Solved Installing linux app - library issues (MySQL-Workbench as example)

ohyes · May 2, 2020

Hello

20200502 - Working with FreeBSD 12.1 amd64

EDIT 20200506: Solved with solution described in this first post, short how-to on third post.

I'm trying to install MySQL-Workbench Linux application (Red Hat 7 app version).
In the past this app was in the FreeBSD ports tree. Maybe I should try to build this app directly from the sources (still available on Oracle's website).

But let say this thread is more generalistic; Speaking about installation of Linux apps and issues.

Setup
First step: the FreeBSD Hanbook related chapter, and do checks

Kernel:

Code:

# kldstat | grep linux
linux_common.ko
linux.ko
    linux64.ko

Linux pkg:

Code:

# pkg info | grep linux
    linux_base-c7-7.7.1908_1

rpm installation pkg:
Code:
```
# pkg info | grep rpm
    rpm4-4.15.1_1
```

Second step: Install a rpm (also described in the Handbook) - Here with MySQL Workbench RPM app

Install:

Code:

# cd /compat/linux
# rpm2cpio /path/mysql-workbench-community-8.0.19-1.el8.x86_64.rpm | cpio -id
397624 blocks

Running app Issue: Command not found

as standard user

Code:

# /compat/linux/bin/mysql-workbench
./mysql-workbench: Command not found.
# ls -l /compat/linux/bin/mysql-workbench
-rwxr-xr-x /compat/linux/bin/mysql-workbench

as root

Code:

# ldd /usr/compat/bin/mysql-workbench
    ldd: mysql-workbench-bin: No such file or directory

probably because it is a Shell script (thanks to vermaden with this thread Fix Broken Dependency on FreeBSD)

So as vermaden explains check the script and get the real app binary file. (extract)

Code:

# cat /compat/linux/bin/mysql-workbench
#!/bin/bash
[...]

export [...]
export MWB_BINARIES_DIR="$destdir/usr/libexec/mysql-workbench"

[...]
$MWB_BINARIES_DIR/mysql-workbench-bin "$@"

We can understand that the binary is: /compat/linux/usr/libexec/mysql-workbench/mysql-workbench-bin

let's do a ldd now (extract)

Code:

# ldd /compat/linux/usr/libexec/mysql-workbench/mysql-workbench-bin
linux_vdso.so.1 => (0x00007ffffffff000)
libsqlide.so.8.0.19 => not found
libwbprivate.so.8.0.19 => not found
libxml2.so.2 => not found
[...]
libmount.so.1 => /lib64/libmount.so.1 (0x0000000805200000)
    libblkid.so.1 => /lib64/libblkid.so.1 (0x0000000805600000)

a lot of libraries not found

Running app Issue: ldd reports library not found
Don't forget to be up-to-date with the pkg update

Solution 1 - Linux library provided by FreeBSD:

example with "libgtk-3.so.0 => not found"
check if there is a pkg that provides the Linux library

Code:

# pkg search linux | grep gtk
    linux-c7-gtk3-3.22.30          GTK+ library, version 3.X (Linux CentOS 7.7.1908)

if yes, then install it pkg install linux-c7-gtk3 and don't forget to check messages after installation

Code:

# pkg install linux-c7-gtk3
[...]
[36/36] Installing linux-c7-gtk3-3.22.30...
[36/36] Extracting linux-c7-gtk3-3.22.30: 100%
=====
Message from linux-c7-dri-18.3.4_1:

This package needs linsysfs mounted on /compat/linux/sys. Add the
following line to /etc/fstab:
linsysfs /compat/linux/sys linsysfs rw 0 0

During the pkg installation process you see that the x11-toolkits/linux-c7-gtk3 pkg will install a lot of others Linux librairies, so after installation redo a ldd to see the updated output
More generally if your Linux app is "complex modern" app you will probably add the emulators/linux-c7 pkg

Solution 2 - Linux library provided by the app itself:

For some libraries it is possible that FreeBSD may not provide them. In my example MySQL-Workbench app have his associated librairies folder

extract

Code:

# ls -l /compat/linux/lib64/mysql-workbench/lib*
lrwxrwxrwx /compat/linux/lib64/mysql-workbench/libantlr4-runtime.so -> libantlr4-runtime.so.4.7.1
-rw-r--r-- /compat/linux/lib64/mysql-workbench/libantlr4-runtime.so.4.7.1
[...]
lrwxrwxrwx /compat/linux/lib64/mysql-workbench/libwbssh.so -> libwbssh.so.8.0.19
-rw-r--r-- /compat/linux/lib64/mysql-workbench/libwbssh.so.8.0.19

So I decide to link those libraries, sample here:

Code:

# cd /compat/linux/usr/lib64
# ln -s mysql-workbench/libwbprivate.so.8.0.19 .

Solution 3 - Linux Labrary as an RPM:

For some libraries it will be necessary to install them with the CentOS rpm package
Get the rpm from CentOS 7 packages, you can also have a look in the CentOS 7 update packages.
Then install (in my case I did that for libgtkmm, libatkmm, libgdkmm, ...)

Solution 4 - FreeBSD Library: (not sure this works)
EDIT 20200506 : See post 3, after a 'reset' I was able to get all need libraries with solution 1/2/3 - all together - solution 4 not necessary

example with "libsecret-1.so.0 => not found"

let see if the library is there somewhere

Code:

# ls -l /compat/linux/lib/libsecret-1.so.0*
    ls: not found

Code:

# ls -l /compat/linux/lib64/libsecret-1.so.0*
    ls: not found

Code:

# ls -l /usr/local/lib/libsecret-1.so.0*
lrwxr-xr-x /usr/local/lib/libsecret-1.so.0 -> libsecret-1.so.0.0.0
    -rwxr-xr-x /usr/local/lib/libsecret-1.so.0.0.0

If you don't find the library you probably need to install it (see also notes below). In my example "libzip" was not install, so I did a pkg install libzip
Then, again the Handbook: "copy all the files in the last column of the output from the Linux® system into /compat/linux".
let's do for libsecret-1.so.0 and check with ldd again as a complete example

before

Code:

# # ldd /compat/linux/usr/libexec/mysql-workbench/mysql-workbench-bin | grep secret
    libsecret-1.so.0 => not found

update

Code:

# cd /compat/linux/lib64
# cp /usr/local/lib/libsecret-1.so.0 .

after

Code:

# ldd /compat/linux/usr/libexec/mysql-workbench/mysql-workbench-bin | grep secret
    (no result here - means now library found)

linking done

Running app Issue: ELF file OS ABI invalid with FreeBSD library

after linking all the missing libraries, you get a new issue

Code:

# ldd /compat/linux/usr/libexec/mysql-workbench/mysql-workbench-bin
    /compat/linux/usr/libexec/mysql-workbench/mysql-workbench-bin: error while loading shared libraries: /lib64/libsecret-1.so.0: ELF file OS ABI invalid

Again the Handbook, "help the FreeBSD kernel distinguish between a FreeBSD ELF binary and a Linux® binary"

Code:

# brandelf -t linux /compat/linux/lib64/libsecret-1.so.0

Running app Issue: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found

Run

Code:

# ./mysql-workbench-bin
./mysql-workbench-bin: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by ./mysql-workbench-bin)
./mysql-workbench-bin: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by ./mysql-workbench-bin)
./mysql-workbench-bin: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by ./mysql-workbench-bin)
[...]
./mysql-workbench-bin: /lib64/libssl.so.1.1: version `OPENSSL_1_1_1' not found (required by /lib64/libmysqlclient.so.21)
./mysql-workbench-bin: /lib64/libssl.so.1.1: version `OPENSSL_1_1_0' not found (required by /lib64/libmysqlclient.so.21)
./mysql-workbench-bin: /lib64/libcrypto.so.1.1: version `OPENSSL_1_1_1' not found (required by /lib64/libmysqlclient.so.21)
./mysql-workbench-bin: /lib64/libcrypto.so.1.1: version `OPENSSL_1_1_0' not found (required by /lib64/libmysqlclient.so.21)
./mysql-workbench-bin: /lib64/libpng15.so.15: version `PNG16_0' not found (required by /lib64/libgdal.so.1)
    ./mysql-workbench-bin: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /lib64/libsqlite3.so)

We can check that for listed libraries if they contain the required version

check (example)

Code:

# strings libstdc++.so.6 | grep GLIBCXX
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
[...]
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBCXX_3.4.18
GLIBCXX_3.4.19

So we can see the wanted version is not present. Then I try to update the library version to the last provided on CentOS 7 archived rpm but the same.
My only solution here is to go with an older version of the Linux app.

Solved for MySQL-Workbench last version - See post 3.

John Zelada · May 5, 2020

Mmmm is quite info to process, I will save your message to consult more carefully later

ohyes · May 6, 2020

I finally get last version of MySQL-Workbench 8.0.20 working.
I did a complete cleaning of Linux installation and restart the procedure as I decribed in first post (see below for quick how-to).

Please (launch as standard user):

Clean Linux:

Code:

# cd /compat

# umount tmpfs
# umount linsysfs
# umount linprocfs

# pkg delete linux-c7-7.7.1908 linux_base-c7-7.7.1908_1
# pkg info | grep linux (to check if there is still a linux pkg, if yes delete)

# rm -rf linux (/!\ take care you don't have personnal data in it before)

Re-install: As decribed in the FreeBSD Hanbook.
In my case I have also added (because I know my app needs them):

Code:

# pkg install linux-c7
# pkg install linux-c7-gtk3

Re-mount Linux stuff:

Code:

# mount tmpfs
# mount linsysfs
# mount linprocfs

Reinstall MySQL-Workbench; As described in first post:

install with the RPM
follow "solution 1/2/3" in this order for missing libraries (solution 4 was finally not necessary)

Edit the MySQL-Workbench start-up script;

first save it

Code:

# cp /compat/linux/usr/bin/mysql-workbench /compat/linux/usr/bin/mysql-workbench.sav

edit with your favorite editor:.
- remove the first line (#!/bin/bash) if you don't have bash installed
- search this line and remplace it
- Code:
```
#destdir="$WB_DEST_DIR"
destdir="/compat/linux"
```

Then start with you standard user and enjoy; /compat/linux/usr/bin/mysql-workbench

Note: I haven't tested all features (db connection) but design DB and save design is ok.
When running I see the ouput:

Code:

ld-elf.so.1: Shared object "libpthread.so.0" not found, required by "libsqlite3.so"

So it means that for some functionalities there is a missing library.

[TODO: investigate and report here]
Save your like/love/life and don't forget to smile to people

Solved Installing linux app - library issues (MySQL-Workbench as example)

ohyes

John Zelada

ohyes