Bash: How to trim/truncate variables / get substrings

In a comment to one of the most useless commands postings was shown how to use the rev command to get the last component of  the path out of a log file:

cat log | grep pattern | rev | cut -d '/' -f 1 | rev

If you only have one variable filled with a path, you can get the last component very easy:

schroff@zerberus:~$ myvar=/ab/cd/ef/gh

schroff@zerberus:~$ echo ${myvar##*\/}
gh

?

## removes the longest matching string for the pattern "*\/" from the beginning (the slash has to be escaped with a backslash).

schroff@zerberus:~$ echo ${myvar#*\/}
ab/cd/ef/gh

# removes the shortest matching pattern. Here only the starting "/"

% and %% removes everything from the end up to the pattern:

schroff@zerberus:~$ echo ${myvar%\/*}
/ab/cd/ef
schroff@zerberus:~$ echo ${myvar%%\/*}

Here the content of the bash manpage:

       ${parameter#word}
       ${parameter##word}
Remove matching prefix pattern.  The word is expanded to produce a pattern just
as in pathname expansion.  If the pattern matches the beginning of the value of
parameter,  then the result of the expansion is the expanded value of parameter
with the shortest matching pattern (the ``#'' case)  or  the  longest  matching
pattern (the ``##'' case) deleted.  If parameter is @ or *, the pattern removal
operation is applied to each positional parameter in turn, and the expansion is
the resultant list.  If parameter is an array variable subscripted with @ or *,
the pattern removal operation is applied to each member of the array  in  turn,
and the expansion is the resultant list.

       ${parameter%word}
       ${parameter%%word}
Remove matching suffix pattern.  The word is expanded to produce a pattern just
as in pathname expansion.  If the pattern matches a  trailing  portion  of  the
expanded  value  of parameter, then the result of the expansion is the expanded
value of parameter with the shortest matching pattern (the ``%'' case)  or  the
longest  matching  pattern  (the ``%%'' case) deleted.  If parameter is @ or *,
the pattern removal operation is applied to each positional parameter in  turn,
and  the  expansion  is  the resultant list.  If parameter is an array variable
subscripted with @ or *, the pattern removal operation is applied to each  mem‐
ber of the array in turn, and the expansion is the resultant list.

Java 9: JDK without subfolder JRE

In older JDK releases the directory structure was:

bin
db
include
jre
lib

With JEP 220 the jre folder was removed.

A JDK image no longer contains a jre subdirectory, as noted above. Existing code that assumes the existence of that directory might not work correctly.

But this does not mean that there is no JRE any more. You can still download the JRE. There are some minor changes to the JRE like:

The bin directory in a JRE image contains a few commands that were previously found only in JDK images, namely appletviewer, idlj,jrunscript, and jstatd. As with the previous item, these changes are a consequence of the way in which components that contain both APIs and tools were modularized.

For both version the files rt.jar, tools.jar and dt.jar are removed:

JDK and JRE images no longer contain the files lib/rt.jar,lib/tools.jar, lib/dt.jar, and other internal JAR files, as noted above. Existing code that assumes the existence of these files might not work correctly.

But this should not be a problem:

Class and resource files previously found in lib/dt.jar and visible only when that file was added to the class path are now visible via the bootstrap class loader and present in both the JRE and the JDK. 

Everyone who delivers Java applications should read  JEP 220 and check, what has to be changed...

Oracle SOA Suite 12c: Configuring the SOA Suite Weblogic Server

After

• Configuring the database via RCU
• Installation of the infrastructure software
• Installation of the SOA Suite software

 i had to run the

./config.sh

inside the home/oracle/Oracle/Middleware/Oracle_Home/oracle_common/common/bin

And then after a

./startWeblogic.sh

inside /bin in the directory, which was configured in the first screenshot of the config.sh, i can open the console:

Oracle SOA Suite: Installing the Fusion Middleware SOA Suite

After the installation of the Fusion Middleware Infrastructur the next step is to install the SOA Suite software.

The software can be found here:

The first try failed with this error:

java -d64 -jar fmw_12.2.1.3.0_soa_quickstart.jar
Launcher-Logdatei ist /tmp/OraInstall2017-10-07_11-47-20PM/launcher2017-10-07_11-47-20PM.log.
Nicht genügend freier Speicherplatz in /tmp/orcl3797124329273264119.tmp, um das Installationsprogramm zu extrahieren. Aktuell 2796 MB. Erforderlich 3532 MB.

Ok. Some cleanups inside /tmp and then:

Next step: Run the config.sh to create a SOA Suite Server....

Docker-CE: How to modify containers with overlays / How to add directories to a standard docker image

After some experiments with docker i wanted to run a tomcat with my own configuration (e.g. memory settings, ports, ...).

My first idea was: Download tomcat, configure everything and then build an image.
BUT: After i learned how to use the -v (--volume) flag for adding some file via the docker command to an image i was wondering, wether creating a new image with only the additional files on top of standard tomcat docker image.

So first step is to take a look at all local images:

# docker images
REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE
558MB
friendlyhello       latest              976ee2bb47bf        3 days ago          148MB
tomcat              latest              11df4b40749f        8 days ago          558MB

I can use tomcat:latest. (if it is not there just pull it: docker pull tomcat)
Next step is to create a directory and add all the directories which you want to override.
For my example:

mkdir conftomcat
cd conftomcat
mkdir bin

Into the bin directory i put all the files from the tomcat standard container:

# ls bin
bootstrap.jar  catalina-tasks.xml  commons-daemon-native.tar.gz  daemon.sh  setclasspath.sh  startup.sh       tool-wrapper.sh
catalina.sh    commons-daemon.jar  configtest.sh                 digest.sh  shutdown.sh      tomcat-juli.jar  version.sh

Inside the catalina.sh i added -Xmx384M.
In conftomcat i created the following Dockerfile:

FROM tomcat:latest
WORKDIR /usr/local/tomcat/bin
ADD status /usr/local/tomcat/webapps/mystatus
ADD bin /usr/local/tomcat/bin
ENTRYPOINT [ "/usr/local/tomcat/bin/catalina.sh" ]
CMD [ "run"]

And as you can see i added my index.jsp which is inside status (s. this posting).
Ok. Let's see, if my plan works:

#docker build  -t  mytomcat .

ending build context to Docker daemon  375.8kB
Step 1/6 : FROM tomcat:latest
 ---> 11df4b40749f
Step 2/6 : WORKDIR /usr/local/tomcat/bin
 ---> Using cache
 ---> 5696a9ab99cb
Step 3/6 : ADD status /usr/local/tomcat/webapps/mystatus
 ---> 1bceea5af515
Step 4/6 : ADD bin /usr/local/tomcat/bin
 ---> e8d3a386a7f0
Step 5/6 : ENTRYPOINT [ "/usr/local/tomcat/bin/catalina.sh" ]
 ---> Running in a04038032bb7
Removing intermediate container a04038032bb7
 ---> 4c8fda05df18
Step 6/6 : CMD [ "run"]
 ---> Running in cce378648e7a
Removing intermediate container cce378648e7a
 ---> 72ecfe2aa4a7
Successfully built 72ecfe2aa4a7
Successfully tagged mytomcat:latest

and then start:

docker run -p 4001:8080 mytomcat

Let's check the memory settings:

$ ps aux|grep java
root      2313 20.7  8.0 2418472 81236 ?       Ssl  19:51   0:02 /docker-java-home/jre/bin/java -Djava.util.logging.config.file=/usr/local/tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xmx394M -Djdk.tls.ephemeralDHKeySize=2048 -Djava.protocol.handler.pkgs=org.apache.catalina.webresources -classpath /usr/local/tomcat/bin/bootstrap.jar:/usr/local/tomcat/bin/tomcat-juli.jar -Dcatalina.base=/usr/local/tomcat -Dcatalina.home=/usr/local/tomcat -Djava.io.tmpdir=/usr/local/tomcat/temp org.apache.catalina.startup.Bootstrap start

Yes - changed to 384M.
And check the jsp:

Yippie!
As you can see, i have the standard tomcat running with an override inside the configuration to 384M. So it should be easy to add certificates, WARs, ... to such a standard container.


Related posts:

• Docker on Ubuntu 
• Running through a tutorial / investigating the processes
• Creating a small linux for my docker cluster (Alpine Linux) 
• How to build a docker swarm 
• Creating a minimal webserver container and deploying it to docker swarm
• Setting up a tomcat with docker  
• Running a swarm with multiple managers 
• Mysql inside a docker container - persistency with docker volumes 
• How to change the configuration of a standard docker container(e.g. changing tomcats memory settings)

Ubuntu Intel Spectre/Meltdown update

One week after the rumors about Spectre and Meltdown (s. Project Zero Blog) my Ubuntu 17.10 got the Intel microcode patch:


root@zerberus:~# apt-get upgrade
Paketlisten werden gelesen... Fertig
Abhängigkeitsbaum wird aufgebaut.      
Statusinformationen werden eingelesen.... Fertig
Paketaktualisierung (Upgrade) wird berechnet... Fertig
Die folgenden Pakete wurden automatisch installiert und werden nicht mehr benötigt:
  linux-headers-4.13.0-17 linux-headers-4.13.0-17-generic
  linux-image-4.13.0-17-generic linux-image-extra-4.13.0-17-generic
Verwenden Sie »apt autoremove«, um sie zu entfernen.
Die folgenden Pakete sind zurückgehalten worden:
  linux-generic linux-headers-generic linux-image-generic
Die folgenden Pakete werden aktualisiert (Upgrade):
  gir1.2-javascriptcoregtk-4.0 gir1.2-poppler-0.18 gir1.2-webkit2-4.0
  intel-microcode libjavascriptcoregtk-4.0-18 libpoppler-glib8 libpoppler68
  libruby2.3 libwebkit2gtk-4.0-37 libwebkit2gtk-4.0-37-gtk2 linux-libc-dev
  poppler-utils ruby2.3
13 aktualisiert, 0 neu installiert, 0 zu entfernen und 3 nicht aktualisiert.
Es müssen 30,5 MB an Archiven heruntergeladen werden.
Nach dieser Operation werden 321 kB Plattenplatz zusätzlich benutzt.
Möchten Sie fortfahren? [J/n]
Holen:1 http://de.archive.ubuntu.com/ubuntu artful-updates/universe amd64 libwebkit2gtk-4.0-37-gtk2 amd64 2.18.5-0ubuntu0.17.10.1 [9.026 kB]
Holen:2 http://de.archive.ubuntu.com/ubuntu artful-updates/main amd64 libwebkit2gtk-4.0-37 amd64 2.18.5-0ubuntu0.17.10.1 [11,2 MB]                                                      
Holen:3 http://de.archive.ubuntu.com/ubuntu artful-updates/main amd64 libjavascriptcoregtk-4.0-18 amd64 2.18.5-0ubuntu0.17.10.1 [4.052 kB]                                              
Holen:4 http://de.archive.ubuntu.com/ubuntu artful-updates/main amd64 gir1.2-webkit2-4.0 amd64 2.18.5-0ubuntu0.17.10.1 [67,6 kB]                                                        
Holen:5 http://de.archive.ubuntu.com/ubuntu artful-updates/main amd64 gir1.2-javascriptcoregtk-4.0 amd64 2.18.5-0ubuntu0.17.10.1 [21,0 kB]                                              
Holen:6 http://de.archive.ubuntu.com/ubuntu artful-updates/main amd64 poppler-utils amd64 0.57.0-2ubuntu4.2 [141 kB]                                                                    
Holen:7 http://de.archive.ubuntu.com/ubuntu artful-updates/main amd64 libpoppler-glib8 amd64 0.57.0-2ubuntu4.2 [108 kB]                                                                 
Holen:8 http://de.archive.ubuntu.com/ubuntu artful-updates/main amd64 libpoppler68 amd64 0.57.0-2ubuntu4.2 [787 kB]                                                                     
Holen:9 http://de.archive.ubuntu.com/ubuntu artful-updates/main amd64 gir1.2-poppler-0.18 amd64 0.57.0-2ubuntu4.2 [18,4 kB]                                                             
Holen:10 http://de.archive.ubuntu.com/ubuntu artful-updates/main amd64 linux-libc-dev amd64 4.13.0-25.29 [963 kB]                                                                       
Holen:11 http://de.archive.ubuntu.com/ubuntu artful-updates/main amd64 intel-microcode amd64 3.20180108.0~ubuntu17.10.1 [1.090 kB]                                                       Holen:12 http://de.archive.ubuntu.com/ubuntu artful-updates/main amd64 libruby2.3 amd64 2.3.3-1ubuntu1.2 [2.972 kB]                                                                     
Holen:13 http://de.archive.ubuntu.com/ubuntu artful-updates/main amd64 ruby2.3 amd64 2.3.3-1ubuntu1.2 [41,0 kB]                                                                         
Es wurden 30,5 MB in 25 s geholt (1.186 kB/s).                                                                                                                                          
(Lese Datenbank ... 391417 Dateien und Verzeichnisse sind derzeit installiert.)
Vorbereitung zum Entpacken von .../00-libwebkit2gtk-4.0-37-gtk2_2.18.5-0ubuntu0.17.10.1_amd64.deb ...
Entpacken von libwebkit2gtk-4.0-37-gtk2:amd64 (2.18.5-0ubuntu0.17.10.1) über (2.18.4-0ubuntu0.17.10.1) ...
Vorbereitung zum Entpacken von .../01-libwebkit2gtk-4.0-37_2.18.5-0ubuntu0.17.10.1_amd64.deb ...
Entpacken von libwebkit2gtk-4.0-37:amd64 (2.18.5-0ubuntu0.17.10.1) über (2.18.4-0ubuntu0.17.10.1) ...
Vorbereitung zum Entpacken von .../02-libjavascriptcoregtk-4.0-18_2.18.5-0ubuntu0.17.10.1_amd64.deb ...
Entpacken von libjavascriptcoregtk-4.0-18:amd64 (2.18.5-0ubuntu0.17.10.1) über (2.18.4-0ubuntu0.17.10.1) ...
Vorbereitung zum Entpacken von .../03-gir1.2-webkit2-4.0_2.18.5-0ubuntu0.17.10.1_amd64.deb ...
Entpacken von gir1.2-webkit2-4.0:amd64 (2.18.5-0ubuntu0.17.10.1) über (2.18.4-0ubuntu0.17.10.1) ...
Vorbereitung zum Entpacken von .../04-gir1.2-javascriptcoregtk-4.0_2.18.5-0ubuntu0.17.10.1_amd64.deb ...
Entpacken von gir1.2-javascriptcoregtk-4.0:amd64 (2.18.5-0ubuntu0.17.10.1) über (2.18.4-0ubuntu0.17.10.1) ...
Vorbereitung zum Entpacken von .../05-poppler-utils_0.57.0-2ubuntu4.2_amd64.deb ...
Entpacken von poppler-utils (0.57.0-2ubuntu4.2) über (0.57.0-2ubuntu4.1) ...
Vorbereitung zum Entpacken von .../06-libpoppler-glib8_0.57.0-2ubuntu4.2_amd64.deb ...
Entpacken von libpoppler-glib8:amd64 (0.57.0-2ubuntu4.2) über (0.57.0-2ubuntu4.1) ...
Vorbereitung zum Entpacken von .../07-libpoppler68_0.57.0-2ubuntu4.2_amd64.deb ...
Entpacken von libpoppler68:amd64 (0.57.0-2ubuntu4.2) über (0.57.0-2ubuntu4.1) ...
Vorbereitung zum Entpacken von .../08-gir1.2-poppler-0.18_0.57.0-2ubuntu4.2_amd64.deb ...
Entpacken von gir1.2-poppler-0.18:amd64 (0.57.0-2ubuntu4.2) über (0.57.0-2ubuntu4.1) ...
Vorbereitung zum Entpacken von .../09-linux-libc-dev_4.13.0-25.29_amd64.deb ...
Entpacken von linux-libc-dev:amd64 (4.13.0-25.29) über (4.13.0-21.24) ...
Vorbereitung zum Entpacken von .../10-intel-microcode_3.20180108.0~ubuntu17.10.1_amd64.deb ...
Entpacken von intel-microcode (3.20180108.0~ubuntu17.10.1) über (3.20170707.1) ...Vorbereitung zum Entpacken von .../11-libruby2.3_2.3.3-1ubuntu1.2_amd64.deb ...
Entpacken von libruby2.3:amd64 (2.3.3-1ubuntu1.2) über (2.3.3-1ubuntu1.1) ...
Vorbereitung zum Entpacken von .../12-ruby2.3_2.3.3-1ubuntu1.2_amd64.deb ...
Entpacken von ruby2.3 (2.3.3-1ubuntu1.2) über (2.3.3-1ubuntu1.1) ...
intel-microcode (3.20180108.0~ubuntu17.10.1) wird eingerichtet ...update-initramfs: deferring update (trigger activated)
intel-microcode: microcode will be updated at next boot
linux-libc-dev:amd64 (4.13.0-25.29) wird eingerichtet ...
gir1.2-javascriptcoregtk-4.0:amd64 (2.18.5-0ubuntu0.17.10.1) wird eingerichtet ...
Trigger für libc-bin (2.26-0ubuntu2) werden verarbeitet ...
Trigger für man-db (2.7.6.1-2) werden verarbeitet ...
libjavascriptcoregtk-4.0-18:amd64 (2.18.5-0ubuntu0.17.10.1) wird eingerichtet ...
libruby2.3:amd64 (2.3.3-1ubuntu1.2) wird eingerichtet ...
libpoppler68:amd64 (0.57.0-2ubuntu4.2) wird eingerichtet ...
libpoppler-glib8:amd64 (0.57.0-2ubuntu4.2) wird eingerichtet ...
poppler-utils (0.57.0-2ubuntu4.2) wird eingerichtet ...
libwebkit2gtk-4.0-37:amd64 (2.18.5-0ubuntu0.17.10.1) wird eingerichtet ...
libwebkit2gtk-4.0-37-gtk2:amd64 (2.18.5-0ubuntu0.17.10.1) wird eingerichtet ...
gir1.2-poppler-0.18:amd64 (0.57.0-2ubuntu4.2) wird eingerichtet ...
ruby2.3 (2.3.3-1ubuntu1.2) wird eingerichtet ...
gir1.2-webkit2-4.0:amd64 (2.18.5-0ubuntu0.17.10.1) wird eingerichtet ...
Trigger für initramfs-tools (0.125ubuntu12) werden verarbeitet ...
update-initramfs: Generating /boot/initrd.img-4.13.0-21-generic
Trigger für libc-bin (2.26-0ubuntu2) werden verarbeitet ...

So note the "intel-microcode" package, which states:
intel-microcode: microcode will be updated at next boot

And after the reboot:
schroff@zerberus:~$ dmesg | grep microcode
[    0.000000] microcode: microcode updated early to revision 0xc2, date = 2017-11-16
[    1.400728] microcode: sig=0x406e3, pf=0x40, revision=0xc2
[    1.401060] microcode: Microcode Update Driver: v2.2.

Oracle SOA Suite: Installing the Fusion Middleware Infrastructure

After setting up the database (installation, instance setup) and the SOA Suite repository (via rcu) the next step is to install the Oracle Weblogic Infrastructure.

The software can be downloaded here:

(You have to choose "Fusion Middleware Infrastructure Installer)

The unzip the downloaded zip:

 fmw_12.2.1.3.0_infrastructure_Disk1_1of1.zip

and run it: 

java -d64 -jar fmw_12.2.1.3.0_infrastructure.jar

Because the Oracle documentation does not contain pictures of the installer, here the screenshots:

Next step is to run the config.sh to configure the Application server domain.
(Not really true: first the SOA Suite software has to be added to the middleware home.)

Review at amazon: Kubernetes: Up & Running

Between christmas and new year i read

The authors state:

"This practical guide shows you how Kubernetes and container technology can help you achieve new levels of velocity, agility, reliability, and efficiency."

I think, yes - this is a practial guide, but within only 166 pages it is far too short to give relevant insights into Kubernetes. There are many commands and YAMLs shown, but the book misses a didactic preparation. Some chapters can only be understand, if you have read some later chapters.

But for only 25€ you get a good start, if you are willing to read the book twice ;-)

If you are interested, take a look at my review at amazon.com. (This time amazon.de refused my review. ;-)

Docker-Swarm: How to run a mysql database...

After several tests with docker swarm (setting up a swarm, running with more than on master, running a webserver in a swarm) i am thinking about running a mysql database in a swarm.

If you are running a mysql database on one docker host, you have to set up a docker volume, because otherwise data inside the container is gone, if you restart your database container. You can follow this tutorial, which says, you have to run

docker run --name=mysql1 -d mysql/mysql-server:tag

but there is the persistent volume missing. If you try this one, you are on the right way:

docker run --name mysqldb --volumes-from mysql_data -v /var/lib/mysql:/var/l
ib/mysql -e MYSQL_USER=mysql -e MYSQL_PASSWORD=mysql -e MYSQL_DATABASE=sample -e MYSQL
_ROOT_PASSWORD=supersecret -it -p 3306:3306 mysql

The problem is, that you have to create a container, mysql_data which contains a volume.

What about running a mysql database just with a volume?

First idea is to create a docker volume:

alpine:~#  docker volume create mysql_data
mysql_data
alpine:~# docker volume ls
DRIVER              VOLUME NAME
local               mysql_data

 And then start the mysql database:

 alpine:~# docker run --name mysqldb  -v mysql_data:/var/lib/mysql -e MYSQL_USER=mysql
-e MYSQL_PASSWORD=mysql -e MYSQL_DATABASE=sample -e MYSQL_ROOT_PASSWORD=supersecret -i
t -p 3306:3306 mysql
Initializing database
2017-12-10T12:25:38.890958Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2017-12-10T12:25:39.114910Z 0 [Warning] InnoDB: New log files created, LSN=45790
2017-12-10T12:25:39.192006Z 0 [Warning] InnoDB: Creating foreign key constraint system tables.
2017-12-10T12:25:39.269224Z 0 [Warning] No existing UUID has been found, so we assume that this is the first time that this server has been started. Generating a new UUID: 3b5276c6-dda5-11e7-847f-0242ac110002.
2017-12-10T12:25:39.293895Z 0 [Warning] Gtid table is not ready to be used. Table 'mysql.gtid_executed' cannot be opened.
2017-12-10T12:25:39.296705Z 1 [Warning] root@localhost is created with an empty password ! Please consider switching off the --initialize-insecure option.
2017-12-10T12:25:39.734384Z 1 [Warning] 'user' entry 'root@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:39.734823Z 1 [Warning] 'user' entry 'mysql.session@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:39.735089Z 1 [Warning] 'user' entry 'mysql.sys@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:39.735325Z 1 [Warning] 'db' entry 'performance_schema mysql.session@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:39.735530Z 1 [Warning] 'db' entry 'sys mysql.sys@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:39.735734Z 1 [Warning] 'proxies_priv' entry '@ root@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:39.735969Z 1 [Warning] 'tables_priv' entry 'user mysql.session@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:39.736171Z 1 [Warning] 'tables_priv' entry 'sys_config mysql.sys@localhost' ignored in --skip-name-resolve mode.
Database initialized
Initializing certificates
Generating a 2048 bit RSA private key
............+++
...........................................................................................................................................................................................................+++
unable to write 'random state'
writing new private key to 'ca-key.pem'
-----
Generating a 2048 bit RSA private key
.......................+++
.......+++
unable to write 'random state'
writing new private key to 'server-key.pem'
-----
Generating a 2048 bit RSA private key
.......................+++
.............+++
unable to write 'random state'
writing new private key to 'client-key.pem'
-----
Certificates initialized
MySQL init process in progress...
2017-12-10T12:25:42.948452Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2017-12-10T12:25:42.949739Z 0 [Note] mysqld (mysqld 5.7.20) starting as process 87 ...
2017-12-10T12:25:42.952799Z 0 [Note] InnoDB: PUNCH HOLE support available
2017-12-10T12:25:42.953188Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2017-12-10T12:25:42.953550Z 0 [Note] InnoDB: Uses event mutexes
2017-12-10T12:25:42.953828Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
2017-12-10T12:25:42.954120Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.3
2017-12-10T12:25:42.954451Z 0 [Note] InnoDB: Using Linux native AIO
2017-12-10T12:25:42.954900Z 0 [Note] InnoDB: Number of pools: 1
2017-12-10T12:25:42.955173Z 0 [Note] InnoDB: Using CPU crc32 instructions
2017-12-10T12:25:42.956841Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
2017-12-10T12:25:42.965639Z 0 [Note] InnoDB: Completed initialization of buffer pool
2017-12-10T12:25:42.969568Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
2017-12-10T12:25:42.982838Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
2017-12-10T12:25:43.001695Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables
2017-12-10T12:25:43.002427Z 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
2017-12-10T12:25:43.028474Z 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
2017-12-10T12:25:43.029519Z 0 [Note] InnoDB: 96 redo rollback segment(s) found. 96 redo rollback segment(s) are active.
2017-12-10T12:25:43.029785Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are active.
2017-12-10T12:25:43.030165Z 0 [Note] InnoDB: Waiting for purge to start
2017-12-10T12:25:43.080873Z 0 [Note] InnoDB: 5.7.20 started; log sequence number 2565377
2017-12-10T12:25:43.085057Z 0 [Note] Plugin 'FEDERATED' is disabled.
2017-12-10T12:25:43.097783Z 0 [Note] InnoDB: Loading buffer pool(s) from /var/lib/mysql/ib_buffer_pool
2017-12-10T12:25:43.111653Z 0 [Note] Found ca.pem, server-cert.pem and server-key.pem in data directory. Trying to enable SSL support using them.
2017-12-10T12:25:43.112695Z 0 [Warning] CA certificate ca.pem is self signed.
2017-12-10T12:25:43.112387Z 0 [Note] InnoDB: Buffer pool(s) load completed at 171210 12:25:43
2017-12-10T12:25:43.122126Z 0 [Warning] 'user' entry 'root@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:43.122654Z 0 [Warning] 'user' entry 'mysql.session@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:43.122922Z 0 [Warning] 'user' entry 'mysql.sys@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:43.123172Z 0 [Warning] 'db' entry 'performance_schema mysql.session@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:43.123424Z 0 [Warning] 'db' entry 'sys mysql.sys@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:43.123655Z 0 [Warning] 'proxies_priv' entry '@ root@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:43.125278Z 0 [Warning] 'tables_priv' entry 'user mysql.session@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:43.125625Z 0 [Warning] 'tables_priv' entry 'sys_config mysql.sys@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:43.130811Z 0 [Note] Event Scheduler: Loaded 0 events
2017-12-10T12:25:43.131463Z 0 [Note] mysqld: ready for connections.
Version: '5.7.20'  socket: '/var/run/mysqld/mysqld.sock'  port: 0  MySQL Community Server (GPL)
2017-12-10T12:25:43.131789Z 0 [Note] Executing 'SELECT * FROM INFORMATION_SCHEMA.TABLES;' to get a list of tables using the deprecated partition engine. You may use the startup option '--disable-partition-engine-check' to skip this check.
2017-12-10T12:25:43.132034Z 0 [Note] Beginning of list of non-natively partitioned tables
2017-12-10T12:25:43.141674Z 0 [Note] End of list of non-natively partitioned tables
Warning: Unable to load '/usr/share/zoneinfo/iso3166.tab' as time zone. Skipping it.
Warning: Unable to load '/usr/share/zoneinfo/leap-seconds.list' as time zone. Skipping it.
Warning: Unable to load '/usr/share/zoneinfo/zone.tab' as time zone. Skipping it.
2017-12-10T12:25:45.325153Z 5 [Warning] 'user' entry 'root@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:45.326169Z 5 [Warning] 'user' entry 'mysql.session@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:45.326766Z 5 [Warning] 'user' entry 'mysql.sys@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:45.327430Z 5 [Warning] 'db' entry 'performance_schema mysql.session@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:45.328439Z 5 [Warning] 'db' entry 'sys mysql.sys@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:45.329236Z 5 [Warning] 'proxies_priv' entry '@ root@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:45.330139Z 5 [Warning] 'tables_priv' entry 'user mysql.session@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:45.330625Z 5 [Warning] 'tables_priv' entry 'sys_config mysql.sys@localhost' ignored in --skip-name-resolve mode.
mysql: [Warning] Using a password on the command line interface can be insecure.
mysql: [Warning] Using a password on the command line interface can be insecure.
mysql: [Warning] Using a password on the command line interface can be insecure.
mysql: [Warning] Using a password on the command line interface can be insecure.
2017-12-10T12:25:45.355944Z 9 [Warning] 'user' entry 'root@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:45.356363Z 9 [Warning] 'user' entry 'mysql.session@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:45.356743Z 9 [Warning] 'user' entry 'mysql.sys@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:45.357080Z 9 [Warning] 'db' entry 'performance_schema mysql.session@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:45.357407Z 9 [Warning] 'db' entry 'sys mysql.sys@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:45.358138Z 9 [Warning] 'proxies_priv' entry '@ root@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:45.358579Z 9 [Warning] 'tables_priv' entry 'user mysql.session@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:45.358825Z 9 [Warning] 'tables_priv' entry 'sys_config mysql.sys@localhost' ignored in --skip-name-resolve mode.

2017-12-10T12:25:45.360088Z 0 [Note] Giving 0 client threads a chance to die gracefully
2017-12-10T12:25:45.360365Z 0 [Note] Shutting down slave threads
2017-12-10T12:25:45.360562Z 0 [Note] Forcefully disconnecting 0 remaining clients
2017-12-10T12:25:45.360757Z 0 [Note] Event Scheduler: Purging the queue. 0 events
2017-12-10T12:25:45.360982Z 0 [Note] Binlog end
2017-12-10T12:25:45.361681Z 0 [Note] Shutting down plugin 'ngram'
2017-12-10T12:25:45.361897Z 0 [Note] Shutting down plugin 'BLACKHOLE'
2017-12-10T12:25:45.362098Z 0 [Note] Shutting down plugin 'partition'
2017-12-10T12:25:45.362285Z 0 [Note] Shutting down plugin 'ARCHIVE'
2017-12-10T12:25:45.362470Z 0 [Note] Shutting down plugin 'INNODB_SYS_VIRTUAL'
2017-12-10T12:25:45.362653Z 0 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
2017-12-10T12:25:45.362844Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACES'
2017-12-10T12:25:45.363019Z 0 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_COLS'
2017-12-10T12:25:45.363206Z 0 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
2017-12-10T12:25:45.363455Z 0 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
2017-12-10T12:25:45.363740Z 0 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
2017-12-10T12:25:45.364038Z 0 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
2017-12-10T12:25:45.364313Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS'
2017-12-10T12:25:45.364603Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
2017-12-10T12:25:45.364886Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE'
2017-12-10T12:25:45.365129Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE'
2017-12-10T12:25:45.365333Z 0 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
2017-12-10T12:25:45.365507Z 0 [Note] Shutting down plugin 'INNODB_FT_BEING_DELETED'
2017-12-10T12:25:45.365678Z 0 [Note] Shutting down plugin 'INNODB_FT_DELETED'
2017-12-10T12:25:45.365846Z 0 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
2017-12-10T12:25:45.366026Z 0 [Note] Shutting down plugin 'INNODB_METRICS'
2017-12-10T12:25:45.366214Z 0 [Note] Shutting down plugin 'INNODB_TEMP_TABLE_INFO'
2017-12-10T12:25:45.366413Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
2017-12-10T12:25:45.366616Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LRU'
2017-12-10T12:25:45.366799Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
2017-12-10T12:25:45.366976Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
2017-12-10T12:25:45.367142Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
2017-12-10T12:25:45.367305Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
2017-12-10T12:25:45.367467Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM'
2017-12-10T12:25:45.367628Z 0 [Note] Shutting down plugin 'INNODB_CMP_RESET'
2017-12-10T12:25:45.367796Z 0 [Note] Shutting down plugin 'INNODB_CMP'
2017-12-10T12:25:45.367978Z 0 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2017-12-10T12:25:45.368141Z 0 [Note] Shutting down plugin 'INNODB_LOCKS'
2017-12-10T12:25:45.368307Z 0 [Note] Shutting down plugin 'INNODB_TRX'
2017-12-10T12:25:45.368469Z 0 [Note] Shutting down plugin 'InnoDB'
2017-12-10T12:25:45.368926Z 0 [Note] InnoDB: FTS optimize thread exiting.
2017-12-10T12:25:45.369212Z 0 [Note] InnoDB: Starting shutdown...
2017-12-10T12:25:45.469927Z 0 [Note] InnoDB: Dumping buffer pool(s) to /var/lib/mysql/ib_buffer_pool
2017-12-10T12:25:45.471353Z 0 [Note] InnoDB: Buffer pool(s) dump completed at 171210 12:25:45
2017-12-10T12:25:47.118138Z 0 [Note] InnoDB: Shutdown completed; log sequence number 12169663
2017-12-10T12:25:47.125477Z 0 [Note] InnoDB: Removed temporary tablespace data file: "ibtmp1"
2017-12-10T12:25:47.126721Z 0 [Note] Shutting down plugin 'MRG_MYISAM'
2017-12-10T12:25:47.127496Z 0 [Note] Shutting down plugin 'MyISAM'
2017-12-10T12:25:47.128253Z 0 [Note] Shutting down plugin 'CSV'
2017-12-10T12:25:47.128958Z 0 [Note] Shutting down plugin 'MEMORY'
2017-12-10T12:25:47.129665Z 0 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
2017-12-10T12:25:47.130679Z 0 [Note] Shutting down plugin 'sha256_password'
2017-12-10T12:25:47.131807Z 0 [Note] Shutting down plugin 'mysql_native_password'
2017-12-10T12:25:47.132756Z 0 [Note] Shutting down plugin 'binlog'
2017-12-10T12:25:47.135910Z 0 [Note] mysqld: Shutdown complete


MySQL init process done. Ready for start up.

2017-12-10T12:25:47.379637Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2017-12-10T12:25:47.381062Z 0 [Note] mysqld (mysqld 5.7.20) starting as process 1 ...
2017-12-10T12:25:47.383987Z 0 [Note] InnoDB: PUNCH HOLE support available
2017-12-10T12:25:47.384373Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2017-12-10T12:25:47.384612Z 0 [Note] InnoDB: Uses event mutexes
2017-12-10T12:25:47.384828Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
2017-12-10T12:25:47.385024Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.3
2017-12-10T12:25:47.385229Z 0 [Note] InnoDB: Using Linux native AIO
2017-12-10T12:25:47.385591Z 0 [Note] InnoDB: Number of pools: 1
2017-12-10T12:25:47.385887Z 0 [Note] InnoDB: Using CPU crc32 instructions
2017-12-10T12:25:47.387049Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
2017-12-10T12:25:47.393069Z 0 [Note] InnoDB: Completed initialization of buffer pool
2017-12-10T12:25:47.395207Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
2017-12-10T12:25:47.406539Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
2017-12-10T12:25:47.417533Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables
2017-12-10T12:25:47.418058Z 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
2017-12-10T12:25:47.433202Z 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
2017-12-10T12:25:47.434200Z 0 [Note] InnoDB: 96 redo rollback segment(s) found. 96 redo rollback segment(s) are active.
2017-12-10T12:25:47.434456Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are active.
2017-12-10T12:25:47.434855Z 0 [Note] InnoDB: Waiting for purge to start
2017-12-10T12:25:47.485468Z 0 [Note] InnoDB: 5.7.20 started; log sequence number 12169663
2017-12-10T12:25:47.487084Z 0 [Note] Plugin 'FEDERATED' is disabled.
2017-12-10T12:25:47.500417Z 0 [Note] Found ca.pem, server-cert.pem and server-key.pem in data directory. Trying to enable SSL support using them.
2017-12-10T12:25:47.502089Z 0 [Note] InnoDB: Loading buffer pool(s) from /var/lib/mysql/ib_buffer_pool
2017-12-10T12:25:47.511981Z 0 [Warning] CA certificate ca.pem is self signed.
2017-12-10T12:25:47.516700Z 0 [Note] Server hostname (bind-address): '*'; port: 3306
2017-12-10T12:25:47.517640Z 0 [Note] IPv6 is available.
2017-12-10T12:25:47.518010Z 0 [Note]   - '::' resolves to '::';
2017-12-10T12:25:47.518467Z 0 [Note] Server socket created on IP: '::'.
2017-12-10T12:25:47.523590Z 0 [Warning] 'user' entry 'root@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:47.524079Z 0 [Warning] 'user' entry 'mysql.session@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:47.524350Z 0 [Warning] 'user' entry 'mysql.sys@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:47.524623Z 0 [Warning] 'db' entry 'performance_schema mysql.session@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:47.524854Z 0 [Warning] 'db' entry 'sys mysql.sys@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:47.525118Z 0 [Warning] 'proxies_priv' entry '@ root@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:47.527817Z 0 [Warning] 'tables_priv' entry 'user mysql.session@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:47.528270Z 0 [Note] InnoDB: Buffer pool(s) load completed at 171210 12:25:47
2017-12-10T12:25:47.528542Z 0 [Warning] 'tables_priv' entry 'sys_config mysql.sys@localhost' ignored in --skip-name-resolve mode.
2017-12-10T12:25:47.532739Z 0 [Note] Event Scheduler: Loaded 0 events
2017-12-10T12:25:47.533402Z 0 [Note] mysqld: ready for connections.
Version: '5.7.20'  socket: '/var/run/mysqld/mysqld.sock'  port: 3306  MySQL Community Server (GPL)
2017-12-10T12:25:47.533772Z 0 [Note] Executing 'SELECT * FROM INFORMATION_SCHEMA.TABLES;' to get a list of tables using the deprecated partition engine. You may use the startup option '--disable-partition-engine-check' to skip this check.
2017-12-10T12:25:47.534079Z 0 [Note] Beginning of list of non-natively partitioned tables
2017-12-10T12:25:47.541968Z 0 [Note] End of list of non-natively partitioned tables

and everything works like expected:

alpine:~# docker ps
CONTAINER ID        IMAGE               COMMAND                  CREATED             STATUS              PORTS                    NAMES
a6d0d908f034        mysql               "docker-entrypoint..."   3 minutes ago       Up 3 minutes        0.0.0.0:3306->3306/tcp   mysqldb
alpine:~# docker exec -it a6d0d908f034  mysql -u root -psupersecret
mysql: [Warning] Using a password on the command line interface can be insecure.
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 4
Server version: 5.7.20 MySQL Community Server (GPL)

Copyright (c) 2000, 2017, Oracle and/or its affiliates. All rights reserved.

Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

mysql> exit
Bye

If i create the following:

mysql> create database mydb;

Query OK, 1 row affected (0.00 sec)
mysql> use mydb
Database changed
mysql> create table mytable ( id int);
Query OK, 0 rows affected (0.03 sec)

and inside the volume:

alpine:/# docker volume inspect mysql_data
[
    {
        "CreatedAt": "2017-12-10T12:30:53Z",
        "Driver": "local",
        "Labels": {},
        "Mountpoint": "/var/lib/docker/volumes/mysql_data/_data",
        "Name": "mysql_data",
        "Options": {},
        "Scope": "local"
    }
]
alpine:/# ls -l /var/lib/docker/volumes/mysql_data/_data/mydb/
total 112
-rw-r-----    1 999      ping            65 Dec 10 12:30 db.opt
-rw-r-----    1 999      ping          8556 Dec 10 12:31 mytable.frm
-rw-r-----    1 999      ping         98304 Dec 10 12:31 mytable.ibd

But after stopping the mysql database, i got the following on the next start:

alpine:~# docker run --name mysqldb  -v mysql_data:/var/lib/mysql -e MYSQL_USER=mysql -e MYSQL_PASSWORD=mysql -e MYSQL_DATABASE=sample -e MYSQL_ROOT_PASSWORD=supersecret -it -p 3306:3306 mysq
l
docker: Error response from daemon: Conflict. The container name "/mysqldb" is already in use by container "a6d0d908f03466181682666affb390650179c322f2848d32f2c72fab828f980c". You have to remove (or rename) that container to be able to reuse that name.
See 'docker run --help'.

 OK. I have to change the "--name" (--> mysqldb2):

alpine:/# docker exec -it mysqldb2  mysql -u root -psupersecret
mysql: [Warning] Using a password on the command line interface can be insecure.
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 3
Server version: 5.7.20 MySQL Community Server (GPL)

Copyright (c) 2000, 2017, Oracle and/or its affiliates. All rights reserved.

Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

mysql> show databases
    -> ;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| mydb               |
| mysql              |
| performance_schema |
| sample             |
| sys                |
+--------------------+
6 rows in set (0.01 sec)

Yippie! The data is still there!







Shortcomings of this approach:

• Each time you start the mysql database on a new host, you have to run "docker volume create..."
  If you create a container with this volume (s. here oder there) you can skip this "docker volume create".
• Both approaches will not work on docker swarm. The data is local to a node and not shared. One idea: Use a NFS mountpoint to redistribute the volume to all nodes.

Related posts:

• Docker on Ubuntu 
• Running through a tutorial / investigating the processes
• Creating a small linux for my docker cluster (Alpine Linux) 
• How to build a docker swarm 
• Creating a minimal webserver container and deploying it to docker swarm
• Setting up a tomcat with docker  
• Running a swarm with multiple managers 
• Mysql inside a docker container - persistency with docker volumes 
• How to change the configuration of a standard docker container(e.g. changing tomcats memory settings)