[Python] cannot allocate memory in static TLS block exception raised when pyarrow is imported before _mysql

[mdobrzanski]

Describe the bug, including details regarding any error messages, version, and platform.

The mysqlclient (MySQLdb) cannot be imported if pyarrow is imported first. An error is raised ImportError: /lib64/libstdc++.so.6: cannot allocate memory in static TLS block

I have experienced Red Hat and Oracle Linux distributions.

Steps to reproduce:

1. start docker container from oracle linux9 image docker run -ti oraclelinux:9 bash
2. install system dependencies

   dnf install -y epel-release 
   dnf config-manager --set-enabled ol9_codeready_builder
   dnf install gcc python3-devel python3-pip
   

   The libmysql is 8.0.32 from oracle linux repositories but I had the same problem with I used libmysql from mysql
   community repository .
3. install python dependencies (pyarrow and mysqlclient aka. MySQLdb)

   pip3 install pyarrow==15.0.0 mysqlclient==2.2.1
   

4. mysql import is fine when pyarrow is not earlier imported

   [root@930fd58ceb8a /]# python3 -c 'import MySQLdb; print("OK")'
   OK
   

5. fails if pyarrow is imported before mysql
   ImportError: /lib64/libstdc++.so.6: cannot allocate memory in static TLS block

   [root@930fd58ceb8a /]# python3 -c 'import pyarrow; import MySQLdb; print("OK")'
   Traceback (most recent call last):
     File "<string>", line 1, in <module>
     File "/usr/local/lib64/python3.9/site-packages/MySQLdb/__init__.py", line 17, in <module>
       from . import _mysql
   ImportError: /lib64/libstdc++.so.6: cannot allocate memory in static TLS block
   

I was probing the installed pyarrow library. The mysql import starts to fail after pyarrow.lib is imported https://github.com/apache/arrow/blob/maint-15.0.0/python/pyarrow/__init__.py#L65

When looking at shared libraries, _mysql, pyarrow.lib as we as libmysqlclient use the same libstdc++.so.6 => /lib64/libstdc++.so.6

[root@930fd58ceb8a /]# ldd /usr/local/lib64/python3.9/site-packages/MySQLdb/_mysql.cpython-39-x86_64-linux-gnu.so 
	linux-vdso.so.1 (0x00007ffda316c000)
	libmysqlclient.so.21 => /usr/lib64/mysql/libmysqlclient.so.21 (0x00007f4c2d672000)
	libc.so.6 => /lib64/libc.so.6 (0x00007f4c2d469000)
	libzstd.so.1 => /lib64/libzstd.so.1 (0x00007f4c2d392000)
	libssl.so.3 => /lib64/libssl.so.3 (0x00007f4c2d2ec000)
	libcrypto.so.3 => /lib64/libcrypto.so.3 (0x00007f4c2ceb9000)
	libresolv.so.2 => /lib64/libresolv.so.2 (0x00007f4c2cea5000)
	libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f4c2cc7c000)
	libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f4c2cc60000)
	/lib64/ld-linux-x86-64.so.2 (0x00007f4c2dd11000)
	libz.so.1 => /lib64/libz.so.1 (0x00007f4c2cc46000)
	libm.so.6 => /lib64/libm.so.6 (0x00007f4c2cb6b000)

[root@930fd58ceb8a /]# ldd /usr/local/lib64/python3.9/site-packages/pyarrow/lib.cpython-39-x86_64-linux-gnu.so 
	linux-vdso.so.1 (0x00007fff96b91000)
	libarrow_python.so => /usr/local/lib64/python3.9/site-packages/pyarrow/libarrow_python.so (0x00007f1798f6b000)
	libarrow_dataset.so.1500 => /usr/local/lib64/python3.9/site-packages/pyarrow/libarrow_dataset.so.1500 (0x00007f1798da1000)
	libparquet.so.1500 => /usr/local/lib64/python3.9/site-packages/pyarrow/libparquet.so.1500 (0x00007f1798538000)
	libarrow_acero.so.1500 => /usr/local/lib64/python3.9/site-packages/pyarrow/libarrow_acero.so.1500 (0x00007f17983c5000)
	libarrow.so.1500 => /usr/local/lib64/python3.9/site-packages/pyarrow/libarrow.so.1500 (0x00007f17957e0000)
	libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f17955b4000)
	libm.so.6 => /lib64/libm.so.6 (0x00007f17954d9000)
	libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f17954bd000)
	libc.so.6 => /lib64/libc.so.6 (0x00007f17952b4000)
	librt.so.1 => /lib64/librt.so.1 (0x00007f17952af000)
	libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f17952aa000)
	libdl.so.2 => /lib64/libdl.so.2 (0x00007f17952a3000)
	/lib64/ld-linux-x86-64.so.2 (0x00007f17994ed000)

[root@930fd58ceb8a /]# ldd /usr/lib64/mysql/libmysqlclient.so.21
	linux-vdso.so.1 (0x00007ffe5cfaa000)
	libzstd.so.1 => /lib64/libzstd.so.1 (0x00007fb1976c3000)
	libssl.so.3 => /lib64/libssl.so.3 (0x00007fb19761d000)
	libcrypto.so.3 => /lib64/libcrypto.so.3 (0x00007fb1971ea000)
	libresolv.so.2 => /lib64/libresolv.so.2 (0x00007fb1971d6000)
	libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fb196faf000)
	libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fb196f93000)
	libc.so.6 => /lib64/libc.so.6 (0x00007fb196d88000)
	libz.so.1 => /lib64/libz.so.1 (0x00007fb196d6e000)
	libm.so.6 => /lib64/libm.so.6 (0x00007fb196c93000)
	/lib64/ld-linux-x86-64.so.2 (0x00007fb197e28000)

Interestingly importing other way round or setting the LD_PRELOAD=/lib64/libstdc++.so.6 makes it work fine

[root@930fd58ceb8a /]# python3 -c 'import MySQLdb; import pyarrow; print("OK")'
OK

[root@930fd58ceb8a /]# LD_PRELOAD=/lib64/libstdc++.so.6 python3 -c 'import pyarrow; import MySQLdb; print("OK")'
OK

Could you help me understand what is going on and what would be the right fix for that?

Component(s)

Python

[xhochy]

This is related to jemalloc/jemalloc#937 and conda-forge/arrow-cpp-feedstock#636

[mdobrzanski]

@xhochy, that's some advanced stuff, I think I didn't get everything that is written in related issues.
What I understood is pyarrow was fixed and it's MySQLdb or even libmysqlclient that has to be fixed. There was an issue with the latter on ubuntu https://bugs.launchpad.net/ubuntu/+source/mysql-8.0/+bug/1889851. Is that right? In your opinion, where the fixes should be done?

[xhochy]

Yes, that sounds related and the fix needs to be done on the MySQLdb side.