sende var mı aynı sorun ama sanırsam anladırım kadarıyla.

atomic ile alakalı

2017-03-14 03:14:14 INFO: pum is called with arguments: ['--update', '--json']
Loading mirror speeds from cached hostfile
* atomic: mirror.veriteknik.net.tr
* base: mirror.venov.net.tr
* epel: mirror.veriteknik.net.tr
* extras: mirror.venov.net.tr
* updates: mirror.dgn.net.tr
2017-03-14 03:14:16 INFO: updating packages: mysql-libs mysql-devel mysql-server mysql
Running rpm_check_debug
Updating: mysql-libs-5.5.54-36.x86_64 165/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 1299/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 1428/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 1604/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 67296/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 132832/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 198368/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 263904/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 329440/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 394976/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 460512/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 526048/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 591584/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 657120/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 722656/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 788192/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 853728/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 919264/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 984800/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 1050336/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 1115872/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 1181408/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 1246944/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 1312480/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 1378016/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 1443552/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 1509088/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 1574624/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 1640160/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 1705696/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 1771232/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 1836768/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 1902304/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 1967840/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 2033376/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 2098912/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 2164448/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 2229984/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 2295520/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 2361056/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 2426592/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 2492128/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 2557664/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 2623200/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 2688736/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 2754272/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 2819808/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 2885344/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 2950880/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 2992496/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 2992640/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 3010779/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 3013428/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 3013886/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 3014016/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 3014156/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 3032611/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 3034505/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 3040186/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 3045848/4296864 [1/8]
Updating: mysql-libs-5.5.54-36.x86_64 3054237/4296864 [1/8]

Cleanup: mysql-devel 100/100 [5/8]
Cleanup: mysql-server 100/100 [6/8]
Cleanup: mysql 100/100 [7/8]
Cleanup: mysql-libs 100/100 [8/8]
Verify: 1/8: mysql-libs.x86_64 0:5.5.54-36 - u
Verify: 2/8: mysql-devel.x86_64 0:5.5.54-36 - u
Verify: 3/8: mysql-server.x86_64 0:5.5.54-36 - u
Verify: 4/8: mysql.x86_64 0:5.5.54-36 - u
Verify: 5/8: mysql-libs.x86_64 0:5.5.52-36.el6.art - ud
Verify: 6/8: mysql.x86_64 0:5.5.52-36.el6.art - ud
Verify: 7/8: mysql-server.x86_64 0:5.5.52-36.el6.art - ud
Verify: 8/8: mysql-devel.x86_64 0:5.5.52-36.el6.art - ud
2017-03-14 03:14:27 INFO: pum completed successfully
2017-03-14 03:14:27 INFO: pum is called with arguments: ['--check']
Loaded plugins: fastestmirror, security

dun gece otomatik olarak yapmış olduğu işlem.

atomic repo kurulu olmayan plesk sunucularda sorun yok.