Jupyter docker stacks with a custom user

Jupyter allows to set a custom user instead of jovyan which is the default for all containers of the Jupyter Docker Stack. You need to change this user or its UID and GID in order to get the permissions right when you mount a volume from the host into the Jupyter container. The following steps are required:

  1. Create an unprivileged user and an asociated group on the host. Here we call the user and the group docker_worker
  2. Add your host user to the group. This gives you the permissions to modify and read the files also on the host. This is useful if your working directory on the hist is under source code control (eg. git)
  3. Launch the container with the correct settings that change the user inside the container

It is important to know that during the launch the container needs root privileges in order to change the settings in the mounted host volume and inside the container. After the permissions have been changed, the user is switched back and does not run with root privileges, but your new user. Thus make sure to secure your Docker service, as the permissions inside the container also apply to the host.

Prepare an unprivileged user on the host

Docker-compose Caveats

It is important to know that docker-compose supports either an array or a dictionary for environment variables (docs).  In the case below we use arrays and we quote all variables. If you accidentally use a dictionary, then the quotes would be passed along to the Jupyter script. You would then see this error message: 

The docker-compose file

Here you can see that we set the variables that cause the container to ditch jovyan in favor of docker_worker.

NB_USER: ‘docker_worker’
NB_UID: 1010
NB_GID: 1020
CHOWN_HOME: ‘yes’
CHOWN_HOME_OPTS: -R

This facilitates easy version control of the working directory of Jupyter. I also added the snipped to my Github Jupyter template.

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Unbrick a Netgear WNR3500L V2

It finally happened… After experimenting with alternative firmware for my WNR3500L router, I uploaded the wrong version and converted the device into a rather expensive paperweight. After some searching, I found this page, explaining how to revitalize the router by using a USB-TTL converter cable. You can get  (e.g. CP2102 Module Modul USB to TTL Converter) for a few bucks Ebay, but expect a few weeks for the delivery from China.  If you follow the tutorial on the OpenRouters page closely, it should work out quite nicely.

Update: 2018-01-21

It happened again. I flashed an unsupported version of LEDE on the device and it did not want to boot again. I followed the same procedure as described here, but the router was complaining about a version missmatch of the device ID and the image ID. Turns out, I had to explicitly use binary mode for FTP. Here are the steps again.

  1. Connect the serial cables as shown
  2. Make sure router is off
  3. Launch minicom in a terminal and make sure the settings are valid for ttyUSB0
  4. Boot the router and immediately press Ctrl+C in the terminal
  5. Type tftpd in the prompt, the router should start a FTP server on 192.168.1.1
  6. Open a second terminal, cd into the directory where the firmware is
  7. Make sure its the right version 🙂
  8. Start the FTP client: ftp 192.168.1.1
  9. Change to binary mode (this is very important): mode binary
  10. Move the file: put FIRMWARE.chr
  11. The router should detect the file and process it
  12. Reboot and enjoy

Connecting a Serial TTYUSB Device to the Router

 

USB-TTL

When you see this message below, you need to abort the boot process.

When pressing Ctrl+C does not work, make sure your minicom settings look like this:

 

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Illegal mix of collations: IntelliJ and UTF8mb4

IntelliJ products do not yet support MySQL’s utf8mb4 character set encodings. The […]

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When using variables inside SQL scripts within IntelliJ products (e.g. DataGrip), certain queries will not work because the encodings of the IntelliJ client and the server missmatch. This occurs for instance when you compare variables. A typical error message looks like this:

IntelliJ products do not yet support MySQL’s utf8mb4 character set encodings. The problem occurs when using variables in queries. Per default. IntelliJ uses a UTF-8 encoding for the connection. When you use utf8mb4 as the database default character set, then variables will be encoded in UTF-8 while the database content remailns in utf8mb4. It is not possible to provide the character set encodings to the IntelliJ settings, as it will refuse to connect.

Check your server settings using the MySQL client:

This seems correct, but when you connect with the IntelliJ client, you will get wrong results when you use variables. Until the products support utf8mb4, you would need to add the following settings to the script in order to force the right settings.

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Flashing a OnePlus One from CM to LineageOS

As Cyanogen Inc closed down its operations in December 2016, CyanogenMod was affected too and my OnePlus One (OPO) did not receive updates anymore. This is not ideal, as new and old bugs have will remain. For instance did my phone often not reconnect to the 4G network, when a wifi connection was lost, This was very annoying. For this reason, if was about time to upgrade to a new OS: LineageOS.

LineageOS

LineageOS is a fork of CyanogenMod and contunes the quite successful project for our benefit. LineageOS 14 is compatible with Android 7.1 and very easy to install. These are the steps which I had to follow.

How to Upgrade

  • Create a backup with Helios. Use the Chrome Helium app if the app on your mobile phone refuses to start.
  • Download and install adb
  • Download the TWRP custom ROM: https://twrp.me/Devices/ 
  • Download LineageOS. The codename for the OPO is bacon.
  • Download the Google apps mini distribution (stock is too large) here.
  • Enable developer tools and connect the phone with a USB cable
  • Reboot the device with adb:  ./adb reboot bootloader 
  • Check if the device is recognized:  ./fastboot devices 
  • Enable OEM unlock:  fastboot oem unlock 
  • Install the custom rom:  fastboot flash recovery twrp-x.x.x-x-bacon.img 
  • Reboot into the new ROM: With the device powered down, hold the Volume Down and Power buttons.

Copy the files to the device

Install both zip files by selecting first the LineageOS and then the Google Apps Zip file

Thats it. Reboot and begin with the setup or restore the backup.

Update 28.09.2017

The problem that the phone would not reconnect to 3G/4G again after losing the Wifi signal still persisted with LineageOS. A friend recommended flashing the firmware of the device. After installing the version 2016_1-25_.4.0.1.c7-00011 downloaded from here solved the issue for now. No more connection problems so far

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Verifying Replication Consistency with Percona’s pt-table-checksum

Replication is an important concept for improving database performance and security. In this blog post, I would like to demonstrate how the consistency between a MySQL master and a slave can be verified. We will create two Docker containers, one for the master one for the slave.

Installing the Percona Toolkit

The Percona Toolkit is a collection of useful utilities, which can be obained for free from the company’s portal. The following commands install the prerequisits, download the package and eventually the package.

Setting up a Test Environment with Docker

The following command creates and starts a docker container. Note that these are minimal examples and are not suitable for a serious environment.

Get the IP address from the master container:

You can connect to this container like this and verify the server id:

We repeat the command for the slave, but use a different id. port and name:

For simplicity, we did not use Docker links, but will rather use IP addresses assigned by Docker directly.

Replication Setup

First, we need to setup a user with replication privileges. This user will connect from the slave to the master.

Now log into the slave container and add the connection details for the master:

Now our simple slave setup is running.

Get some test data

Lets download the Sakila test database and import it into the master. It will be replicated immediately.

Verify that the data is on the slave as well:

After our setup is completed, we can proceed with Percona pt-table checksum.

Percona pt-table-checksum

The Percona pt-table-checksum tool requires the connection information of the master and the slave in a specific format. This is called the DSN (data source name), which is a coma separated string. We can store this information in a dedicated database called percona in a table called dsns. We create this table on the master. Note that the data gets replicated to the slave within the blink of an eye.

The next step involves creating permissions on the slave and the master!

The percona user is needed to run the script. Note that the IP address is this time from the (Docker) host, having the IP 172.17.0.1 by default. In real world scenarios, this script would either be run on the master or on the slave directly.

Now we need to add the information about the slave to the table we created. The Percona tool could also read this from the process list, but it is more reliable if we add the information ourselves. To do so, we add a record to the table we just created, which describes the slave DSN:

The pt-table-checksum tool the connects to the master instance and the the slave. It computes checksums of all databases and tables and compares results. You can use the tool like this:

The result shows a difference in the MySQL internal table for permissions. This is obviously not what we are interested in, as permissions are individual to a host. So we rather exclude the MySQL internal database and also the percona database, because it is not what we are interested in. Also in order to test it the tool works, we delete the last five category assignments from the table  with mysql -u root -h 172.17.0.3 -e "DELETE FROM sakila.film_category WHERE film_id > 995;" and update a row in the city table with 

Now execute the command again:

You see that there is a difference in the tables sakila.city and in the table sakila.film_category. The tool does not report the actual number of differences, but rather the number of different chunks. To get the actual differences, we need to use a different tool, which utilises the checksum table that the previous step created.

Show the differences with pt-tabel-sync

The pt-table-sync tool is the counter part for the pt-table-checksum util. It can print or even replay the SQL statements that would render the slave the same state again to be in sync with the master. We can run a dry-run first, as the tool is potentially dangerous.

With –dry-run, you only see affected tables, but not the actual data because it does not really access the databases tables in question. Use –print additionally or instead of dry-run to get a list:

The command shows how we can rename back from Innsbruck to Yuncheng again and also provides the INSERT statements to get the deleted records back.When we replace –print with –execute, the data gets written to the master and replicated to the slave. To allow this, we need to set the permissions on the master

This error indicates that updating the city table has consequences, because it is a FK to child tables. In this example, we are bold and ignore this warning. This is absolutely not recommended for real world scenarios.

The command –no-check-child-tables ignores child tables and the command –no-foreign-key-checks ignores foreign keys.

Run the checksum command again to verify that the data has been restored:

0 DIFFS, we are done!

 

 

 

 

 

 

 

 

 

 

 

 

 

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