How to Solve Error yum error: Failed to initialize NSS library

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Introduction

This is an article for solving error as it shows in the title part. Particularly, the error is the impact of erasing the package as it also shows in the article in this link. The error is an output of executing a yum command. Below is an output present after performing the ‘yum’ command :

[root@localhost dracut.conf.d]# yum clean all
error: Failed to initialize NSS library
There was a problem importing one of the Python modules
required to run yum. The error leading to this problem was:

   cannot import name ts

Please install a package which provides this module, or
verify that the module is installed correctly.

It's possible that the above module doesn't match the
current version of Python, which is:
2.7.5 (default, Jul 13 2018, 13:06:57) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-28)]

If you cannot solve this problem yourself, please go to 
the yum faq at:
  http://yum.baseurl.org/wiki/Faq
  

[root@localhost dracut.conf.d]#

Basically, it is not just the ‘yum clean all’ command. All of the command using ‘yum’ with any type of parameter will present the above error messages.

Solving the problem

Remember that the option for reinstalling the already removed package cannot be done because the ‘yum’ utility is broken. So, in order to solve it manually, the only method to accomplish it is by copying the related files manually.

Those package removal accidents is mentioned clearly in the article in this link. In this case, the operating system is CentOS. So, for further revival, search the related files of the two packages accident removal. Those two packages are the ‘libgomp and the ‘nss-softokn-freebl.

First of all, it is the first package with the name of ‘libgomp’.The related file of the package is libfreebl3.so. It exists in the /usr/lib64 folder.

The second package, it is the the package with the name of nss-softokn-freebl. Try to recover it manually by copying all the files which related to the package. Find it by searching the related files in the rpm package search page. For an example in this link. In the ‘Files’ section on the page in that link, it lists all of the related files :

/etc/prelink.conf.d
/etc/prelink.conf.d/nss-softokn-prelink.conf
/usr/lib/dracut/dracut.conf.d/50-nss-softokn.conf
/usr/lib/dracut/modules.d/05nss-softokn
/usr/lib/dracut/modules.d/05nss-softokn/module-setup.sh
/usr/lib64/libfreebl3.chk
/usr/lib64/libfreebl3.so
/usr/lib64/libfreeblpriv3.chk
/usr/lib64/libfreeblpriv3.so

Screenshot image of the ‘Files’ section as follows :

How to Solve Error  SSH Remote Access Permission denied, please try again

Similarly, all of the information containing list of related files also exists in this link. Also, In the ‘Files’ section on the page in the mentioned link before, the lists below is the affected files for installing nss-softokn-freebl package.

/etc/prelink.conf.d/nss-softokn-prelink.conf
/usr/lib/dracut/dracut.conf.d/50-nss-softokn.conf
/usr/lib/dracut/modules.d/05nss-softokn/module-setup.sh
/usr/lib64/libfreebl3.chk
/usr/lib64/libfreebl3.so
/usr/lib64/libfreeblpriv3.chk
/usr/lib64/libfreeblpriv3.so

In the mentioned link above, list of the related files with nss-softokn-freebl package exists below in the image screenshot :

How to Solve Error  SSH Remote Access Permission denied, please try again
How to Solve Error SSH Remote Access Permission denied, please try again

Copy all of the necessary files into the correct location from another server with the same operating system or environment.

Executing the solution for solving the problem

After deciding the solution in the previous section by copying several files, in the next section there are description of steps to achieve it in a systematic order.So, reviving ‘libgomp’ and ‘nss-softokn-freebl’ package by manually copying related file can be done if the ‘yum’ utility is broken. Those files are the ‘nss-softokn-prelink.conf, 50-nss-softokn.conf, module-setup.sh, libfreebl3.chk, libfreebl3.so, libfreeblpriv3.chk and libfreeblpriv3.so with their respective paths.

Copy the first file, the nss-softokn-prelink.conf file

Start checking the condition in the target or the problematic server location before copying the first file, the nss-softokn-prelink.conf, below is :

[root@target lib]# cd /etc/prelink.conf.d/
[root@target prelink.conf.d]# ls
fipscheck.conf  grub2.conf
[root@target prelink.conf.d]#

There is no nss-fotokn-prelink.conf exist according to the output above. So, copy the first file, the nss-softokn-prelink.conf from source server to the problematic or the target server location :

[root@source prelink.conf.d]# scp nss-softokn-prelink.conf user@xxx.xxx.xxx.xxx:/home/user
user@xxx.xxx.xxx.xxx's password: 
nss-softokn-prelink.conf                                                                                                                                                   100%  xxxxx xxxx/s   00:00    
[root@source prelink.conf.d]$

After finishing the copy process of the first file, below is the condition in the problematic or the target server location :

[root@target prelink.conf.d]# mv /home/user/nss-softokn-prelink.conf . 
[root@target prelink.conf.d]# ls -al
total 24
drwxr-xr-x.  2 root root   78 Feb  4 09:33 .
drwxr-xr-x. 76 root root 8192 Feb  4 07:50 ..
-rw-r--r--.  1 root root   57 Aug  2 2017 fipscheck.conf
-rw-r--r--.  1 root root  220 Oct 21 2017 grub2.conf
-rw-r--r--.  1 root root  184 Feb  4 09:30 nss-softokn-prelink.conf
[root@target prelink.conf.d]#

As the output above, at last the file exists.

Copy the second file, the 50-nss-softokn.conf file

Similarly, before copying the second file just check the condition in the target or the problematic server location :

[root@target dracut]# cd dracut.conf.d/
[root@target dracut.conf.d]# ls
01-dist.conf  01-microcode.conf  02-rescue.conf  76-phys-port-name.conf
[root@target dracut.conf.d]#

In the output above, there is no file with the name of 50-nss-softokn.conf, so copy the second file from source server to the problematic or the target server location :

[root@source dracut.conf.d]# scp 50-nss-softokn.conf user@xxx.xxx.xxx.xxx:/home/user
user@xxx.xxx.xxx.xxx's password: 
50-nss-softokn.conf                                                                                                                                                   100%  xxxxx xxxx/s   00:00    
root@source dracut.conf.d]#

After the copy process of the second file, don’t forget to check the condition of the problematic or the target server location :

[root@target prelink.conf.d]# mv /home/user/50-nss-softokn.conf . 
[root@target dracut.conf.d]# ls -al
total 20
drwxr-xr-x. 2 root root 130 Feb  4 09:37 .
drwxr-xr-x. 4 root root 236 Jul 16 2018 ..
-rw-r--r--. 1 root root 524 Apr 11 2018 01-dist.conf
-rw-r--r--. 1 root root  22 May 24 2018 01-microcode.conf
-rw-r--r--. 1 root root  26 Apr 11 2018 02-rescue.conf
-rw-r--r--. 1 root root  65 Feb  4 09:36 50-nss-softokn.conf
-rw-r--r--. 1 root root 117 Apr 11 2018 76-phys-port-name.conf
[root@target dracut.conf.d]#

Finally, the file with the name of 50-nss-softokn.conf exist.

Copy the third file, the module-setup.sh file

Check the availability of the third file which is the module-setup.sh file. It is done by checking the condition in the target or the problematic server location :

[root@target prelink.conf.d]# cd /usr/lib/dracut/
[root@target dracut]# ls
dracut.conf.d  dracut-functions  dracut-functions.sh  dracut-initramfs-restore  dracut-init.sh  dracut-install  dracut-logger.sh  dracut-version.sh  modules.d  skipcpio
[root@target dracut]# cd modules.d/
[root@target modules.d]# ls -al
total 16
drwxr-xr-x. 64 root root 4096 Feb  4 07:50 .
drwxr-xr-x.  4 root root  236 Jul 16 2018 ..
drwxr-xr-x.  2 root root   29 Jul 16 2018 00bash
drwxr-xr-x.  2 root root   29 Jul 16 2018 00systemd-bootchart
drwxr-xr-x.  2 root root   57 Jul 16 2018 03modsign
drwxr-xr-x.  2 root root   29 Jul 16 2018 03rescue
drwxr-xr-x.  2 root root   72 Jul 16 2018 04watchdog
drwxr-xr-x.  2 root root   29 Jul 16 2018 05busybox
drwxr-xr-x.  2 root root  111 Jul 16 2018 10i18n
drwxr-xr-x.  2 root root   72 Jul 16 2018 30convertfs
....
drwxr-xr-x.  2 root root  227 Jul 16 2018 99kdumpbase
drwxr-xr-x.  2 root root   48 Jul 16 2018 99shutdown
drwxr-xr-x.  2 root root   48 Jul 16 2018 99uefi-lib
[root@target modules.d]#

Before copying the third file, create the folder to place the module-setup.sh file in the target or the problematic server location :

[root@source modules.d]# mkdir 05nss-softokn
[root@source modules.d]# chmod -Rv 755 05nss-softokn/
mode of ‘05nss-softokn/’ retained as 0755 (rwxr-xr-x)
[root@source modules.d]# cd 05nss-softokn/
[root@source 05nss-softokn]# ls -al
total 4
drwxr-xr-x.  2 root root    6 Feb  4 09:34 .
drwxr-xr-x. 65 root root 4096 Feb  4 09:34 ..
[root@source 05nss-softokn]#

Afterwards, continuing the above step copy the third file, the module-setup.sh to the target or the problematic server :

[root@source 05nss-softokn]# scp 05nss-softokn/module-setup.sh user@xxx.xxx.xxx.xxx:/home/user
user@xxx.xxx.xxx.xxx's password: 
module-setup.sh                                                                                                                                                   100%  xxxxx xxxx/s   00:00  
[root@source 05nss-softokn]#

In the end, don’t forget to check the problematic server after copying the third file for the availability of the file :

[root@target 05nss-softokn]# ls
[root@target 05nss-softokn]# mv /home/user/module-setup.sh . 
[root@target 05nss-softokn]# ls -al
total 8
drwxr-xr-x.  2 root root   29 Feb  4 09:35 .
drwxr-xr-x. 65 root root 4096 Feb  4 09:34 ..
-rw-r--r--.  1 root root  293 Feb  4 09:34 module-setup.sh
[root@target 05nss-softokn]#

Copy the rest of the files, the libfreebl3.so, libfreebl3.chk, libfreeblpriv3.chk and libfreeblpriv3.so files

As the previous steps, check first the condition of the target or the problematic server before copying all those files :

[root@target lib64]# ls -al
total 62072
dr-xr-xr-x. 40 root root   20480 Feb  4 09:40 .
drwxr-xr-x. 15 root root     188 Jul 30 2018 ..
drwxr-xr-x.  2 root root       6 Jun 10 2014 apr-util-1
drwxr-xr-x.  2 root root      28 Jul 16 2018 audit
...
-r-xr-xr-x.  1 root root  356120 Apr 11 2018 libdevmapper.so.1.02
...
-rwxr-xr-x.  1 root root   72192 Sep  7 2017 libformw.so.5.9
...
-rwxr-xr-x.  1 root root  535064 Aug  2 2017 libgcrypt.so.11.8.2
...
-rwxr-xr-x.  1 root root  339104 Apr 11 2018 libgobject-2.0.so.0.5400.2
...
drwxr-xr-x.  2 root root    4096 Jul 16 2018 xtables
[root@target lib64]# 

In the above output, there are no related files with the nss-softokn-freebl package. So, copy all of those files from the source server to the target or problematic server :

[root@localhost dracut.conf.d]# cd /usr/lib64/
[root@localhost lib64]# scp libfreebl3.so libfreebl3.chk libfreeblpriv3.so libfreeblpriv3.chk 
user@xxx.xxx.xxx.xxx's password: 
libfreebl3.so                                                                                                                                                   100%  xxxxx xxxx/s   00:00 
libfreebl3.chk                                                                                                                                                   100%  xxxxx xxxx/s   00:00  
libfreeblpriv3.so                                                                                                                                                   100%  xxxxx xxxx/s   00:00 
libfreeblpriv3.chk                                                                                                                                                   100%  xxxxx xxxx/s   00:00 
[root@localhost lib64]#

The last output in this article. It is to make sure that the content in the target or the problematic server have the libfreebl3.chk, libfreebl3.so, libfreeblpriv3.chk and libfreeblpriv3.so file exist in it :

[root@localhost lib64]# ls -al
total 62072
dr-xr-xr-x. 40 root root   20480 Feb  4 09:40 .
drwxr-xr-x. 15 root root     188 Jul 30 2018 ..
drwxr-xr-x.  2 root root       6 Jun 10 2014 apr-util-1
drwxr-xr-x.  2 root root      28 Jul 16 2018 audit
...
-rwxr-xr-x.  1 root root   72192 Sep  7 2017 libformw.so.5.9
-rw-r--r--.  1 root root     899 Feb  4 09:39 libfreebl3.chk
-rwxr-xr-x.  1 root root   11448 Feb  4 09:04 libfreebl3.so
-rw-r--r--.  1 root root     899 Feb  4 09:39 libfreeblpriv3.chk
-rw-r--r--.  1 root root  551840 Feb  4 09:39 libfreeblpriv3.so
...
drwxr-xr-x.  2 root root    4096 Jul 16 2018 xtables
[root@localhost lib64]#

Finishing solution

Finally, execute the ‘yum’ command again. The following is the output of it after copying all the related files above :

[root@localhost lib64]# yum update
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
 * base: xxxxxxx.xxxxx.xxx.xx
 * epel: xxxxxxx.xxx.xxx.xx
 * extras: xxxxxxx.xxxx.xxx.xx
 * ius: xxx.xxxxxxx.xx
 * updates: xxxxxxx.xxxx.xx.xx
Resolving Dependencies
--> Running transaction check
---> Package NetworkManager.x86_64 1:1.10.2-16.el7_5 will be updated
---> Package NetworkManager.x86_64 1:1.12.0-8.el7_6 will be an update
--> Processing Dependency: glib2 >= 2.56.1 for package: 
...
---> Package bind-license.noarch 32:9.9.4-61.el7 will be updated
---> Package bind-license.noarch 32:9.9.4-73.el7_6 will be an update
---> Package cronie.x86_64 0:1.4.11-19.el7 will be updated
---> Package cronie.x86_64 0:1.4.11-20.el7_6 will be an update
---> Package cronie-anacron.x86_64 0:1.4.11-19.el7 will be updated
...
---> Package python2-psutil.x86_64 0:2.2.1-4.el7 will be installed
---> Package selinux-policy.noarch 0:3.13.1-229.el7_6.9 will be an update
--> Processing Dependency: libsemanage >= 2.5-13 for package: selinux-policy-3.13.1-229.el7_6.9.noarch
---> Package systemd.x86_64 0:219-62.el7_6.3 will be an update
--> Processing Dependency: libcryptsetup.so.12(CRYPTSETUP_2.0)(64bit) for package: systemd-219-62.el7_6.3.x86_64
--> Processing Dependency: libcryptsetup.so.12()(64bit) for package: systemd-219-62.el7_6.3.x86_64
--> Finished Dependency Resolution
...
Error: Package: kernel-3.10.0-957.5.1.el7.x86_64 (updates)
           Requires: linux-firmware >= 20180911-68
           Installed: linux-firmware-20180220-62.2.git6d51311.el7_5.noarch (@updates)
               linux-firmware = 20180220-62.2.git6d51311.el7_5
           Available: linux-firmware-20180220-62.git6d51311.el7.noarch (base)
               linux-firmware = 20180220-62.git6d51311.el7
Error: Package: systemd-219-62.el7_6.3.x86_64 (updates)
           Requires: libcryptsetup.so.12()(64bit)
Error: Package: systemd-219-62.el7_6.3.x86_64 (updates)
           Requires: libcryptsetup.so.12(CRYPTSETUP_2.0)(64bit)
 You could try using --skip-broken to work around the problem
** Found 8 pre-existing rpmdb problem(s), 'yum check' output follows:
gettext-0.19.8.1-2.el7.x86_64 has missing requires of libgomp.so.1()(64bit)
gettext-0.19.8.1-2.el7.x86_64 has missing requires of libgomp.so.1(GOMP_1.0)(64bit)
gettext-libs-0.19.8.1-2.el7.x86_64 has missing requires of libgomp.so.1()(64bit)
glibc-2.17-222.el7.x86_64 has missing requires of libfreebl3.so()(64bit)
glibc-2.17-222.el7.x86_64 has missing requires of libfreebl3.so(NSSRAWHASH_3.12.3)(64bit)
nss-softokn-3.36.0-5.el7_5.x86_64 has missing requires of nss-softokn-freebl(x86-64) >= ('0', '3.36.0', '5.el7_5')
p11-kit-trust-0.23.5-3.el7.x86_64 has missing requires of libfreebl3.so()(64bit)
p11-kit-trust-0.23.5-3.el7.x86_64 has missing requires of libfreebl3.so(NSSRAWHASH_3.12.3)(64bit)
[root@localhost lib64]#

Execute the ‘yum check’ to inspect the problem further as follows :

[root@localhost lib64]# yum check
Loaded plugins: fastestmirror
gettext-0.19.8.1-2.el7.x86_64 has missing requires of libgomp.so.1()(64bit)
gettext-0.19.8.1-2.el7.x86_64 has missing requires of libgomp.so.1(GOMP_1.0)(64bit)
gettext-libs-0.19.8.1-2.el7.x86_64 has missing requires of libgomp.so.1()(64bit)
glibc-2.17-222.el7.x86_64 has missing requires of libfreebl3.so()(64bit)
glibc-2.17-222.el7.x86_64 has missing requires of libfreebl3.so(NSSRAWHASH_3.12.3)(64bit)
nss-softokn-3.36.0-5.el7_5.x86_64 has missing requires of nss-softokn-freebl(x86-64) >= ('0', '3.36.0', '5.el7_5')
p11-kit-trust-0.23.5-3.el7.x86_64 has missing requires of libfreebl3.so()(64bit)
p11-kit-trust-0.23.5-3.el7.x86_64 has missing requires of libfreebl3.so(NSSRAWHASH_3.12.3)(64bit)
Error: check all
[root@localhost lib64]#

Copy another file, the libgomp.so.1

Apparently, according to the output in the previous section above, there is still a missing file related to the libgomp package. That file name is libgomp.so.1. For an easy solution, just copy it manually again.

From the source of another server with the same operating system or environment :

[root@source lib64]#  scp libgomp.so.1 user@xxx.xxx.xxx.xxx:/home/user
user@xxx.xxx.xxx.xxx's password: 
libgomp.so.1                                                                                                                                                   100%  xxxxx xxxx/s   00:00 
[root@source lib64]#

Properly copy and modify the file permission in the target or problematic server :

[root@target lib64]# mv /home/user/libgomp.so.1 . 
[root@target lib64]# chmod +x libgomp.so.1 
[root@target lib64]#

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