Getting GDB to work on Mac OS X Mojave

How to get GDB to work on MacOSX Mojave

Starting from Mac OS X 10.5 (Leopard), Apple starts to lock down the system further and debuggers like GDB now have to be code signed. There is a great article describing steps to get it to work. However, there are a lot of conflicting information on the web and people are having trouble with some of those instructions, myself included. So I’d like to document what I did to get it to work, and highlight the issues I ran into:

On a high-level you need to perform these steps:

  1. You need to create a certificate in System Keychain that is self-sign and always trust for code signing
  2. Sign the GDB binary with the certificate. Include proper entitlements if you are on 10.14+.
  3. Reboot

The article has detailed steps on these steps so I’m not going to repeat them.

A few gotchas that I ran into myself:

  1. If you see this error complaining about code signing even though you had signed the GDB executable:
Starting program: /Users/yzha/github/mysql-server/debug/runtime_output_directory/mysqld
Unable to find Mach task port for process-id 55009: (os/kern) failure (0x5).
 (please check gdb is codesigned - see taskgated(8))

Double check if you had the proper entitlements in a XML file and pass to codesign when you are signing GDB. Many articles on the web in fact didn’t have the entitlement step as it likely is a new requirement 10.14+.

  1. If you are seeing this error even if you had signed with proper entitlements:
During startup program terminated with signal ?, Unknown signal.

or this:

/Users/yizhang/github/leveldb/debug/db_test": not in executable format: file format not recognized

Make sure you stay off GDB 8.2! Upgrade to 8.3 (available in Homebrew already) or downgrade to 8.0.

Sorting structured data using memcmp-friendly encoding part 2 - floats

Sorting structured data using memcmp-friendly encoding part 2 - sorting floats

In the last post we’ve discussed converting integers and strings into a memcmp / byte-comparable format for faster comparison (but at the trade off of doing decoding/encoding at reading/writing). In this post let’s take a look at how do we do the same for floating pointers.

Get cherry-pick to work across file renames

Making cherry-pick work across file renames

Recently I need to port over some changes using cherry-pick and that usually works fine without any issues (except for occasional conflicts), but this time the actual file was renamed to In such case git cherry-pick simply gives up and simply tells you the old file you are changing has been deleted. As far as I can tell there isn’t a good way to resolve the conflict.

There are a couple of ways to address this issue. But the easiest way I found is to just rename the file back to the original name where you had made the change on, in order to make git happy. Once that’s done, cherry-picking would work fine as usual. Now just rename the file back to the ‘new’ name. Squash the change.

This can be illustrated in following example - assuming:

  1. Your commit modifies
  2. In the target branch (that you want to cherry-pick) renames to
# Create the target branch as usual
git checkout -b your-target-branch

# Rename back to to make git cherry-pick happy
git mv 
git commit -m "Make git happy"

# Cherry-pick as usual
git cherry-pick -x <commit>

# Rename it back
git mv 
git commit -m "Rename back"

# Squash the 3 commits into one
git rebase -i HEAD~3

In the rebase file, you’ll see:

pick 95be80db682 Make git happy
pick 3d74c6c9e13 Cherry-pick commit blah
pick 238e3c51354 Rename back

Change to:

pick 95be80db682 Make git happy
s 3d74c6c9e13 Cherry-pick commit blah
s 238e3c51354 Rename back

Here s means squash with previous commit.

Just remember in commit message deleting the first and third unrelated commit.

And now you are all set!

Repeatable reads in InnoDB comes with a catch

A few days ago I was looking into a deadlock issue that is caused by a behavioral difference between MySQL storage engine transaction behavior in repeatable reads. This leads me to dig deeper into repeatable read behavior in InnoDB and what I found is quite interesting:

The basics

Before we dig deeper, let’s revisit some of the basics of database isolation levels. You can refer to my earlier post for a more detailed explanation / comparison. Database isolation level defines the behavior of data read/write operations within transactions, and those can have a signficant impact to protecting the data integrity of your application. Repeatable reads guaratees that you would always observe the same value once you read it, and it would never change unless you’ve made the change yourself, giving you the illusion that it is exclusively owned by you and there is no one else. Of course, this isn’t true in practice as there are pessimistic locking and optimistic locking that defines the behavior when write conflict occurs.

Diagnosing interesting MySQL client connection error in localhost through the source code

The art of argument parsing and policy transparency

When working with MySQL the often most frustrating part is getting strange connection errors. I’ve wasted two hours trying to connect to a MySQL server using TCP port (unix domain sockets works fine) and I’ll talk about why it didn’t work, and as usual we’ll dive into the code to understand exactly why.

To simplify the problem, let’s say I have MySQL server at port 13010 and bound to localhost, with user name root and empty password (don’t do that in production):

[~/mysql]: mysql -p 13010 -h localhost -u root
Enter password:
ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2)

This is typical error many people will run into and you can find many similar posts that discuss the problem but few ever got to the bottom of it. Let’s jump right in.

-p and -P

Obviously when I write -p 13010 I meant to tell mysql client to connect to server using port 13010, but that’s not quite right:

[~/mysql]: mysql --help
  -p, --password[=name]
                      Password to use when connecting to server. If password is
  -P, --port=#        Port number to use for connection or 0 for default

So I actually told mysql the password is 13010 instead. Supporting both -p and -P is a apparently very bad idea.

Linux tools often have excessive amount of short options, like this one from man page for ls:

ls [[email protected]] [file …]

Personally I think they should go easy and only include the most common ones rather than using the entire alphabet.

However, the mystery is not yet solved. Note that we have been asked to enter the password, which explains why most people never suspected -p actually means password. Put in other words - if -p means password, why is this command is still asking for password?

The answer lies in the source code:

  for (optend= cur_arg; *optend; optend++)
	  opt_found= 0;
	  for (optp= longopts; optp->name; optp++)
	    if (optp->id && optp->id == (int) (uchar) *optend)
	      /* Option recognized. Find next what to do with it */
	      opt_found= 1;
	      if (optp->arg_type == REQUIRED_ARG ||
		        optp->arg_type == OPT_ARG)
					if (*(optend + 1))
						/* The rest of the option is option argument */
						argument= optend + 1;
						/* This is in effect a jump out of the outer loop */
						optend= (char*) " ";
						if (optp->arg_type == OPT_ARG)
							if (optp->var_type == GET_BOOL)
								*((my_bool*) optp->value)= (my_bool) 1;
							if (get_one_option && get_one_option(optp->id, optp, argument))
						/* Check if there are more arguments after this one */
      		  argument= *++pos;

The *(optend + 1) is the most interesting part. If a short-form option is being recognized, the rest immediately following the short option is treated as argument:

					if (*(optend + 1))
						/* The rest of the option is option argument */
						argument= optend + 1;
						/* This is in effect a jump out of the outer loop */
						optend= (char*) " ";

Given that we are not passing -p13010, the 13010 part is ignored.

But wait, why does -h localhost work fine?

Just keep looking:

						if (optp->arg_type == OPT_ARG)
							if (optp->var_type == GET_BOOL)
								*((my_bool*) optp->value)= (my_bool) 1;
							if (get_one_option && get_one_option(optp->id, optp, argument))
						/* Check if there are more arguments after this one */
						if (!pos[1])
              return EXIT_ARGUMENT_REQUIRED;
      		  argument= *++pos;

So if the argument is an optional arg, it’ll give up and only check for immediate following argument. Otherwise, for OPT_REQUIRED, it assumes the next one is the argument.

Let’s take a look at where they are defined:

  {"password", 'p',
   "Password to use when connecting to server. If password is not given it's asked from the tty.",
   0, 0, 0, GET_PASSWORD, OPT_ARG, 0, 0, 0, 0, 0, 0},
  {"host", 'h', "Connect to host.", &current_host,
   &current_host, 0, GET_STR_ALLOC, REQUIRED_ARG, 0, 0, 0, 0, 0, 0},

As expected, password is optional and host is required.

Also, note that how it never checked for ‘=’? So the syntax -p=abc wouldn’t work as expected as well. And hilariously =abc would become the password. For arguments with a bit more error checking like port, the error message is a bit better:

[~/mysql]: mysql -P=13010 
mysql: [ERROR] Unknown suffix '=' used for variable 'port' (value '=13010')
mysql: [ERROR] mysql: Error while setting value '=13010' to 'port'

Note the ‘=13010’ part?

Default protocol

OK. Let’s try again:

[~/mysql/mysql-fork]: mysql -P 13010 -h localhost -u root
ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2)

Still doesn’t work. We know it’s not the parsing of -P because port is OPT_REQUIRED:

  {"port", 'P', "Port number to use for connection or 0 for default to, in "
   "order of preference, my.cnf, $MYSQL_TCP_PORT, "
   "/etc/services, "
   "built-in default (" STRINGIFY_ARG(MYSQL_PORT) ").",
   &opt_mysql_port, 0, GET_UINT, REQUIRED_ARG, 0, 0, 0, 0, 0,  0},

Note the error message socket '/var/lib/mysql/mysql.sock. This is for domain socket.

To confirm this is the issue, let’s search for the actual error message:

const char *client_errors[]=
  "Unknown MySQL error",
  "Can't create UNIX socket (%d)",
  "Can't connect to local MySQL server through socket '%-.100s' (%d)",

The client_errors are looked up from error codes:

#define ER(X) (((X) >= CR_ERROR_FIRST && (X) <= CR_ERROR_LAST)? \
               client_errors[(X)-CR_ERROR_FIRST]: client_errors[CR_UNKNOWN_ERROR])

And the 3rd error is CR_SOCKET_CREATE_ERROR:

#define CR_ERROR_FIRST  	2000 /*Copy first error nr.*/
#define CR_UNKNOWN_ERROR	2000

Searching for that leads us back to

  if (!net->vio &&
      (!mysql->options.protocol ||
       mysql->options.protocol == MYSQL_PROTOCOL_SOCKET) &&
      (unix_socket || mysql_unix_port) &&
      (!host || !strcmp(host,LOCAL_HOST)))
    my_socket sock= socket(AF_UNIX, SOCK_STREAM, 0);
    DBUG_PRINT("info", ("Using socket"));
    if (sock == SOCKET_ERROR)
      set_mysql_extended_error(mysql, CR_SOCKET_CREATE_ERROR,

So this means by default we are connecting using Unix domain socket, and only if host is not specifed or is localhost!

Programs should be transparent about its policies, and give information about what it is doing. If that can end up being too verbose, add a verbose option. I’ll write a separate post about this because I’ve been bitten too many times by similar issues and now my favorite past-time is to add print/printf.

So there are two ways to fix this:

  1. Instead of local host, use This fails the UNIX socket check and will fallback to TCP.
  2. Use --protocol tcp to force using TCP.

So the right command would be:

mysql -P 13010 -h localhost -u root --protocol tcp 


mysql -P 13010 -h -u root


These two problems can be easily avoided by adding more messages to the mysql client, such as:

Trying to connect to UNIX domain socket localhost...
Connecting to database `12310`. 

These would’ve avoided wasting collectively god knows how much time wasted. Maybe I should submit a patch when I get a chance.

The gotchas:

  1. mysql short-option with optional args only accept arguments when they immediately follow the option, such as ‘-pmypassword’. Specifying as ‘-p blah’ and blah will be interpreted as current database. Short option with required args don’t have this problem.

  2. When there is no protocol specified, mysql will try to connect as UNIX domain socket if connecting to localhost or host isn’t specified. To work around it, use IP address instead of localhost, or specify protocol explicitly using --protocol.