Percona Live Data Performance Conference 2016 - CFP and Community voting

The call for participation for Percona Live Data Performance Conference 2016 is still open. Deadline for submission is November 29th.

There are two immediately noticeable novelties in this edition:

• The name change. Not "MySQL & Expo" but "Data Performance Conference." It makes the conference open to a broader set of topics.
• The community voting. Proposals can get evaluated by the community before the review committee takes decisions.

I think it's a good choice. Other conferences adopt the same method. The attendees choose what they want to see and hear. In this case, it's mixed method, where the community voting is used as an indication for the review committee, which, by my understanding, has the final say.

Vote for my proposals!

Below are my proposals. Clicking on the links below will take you to the conference site, where you can say if you want to see these talks or not. You will need to register (to the site, not yet to the conference) in order to cast votes.

• MySQL Replication, the community sceptic roundup

Here is a talk that is in continuous evolution. It discusses the latest advances in replication, and gives an honest evaluation of the features from a new user standpoint. This talk, if accepted, will be updated with the latest novelties in MariaDB and MySQL, if they come out in time for the conference. You can see in my blog six articles covering related matters.

• MySQL operations in Docker

Another tutorial, this one aimed at users of containers who want to get started with this exciting technology. Also for this topic I have written a few articles.

• MySQL deployment methods - whole servers, sandboxes, virtual machines, containers

This is a short talk that wants to explain the differences between deployment methods. Standalone physical servers, sandboxes, virtual machines, and containers are choices that require some information to get started. This talk, for which I also wrote an article, wants to show the good and bad of each choice.

• The geeky pleasure of wet shaving

This is a lightning talk, which is not about data performance, but it's a geeky topic and I was asked to submit it. So here it is!

MySQL and Docker on a Mac: networking oddity

This is a quick post only indirectly related to the series of articles about Docker that I have written recently.

Yesterday I was giving a presentation about Docker in Buenos Aires, and as usual I included a long live demo. Almost all went as expected. There was one step that I tried some time ago, and had always worked well, but when I tried to repeat it on stage, it failed miserably:

• Step 1: run the container

$ docker run  -d --name mybox -e MYSQL_ROOT_PASSWORD=secret mysql/mysql-server
50acff1c7d237b2944f3fbdd5d230e4ecca2bcccd4e4ba06aa778ee20d41631e

• Step 2: get the IP address

$ docker inspect --format '{{ .NetworkSettings.IPAddress}}'  mybox
172.17.0.2

• Step 3: connect to the container from a local client.

$ mysql -h 172.17.0.2 -u root -psecret
Enter Password:

And here the connection hangs.

That was odd. This operation was working fine at home. I have it pasted into my first article of the series. Why it did not work here?

I could not solve the issue on stage. I had to go on with my presentation. The installation of three nodes in replication went well. Everything that I tried at home was working, except connecting from the external client to the server inside a container.

When I came back to the hotel, I realised what was different: I had done all the tests for the first article on Linux only, and I started testing on Mac when using the material for the second article. Thus I hadn't tried this particular example on a Mac until I went on stage. And of course it did not work: I was trying to connect from my Mac to a container inside a virtual machine which uses a different subnet and cannot be reached without indirection.

The only way of connecting a local client to the container is by exposing explicitly the MySQL port to the external (and in this case the "external" is the virtual machine itself) and then connect to the virtual machine.

This approach works:

$ docker rm -v -f mybox
mybox

$ docker run -p 3306:3306 -d --name mybox -e MYSQL_ROOT_PASSWORD=secret mysql/mysql-server
2798f4d1b9abb023453b1141a808014fdf7666221498b42c96e2a5d58fc6ce65

Here the port 3306 of the container is attached to the port 3306 to the host (= the virtual machine).

$ docker-machine ip default
192.168.99.100

Now we get the address of the virtual machine, so that we can connect to its MySQL port.

$ mysql -h 192.168.99.100 -u root -psecret
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 2
Server version: 5.7.9-log MySQL Community Server (GPL)

Copyright (c) 2000, 2015, 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>

And the connection now works!

I owe it to the attendees to my talk to explain the oddity, but I believe it could be useful for others out there as well.

Default users in MySQL 5.7

Among the many New features introduced by MySQL 5.7, we can notice a strong trend towards improving the server security by default. Two features stand out in this respect:

• A password-less root is no longer the default for new installations. Unless you say otherwise, the default installers mysqld --initialize and the deprecated mysql_install_db will generate a random password which the user needs to change.
• The anonymous accounts are no longer created by default. When you start MySQL, you only get the root user (and a new one: read on).

The above features are a great advance not only for security but also for usability. The anonymous users were a continuous source of mismatched connections, with difficult to explain errors, and confusion for beginners and experts alike. That's why MySQL-Sandbox has removed the anonymous accounts since its first release.

There are, however, two more changes in the privileges tables:

1. We have a new user, mysql.sys, which is not a usable account, as it comes with a deliberately invalid password. Its role is only to allow the sys objects to have an owner different from root. This novelty has caught me by surprise, and I had to adjust the management of users in MySQL-Sandbox, to prevent removal of this account attributes from various mysql tables: user, db, tables_priv. In fact, since we don't have anonymous accounts anymore, MySQL-Sandbox does not remove rows from db and tables_priv. (The changes were apparently new for the team maintaining MySQL images on Docker, as this user is not available on Docker MySQL containers: the entrypoint file removes all accounts from the user file.)
2. The test database is removed by default. This is, in my opinion, a mistake. The reason for the vulnerability of the test database was that it was open to use for the anonymous users. But since we don't have anonymous users anymore, deleting the test database is like obeying a superstitious belief.

Anyway, MySQL-Sandbox 3.1.02 comes with a few small bug fixes, among which is the preservation of the mysql.sys user and a few adjustments to the tests to take into account the latest change. The test database is always present in sandboxes, despite the above mentioned irrational removal.

Let me demonstrate the issue. In a brand new installation, we create an anonymous user and the test database:

mysql> create user '';
Query OK, 0 rows affected (0.02 sec)

mysql> select host,user from user;
+------+------+
| host | user |
+------+------+
| %    |      |
| %    | root |
+------+------+
2 rows in set (0.00 sec)

mysql> create schema test;
Query OK, 1 row affected (0.01 sec)

Then we try to access the server

# mysql -user=''
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5
Server version: 5.7.9-log MySQL Community Server (GPL)

Copyright (c) 2000, 2015, 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> use test
ERROR 1044 (42000): Access denied for user ''@'%' to database 'test'
mysql> use performance_schema
ERROR 1044 (42000): Access denied for user ''@'%' to database 'performance_schema'
mysql> use sys;
ERROR 1044 (42000): Access denied for user ''@'%' to database 'sys'

mysql> show schemas;
+--------------------+
| Database           |
+--------------------+
| information_schema |
+--------------------+
1 row in set (0.00 sec)

mysql> select table_schema,engine,count(*) from information_schema.tables group by table_schema,engine;
+--------------------+--------+----------+
| table_schema       | engine | count(*) |
+--------------------+--------+----------+
| information_schema | InnoDB |       10 |
| information_schema | MEMORY |       51 |
+--------------------+--------+----------+
2 rows in set (0.00 sec)

mysql> show grants for '';
+------------------------------+
| Grants for @%                |
+------------------------------+
| GRANT USAGE ON *.* TO ''@'%' |
+------------------------------+
1 row in set (0.00 sec)

So, the anonymous user is unable to do harm, as it can't even see the databases. The only effective measure was cleaning up the table mysql.db, which was the one giving access to the test database to the anonymous users.

MySQL-Docker operations. - Part 4: Sandboxes, virtual machines, containers.

Previous episodes:

• MySQL-Docker operations. - Part 1: Getting started with MySQL in Docker.
• MySQL-Docker operations. - Part 2: Customizing MySQL in Docker.
• MySQL-Docker operations. - Part 3: MySQL replication in Docker.

We're going to explore the choices and the differences between various types of deployments. We will consider four use cases:

1. [Friendly]: Testing an application on a server where a different version of the same application is already installed (examples: a Python app requiring many libraries, a MySQL server);
2. [Intrusive]: Testing a potentially intrusive application (anything that changes your general settings in /usr or /etc);
3. [Conflicting]: Running a service that has lots of conflicting dependencies (an updated database driver compiled with a version of MySQL different from what you have installed);
4. [Intractable]: Running an intractable service, one of those that require a specific user to run and assume they have full control of the operating system (e.g. Postgresql, Oracle).

For each case, we need to determine the impact on our well being. We assume that the user starts with one reasonably powerful server.

The method used will affect our operations in several ways:

1. Cost: How much would it cost to implement this method.
2. Time: How much time will be needed to get things done.
3. Performance: Can we run things as fast as we need.
4. Ease of use: Can we get things done without reading a lengthy manual or using an unforgiving and complicated procedure;
5. Isolation: Can you run your server without affecting other servers?
6. Storage: Can we add or change storage easily?
7. Scalability: Can we easily repeat the procedure as many times as needed.
8. Availability: Can we run any service using this method?
9. Portability: Can we run this service on several operating systems?
10. Networking: Can we use this method to run operations that require a network?

Running servers on a regular host

The first possibility to solve our problem is simple. Take an empty server, install the service, run it. Until not long ago, before the advent of cloud computing, this was the only way to run operations: if your server is not enough, buy a bigger one, or buy many small ones and get smarter with them. But inevitably, whether we wanted to install a new service or test a new version of a known application, we needed to find money and physical space to get the job done.

Figure 1 : Applications within a server share the operating system and library resources

In this configuration, everything is by the book. We assume that we will use one physical host to run a main service, using the best configuration we can get to achieve the purpose.

The evaluations in the following table are based on my own experience and may differ from what others feel or need.

Requirement	score	notes
Cost	–10	You need to own a new server
Time	8	You need to install it, but it can be easily automated
Performance	10	Nothing beats bare metal
Ease of use	8	As easy as the installation procedure makes it.
Isolation	10	Not going to affect services in other machines.
Storage	–10	Changing storage requires physical manipulation
Scalability	–10	Every new server requires a new purchase
Availability	10	We can run anything.
Portability	10	We can install the O.S. that we need, and the services on top of it
Networking	0	We can use, but can't create or simulate networking.
Total	+56 / -30

The negative results should be considered separately from the positive ones. What could be a prohibitive condition for an individual could be merely a nuisance for someone in a stronger position. For example, if you already have access to bare metal servers for the next two years, thanks to an advantageous merger, you may not feel the cost factor to affect you too much.

Evaluation for the bare metal servers usability:

• [Friendly]: easily used. No problems here.
• [Intrusive]: difficult to use. Installing one of those means that you may have trouble installing anything else.
• [Conflicting]: Extremely difficult. You may end up with the inability of upgrading a given service unless you also upgrade all the dependencies, and end up upgrading the whole operating system out of desperation.
• [Intractable]: Extremely difficult. Once you install one of those, you may not be able to use the server for anything else.

Running servers in a sandbox

In this context, by sandbox I mean an application that runs on a server with strict configuration settings that prevent it from misbehaving. One example for this category is MySQL-Sandbox, where one or more MySQL servers are installed in a host, each of them configured in such a way that it does not clash with the others.

Figure 2 : Sandboxes are regular applications that were carefully configured to behave well without disturbing the neighbors.

While MySQL-Sandbox is designed for testing, deploying several production servers on the same host is a common practice. The main reason for it is that commodity servers have become more and more powerful, but the software hasn't caught up to utilise such power to its fullest. In this context, using a single server on such powerful hosts would be a waste, while installing two or three servers would provide for better effectiveness.

This type is similar to running a plain bare metal server. You are running your MySQL server very close to the metal, as there is no software layer between the server and the operating system. Applications configured this way are as fast as the hardware allows. However, they are not as secure. While a lonely server running inside its dedicated host does not have to worry about clashing, a sandbox is sharing libraries and other operating system resources to other similar servers, and a clash is easy to provoke. It would be enough to mix up the configuration settings, and one or more of them would either stop working or corrupt data. Or it could happen that a sandbox could drain all the resources (e.g. the main memory) leaving all the other contenders in the cold.

Requirement	score	notes
Cost	10	No investment required
Time	8	As easy as the installation procedure makes it
Performance	10	Still bare metal, even if there is potential concurrency.
Ease of use	10	As easy as the manual says it is
Isolation	-5	Depends on the service configuration. Although it is functionally independent, the services can clash.
Storage	5	Sandboxes can be resized at will (within the limits of existing storage).
Scalability	10	Deployment of new instances is only limited by the host resources.
Availability	5	We can run only applications that are fully configurable.
Portability	-5	We can only run applications for the host O.S.
Networking		We can use but can't create or simulate networking.
Total	+58 / -10

There are several advantages to using sandboxes instead of a dedicated host, such as being able to deploy multiple servers without buying new hardware or installing virtual machines. There are, however, obvious limitations, like the lack of isolation mentioned above and the fact that only applications compiled for the host operating system can run in this fashion.

Evaluation for the sandboxes usability:

• [Friendly]: easily used. This is the strong point of sandboxed applications.
• [Intrusive]: Difficult to use. Sometimes impossible.
• [Conflicting]: Difficult but possible to use. It's one of the case where having a conflicting application used in a parallel environment could be beneficial.
• [Intractable]: Almost impossible to reduce to a sandboxed environment.

Running servers in virtual machines

Figure 3 : A virtual machine isolates the application and the operating system.

Virtual machines are the heart of current cloud computing strategies. The ability of creating servers that behave almost like bare metal ones –without need for physically buying them and transporting into a data center– has changed the economy of most companies in the past decade.

Requirement	score	notes
Cost	-5	Moderate investment required
Time		As easy as the installation procedure makes it. But the O.S. must be installed as well
Performance	-10	There is much overhead from the additional layers and the need of having a full O.S..
Ease of use	8	Everything that is allowed through the interface.
Isolation	9	It can be as good as a physical host. There is still the risk of a VM affecting negatively others.
Storage	5	V.M.s can be resized at will (within the limits of existing storage).
Scalability	10	Deployment of new instances is only limited by the host resources.
Availability	10	We can run anything.
Portability	10	We can install the O.S. that we need, and the services on top of it
Networking	10	We can use and create networks.
Total	+62 / -15

Compared to bare metal, virtual machines can scale at will. You can deploy in a few minutes a new VM of the size that is needed for your current business, and get rid of it when the need ends. Unlike sandboxes, you can run any operating system and any application. In addition, you can have a network for public and private communication between servers.

There are prices to pay. First of all, it will cost you. Depending on the usage, they could be much cheaper than buying and storing your own physical servers, but they won't be free. Sure, you can install a virtual machine in your initial server, the same way that you can do it for a sandbox, but then you get into the second great limitation: performance. Even with the best software available today, the performance of a server running in a VM is greatly inferior to a server on bare metal.

You can compensate for performance by splitting the job into many parts and deploying many small virtual machines that will work in parallel. When a solution like this is successfully deployed, the performance of the group of virtual machines can surpass that of a single bare metal server. Unfortunately, to achieve this goal, you would incur more costs than buying a single server, and your application will need to be adapted to working in a distributed environment. This solution can work, and it has been deployed successfully in many cases, but it is not a one-size-fits-all, and done with poor planning can backfire.

Evaluation for the virtual machines usability:

• [Friendly]: easily used. No problems here.
• [Intrusive]: Easily used with overhead. Just install another virtual machine.
• [Conflicting]: Easily used with overhead.
• [Intractable]: Easily used with overhead.

Running servers in containers

Figure 4 : Docker containers are thin layers of libraries and applications on top of a common kernel.

Containers are a growing trend in the virtualization ecosystem. If, by the previous statement, you believe that containers are virtual machines, you need to reconsider immediately, or risk failing to understand this technology. Containers are not virtual machines, although they have many things in common. Like virtual machines, containers are entities that are not in the host computer, can be deployed in a package, started, and the service inside it can be used more or less like a server on bare metal.

The differences between virtual machines and containers are a few, and very important:

• A container does not pack a full operating system, but just a thin layer of the needed libraries to run the service in it;
• The service itself is often a stripped down version of the original application.
• Most important, the software in the container uses the host kernel directly, without any intermediate layer.
• For the above reasons, while a virtual machine starts up in minutes, a container starts up in less than a second.

A container is a well packaged application that can be downloaded very quickly, and once downloaded can be instantiated several times with incredible speed.

Another notable difference between containers and virtual machines is that containers are less isolated, because they use the same kernel as the host, rather than a virtualized one. On one hand, this makes containers less secure, on the other hand, they are blazingly fast.

Figure 5 : Docker containers can share libraries and other image layers

There is another reason for containers speed and low storage occupancy. Docker containers are deployed in layers. Some of those layers can be used by a single container, others could be in common between two or more containers. While a virtual machine is an enormous blob which can reach several GB, a container could be a thin modification of an existing image, and thus can be downloaded in seconds and deployed even faster.

Requirement	score	notes
Cost	10	No investment required
Time	10	Fast, fast, fast!
Performance	9	Almost as fast as running on bare metal. Tiny overhead.
Ease of use	3	Requires some learning and new workflows.
Isolation	7	Much better than a sandbox. Less than a V.M., because containers use the same kernel.
Storage	5	Containers can be resized at will (within the limits of existing storage).
Scalability	10	Deployment of new instances is only limited by the host resources.
Availability	3	We can run only applications that have been adapted for containers.
Portability	-5	We can only run applications for the host O.S.
Networking	10	We can create and use netweoks.
Total	+67 / -5

What are the strong points of containers? Low cost (or no cost, if all you need is what fits in your current server), good performance, private networking, easy to scale.

The limitations, as of today, are portability (applications can only run in the same OS as the host) and the ease of use. This is a point that is going to change. Using containers requires some changes in the applications (or finding ready made images) and an understanding of the environment, which could be intimidating for people used to the old ways. But once you get past the initial learning phase, everything feels very easy, and eventually the usage will be far easier than the old ways.

Evaluation for the containers usability:

• [Friendly]: easily used. No problems here.
• [Intrusive]: easily used, with little or no overhead.
• [Conflicting]: easily used with little or no overhead.
• [Intractable]: difficult to use, sometimes impossible if the intractable application or service was built without flexibility in mind.

All solutions comparison

For convenience, I made a table with a comparison of the solutions examined above.

I must stress that these evaluations are my own, very much subjective, based on my experience. The evaluations may differ from others, and possibly also from my own in a few years or months. Talking about Docker is like catching eels: it's a moving target where the technology evolves and improves daily. This fluidity is possibly the most appealing characteristic of Docker and the container related technology: its evolution has been and continues to be fast and effective, addressing the users needs at incredible speed.

Requirement	Bare metal	Sandbox	Virtual machine	Container
Cost	–10	10	–5	10
Time	8	8	0	10
Performance	10	10	–10	8
Ease of use	8	10	8	3
Isolation	10	–5	9	7
Storage	–10	5	5	5
Scalability	–10	10	10	10
Availability	10	5	10	3
Portability	10	–5	10	–5
Networking	0	0	10	10
Total	+56 –30	+58 –10	+62 –15	+66 –5

I believe we haven't seen the end of this trend yet. What we have seen so far with containers and virtual machines seems to aim at an architecture built on micro services. Containers could take a substantial role in the transition towards that reality.

What can we take away from this analysis?

• Bare metal servers are not outdated yet. There are still cases where they are irreplaceable. Despite the cost associated with their usage, they are not extinct yet, but just.
• Virtual machines are still in charge of the scalability department in many cases. However, they feel the advance of containers and need to either evolve or merge into a more flexible architecture to deal with increasing demands from users.
• Containers are the new force in IT. They can play well with both bare metal servers and virtual machines, waiting for the rise of container-oriented operating systems, which already exist and aim at world domination in a not distant future.

I see a future where the rise of containers and micro systems will force software makers to simplify their products and make them more modular and easy to play with. This trend is important in the current cloud architecture and will become vital when containers take over.

In the meantime, I am not giving up MySQL-Sandbox, which is still indispensable I'm most scenarios, but I am starting to rethink the architecture to fit smarter future uses.

MySQL deployment summary

With all the above considerations, where do we stand with MySQL? My view is that we're still in middle ground. MySQL is still used heavily on bare metal, either as a stand-alone server or as a part of multi server deployments in the same host.

It is also massively employed in the cloud, where it offers many advantages for deployment flexibility and ease of scalability. Yet it still lacks the agility necessary to be a native cloud component. There are several attempts at creating a better cloud player out of MySQL, some successful, some less so.

When it comes to containers, MySQL has still much work to do to become an efficient building block in the new ebullient architecture expansion. The MySQL team provides an official package, which is a first step towards becoming a good player. But in the near future there will be demands of more integration and better modularity than what's available today. Looking at the internals of MySQL deployment in a container shows that the system is struggling to adapt to the new medium. I see the container revolution as an opportunity for established applications like MySQL to improve their usability and increase their ability to play well with other components of the emerging IT infrastructure.

What's next

In the next (and last) episode we will see MySQL, Docker and orchestrating tools playing together to deliver faster and more powerful operations.

MySQL-Docker operations. - Part 3: MySQL replication in Docker

Previous Episodes:

• MySQL-Docker operations. - Part 1: Getting started with MySQL in Docker
• MySQL-Docker operations. - Part 2: Customizing MySQL in Docker

With the material covered in the first two articles, we have all the elements needed to set up replication in Docker. We just need to put the pieces together.
If you want to do everything by hand, it will only take a few minutes. The steps are not complicated. If you have followed the reasoning in the past episodes, you will know what to do.
Or, you can make your life easier by using the ready-made scripts available in Github as MySQL replication samples. In fact, what this article will do in practice is adding comments to a stripped down version of the deployment script, which will make things clear.
First, we will use two templates for the configuration files. Notice that the server-id value is replaced by a placeholder. We will also use a smaller options file for the client's username and password.

$ cat my-template.cnf
[mysqld]
user  = mysql
port  = 3306
log-bin  = mysql-bin
relay-log = mysql-relay
server-id = _SERVERID_
master-info-repository=table
relay-log-info-repository=table
gtid_mode=ON
enforce-gtid-consistency

$ cat node-my.cnf 
[client]
user=root
password=secret

First phase: deploying the containers

Note: Don't try to copy-and-paste the code below. It is a reduced version that is used here only for the sake of commenting it. I have deliberately added line numbers to make copy-and-paste harder. Take the code from github instead.

MySQL-Docker operations. - Part 2: Customizing MySQL in Docker

Previous Episodes:

• MySQL-Docker operations. - Part 1: Getting started with MySQL in Docker

After seeing the basics of deploying a MySQL server in Docker, in this article we will lay the foundations to customising a node and eventually using more than one server, so that we can cover replication in the next one.

Enabling GTID: the dangerous approach.

To enable GTID, you need to set five variables in the database server:

• master-info-repository=table
• relay-log-info-repository=table
• enforce-gtid-consistency
• gtid_mode=ON
• log-bin=mysql-bin

For MySQL 5.6, you also need to set log-slave-updates, but we won't deal with such ancient versions here.
Using the method that we've seen in Part 1, we can use a volume to change the default /etc/my.cnf with our own.

$ cat my-gtid.cnf
[mysqld]
user  = mysql
port  = 3306
log-bin  = mysql-bin
relay-log = mysql-relay
server-id = 12345

master-info-repository=table
relay-log-info-repository=table
gtid_mode=ON
enforce-gtid-consistency

However, this approach may fail. It will work with some MySQL images, but depending on how the image is built, the server may not install at all.

$ docker run --name boxedmysql \
    -e MYSQL_ROOT_PASSWORD=secret \
    -v $PWD/my-gtid.cnf:/etc/my.cnf \
    -d mysql/mysql-server
b9c15ed3c40c078db5335dcb76c10da1788cee43b3e32e20c22b937af50248c5

$ docker exec -it boxedmysql bash
Error response from daemon: Container boxedmysql is not running

The reason for the failure is Bug#78957. When my.cnf contains log-bin and mysql is called prior to the installation to perform some detection tasks, the server creates the binary log index in the data directory. After that, the installation task will abort because the data directory is not empty. It sounds as if there is a set of unnecessary actions here (the server should not create the index without other components in place, and the installer should not complain about finding a harmless file in the data directory) but this is the way it is, and we should work around it. At the time of writing, the bug has received a temporary fix and the installation now works.
All considered, it's best that we are forced to run things this way, because there are side effects of enabling GTIDs at startup: there will be unwanted GTID sets in the server, and that could be annoying.