Several days ago, I run 'yum update' while failed:
error: Couldn't fork %pre(php71u-fpm-7.1.14-1.ius.centos6.x86_64): Cannot allocate memory Error in PREIN scriptlet in rpm package php71u-fpm-7.1.14-1.ius.centos6.x86_64 error: install: %pre scriptlet failed (2), skipping php71u-fpm-7.1.14-1.ius.centos6 Updating : php71u-pecl-apcu-5.1.10-1.ius.centos6.x86_64
Just now when I checked the log, I found similar errors happened many times while unfortunately at that time I just thought maybe one package failed.
I did not know why I got this error as there should be enough memory:
[root@www ~]# free
total used free shared buffers cached
Mem: 1019932 778860 241072 56920 14732 182964
-/+ buffers/cache: 581164 438768
Swap: 0 0 0Anyway, I stopped mysql and nginx and tried to run 'yum update' again, and got this:
Resolving Dependencies There are unfinished transactions remaining. You might consider running yum-complete-transaction first to finish them. --> Running transaction check ---> Package kernel-headers.x86_64 0:2.6.32-696.16.1.el6 will be updated ---> Package kernel-headers.x86_64 0:2.6.32-696.20.1.el6 will be an update ---> Package mysql-community-server.x86_64 0:5.7.20-1.el6 will be updated ---> Package mysql-community-server.x86_64 0:5.7.21-1.el6 will be an update ---> Package ntpdate.x86_64 0:4.2.6p5-12.el6.centos.1 will be updated --> Processing Dependency: ntpdate = 4.2.6p5-12.el6.centos.1 for package: ntp-4.2.6p5-12.el6.centos.1.x86_64 ---> Package ntpdate.x86_64 0:4.2.6p5-12.el6.centos.2 will be an update ---> Package php71u-cli.x86_64 0:7.1.11-1.ius.centos6 will be updated ---> Package php71u-cli.x86_64 0:7.1.14-1.ius.centos6 will be an update ---> Package php71u-fpm.x86_64 0:7.1.11-1.ius.centos6 will be updated ---> Package php71u-fpm.x86_64 0:7.1.14-1.ius.centos6 will be an update ---> Package php71u-intl.x86_64 0:7.1.11-1.ius.centos6 will be updated ---> Package php71u-intl.x86_64 0:7.1.14-1.ius.centos6 will be an update ---> Package php71u-json.x86_64 0:7.1.11-1.ius.centos6 will be updated ---> Package php71u-json.x86_64 0:7.1.14-1.ius.centos6 will be an update ---> Package php71u-mbstring.x86_64 0:7.1.11-1.ius.centos6 will be updated ---> Package php71u-mbstring.x86_64 0:7.1.14-1.ius.centos6 will be an update ---> Package php71u-tidy.x86_64 0:7.1.11-1.ius.centos6 will be updated ---> Package php71u-tidy.x86_64 0:7.1.14-1.ius.centos6 will be an update ---> Package selinux-policy-targeted.noarch 0:3.7.19-307.el6_9.2 will be updated ---> Package selinux-policy-targeted.noarch 0:3.7.19-307el6_9.3 will be an update ---> Package tzdata.noarch 0:2017c-1.el6 will be updated ---> Package tzdata.noarch 0:2018c-1.el6 will be an update --> Finished Dependency Resolution Error: Package: ntp-4.2.6p5-12.el6.centos.1.x86_64 (@updates) Requires: ntpdate = 4.2.6p5-12.el6.centos.1 Removing: ntpdate-4.2.6p5-12.el6.centos.1.x86_64 (@updates) ntpdate = 4.2.6p5-12.el6.centos.1 Updated By: ntpdate-4.2.6p5-12.el6.centos.2.x86_64 (updates) ntpdate = 4.2.6p5-12.el6.centos.2 Available: ntpdate-4.2.6p5-10.el6.centos.2.x86_64 (base) ntpdate = 4.2.6p5-10.el6.centos.2 You could try using --skip-broken to work around the problem ** Found 31 pre-existing rpmdb problem(s), 'yum check' output follows: GeoIP-GeoLite-data-2018.01-1.el6.noarch is a duplicate with GeoIP-GeoLite-data-2017.07-1.el6.noarch GeoIP-GeoLite-data-extra-2018.01-1.el6.noarch is a duplicate with GeoIP-GeoLite-data-extra-2017.07-1.el6.noarch kernel-firmware-2.6.32-696.20.1.el6.noarch is a duplicate with kernel-firmware-2.6.32-696.16.1.el6.noarch libblkid-2.17.2-12.28.el6_9.2.x86_64 is a duplicate with libblkid-2.17.2-12.28.el6_9.1.x86_64 libuuid-2.17.2-12.28.el6_9.2.x86_64 is a duplicate with libuuid-2.17.2-12.28.el6_9.1.x86_64 mysql-community-client-5.7.21-1.el6.x86_64 is a duplicate with mysql-community-client-5.7.20-1.el6.x86_64 mysql-community-common-5.7.21-1.el6.x86_64 is a duplicate with mysql-community-common-5.7.20-1.el6.x86_64 mysql-community-libs-5.7.21-1.el6.x86_64 is a duplicate with mysql-community-libs-5.7.20-1.el6.x86_64 ntp-4.2.6p5-12.el6.centos.2.x86_64 is a duplicate with ntp-4.2.6p5-12.el6.centos.1.x86_64 ntp-4.2.6p5-12.el6.centos.2.x86_64 has missing requires of ntpdate = ('0', '4.2.6p5', '12.el6.centos.2') php71u-common-7.1.14-1.ius.centos6.x86_64 has installed conflicts php-common < ('0', '7.1.14', '1.ius.centos6'): php71u-common-7.1.11-1.ius.centos6.x86_64 php71u-common-7.1.14-1.ius.centos6.x86_64 is a duplicate with php71u-common-7.1.11-1.ius.centos6.x86_64 php71u-gd-7.1.14-1.ius.centos6.x86_64 has installed conflicts php-gd < ('0', '7.1.14', '1.ius.centos6'): php71u-gd-7.1.11-1.ius.centos6.x86_64 php71u-gd-7.1.14-1.ius.centos6.x86_64 is a duplicate with php71u-gd-7.1.11-1.ius.centos6.x86_64 php71u-mysqlnd-7.1.14-1.ius.centos6.x86_64 has installed conflicts php-mysqlnd < ('0', '7.1.14', '1.ius.centos6'): php71u-mysqlnd-7.1.11-1.ius.centos6.x86_64 php71u-mysqlnd-7.1.14-1.ius.centos6.x86_64 is a duplicate with php71u-mysqlnd-7.1.11-1.ius.centos6.x86_64 php71u-opcache-7.1.14-1.ius.centos6.x86_64 has installed conflicts php-opcache < ('0', '7.1.14', '1.ius.centos6'): php71u-opcache-7.1.11-1.ius.centos6.x86_64 php71u-opcache-7.1.14-1.ius.centos6.x86_64 is a duplicate with php71u-opcache-7.1.11-1.ius.centos6.x86_64 php71u-pdo-7.1.14-1.ius.centos6.x86_64 has installed conflicts php-pdo < ('0', '7.1.14', '1.ius.centos6'): php71u-pdo-7.1.11-1.ius.centos6.x86_64 php71u-pdo-7.1.14-1.ius.centos6.x86_64 is a duplicate with php71u-pdo-7.1.11-1.ius.centos6.x86_64 php71u-pecl-apcu-5.1.10-1.ius.centos6.x86_64 has installed conflicts php-pecl-apcu < ('0', '5.1.10', None): php71u-pecl-apcu-5.1.8-1.ius.centos6.x86_64 php71u-pecl-apcu-5.1.10-1.ius.centos6.x86_64 is a duplicate with php71u-pecl-apcu-5.1.8-1.ius.centos6.x86_64 php71u-pecl-igbinary-2.0.5-2.ius.centos6.x86_64 is a duplicate with php71u-pecl-igbinary-2.0.5-1.ius.centos6.x86_64 php71u-pecl-redis-3.1.6-2.ius.centos6.x86_64 has installed conflicts php-pecl-redis < ('0', '3.1.6', None): php71u-pecl-redis-3.1.4-2.ius.centos6.x86_64 php71u-pecl-redis-3.1.6-2.ius.centos6.x86_64 is a duplicate with php71u-pecl-redis-3.1.4-2.ius.centos6.x86_64 php71u-process-7.1.14-1.ius.centos6.x86_64 has installed conflicts php-process < ('0', '7.1.14', '1.ius.centos6'): php71u-process-7.1.11-1.ius.centos6.x86_64 php71u-process-7.1.14-1.ius.centos6.x86_64 is a duplicate with php71u-process-7.1.11-1.ius.centos6.x86_64 php71u-xml-7.1.14-1.ius.centos6.x86_64 has installed conflicts php-xml < ('0', '7.1.14', '1.ius.centos6'): php71u-xml-7.1.11-1.ius.centos6.x86_64 php71u-xml-7.1.14-1.ius.centos6.x86_64 is a duplicate with php71u-xml-7.1.11-1.ius.centos6.x86_64 selinux-policy-3.7.19-307el6_9.3.noarch is a duplicate with selinux-policy-3.7.19-307.el6_9.2.noarch util-linux-ng-2.17.2-12.28.el6_9.2.x86_64 is a duplicate with util-linux-ng-2.17.2-12.28.el6_9.1.x86_64
OK, run 'yum-complete-transaction':
[root@www ~]# yum-complete-transactionn Loaded plugins: fastestmirror Loading mirror speeds from cached hostfile * base: mirrors.zju.edu.cn * epel: ftp.cuhk.edu.hk * extras: ftp.sjtu.edu.cn * ius: hkg.mirror.rackspace.com * updates: ftp.sjtu.edu.cn There are 1 outstanding transactions to complete. Finishing the most recent one The remaining transaction had 40 elements left to run --> Running transaction check ---> Package GeoIP-GeoLite-data.noarch 0:2017.07-1.el6 will be erased ---> Package GeoIP-GeoLite-data-extra.noarch 0:2017.07-1.el6 will be erased ---> Package kernel.x86_64 0:2.6.32-642.13.1.el6 will be erased ---> Package kernel-firmware.noarch 0:2.6.32-696.16.1.el6 will be erased ---> Package kernel-headers.x86_64 0:2.6.32-696.16.1.el6 will be updated ---> Package kernel-headers.x86_64 0:2.6.32-696.20.1.el6 will be an update ---> Package libblkid.x86_64 0:2.17.2-12.28.el6_9.1 will be erased ---> Package libuuid.x86_64 0:2.17.2-12.28.el6_9.1 will be erased ---> Package mysql-community-client.x86_64 0:5.7.20-1.el6 will be erased ---> Package mysql-community-common.x86_64 0:5.7.20-1.el6 will be erased ---> Package mysql-community-libs.x86_64 0:5.7.20-1.el6 will be erased ---> Package mysql-community-server.x86_64 0:5.7.20-1.el6 will be erased ---> Package ntp.x86_64 0:4.2.6p5-12.el6.centos.1 will be erased ---> Package ntpdate.x86_64 0:4.2.6p5-12.el6.centos.1 will be erased ---> Package php71u-cli.x86_64 0:7.1.11-1.ius.centos6 will be updated ---> Package php71u-cli.x86_64 0:7.1.14-1.ius.centos6 will be an update ---> Package php71u-common.x86_64 0:7.1.11-1.ius.centos6 will be erased ---> Package php71u-fpm.x86_64 0:7.1.11-1.ius.centos6 will be erased ---> Package php71u-gd.x86_64 0:7.1.11-1.ius.centos6 will be erased ---> Package php71u-intl.x86_64 0:7.1.11-1.ius.centos6 will be updated ---> Package php71u-intl.x86_64 0:7.1.14-1.ius.centos6 will be an update ---> Package php71u-json.x86_64 0:7.1.11-1.ius.centos6 will be updated ---> Package php71u-json.x86_64 0:7.1.14-1.ius.centos6 will be an update ---> Package php71u-mbstring.x86_64 0:7.1.11-1.ius.centos6 will be updated ---> Package php71u-mbstring.x86_64 0:7.1.14-1.ius.centos6 will be an update ---> Package php71u-mysqlnd.x86_64 0:7.1.11-1.ius.centos6 will be erased ---> Package php71u-opcache.x86_64 0:7.1.11-1.ius.centos6 will be erased ---> Package php71u-pdo.x86_64 0:7.1.11-1.ius.centos6 will be erased ---> Package php71u-pecl-apcu.x86_64 0:5.1.8-1.ius.centos6 will be erased ---> Package php71u-pecl-igbinary.x86_64 0:2.0.5-1.ius.centos6 will be erased ---> Package php71u-pecl-redis.x86_64 0:3.1.4-2.ius.centos6 will be erased ---> Package php71u-process.x86_64 0:7.1.11-1.ius.centos6 will be erased ---> Package php71u-tidy.x86_64 0:7.1.11-1.ius.centos6 will be updated ---> Package php71u-tidy.x86_64 0:7.1.14-1.ius.centos6 will be an update ---> Package php71u-xml.x86_64 0:7.1.11-1.ius.centos6 will be erased ---> Package selinux-policy.noarch 0:3.7.19-307.el6_9.2 will be erased ---> Package selinux-policy-targeted.noarch 0:3.7.19-307.el6_9.2 will be erased ---> Package tzdata.noarch 0:2017c-1.el6 will be updated ---> Package tzdata.noarch 0:2018c-1.el6 will be an update ---> Package util-linux-ng.x86_64 0:2.17.2-12.28.el6_9.1 will be erased --> Finished Dependency Resolution Dependencies Resolved ====================================================================================================================================================================================================== Package Arch Version Repository Size ====================================================================================================================================================================================================== Updating: kernel-headers x86_64 2.6.32-696.20.1.el6 updates 4.5 M php71u-cli x86_64 7.1.14-1.ius.centos6 ius 4.1 M php71u-intl x86_64 7.1.14-1.ius.centos6 ius 200 k php71u-json x86_64 7.1.14-1.ius.centos6 ius 64 k php71u-mbstring x86_64 7.1.14-1.ius.centos6 ius 988 k php71u-tidy x86_64 7.1.14-1.ius.centos6 ius 65 k tzdata noarch 2018c-1.el6 updates 492 k Removing: GeoIP-GeoLite-data noarch 2017.07-1.el6 @epel 1.1 M GeoIP-GeoLite-data-extra noarch 2017.07-1.el6 @epel 49 M kernel x86_64 2.6.32-642.13.1.el6 @updates 131 M kernel-firmware noarch 2.6.32-696.16.1.el6 @updates 58 M libblkid x86_64 2.17.2-12.28.el6_9.1 @updates 133 k libuuid x86_64 2.17.2-12.28.el6_9.1 @updates 16 k mysql-community-client x86_64 5.7.20-1.el6 @mysql57-community 100 M mysql-community-common x86_64 5.7.20-1.el6 @mysql57-community 2.5 M mysql-community-libs x86_64 5.7.20-1.el6 @mysql57-community 8.9 M mysql-community-server x86_64 5.7.20-1.el6 @mysql57-community 771 M ntp x86_64 4.2.6p5-12.el6.centos.1 @updates 1.6 M ntpdate x86_64 4.2.6p5-12.el6.centos.1 @updates 123 k php71u-common x86_64 7.1.11-1.ius.centos6 @ius 8.1 M php71u-fpm x86_64 7.1.11-1.ius.centos6 @ius 4.0 M php71u-gd x86_64 7.1.11-1.ius.centos6 @ius 731 k php71u-mysqlnd x86_64 7.1.11-1.ius.centos6 @ius 814 k php71u-opcache x86_64 7.1.11-1.ius.centos6 @ius 791 k php71u-pdo x86_64 7.1.11-1.ius.centos6 @ius 345 k php71u-pecl-apcu x86_64 5.1.8-1.ius.centos6 @ius 263 k php71u-pecl-igbinary x86_64 2.0.5-1.ius.centos6 @ius 134 k php71u-pecl-redis x86_64 3.1.4-2.ius.centos6 @ius 964 k php71u-process x86_64 7.1.11-1.ius.centos6 @ius 148 k php71u-xml x86_64 7.1.11-1.ius.centos6 @ius 788 k selinux-policy noarch 3.7.19-307.el6_9.2 @updates 9.0 M selinux-policy-targeted noarch 3.7.19-307.el6_9.2 @updates 3.5 M util-linux-ng x86_64 2.17.2-12.28.el6_9.1 @updates 5.9 M Transaction Summary ====================================================================================================================================================================================================== Upgrade 7 Package(s) Remove 26 Package(s) Total size: 10 M Is this ok [y/N]: y Downloading Packages: Running rpm_check_debug ERROR with rpm_check_debug vs depsolve: ntpdate = 4.2.6p5-12.el6.centos.2 is needed by (installed) ntp-4.2.6p5-12.el6.centos.2.x86_64 Complete! Not removing old transaction files
Do you find something wrong? I should read the output more carefully but I did not.
I wanted to finish the update in a short time so I did some attempts and had to remove the ntp package and finally run the 'yum update' successfully.
............ Removed: GeoIP-GeoLite-data.noarch 0:2017.07-1.el6 GeoIP-GeoLite-data-extra.noarch 0:2017.07-1.el6 kernel.x86_64 0:2.6.32-642.13.1.el6 kernel-firmware.noarch 0:2.6.32-696.16.1.el6 libblkid.x86_64 0:2.17.2-12.28.el6_9.1 libuuid.x86_64 0:2.17.2-12.28.el6_9.1 mysql-community-client.x86_64 0:5.7.20-1.el6 mysql-community-common.x86_64 0:5.7.20-1.el6 mysql-community-libs.x86_64 0:5.7.20-1.el6 mysql-community-server.x86_64 0:5.7.20-1.el6 ntpdate.x86_64 0:4.2.6p5-12.el6.centos.1 php71u-common.x86_64 0:7.1.11-1.ius.centos6 php71u-fpm.x86_64 0:7.1.11-1.ius.centos6 php71u-gd.x86_64 0:7.1.11-1.ius.centos6 php71u-mysqlnd.x86_64 0:7.1.11-1.ius.centos6 php71u-opcache.x86_64 0:7.1.11-1.ius.centos6 php71u-pdo.x86_64 0:7.1.11-1.ius.centos6 php71u-pecl-apcu.x86_64 0:5.1.8-1.ius.centos6 php71u-pecl-igbinary.x86_64 0:2.0.5-1.ius.centos6 php71u-pecl-redis.x86_64 0:3.1.4-2.ius.centos6 php71u-process.x86_64 0:7.1.11-1.ius.centos6 php71u-xml.x86_64 0:7.1.11-1.ius.centos6 selinux-policy.noarch 0:3.7.19-307.el6_9.2 selinux-policy-targeted.noarch 0:3.7.19-307.el6_9.2 util-linux-ng.x86_64 0:2.17.2-12.28.el6_9.1 Updated: kernel-headers.x86_64 0:2.6.32-696.20.1.el6 php71u-cli.x86_64 0:7.1.14-1.ius.centos6 php71u-intl.x86_64 0:7.1.14-1.ius.centos6 php71u-json.x86_64 0:7.1.14-1.ius.centos6 php71u-mbstring.x86_64 0:7.1.14-1.ius.centos6 php71u-tidy.x86_64 0:7.1.14-1.ius.centos6 tzdata.noarch 0:2018c-1.el6 Complete! Cleaning up completed transaction file
I did not find lots of packages were removed wrongly. 
Then I installed the ntp again and run the 'yum update' to confirm all the packages were the latest ones:
[root@www ~]# yum update Loaded plugins: fastestmirror Setting up Update Process Loading mirror speeds from cached hostfile * base: mirrors.zju.edu.cn * epel: ftp.cuhk.edu.hk * extras: ftp.sjtu.edu.cn * ius: hkg.mirror.rackspace.com * updates: ftp.sjtu.edu.cn No Packages marked for Update
Then I rebooted the server and lost access to it.
From the console, I got the error messages similar with below:
Kernel Panic - not syncing: Attempted to kill init! Pid: 1 comm: init Not tainted 2.6.32-358.6.2.e16.x86_64 #1 Call Trace: [] ? panic+0xs7/0x16f [] ? do_exit+0x862/0x870 [] ? fput+0x25/0x30 [] ? do_group_exit+0x58/0xd0 [] ? sys_exit_group+0x17/0x20 [] ? system_call_fastpath+0x16/0x1b
I could not boot an Linux image to the rescue mode and at last I found one way to boot the system by adding kernel parameter selinux=0.
And removed the rhgb and quiet boot options, I found the root cause was the system could not load selinux policy, so I tried to regenerate the selinux policy by 'semodule -B'. I got some errors as some folders did not exist, so created them and run it finally.
While if I enabled the selinux, I would fail to boot the system again so temporarily I had to disable it.
Then I found mysql and php-fpm were not installed so had to reinstalled them to make my website work and had to restore some configuration files.
I was so tried these days that I wrote this note late, but currently I still do not know why 'yum update' did not upgrade those packages but removed them? Bug?
