef, 2, "/var/cpanel/databases/humboldt.json", CODE(0x2bfa6d0), "safesysopen") called at /usr/local/cpanel/Cpanel/SafeFile.pm line 213
        eval {...} called at /usr/local/cpanel/Cpanel/SafeFile.pm line 212
        Cpanel::SafeFile::safesysopen(undef, "/var/cpanel/databases/humboldt.json", 2, 416) called at /usr/local/cpanel/Cpanel/SafeFile.pm line 126
        Cpanel::SafeFile::safesysopen_no_warn_on_fail(undef, "/var/cpanel/databases/humboldt.json", 2, 416) called at /usr/local/cpanel/Cpanel/Transaction/File/Base.pm line 137
        Cpanel::Transaction::File::Base::new("Cpanel::Transaction::File::JSON", "path", "/var/cpanel/databases/humboldt.json", "permissions", 416, "ownership", ARRAY(0x2ba4230), "sysopen_flags", ...) called at /usr/local/cpanel/Cpanel/DB/Map.pm line 201
        Cpanel::DB::Map::_open_transaction(Cpanel::DB::Map=HASH(0x2b7db78), "sysopen_flags", 0) called at /usr/local/cpanel/Cpanel/DB/Map.pm line 214
        Cpanel::DB::Map::_initialize_data(Cpanel::DB::Map=HASH(0x2b7db78)) called at /usr/local/cpanel/Cpanel/DB/Map.pm line 119
        Cpanel::DB::Map::new("Cpanel::DB::Map", HASH(0x2b782c0)) called at /usr/local/cpanel/Cpanel/DBAdmin.pm line 238
        Cpanel::DBAdmin::_get_map(Cpanel::Mysql=HASH(0x2b78818)) called at /usr/local/cpanel/Cpanel/Mysql.pm line 418
        Cpanel::Mysql::updateprivs(Cpanel::Mysql=HASH(0x2b78818)) called at /usr/local/cpanel/Cpanel/Mysql.pm line 1076
        Cpanel::Mysql::dbcache(Cpanel::Mysql=HASH(0x2b78818), "") called at bin/admin/Cpanel/cpmysql.pl line 387
Invalid grant string: GRANT geo TO 'humboldt_dbuser'@'localhost'
[2019-05-15 10:03:14 -0500] warn [cpanel] Cpanel::Wrap::send_cpwrapd_request adminbin Cpanel/cpmysql/DBCACHE: exit 11: namespace=[Cpanel] module=[cpmysql] function=[DBCACHE]: set error in context mysql: raw_response=[{"status":1,"mode":"simple","statusmsg":"adminbin Cpanel/cpmysql/DBCACHE: exit 11","error":1,"exit_code":2816,"action":"run","version":"2.4","data":"DBDISKUSED\ttest_humboldt_sublymecart\t339403929\nDBDISKUSED\thumboldt_live\t866075021\nDBDISKUSED\thumboldt_sublymecart\t464615350\nDBDISKUSED\thumboldt_staging\t0\nDBDISKUSED\thumboldt_isodocs\t52463\nDBDISKUSED\thumboldt_wp811\t1071956\nDBDISKUSED\thumboldt_craft\t28545043\nDISKUSED\t1699763762\nDB\thumboldt_craft\nDBUSER\thumboldt_craft\thumboldt_dbuser\nDB\thumboldt_live\nDBUSER\thumboldt_live\thumboldt_dbuser\nDB\thumboldt_wp811\nDBUSER\thumboldt_wp811\thumboldt_wp811\nDB\thumboldt_staging\nDBUSER\thumboldt_staging\thumboldt_dbuser\nDB\thumboldt_sublymecart\nDBUSER\thumboldt_sublymecart\thumboldt_dbuser\nDB\thumboldt_isodocs\nDBUSER\thumboldt_isodocs\thumboldt_dbuser\nUSER\thumboldt_onyxa\nUSER\thumboldt_dbuser\n","timeout":0}] at /usr/local/cpanel/Cpanel/Wrap.pm line 119, <$socket> line 1.
        Cpanel::Wrap::send_cpwrapd_request("namespace", "Cpanel", "module", "cpmysql", "function", "DBCACHE", "data", "", ...) called at /usr/local/cpanel/Cpanel/AdminBin.pm line 57
        Cpanel::AdminBin::adminrun("cpmysql", "DBCACHE", "") called at /usr/local/cpanel/Cpanel/MysqlFE/DB.pm line 233
        Cpanel::MysqlFE::DB::_initcache("") called at cpanel.pl line 2506
        cpanel::cpanel::domysql("initcache", ARRAY(0x31deb38)) called at cpanel.pl line 1840
        eval {...} called at cpanel.pl line 1840
        cpanel::cpanel::_api1("Mysql", "mysql", "initcache()", "initcache", ARRAY(0x31deb38), "safe_html_encode") called at /usr/local/cpanel/Cpanel/Template/Plugin/Api1.pm line 93
        eval {...} called at /usr/local/cpanel/Cpanel/Template/Plugin/Api1.pm line 93
        Cpanel::Template::Plugin::Api1::_api1_exec(0, "Mysql", "initcache", ARRAY(0x31deb38)) called at /usr/local/cpanel/Cpanel/Template/Plugin/Api1.pm line 47
        Cpanel::Template::Plugin::Api1::_captured_api1_exec("Mysql", "initcache", ARRAY(0x31deb38)) called at /var/cpanel/template_compiles//usr/local/cpanel/base/frontend/paper_lantern/sql/index.html.tt line 1
        eval {...} called at /var/cpanel/template_compiles//usr/local/cpanel/base/frontend/paper_lantern/sql/index.html.tt line 1
        eval {...} called at /var/cpanel/template_compiles//usr/local/cpanel/base/frontend/paper_lantern/sql/index.html.tt line 1
        Template::Provider::__ANON__(Template::Context=HASH(0x31d2a80)) called at /usr/local/cpanel/3rdparty/perl/528/lib/perl5/cpanel_lib/x86_64-linux-64int/Template/Document.pm line 162
        eval {...} called at /usr/local/cpanel/3rdparty/perl/528/lib/perl5/cpanel_lib/x86_64-linux-64int/Template/Document.pm line 160
        Template::Document::process(Template::Document=HASH(0x3271c38), Template::Context=HASH(0x31d2a80)) called at /usr/local/cpanel/3rdparty/perl/528/lib/perl5/cpanel_lib/x86_64-linux-64int/Template/Context.pm line 357
        eval {...} called at /usr/local/cpanel/3rdparty/perl/528/lib/perl5/cpanel_lib/x86_64-linux-64int/Template/Context.pm line 327
        Template::Context::process(Template::Context=HASH(0x31d2a80), Template::Document=HASH(0x3271c38)) called at /usr/local/cpanel/3rdparty/perl/528/lib/perl5/cpanel_lib/x86_64-linux-64int/Template/Service.pm line 94
        eval {...} called at /usr/local/cpanel/3rdparty/perl/528/lib/perl5/cpanel_lib/x86_64-linux-64int/Template/Service.pm line 91
        Template::Service::process(Template::Service=HASH(0x31d2648), "/usr/local/cpanel/base/frontend/paper_lantern/sql/index.html.tt", HASH(0x31d9430)) called at /usr/local/cpanel/3rdparty/perl/528/lib/perl5/cpanel_lib/x86_64-linux-64int/Template.pm line 64
        Template::process(Template=HASH(0x31d9958), "/usr/local/cpanel/base/frontend/paper_lantern/sql/index.html.tt", HASH(0x31d9430), SCALAR(0x1408d40)) called at /usr/local/cpanel/Cpanel/Template.pm line 477
        Cpanel::Template::process_template("cpanel", HASH(0x31d9430), HASH(0x1434ab0)) called at cpanel.pl line 1058
        cpanel::cpanel::cptt_exectag("/usr/local/cpanel/base/frontend/paper_lantern/sql/index.html.tt", 1) called at cpanel.pl line 4409
        cpanel::cpanel::run_standard_mode() called at cpanel.pl line 878
        cpanel::cpanel::script("cpanel::cpanel", "./frontend/paper_lantern/sql/index.html.tt") called at cpanel.pl line 321
[2019-05-15 10:03:14 -0500] warn [cpanel] Cpanel::Wrap::send_cpwrapd_request error: namespace=[Cpanel] module=[cpmysql] function=[DBCACHE]: set error in context mysql: statusmsg=[adminbin Cpanel/cpmysql/DBCACHE: exit 11] at /usr/local/cpanel/Cpanel/Wrap.pm line 128, <$socket> line 1.
        Cpanel::Wrap::send_cpwrapd_request("namespace", "Cpanel", "module", "cpmysql", "function", "DBCACHE", "data", "", ...) called at /usr/local/cpanel/Cpanel/AdminBin.pm line 57
        Cpanel::AdminBin::adminrun("cpmysql", "DBCACHE", "") called at /usr/local/cpanel/Cpanel/MysqlFE/DB.pm line 233
        Cpanel::MysqlFE::DB::_initcache("") called at cpanel.pl line 2506
        cpanel::cpanel::domysql("initcache", ARRAY(0x31deb38)) called at cpanel.pl line 1840
        eval {...} called at cpanel.pl line 1840
        cpanel::cpanel::_api1("Mysql", "mysql", "initcache()", "initcache", ARRAY(0x31deb38), "safe_html_encode") called at /usr/local/cpanel/Cpanel/Template/Plugin/Api1.pm line 93
        eval {...} called at /usr/local/cpanel/Cpanel/Template/Plugin/Api1.pm line 93
        Cpanel::Template::Plugin::Api1::_api1_exec(0, "Mysql", "initcache", ARRAY(0x31deb38)) called at /usr/local/cpanel/Cpanel/Template/Plugin/Api1.pm line 47
        Cpanel::Template::Plugin::Api1::_captured_api1_exec("Mysql", "initcache", ARRAY(0x31deb38)) called at /var/cpanel/template_compiles//usr/local/cpanel/base/frontend/paper_lantern/sql/index.html.tt line 1
        eval {...} called at /var/cpanel/template_compiles//usr/local/cpanel/base/frontend/paper_lantern/sql/index.html.tt line 1
        eval {...} called at /var/cpanel/template_compiles//usr/local/cpanel/base/frontend/paper_lantern/sql/index.html.tt line 1
        Template::Provider::__ANON__(Template::Context=HASH(0x31d2a80)) called at /usr/local/cpanel/3rdparty/perl/528/lib/perl5/cpanel_lib/x86_64-linux-64int/Template/Document.pm line 162
        eval {...} called at /usr/local/cpanel/3rdparty/perl/528/lib/perl5/cpanel_lib/x86_64-linux-64int/Template/Document.pm line 160
        Template::Document::process(Template::Document=HASH(0x3271c38), Template::Context=HASH(0x31d2a80)) called at /usr/local/cpanel/3rdparty/perl/528/lib/perl5/cpanel_lib/x86_64-linux-64int/Template/Context.pm line 357
        eval {...} called at /usr/local/cpanel/3rdparty/perl/528/lib/perl5/cpanel_lib/x86_64-linux-64int/Template/Context.pm line 327
        Template::Context::process(Template::Context=HASH(0x31d2a80), Template::Document=HASH(0x3271c38)) called at /usr/local/cpanel/3rdparty/perl/528/lib/perl5/cpanel_lib/x86_64-linux-64int/Template/Service.pm line 94
        eval {...} called at /usr/local/cpanel/3rdparty/perl/528/lib/perl5/cpanel_lib/x86_64-linux-64int/Template/Service.pm line 91
        Template::Service::process(Template::Service=HASH(0x31d2648), "/usr/local/cpanel/base/frontend/paper_lantern/sql/index.html.tt", HASH(0x31d9430)) called at /usr/local/cpanel/3rdparty/perl/528/lib/perl5/cpanel_lib/x86_64-linux-64int/Template.pm line 64
        Template::process(Template=HASH(0x31d9958), "/usr/local/cpanel/base/frontend/paper_lantern/sql/index.html.tt", HASH(0x31d9430), SCALAR(0x1408d40)) called at /usr/local/cpanel/Cpanel/Template.pm line 477
        Cpanel::Template::process_template("cpanel", HASH(0x31d9430), HASH(0x1434ab0)) called at cpanel.pl line 1058
        cpanel::cpanel::cptt_exectag("/usr/local/cpanel/base/frontend/paper_lantern/sql/index.html.tt", 1) called at cpanel.pl line 4409
        cpanel::cpanel::run_standard_mode() called at cpanel.pl line 878
        cpanel::cpanel::script("cpanel::cpanel", "./frontend/paper_lantern/sql/index.html.tt") called at cpanel.pl line 321
[2019-05-15 10:03:14 -0500] warn [cpanel] Encountered error in Mysql::initcache: Mysql::initcache failed: DBDISKUSED    test_humboldt_sublymecart       339403929
DBDISKUSED      humboldt_live   866075021
DBDISKUSED      humboldt_sublymecart    464615350
DBDISKUSED      humboldt_staging        0
DBDISKUSED      humboldt_isodocs        52463
DBDISKUSED      humboldt_wp811  1071956
DBDISKUSED      humboldt_craft  28545043
DISKUSED        1699763762
DB      humboldt_craft
DBUSER  humboldt_craft  humboldt_dbuser
DB      humboldt_live
DBUSER  humboldt_live   humboldt_dbuser
DB      humboldt_wp811
DBUSER  humboldt_wp811  humboldt_wp811
DB      humboldt_staging
DBUSER  humboldt_staging        humboldt_dbuser
DB      humboldt_sublymecart
DBUSER  humboldt_sublymecart    humboldt_dbuser
DB      humboldt_isodocs
DBUSER  humboldt_isodocs        humboldt_dbuser
USER    humboldt_onyxa
USER    humboldt_dbuser
 at /usr/local/cpanel/Cpanel/EventHandler.pm line 112.
        Cpanel::EventHandler::post_event(1, "post", "Mysql", "initcache", ARRAY(0x31deb38), ARRAY(0x31d43c0)) called at cpanel.pl line 1440
        cpanel::cpanel::__ANON__(__CPANEL_HIDDEN__) called at cpanel.pl line 1889
        cpanel::cpanel::_api1("Mysql", "mysql", "initcache()", "initcache", ARRAY(0x31deb38), "safe_html_encode") called at /usr/local/cpanel/Cpanel/Template/Plugin/Api1.pm line 93
        eval {...} called at /usr/local/cpanel/Cpanel/Template/Plugin/Api1.pm line 93
        Cpanel::Template::Plugin::Api1::_api1_exec(0, "Mysql", "initcache", ARRAY(0x31deb38)) called at /usr/local/cpanel/Cpanel/Template/Plugin/Api1.pm line 47
        Cpanel::Template::Plugin::Api1::_captured_api1_exec("Mysql", "initcache", ARRAY(0x31deb38)) called at /var/cpanel/template_compiles//usr/local/cpanel/base/frontend/paper_lantern/sql/index.html.tt line 1
        eval {...} called at /var/cpanel/template_compiles//usr/local/cpanel/base/frontend/paper_lantern/sql/index.html.tt line 1
        eval {...} called at /var/cpanel/template_compiles//usr/local/cpanel/base/frontend/paper_lantern/sql/index.html.tt line 1
        Template::Provider::__ANON__(Template::Context=HASH(0x31d2a80)) called at /usr/local/cpanel/3rdparty/perl/528/lib/perl5/cpanel_lib/x86_64-linux-64int/Template/Document.pm line 162
        eval {...} called at /usr/local/cpanel/3rdparty/perl/528/lib/perl5/cpanel_lib/x86_64-linux-64int/Template/Document.pm line 160
        Template::Document::process(Template::Document=HASH(0x3271c38), Template::Context=HASH(0x31d2a80)) called at /usr/local/cpanel/3rdparty/perl/528/lib/perl5/cpanel_lib/x86_64-linux-64int/Template/Context.pm line 357
        eval {...} called at /usr/local/cpanel/3rdparty/perl/528/lib/perl5/cpanel_lib/x86_64-linux-64int/Template/Context.pm line 327
        Template::Context::process(Template::Context=HASH(0x31d2a80), Template::Document=HASH(0x3271c38)) called at /usr/local/cpanel/3rdparty/perl/528/lib/perl5/cpanel_lib/x86_64-linux-64int/Template/Service.pm line 94
        eval {...} called at /usr/local/cpanel/3rdparty/perl/528/lib/perl5/cpanel_lib/x86_64-linux-64int/Template/Service.pm line 91
        Template::Service::process(Template::Service=HASH(0x31d2648), "/usr/local/cpanel/base/frontend/paper_lantern/sql/index.html.tt", HASH(0x31d9430)) called at /usr/local/cpanel/3rdparty/perl/528/lib/perl5/cpanel_lib/x86_64-linux-64int/Template.pm line 64
        Template::process(Template=HASH(0x31d9958), "/usr/local/cpanel/base/frontend/paper_lantern/sql/index.html.tt", HASH(0x31d9430), SCALAR(0x1408d40)) called at /usr/local/cpanel/Cpanel/Template.pm line 477
        Cpanel::Template::process_template("cpanel", HASH(0x31d9430), HASH(0x1434ab0)) called at cpanel.pl line 1058
        cpanel::cpanel::cptt_exectag("/usr/local/cpanel/base/frontend/paper_lantern/sql/index.html.tt", 1) called at cpanel.pl line 4409
        cpanel::cpanel::run_standard_mode() called at cpanel.pl line 878
        cpanel::cpanel::script("cpanel::cpanel", "./frontend/paper_lantern/sql/index.html.tt") called at cpanel.pl line 321
[2019-05-15 10:03:15 -0500] info [gather-update-logs] File /usr/local/cpanel/logs/update_analysis/2019-05-15T15:03:11Z.tar.gz has been sent successfully to updatelogdrop.cpanel.net.

Any help is appreciated. My hosting company wants to reboot the server. Is there not a better way? Will that even do anything?

RickKukiela

May 16, 2019 14:08

For anyone else that runs into this problem. I opened a ticket and they fixed the issue by running the command:


/scripts/rebuild_dbmap

For the user in question. This did lose some database user information. I'm waiting on reply as to what to do about that.

cPanelMichael

May 16, 2019 22:19

Hello @RickKukiela, Per your support ticket, it looks like you were able to fix the missing database user information by reapplying the privileges for the database user to the database using the cPanel >> MySQL Databases interface. Can you confirm if the issue is now solved? Thank you.

Encountered error in Mysql::initcache

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