Memory corruption during pdm sync

[lambda]

• I have searched the issue tracker and believe that this is not a duplicate.

Make sure you run commands with -v flag before pasting the output.

Steps to reproduce

Twice in the past 24 hours, I have seen PDM exhibit a memory corruption related crash in my CI jobs.

I do not yet know how to reproduce this issue reliably. Re-running the same job a second time can work successfully; this problem is not deterministic. Filing it in case there might be something suspicious that you can think of, and to provide a place to keep track of further instances to collect more information.

In a Python 3.11 CI job yesterday:

$ if [ -f pdm.lock ]; then pdm sync --no-editable -v; else pip install .; fi
STATUS: Resolving packages from lockfile...
STATUS: Fetching hashes for resolved packages...
Synchronizing working set with resolved packages: 114 to add, 0 to update, 0 to remove
realloc(): invalid next size
/usr/bin/bash: line 277:   214 Aborted                 (core dumped) pdm sync --no-editable -v

In a Python 3.12 CI job today (for a different project):

$ if [ -f pdm.lock ]; then pdm sync --no-editable -v; else pip install .; fi
STATUS: Resolving packages from lockfile...
Synchronizing working set with resolved packages: 122 to add, 0 to update, 0 to remove
double free or corruption (fasttop)
/usr/bin/bash: line 278:   194 Aborted                 (core dumped) pdm sync --no-editable -v

Actual behavior

PDM sometimes dumps core due to memory corruption issues.

Expected behavior

PDM doesn't crash and installs the files.

Environment Information

Here is how PDM is installed and set up in these CI jobs:

$ PIP_INDEX_URL= pip install --upgrade pip setuptools wheel
Requirement already satisfied: pip in /usr/local/lib/python3.11/site-packages (23.2.1)
Collecting pip
  Obtaining dependency information for pip from https://files.pythonhosted.org/packages/8a/6a/19e9fe04fca059ccf770861c7d5721ab4c2aebc539889e97c7977528a53b/pip-24.0-py3-none-any.whl.metadata
  Downloading pip-24.0-py3-none-any.whl.metadata (3.6 kB)
Requirement already satisfied: setuptools in /usr/local/lib/python3.11/site-packages (65.5.1)
Collecting setuptools
  Obtaining dependency information for setuptools from https://files.pythonhosted.org/packages/de/88/70c5767a0e43eb4451c2200f07d042a4bcd7639276003a9c54a68cfcc1f8/setuptools-70.0.0-py3-none-any.whl.metadata
  Downloading setuptools-70.0.0-py3-none-any.whl.metadata (5.9 kB)
Requirement already satisfied: wheel in /usr/local/lib/python3.11/site-packages (0.42.0)
Collecting wheel
  Obtaining dependency information for wheel from https://files.pythonhosted.org/packages/7d/cd/d7460c9a869b16c3dd4e1e403cce337df165368c71d6af229a74699622ce/wheel-0.43.0-py3-none-any.whl.metadata
  Downloading wheel-0.43.0-py3-none-any.whl.metadata (2.2 kB)
Downloading pip-24.0-py3-none-any.whl (2.1 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 31.0 MB/s eta 0:00:00
Downloading setuptools-70.0.0-py3-none-any.whl (863 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 863.4/863.4 kB 31.2 MB/s eta 0:00:00
Downloading wheel-0.43.0-py3-none-any.whl (65 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 65.8/65.8 kB 5.8 MB/s eta 0:00:00
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: wheel
    Found existing installation: wheel 0.42.0
    Uninstalling wheel-0.42.0:
      Successfully uninstalled wheel-0.42.0
  Attempting uninstall: setuptools
    Found existing installation: setuptools 65.5.1
    Uninstalling setuptools-65.5.1:
      Successfully uninstalled setuptools-65.5.1
  Attempting uninstall: pip
    Found existing installation: pip 23.2.1
    Uninstalling pip-23.2.1:
      Successfully uninstalled pip-23.2.1
Successfully installed pip-24.0 setuptools-70.0.0 wheel-0.43.0
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
$ if [ -f pdm.lock ]; then pip install pdm~=$PDM_VERSION; fi
Looking in indexes: https://gitlab-ci-token:****@gitlab.<REDACTED>
Collecting pdm~=2.15.0
  Downloading pdm-2.15.4-py3-none-any.whl.metadata (10 kB)
Collecting blinker (from pdm~=2.15.0)
  Downloading blinker-1.8.2-py3-none-any.whl.metadata (1.6 kB)
Collecting packaging!=22.0,>=20.9 (from pdm~=2.15.0)
  Downloading packaging-24.1-py3-none-any.whl.metadata (3.2 kB)
Collecting platformdirs (from pdm~=2.15.0)
  Downloading platformdirs-4.2.2-py3-none-any.whl.metadata (11 kB)
Collecting rich>=12.3.0 (from pdm~=2.15.0)
  Downloading rich-13.7.1-py3-none-any.whl.metadata (18 kB)
Collecting virtualenv>=20 (from pdm~=2.15.0)
  Downloading virtualenv-20.26.2-py3-none-any.whl.metadata (4.4 kB)
Collecting pyproject-hooks (from pdm~=2.15.0)
  Downloading pyproject_hooks-1.1.0-py3-none-any.whl.metadata (1.3 kB)
Collecting unearth>=0.15.0 (from pdm~=2.15.0)
  Downloading unearth-0.15.4-py3-none-any.whl.metadata (3.8 kB)
Collecting dep-logic<1.0,>=0.2.0 (from pdm~=2.15.0)
  Downloading dep_logic-0.2.0-py3-none-any.whl.metadata (2.7 kB)
Collecting findpython<1.0.0a0,>=0.6.0 (from pdm~=2.15.0)
  Downloading findpython-0.6.1-py3-none-any.whl.metadata (5.3 kB)
Collecting tomlkit<1,>=0.11.1 (from pdm~=2.15.0)
  Downloading tomlkit-0.12.5-py3-none-any.whl.metadata (2.7 kB)
Collecting shellingham>=1.3.2 (from pdm~=2.15.0)
  Downloading shellingham-1.5.4-py2.py3-none-any.whl.metadata (3.5 kB)
Collecting python-dotenv>=0.15 (from pdm~=2.15.0)
  Downloading python_dotenv-1.0.1-py3-none-any.whl.metadata (23 kB)
Collecting resolvelib>=1.0.1 (from pdm~=2.15.0)
  Downloading resolvelib-1.0.1-py2.py3-none-any.whl.metadata (4.0 kB)
Collecting installer<0.8,>=0.7 (from pdm~=2.15.0)
  Downloading installer-0.7.0-py3-none-any.whl.metadata (936 bytes)
Collecting truststore (from pdm~=2.15.0)
  Downloading truststore-0.9.1-py3-none-any.whl.metadata (4.5 kB)
Collecting hishel<0.1.0,>=0.0.24 (from pdm~=2.15.0)
  Downloading hishel-0.0.27-py3-none-any.whl.metadata (10 kB)
Collecting msgpack>=1.0 (from pdm~=2.15.0)
  Downloading msgpack-1.0.8-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.1 kB)
Collecting pbs-installer (from pdm~=2.15.0)
  Downloading pbs_installer-2024.4.24-py3-none-any.whl.metadata (990 bytes)
Collecting httpx<1,>0.20 (from httpx[socks]<1,>0.20->pdm~=2.15.0)
  Downloading httpx-0.27.0-py3-none-any.whl.metadata (7.2 kB)
Collecting filelock>=3.13 (from pdm~=2.15.0)
  Downloading filelock-3.15.1-py3-none-any.whl.metadata (2.8 kB)
Collecting typing-extensions>=4.8.0 (from hishel<0.1.0,>=0.0.24->pdm~=2.15.0)
  Downloading typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 kB)
Collecting anyio (from httpx<1,>0.20->httpx[socks]<1,>0.20->pdm~=2.15.0)
  Downloading anyio-4.4.0-py3-none-any.whl.metadata (4.6 kB)
Collecting certifi (from httpx<1,>0.20->httpx[socks]<1,>0.20->pdm~=2.15.0)
  Downloading certifi-2024.6.2-py3-none-any.whl.metadata (2.2 kB)
Collecting httpcore==1.* (from httpx<1,>0.20->httpx[socks]<1,>0.20->pdm~=2.15.0)
  Downloading httpcore-1.0.5-py3-none-any.whl.metadata (20 kB)
Collecting idna (from httpx<1,>0.20->httpx[socks]<1,>0.20->pdm~=2.15.0)
  Downloading idna-3.7-py3-none-any.whl.metadata (9.9 kB)
Collecting sniffio (from httpx<1,>0.20->httpx[socks]<1,>0.20->pdm~=2.15.0)
  Downloading sniffio-1.3.1-py3-none-any.whl.metadata (3.9 kB)
Collecting h11<0.15,>=0.13 (from httpcore==1.*->httpx<1,>0.20->httpx[socks]<1,>0.20->pdm~=2.15.0)
  Downloading h11-0.14.0-py3-none-any.whl.metadata (8.2 kB)
Collecting socksio==1.* (from httpx[socks]<1,>0.20->pdm~=2.15.0)
  Downloading socksio-1.0.0-py3-none-any.whl.metadata (6.1 kB)
Collecting markdown-it-py>=2.2.0 (from rich>=12.3.0->pdm~=2.15.0)
  Downloading markdown_it_py-3.0.0-py3-none-any.whl.metadata (6.9 kB)
Collecting pygments<3.0.0,>=2.13.0 (from rich>=12.3.0->pdm~=2.15.0)
  Downloading pygments-2.18.0-py3-none-any.whl.metadata (2.5 kB)
Collecting distlib<1,>=0.3.7 (from virtualenv>=20->pdm~=2.15.0)
  Downloading distlib-0.3.8-py2.py3-none-any.whl.metadata (5.1 kB)
Collecting mdurl~=0.1 (from markdown-it-py>=2.2.0->rich>=12.3.0->pdm~=2.15.0)
  Downloading mdurl-0.1.2-py3-none-any.whl.metadata (1.6 kB)
Downloading pdm-2.15.4-py3-none-any.whl (258 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 258.5/258.5 kB 13.6 MB/s eta 0:00:00
Downloading dep_logic-0.2.0-py3-none-any.whl (26 kB)
Downloading filelock-3.15.1-py3-none-any.whl (15 kB)
Downloading findpython-0.6.1-py3-none-any.whl (20 kB)
Downloading hishel-0.0.27-py3-none-any.whl (38 kB)
Downloading httpx-0.27.0-py3-none-any.whl (75 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 75.6/75.6 kB 7.0 MB/s eta 0:00:00
Downloading httpcore-1.0.5-py3-none-any.whl (77 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 77.9/77.9 kB 6.4 MB/s eta 0:00:00
Downloading socksio-1.0.0-py3-none-any.whl (12 kB)
Downloading installer-0.7.0-py3-none-any.whl (453 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 453.8/453.8 kB 28.8 MB/s eta 0:00:00
Downloading msgpack-1.0.8-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (409 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 409.3/409.3 kB 24.1 MB/s eta 0:00:00
Downloading packaging-24.1-py3-none-any.whl (53 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 54.0/54.0 kB 4.9 MB/s eta 0:00:00
Downloading python_dotenv-1.0.1-py3-none-any.whl (19 kB)
Downloading resolvelib-1.0.1-py2.py3-none-any.whl (17 kB)
Downloading rich-13.7.1-py3-none-any.whl (240 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 240.7/240.7 kB 15.8 MB/s eta 0:00:00
Downloading shellingham-1.5.4-py2.py3-none-any.whl (9.8 kB)
Downloading tomlkit-0.12.5-py3-none-any.whl (37 kB)
Downloading unearth-0.15.4-py3-none-any.whl (47 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.0/47.0 kB 3.1 MB/s eta 0:00:00
Downloading virtualenv-20.26.2-py3-none-any.whl (3.9 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.9/3.9 MB 39.0 MB/s eta 0:00:00
Downloading platformdirs-4.2.2-py3-none-any.whl (18 kB)
Downloading blinker-1.8.2-py3-none-any.whl (9.5 kB)
Downloading pbs_installer-2024.4.24-py3-none-any.whl (42 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 42.3/42.3 kB 2.1 MB/s eta 0:00:00
Downloading pyproject_hooks-1.1.0-py3-none-any.whl (9.2 kB)
Downloading truststore-0.9.1-py3-none-any.whl (17 kB)
Downloading distlib-0.3.8-py2.py3-none-any.whl (468 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 468.9/468.9 kB 22.1 MB/s eta 0:00:00
Downloading markdown_it_py-3.0.0-py3-none-any.whl (87 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 87.5/87.5 kB 4.9 MB/s eta 0:00:00
Downloading pygments-2.18.0-py3-none-any.whl (1.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 32.9 MB/s eta 0:00:00
Downloading typing_extensions-4.12.2-py3-none-any.whl (37 kB)
Downloading anyio-4.4.0-py3-none-any.whl (86 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 86.8/86.8 kB 5.1 MB/s eta 0:00:00
Downloading idna-3.7-py3-none-any.whl (66 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 66.8/66.8 kB 4.4 MB/s eta 0:00:00
Downloading sniffio-1.3.1-py3-none-any.whl (10 kB)
Downloading certifi-2024.6.2-py3-none-any.whl (164 kB)
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Downloading h11-0.14.0-py3-none-any.whl (58 kB)
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Downloading mdurl-0.1.2-py3-none-any.whl (10.0 kB)
Installing collected packages: resolvelib, distlib, typing-extensions, truststore, tomlkit, socksio, sniffio, shellingham, python-dotenv, pyproject-hooks, pygments, platformdirs, pbs-installer, packaging, msgpack, mdurl, installer, idna, h11, filelock, certifi, blinker, virtualenv, markdown-it-py, httpcore, findpython, dep-logic, anyio, rich, httpx, unearth, hishel, pdm
Successfully installed anyio-4.4.0 blinker-1.8.2 certifi-2024.6.2 dep-logic-0.2.0 distlib-0.3.8 filelock-3.15.1 findpython-0.6.1 h11-0.14.0 hishel-0.0.27 httpcore-1.0.5 httpx-0.27.0 idna-3.7 installer-0.7.0 markdown-it-py-3.0.0 mdurl-0.1.2 msgpack-1.0.8 packaging-24.1 pbs-installer-2024.4.24 pdm-2.15.4 platformdirs-4.2.2 pygments-2.18.0 pyproject-hooks-1.1.0 python-dotenv-1.0.1 resolvelib-1.0.1 rich-13.7.1 shellingham-1.5.4 sniffio-1.3.1 socksio-1.0.0 tomlkit-0.12.5 truststore-0.9.1 typing-extensions-4.12.2 unearth-0.15.4 virtualenv-20.26.2
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
$ python -m venv $VENV_NAME
$ source ${VENV_NAME}/bin/activate
$ if [ -f pdm.lock ]; then pdm use --ignore-remembered --first $VENV_NAME/bin/python; fi
Using Python interpreter: /builds/<REDACTED>/.venv/bin/python (3.11)
$ pip install setuptools wheel
Looking in indexes: https://gitlab-ci-token:****@gitlab.<REDACTED>
Requirement already satisfied: setuptools in ./.venv/lib/python3.11/site-packages (65.5.0)
Collecting wheel
  Obtaining dependency information for wheel from https://files.pythonhosted.org/packages/7d/cd/d7460c9a869b16c3dd4e1e403cce337df165368c71d6af229a74699622ce/wheel-0.43.0-py3-none-any.whl.metadata
  Using cached wheel-0.43.0-py3-none-any.whl.metadata (2.2 kB)
Using cached wheel-0.43.0-py3-none-any.whl (65 kB)
Installing collected packages: wheel
Successfully installed wheel-0.43.0
[notice] A new release of pip is available: 23.2.1 -> 24.0
[notice] To update, run: pip install --upgrade pip
$ if [ -f pdm.lock ]; then pdm sync --no-editable -v; else pip install .; fi
STATUS: Resolving packages from lockfile...
STATUS: Fetching hashes for resolved packages...
Synchronizing working set with resolved packages: 114 to add, 0 to update, 0 to remove
realloc(): invalid next size
/usr/bin/bash: line 277:   214 Aborted                 (core dumped) pdm sync --no-editable -v

[lambda]

I've reproduce this a few times in ~1000 attempts. I have reproduced it on a couple of different versions of Python, ranging from 3.10 to 3.12, and both inside a container that derived from the official Python Docker container and on my host system, an Ubuntu 22.04 system running Python 3.12 from the deadsnakes ppa.

Reproduced by running the following in a project that has exhibited the issue:

trap 'exit_code=$?; echo "exit code: $exit_code"; echo; if [ $exit_code -ne 143 ]; then break; fi' ERR
for i in {1..500}; do (set -o pipefail; rm -rf .venv; python3.12 -m venv .venv; pdm use --ignore-remembered --first .venv/bin/python; pdm sync --no-editable -vv 2>&1 | (while read l; do echo "$l"; if (echo "$l" | grep -q "Install .* successful"); then pkill -s0 pdm; echo; break; fi; done)); done

This eventually produced:

Using Python interpreter: /home/brcampbell/tmp/<REDACTED>/.venv/bin/python (3.12)
STATUS: Resolving packages from lockfile...
Synchronizing working set with resolved packages: 122 to add, 0 to update, 0 to remove

unearth.collector: Collecting links from https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/aiobotocore/
unearth.auth: Found index url https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/
unearth.collector: Collecting links from https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/aiohttp/
unearth.auth: Found index url https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/
unearth.auth: Found credentials in netrc for gitlab.<REDACTED>
unearth.auth: Found credentials in netrc for gitlab.<REDACTED>
unearth.collector: Collecting links from https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/aiosignal/
unearth.collector: Collecting links from https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/aioitertools/
unearth.auth: Found index url https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/
unearth.collector: Collecting links from https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/annotated-types/
unearth.auth: Found index url https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/
unearth.collector: Collecting links from https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/argparse-addons/
unearth.collector: Collecting links from https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/attrs/
unearth.auth: Found credentials in netrc for gitlab.<REDACTED>
unearth.auth: Found index url https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/
unearth.collector: Collecting links from https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/babel/
unearth.collector: Collecting links from https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/<REDACTED>/
unearth.auth: Found index url https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/
unearth.collector: Collecting links from https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/<REDACTED>/
unearth.auth: Found index url https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/
unearth.collector: Collecting links from https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/bitstruct/
unearth.collector: Collecting links from https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/boto3/
unearth.collector: Collecting links from https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/botocore/
unearth.auth: Found credentials in netrc for gitlab.<REDACTED>
unearth.collector: Collecting links from https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/bracex/
unearth.auth: Found index url https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/
unearth.collector: Collecting links from https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/cachetools/
unearth.auth: Found index url https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/
unearth.collector: Collecting links from https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/cerberus/
unearth.auth: Found credentials in netrc for gitlab.<REDACTED>
unearth.auth: Found index url https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/
unearth.collector: Collecting links from https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/certifi/
unearth.collector: Collecting links from https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/charset-normalizer/
unearth.collector: Collecting links from https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/click/
unearth.auth: Found credentials in netrc for gitlab.<REDACTED>
unearth.collector: Collecting links from https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/colorama/
unearth.auth: Found index url https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/
unearth.auth: Found index url https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/
unearth.auth: Found index url https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/
unearth.auth: Found credentials in netrc for gitlab.<REDACTED>
unearth.auth: Found index url https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/
unearth.auth: Found index url https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/
unearth.auth: Found index url https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/
unearth.auth: Found credentials in netrc for gitlab.<REDACTED>
unearth.auth: Found credentials in netrc for gitlab.<REDACTED>
unearth.auth: Found index url https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/
unearth.auth: Found index url https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/
unearth.auth: Found credentials in netrc for gitlab.<REDACTED>
unearth.auth: Found index url https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/
unearth.auth: Found index url https://gitlab.<REDACTED>/api/v4/projects/<REDACTED>/packages/pypi/simple/
unearth.auth: Found credentials in netrc for gitlab.<REDACTED>
unearth.auth: Found credentials in netrc for gitlab.<REDACTED>
unearth.auth: Found credentials in netrc for gitlab.<REDACTED>
unearth.auth: Found credentials in netrc for gitlab.<REDACTED>
unearth.auth: Found credentials in netrc for gitlab.<REDACTED>
unearth.auth: Found credentials in netrc for gitlab.<REDACTED>
unearth.auth: Found credentials in netrc for gitlab.<REDACTED>
unearth.auth: Found credentials in netrc for gitlab.<REDACTED>
unearth.auth: Found credentials in netrc for gitlab.<REDACTED>
unearth.auth: Found credentials in netrc for gitlab.<REDACTED>
exit code: 139

The project is proprietary, and pointing at our internal pypi repository, hosted on a GitLab package registry. Working on minimizing the repro example to see if I can do it without those factors.

[mikecowie-seequent]

Great reproduction @lambda

We have experienced a very similar symtom.

• same error
• random and very occasional in CI so hard to reproduce (github actions, default ubuntu runner). Have not seen locally.
• lockfile and venv are in place and up to date (pdm lock --check) returns no errors
• we are not using a private package repository for this
• pyproject.toml with redactions below:
• pdm.lock also attached (I had to add a .txt to the filename because github limits attachment suffixes)
• pdm is installed in github actions by pdm-project/setup-pdm@v3 (that will be updated but I'm doubtful the out of date action would be the cause.
• noting the dependency list is pretty small; this case it was just setting up and running a small script.
• we are running just pdm install

[project]
name = "redacted"
version = "redacted"
description = "redacted"
authors = [
    {name = "redacted", email = "redacted"},
]
dependencies = [
    "pydantic>=2.5.2",
    "PyYAML~=6.0.1",
    "requests>=2.31.0",
]
requires-python = "==3.12.*"
readme = "README.md"
license = {text = "redacted"}


[project.optional-dependencies]
dev = [
    "pytest>=8.2.1",
    "ruff>=0.2.2",
    "pydantic>=2.5.2",
    "pytest-cov>=5.0.0",
    "requests-mock>=1.12.1",
    "ipython>=8.25.0",
]
[tool.pdm]
distribution = false

PDM Lockfile

I am attempting @lambda 's brute force attempt at local recreation and will update if I can get it.

Edit - no luck in reproduction. I'll leave it running over lunch.

[lambda]

Ah, nice to know that we're not the only ones hitting this.

Seeing this new comment prompted me to try again, and I just reproduced it again, this time with no reference to internal packages or our internal package registry.

Here is my most recent pyproject.toml with which I was able to reproduce it (not really fully minimal, going to continue trying to cut it down but given how long it takes to repro that can take a while):

[build-system]
requires = ["pdm-pep517"]
build-backend = "pdm.pep517.api"

[tool.pdm.dev-dependencies]
dev = [
    "flake8>=4.0.1",
    "pep8-naming>=0.13.1",
    "flake8-docstrings>=1.6.0",
    "pytest>=7.1.2",
    "pytest-cov>=3.0.0",
    "pytest-xdist>=2.5.0",
    "mypy>=0.971",
    "types-requests>=2.28.2",
    "types-mock>=4.0.15",
    "isort>=5.10.1",
    "black>=22.6.0",
    "docformatter>=1.5.0, !=1.5.1",
]
docs = [
    # base tool
    "mkdocs>=1.3.1",
    # theme
    "mkdocs-material>=8.3.9",
    # api reference
    "mkdocstrings[python]>=0.19.0",
    "mkdocs-gen-files>=0.3.5",
    "mkdocs-literate-nav>=0.4.1",
    "mkdocs-section-index>=0.3.4",
    # include files
    "mkdocs-include-markdown-plugin>=3.6.1",
    # cli reference
    "mkdocs-click>=0.8.0",
]

[project]
name = "pdm-memory-corruption"
requires-python = ">=3.8"
version = "1.0.0"
dependencies = [
    "python-gitlab>=3.6.0",
    "click>=8.1.3",
    "more-itertools>=8.13.0",
    "packaging>=21.3",
    "markdown-it-py>=2.1.0",
    "backoff>=2.1.2",
]

pdm.lock contents

# This file is @generated by PDM.
# It is not intended for manual editing.

[[package]]
name = "attrs"
version = "22.2.0"
requires_python = ">=3.6"
summary = "Classes Without Boilerplate"

[[package]]
name = "backoff"
version = "2.2.1"
requires_python = ">=3.7,<4.0"
summary = "Function decoration for backoff and retry"

[[package]]
name = "black"
version = "23.1.0"
requires_python = ">=3.7"
summary = "The uncompromising code formatter."
dependencies = [
    "click>=8.0.0",
    "mypy-extensions>=0.4.3",
    "packaging>=22.0",
    "pathspec>=0.9.0",
    "platformdirs>=2",
    "tomli>=1.1.0; python_version < \"3.11\"",
    "typing-extensions>=3.10.0.0; python_version < \"3.10\"",
]

[[package]]
name = "certifi"
version = "2022.12.7"
requires_python = ">=3.6"
summary = "Python package for providing Mozilla's CA Bundle."

[[package]]
name = "charset-normalizer"
version = "3.0.1"
summary = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."

[[package]]
name = "click"
version = "8.1.3"
requires_python = ">=3.7"
summary = "Composable command line interface toolkit"
dependencies = [
    "colorama; platform_system == \"Windows\"",
]

[[package]]
name = "colorama"
version = "0.4.6"
requires_python = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
summary = "Cross-platform colored terminal text."

[[package]]
name = "coverage"
version = "7.2.0"
requires_python = ">=3.7"
summary = "Code coverage measurement for Python"

[[package]]
name = "coverage"
version = "7.2.0"
extras = ["toml"]
requires_python = ">=3.7"
summary = "Code coverage measurement for Python"
dependencies = [
    "coverage==7.2.0",
    "tomli; python_full_version <= \"3.11.0a6\"",
]

[[package]]
name = "docformatter"
version = "1.5.0"
requires_python = ">=3.6,<4.0"
summary = "Formats docstrings to follow PEP 257"
dependencies = [
    "tomli<3.0.0,>=2.0.0; python_version >= \"3.7\"",
    "untokenize<0.2.0,>=0.1.1",
]

[[package]]
name = "exceptiongroup"
version = "1.1.0"
requires_python = ">=3.7"
summary = "Backport of PEP 654 (exception groups)"

[[package]]
name = "execnet"
version = "1.9.0"
requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
summary = "execnet: rapid multi-Python deployment"

[[package]]
name = "flake8"
version = "5.0.4"
requires_python = ">=3.6.1"
summary = "the modular source code checker: pep8 pyflakes and co"
dependencies = [
    "mccabe<0.8.0,>=0.7.0",
    "pycodestyle<2.10.0,>=2.9.0",
    "pyflakes<2.6.0,>=2.5.0",
]

[[package]]
name = "flake8-docstrings"
version = "1.7.0"
requires_python = ">=3.7"
summary = "Extension for flake8 which uses pydocstyle to check docstrings"
dependencies = [
    "flake8>=3",
    "pydocstyle>=2.1",
]

[[package]]
name = "ghp-import"
version = "2.1.0"
summary = "Copy your docs directly to the gh-pages branch."
dependencies = [
    "python-dateutil>=2.8.1",
]

[[package]]
name = "griffe"
version = "0.25.4"
requires_python = ">=3.7"
summary = "Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API."
dependencies = [
    "colorama>=0.4",
]

[[package]]
name = "idna"
version = "3.4"
requires_python = ">=3.5"
summary = "Internationalized Domain Names in Applications (IDNA)"

[[package]]
name = "importlib-metadata"
version = "6.0.0"
requires_python = ">=3.7"
summary = "Read metadata from Python packages"
dependencies = [
    "zipp>=0.5",
]

[[package]]
name = "iniconfig"
version = "2.0.0"
requires_python = ">=3.7"
summary = "brain-dead simple config-ini parsing"

[[package]]
name = "isort"
version = "5.12.0"
requires_python = ">=3.8.0"
summary = "A Python utility / library to sort Python imports."

[[package]]
name = "jinja2"
version = "3.1.2"
requires_python = ">=3.7"
summary = "A very fast and expressive template engine."
dependencies = [
    "MarkupSafe>=2.0",
]

[[package]]
name = "markdown"
version = "3.3.7"
requires_python = ">=3.6"
summary = "Python implementation of Markdown."
dependencies = [
    "importlib-metadata>=4.4; python_version < \"3.10\"",
]

[[package]]
name = "markdown-it-py"
version = "2.2.0"
requires_python = ">=3.7"
summary = "Python port of markdown-it. Markdown parsing, done right!"
dependencies = [
    "mdurl~=0.1",
]

[[package]]
name = "markupsafe"
version = "2.1.2"
requires_python = ">=3.7"
summary = "Safely add untrusted strings to HTML/XML markup."

[[package]]
name = "mccabe"
version = "0.7.0"
requires_python = ">=3.6"
summary = "McCabe checker, plugin for flake8"

[[package]]
name = "mdurl"
version = "0.1.2"
requires_python = ">=3.7"
summary = "Markdown URL utilities"

[[package]]
name = "mergedeep"
version = "1.3.4"
requires_python = ">=3.6"
summary = "A deep merge function for 🐍."

[[package]]
name = "mkdocs"
version = "1.4.2"
requires_python = ">=3.7"
summary = "Project documentation with Markdown."
dependencies = [
    "click>=7.0",
    "colorama>=0.4; platform_system == \"Windows\"",
    "ghp-import>=1.0",
    "importlib-metadata>=4.3; python_version < \"3.10\"",
    "jinja2>=2.11.1",
    "markdown<3.4,>=3.2.1",
    "mergedeep>=1.3.4",
    "packaging>=20.5",
    "pyyaml-env-tag>=0.1",
    "pyyaml>=5.1",
    "watchdog>=2.0",
]

[[package]]
name = "mkdocs-autorefs"
version = "0.4.1"
requires_python = ">=3.7"
summary = "Automatically link across pages in MkDocs."
dependencies = [
    "Markdown>=3.3",
    "mkdocs>=1.1",
]

[[package]]
name = "mkdocs-click"
version = "0.8.0"
requires_python = ">=3.7"
summary = "An MkDocs extension to generate documentation for Click command line applications"
dependencies = [
    "click~=8.1",
    "markdown==3.*",
]

[[package]]
name = "mkdocs-gen-files"
version = "0.4.0"
requires_python = ">=3.7,<4.0"
summary = "MkDocs plugin to programmatically generate documentation pages during the build"
dependencies = [
    "mkdocs<2.0.0,>=1.0.3",
]

[[package]]
name = "mkdocs-include-markdown-plugin"
version = "3.9.1"
requires_python = ">=3.6"
summary = "Mkdocs Markdown includer plugin."

[[package]]
name = "mkdocs-literate-nav"
version = "0.6.0"
requires_python = ">=3.7"
summary = "MkDocs plugin to specify the navigation in Markdown instead of YAML"
dependencies = [
    "mkdocs>=1.0.3",
]

[[package]]
name = "mkdocs-material"
version = "9.0.14"
requires_python = ">=3.7"
summary = "Documentation that simply works"
dependencies = [
    "colorama>=0.4",
    "jinja2>=3.0",
    "markdown>=3.2",
    "mkdocs-material-extensions>=1.1",
    "mkdocs>=1.4.2",
    "pygments>=2.14",
    "pymdown-extensions>=9.9.1",
    "regex>=2022.4.24",
    "requests>=2.26",
]

[[package]]
name = "mkdocs-material-extensions"
version = "1.1.1"
requires_python = ">=3.7"
summary = "Extension pack for Python Markdown and MkDocs Material."

[[package]]
name = "mkdocs-section-index"
version = "0.3.5"
requires_python = ">=3.7"
summary = "MkDocs plugin to allow clickable sections that lead to an index page"
dependencies = [
    "mkdocs>=1.0.3",
]

[[package]]
name = "mkdocstrings"
version = "0.20.0"
requires_python = ">=3.7"
summary = "Automatic documentation from sources, for MkDocs."
dependencies = [
    "Jinja2>=2.11.1",
    "Markdown>=3.3",
    "MarkupSafe>=1.1",
    "mkdocs-autorefs>=0.3.1",
    "mkdocs>=1.2",
    "pymdown-extensions>=6.3",
]

[[package]]
name = "mkdocstrings-python"
version = "0.8.3"
requires_python = ">=3.7"
summary = "A Python handler for mkdocstrings."
dependencies = [
    "griffe>=0.24",
    "mkdocstrings>=0.19",
]

[[package]]
name = "mkdocstrings"
version = "0.20.0"
extras = ["python"]
requires_python = ">=3.7"
summary = "Automatic documentation from sources, for MkDocs."
dependencies = [
    "mkdocstrings-python>=0.5.2",
    "mkdocstrings==0.20.0",
]

[[package]]
name = "more-itertools"
version = "9.0.0"
requires_python = ">=3.7"
summary = "More routines for operating on iterables, beyond itertools"

[[package]]
name = "mypy"
version = "1.0.1"
requires_python = ">=3.7"
summary = "Optional static typing for Python"
dependencies = [
    "mypy-extensions>=0.4.3",
    "tomli>=1.1.0; python_version < \"3.11\"",
    "typing-extensions>=3.10",
]

[[package]]
name = "mypy-extensions"
version = "1.0.0"
requires_python = ">=3.5"
summary = "Type system extensions for programs checked with the mypy type checker."

[[package]]
name = "packaging"
version = "23.0"
requires_python = ">=3.7"
summary = "Core utilities for Python packages"

[[package]]
name = "pathspec"
version = "0.11.0"
requires_python = ">=3.7"
summary = "Utility library for gitignore style pattern matching of file paths."

[[package]]
name = "pep8-naming"
version = "0.13.3"
requires_python = ">=3.7"
summary = "Check PEP-8 naming conventions, plugin for flake8"
dependencies = [
    "flake8>=5.0.0",
]

[[package]]
name = "platformdirs"
version = "3.0.0"
requires_python = ">=3.7"
summary = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."

[[package]]
name = "pluggy"
version = "1.0.0"
requires_python = ">=3.6"
summary = "plugin and hook calling mechanisms for python"

[[package]]
name = "pycodestyle"
version = "2.9.1"
requires_python = ">=3.6"
summary = "Python style guide checker"

[[package]]
name = "pydocstyle"
version = "6.3.0"
requires_python = ">=3.6"
summary = "Python docstring style checker"
dependencies = [
    "snowballstemmer>=2.2.0",
]

[[package]]
name = "pyflakes"
version = "2.5.0"
requires_python = ">=3.6"
summary = "passive checker of Python programs"

[[package]]
name = "pygments"
version = "2.14.0"
requires_python = ">=3.6"
summary = "Pygments is a syntax highlighting package written in Python."

[[package]]
name = "pymdown-extensions"
version = "9.9.2"
requires_python = ">=3.7"
summary = "Extension pack for Python Markdown."
dependencies = [
    "markdown>=3.2",
]

[[package]]
name = "pytest"
version = "7.2.1"
requires_python = ">=3.7"
summary = "pytest: simple powerful testing with Python"
dependencies = [
    "attrs>=19.2.0",
    "colorama; sys_platform == \"win32\"",
    "exceptiongroup>=1.0.0rc8; python_version < \"3.11\"",
    "iniconfig",
    "packaging",
    "pluggy<2.0,>=0.12",
    "tomli>=1.0.0; python_version < \"3.11\"",
]

[[package]]
name = "pytest-cov"
version = "4.0.0"
requires_python = ">=3.6"
summary = "Pytest plugin for measuring coverage."
dependencies = [
    "coverage[toml]>=5.2.1",
    "pytest>=4.6",
]

[[package]]
name = "pytest-xdist"
version = "3.2.0"
requires_python = ">=3.7"
summary = "pytest xdist plugin for distributed testing, most importantly across multiple CPUs"
dependencies = [
    "execnet>=1.1",
    "pytest>=6.2.0",
]

[[package]]
name = "python-dateutil"
version = "2.8.2"
requires_python = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
summary = "Extensions to the standard Python datetime module"
dependencies = [
    "six>=1.5",
]

[[package]]
name = "python-gitlab"
version = "3.13.0"
requires_python = ">=3.7.0"
summary = "Interact with GitLab API"
dependencies = [
    "requests-toolbelt>=0.10.1",
    "requests>=2.25.0",
]

[[package]]
name = "pyyaml"
version = "6.0"
requires_python = ">=3.6"
summary = "YAML parser and emitter for Python"

[[package]]
name = "pyyaml-env-tag"
version = "0.1"
requires_python = ">=3.6"
summary = "A custom YAML tag for referencing environment variables in YAML files. "
dependencies = [
    "pyyaml",
]

[[package]]
name = "regex"
version = "2022.10.31"
requires_python = ">=3.6"
summary = "Alternative regular expression module, to replace re."

[[package]]
name = "requests"
version = "2.28.2"
requires_python = ">=3.7, <4"
summary = "Python HTTP for Humans."
dependencies = [
    "certifi>=2017.4.17",
    "charset-normalizer<4,>=2",
    "idna<4,>=2.5",
    "urllib3<1.27,>=1.21.1",
]

[[package]]
name = "requests-toolbelt"
version = "0.10.1"
requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
summary = "A utility belt for advanced users of python-requests"
dependencies = [
    "requests<3.0.0,>=2.0.1",
]

[[package]]
name = "six"
version = "1.16.0"
requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
summary = "Python 2 and 3 compatibility utilities"

[[package]]
name = "snowballstemmer"
version = "2.2.0"
summary = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."

[[package]]
name = "tomli"
version = "2.0.1"
requires_python = ">=3.7"
summary = "A lil' TOML parser"

[[package]]
name = "types-mock"
version = "5.0.0.5"
summary = "Typing stubs for mock"

[[package]]
name = "types-requests"
version = "2.28.11.14"
summary = "Typing stubs for requests"
dependencies = [
    "types-urllib3<1.27",
]

[[package]]
name = "types-urllib3"
version = "1.26.25.7"
summary = "Typing stubs for urllib3"

[[package]]
name = "typing-extensions"
version = "4.5.0"
requires_python = ">=3.7"
summary = "Backported and Experimental Type Hints for Python 3.7+"

[[package]]
name = "untokenize"
version = "0.1.1"
summary = "Transforms tokens into original source code (while preserving whitespace)."

[[package]]
name = "urllib3"
version = "1.26.14"
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    {url = "https://files.pythonhosted.org/packages/be/70/5b249f88d4c4fa5235ef524c8591f2d186c611bb93946643eaca301936b5/watchdog-2.3.0-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:15bf5b165d7a6b48265411dad74fb0d33053f8270eb6575faad0e016035cf9f7"},
    {url = "https://files.pythonhosted.org/packages/c1/d0/cd7661148127d5dda9bffeb70777541a70623be1abdc9463e0a82aaca33d/watchdog-2.3.0-py3-none-manylinux2014_x86_64.whl", hash = "sha256:7767a3da3307d9cf597832f692702441a97c259e5d0d560f2e57c43ad0d191d2"},
    {url = "https://files.pythonhosted.org/packages/c2/87/5d651cb0aab9a42b13e9a557021b6498ea45fc9f72ba6b37bbdbcffe907c/watchdog-2.3.0-py3-none-win_amd64.whl", hash = "sha256:6d79b5954db8f41d6a7f5763042b988f7a4afd40b7d141456061fa7c5b7f2159"},
    {url = "https://files.pythonhosted.org/packages/ce/8b/90c2611473594857c3548ad895dc8ca3dde0d5240b4f3ef01eb6c5bbeef9/watchdog-2.3.0-py3-none-win_ia64.whl", hash = "sha256:a3559ee82a10976de1ec544b6ebe3b4aa398d491860a283d80ec0f550076d068"},
    {url = "https://files.pythonhosted.org/packages/cf/b0/4bc82402b2ef7aea5c14c6665222d6cb97ff4997d693e70d2ae45315e8f1/watchdog-2.3.0-py3-none-manylinux2014_i686.whl", hash = "sha256:f1a655f4a49f9232311b9967f42cc2eaf43fd4903f3bed850dd4570fda5d5eff"},
    {url = "https://files.pythonhosted.org/packages/d1/77/6451ac9c31630bab57e4dcd25e701c379547ccc0974d7d6d94b97e46ca7f/watchdog-2.3.0.tar.gz", hash = "sha256:9d39effe6909be898ba3e7286a9e9b17a6a9f734fb1ef9dde3e9bb68715fca39"},
    {url = "https://files.pythonhosted.org/packages/d6/a9/c5ce07886321f043fcf58a72f20096cf72113b05d204a8efa06f5006f1e2/watchdog-2.3.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:d04662017efd00a014cff9068708e085d67f2fac43f48bbbb95a7f97490487f3"},
    {url = "https://files.pythonhosted.org/packages/e3/cc/3c5e4a97d67d6e7ae360891fc59db6c5faa8154c19b74cddc99cc4d027ca/watchdog-2.3.0-py3-none-manylinux2014_aarch64.whl", hash = "sha256:1d9c656495172873bf1ddc7e39e80055fcdd21c4608cf68f23a28116dcba0b43"},
    {url = "https://files.pythonhosted.org/packages/ee/ed/b47a369557d46e1dd336bf91733fba97416dbfa56e859606ed77876f78b3/watchdog-2.3.0-pp38-pypy38_pp73-macosx_10_9_x86_64.whl", hash = "sha256:5ddbbe87f9ed726940d174076da030cd01ec45433ef2b1b2e6094c84f2af17f1"},
]
"zipp 3.14.0" = [
    {url = "https://files.pythonhosted.org/packages/a8/7d/90189265f0a9bcdf79b1143b77b0ef6dca0a5f13783f1e1efa4d7d7eafca/zipp-3.14.0-py3-none-any.whl", hash = "sha256:188834565033387710d046e3fe96acfc9b5e86cbca7f39ff69cf21a4128198b7"},
    {url = "https://files.pythonhosted.org/packages/ab/47/b47d02b741e0aa6f998fc80457d3dfc05cb7732ef480597c2971cbc79260/zipp-3.14.0.tar.gz", hash = "sha256:9e5421e176ef5ab4c0ad896624e87a7b2f07aca746c9b2aa305952800cb8eecb"},
]

And here's the result; amazingly, I hit it on the first iteration of this test, but it frequently takes hundreds or thousands of runs before I hit it.

brcampbell@BETA-0661:~/tmp/pdm-memory-corruption$ for i in {1..500}; do (set -o pipefail; rm -rf .venv; python3.12 -m venv .venv; pdm use --ignore-remembered --first .venv/bin/python; pdm sync --no-editable -vv 2>&1 | (while read l; do echo "$l"; if (echo "$l" | grep -q "Install .* successful"); then pkill -s0 pdm; echo; break; fi; done)); done
Using Python interpreter: /home/brcampbell/tmp/pdm-memory-corruption/.venv/bin/python (3.12)
INFO: PDM 2.15.4 is installed, while 2.17.1 is available.
Please run `pipx upgrade pdm` to upgrade.
Run `pdm config check_update false` to disable the check.
WARNING: Lockfile is generated on an older version of PDM
STATUS: Resolving packages from lockfile...
STATUS: Fetching hashes for resolved packages...
Synchronizing working set with resolved packages: 68 to add, 0 to update, 0 to remove

unearth.collector: Collecting links from https://pypi.org/simple/attrs/
unearth.auth: Found index url https://pypi.org/simple/
unearth.collector: Collecting links from https://pypi.org/simple/certifi/
unearth.auth: Found index url https://pypi.org/simple/
unearth.collector: Collecting links from https://pypi.org/simple/black/
unearth.auth: Found index url https://pypi.org/simple/
unearth.collector: Collecting links from https://pypi.org/simple/charset-normalizer/
unearth.auth: Found index url https://pypi.org/simple/
unearth.collector: Collecting links from https://pypi.org/simple/click/
unearth.auth: Found index url https://pypi.org/simple/
unearth.collector: Collecting links from https://pypi.org/simple/backoff/
unearth.auth: Found index url https://pypi.org/simple/
unearth.collector: Collecting links from https://pypi.org/simple/colorama/
unearth.auth: Found index url https://pypi.org/simple/
unearth.collector: Collecting links from https://pypi.org/simple/coverage/
unearth.auth: Found index url https://pypi.org/simple/
unearth.collector: Collecting links from https://pypi.org/simple/docformatter/
unearth.auth: Found index url https://pypi.org/simple/
unearth.collector: Collecting links from https://pypi.org/simple/execnet/
unearth.auth: Found index url https://pypi.org/simple/
unearth.collector: Collecting links from https://pypi.org/simple/flake8/
unearth.auth: Found index url https://pypi.org/simple/
unearth.collector: Collecting links from https://pypi.org/simple/flake8-docstrings/
unearth.collector: Collecting links from https://pypi.org/simple/ghp-import/
unearth.auth: Found index url https://pypi.org/simple/
unearth.auth: Found index url https://pypi.org/simple/
unearth.collector: Collecting links from https://pypi.org/simple/griffe/
unearth.collector: Collecting links from https://pypi.org/simple/idna/
unearth.auth: Found index url https://pypi.org/simple/
unearth.collector: Collecting links from https://pypi.org/simple/iniconfig/
unearth.collector: Collecting links from https://pypi.org/simple/isort/
unearth.collector: Collecting links from https://pypi.org/simple/jinja2/
unearth.auth: Found index url https://pypi.org/simple/
unearth.collector: Collecting links from https://pypi.org/simple/markdown/
unearth.collector: Collecting links from https://pypi.org/simple/markdown-it-py/
unearth.auth: Found index url https://pypi.org/simple/
unearth.auth: Found index url https://pypi.org/simple/
unearth.auth: Found index url https://pypi.org/simple/
unearth.auth: Found index url https://pypi.org/simple/
unearth.auth: Found index url https://pypi.org/simple/
exit code: 139

[mikecowie-seequent]

Aye, I had no luck on reproduction, but that's a good job @lambda .

So establishing

• Looks unlikely to be deeply linked to the package set or index server.
• It seems to happen either during or straight after Synchronizing working set

Being such a low-level error and PDM apparently being pure-python - somehow it's triggering something quite low down (seemingly in python itself?). That takes it a bit out of my skillset to debug more deeply.

[apollo13]

@lambda I cannot even install your project because it fails with pyyaml :/ Apparently there is a dependency issue between pyyaml and cython. I will try python 3.10 instead of 3.12 which has wheels for pyyaml…

$ pdm sync --no-editable                                                                                                                                                                                                                 WARNING: Lockfile is generated on an older version of PDM
Synchronizing working set with resolved packages: 1 to add, 0 to update, 0 to remove

  ✖ Install pyyaml 6.0 failed
  ✖ Install pyyaml 6.0 failed

ERRORS:
add pyyaml failed:
Traceback (most recent call last):
  File "/usr/lib64/python3.12/concurrent/futures/thread.py", line 58, in run
    result = self.fn(*self.args, **self.kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/florian/.local/share/pipx/venvs/pdm/lib64/python3.12/site-packages/pdm/installers/synchronizers.py", line 228, in install_candidate
    self.manager.install(can)
  File "/home/florian/.local/share/pipx/venvs/pdm/lib64/python3.12/site-packages/pdm/installers/manager.py", line 33, in install
    prepared.build(),
    ^^^^^^^^^^^^^^^^
  File "/home/florian/.local/share/pipx/venvs/pdm/lib64/python3.12/site-packages/pdm/models/candidates.py", line 411, in build
    self._cached = Path(builder.build(build_dir, metadata_directory=self._metadata_dir))
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/florian/.local/share/pipx/venvs/pdm/lib64/python3.12/site-packages/pdm/builders/base.py", line 84, in wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/home/florian/.local/share/pipx/venvs/pdm/lib64/python3.12/site-packages/pdm/builders/wheel.py", line 24, in build
    requires = self._hook.get_requires_for_build_wheel(self.config_settings)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/florian/.local/share/pipx/venvs/pdm/lib64/python3.12/site-packages/pyproject_hooks/_impl.py", line 196, in get_requires_for_build_wheel
    return self._call_hook(
           ^^^^^^^^^^^^^^^^
  File "/home/florian/.local/share/pipx/venvs/pdm/lib64/python3.12/site-packages/pyproject_hooks/_impl.py", line 392, in _call_hook
    self._subprocess_runner(
  File "/home/florian/.local/share/pipx/venvs/pdm/lib64/python3.12/site-packages/pdm/builders/base.py", line 281, in subprocess_runner
    return log_subprocessor(cmd, cwd, extra_environ=env)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/florian/.local/share/pipx/venvs/pdm/lib64/python3.12/site-packages/pdm/builders/base.py", line 128, in log_subprocessor
    raise build_error(e) from None
pdm.exceptions.BuildError: Build backend raised error: Showing the last 10 lines of the build output:
    super().add_defaults()
  File "/tmp/pdm-build-env-i9wa_tsb-shared/lib/python3.12/site-packages/setuptools/_distutils/command/sdist.py", line 250, in add_defaults
    self._add_defaults_ext()
  File "/tmp/pdm-build-env-i9wa_tsb-shared/lib/python3.12/site-packages/setuptools/_distutils/command/sdist.py", line 335, in _add_defaults_ext
    self.filelist.extend(build_ext.get_source_files())
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<string>", line 204, in get_source_files
  File "/tmp/pdm-build-env-i9wa_tsb-shared/lib/python3.12/site-packages/setuptools/_distutils/cmd.py", line 107, in __getattr__
    raise AttributeError(attr)
AttributeError: cython_sources

[apollo13]

So here are some further thoughts while I try to reproduce:

• Upgrade your pdm to the latest version (I doubt it makes a diff, but maybe…)
• You said you could reproduce on your Ubuntu box -- did systemd-coredump record anything (coredumpctl would show you). If not get your system configured to capture those. Having a coredump will make a massive difference in debugging.

[apollo13]

Further things that would be helpful:

• Narrow the package set down (I know that can take some time) but with a binary search you should get there relatively fast and every iteration will increase reproduction speed.
• Generate a lock file that solely has python 3.10 - 3.12 support in it via a new PDM version. This way we also reduce the work that is needed.
• pdm sync -r would reinstall the files, does this work as well, would probably make reproduction also faster

If the segfault is still triggered afterwards we are already in a better position… Although if it is a memory corruption the backtrace is most likely useless. But maybe it is always at the same location and gives some hints?

[FaitAccompli]

@lambda @mikecowie-seequent, our team is experiencing this issue as well. Were you guys able to figure out the cause?

[mikecowie-seequent]

@FaitAccompli , no sadly, it's something we've been tolerating as contributing to CI flakiness . It's rare enough to not be a priority...

I might well be imagining it, but it feels like I might have seen it less in the past few weeks?

[lambda]

Yeah, we weren't able to reproduce it reliably enough to track it down; it's still happening, but so infrequently that reproducing it and getting better debugging data is really elusive.

[mikecowie-seequent]

So ... just to update, we stopped tolerating this and moved to uv ... we haven't looked back.

[lambda]

The frequency that this happens at has gone down, making it harder to reproduce and get good info from, but it hasn't gone away. Just got it again with PDM 2.22.2.

$ if [ -f pdm.lock ]; then pdm sync --no-editable -v; else pip install .; fi
STATUS: Resolving packages from lockfile...
All packages are synced to date, nothing to do.
unearth.preparer: The file . is a local directory, use it directly
pdm.termui: Running PEP 517 backend to get metadata for <Link file:///builds/software/beta-can-dbc (from None)>
pdm.termui: Preparing environment(Isolated mode) for PEP 517 build...
pdm.termui: ======== Start resolving requirements ========
pdm.termui:   Adding requirement python==3.11.11
pdm.termui:   Adding requirement hatchling
pdm.termui:   Adding requirement hatch-vcs
pdm.termui:   Adding requirement py-beta-common>=1.11.1
unearth.preparer: Downloading <Link https://gitlab.beta.team/api/v4/projects/328/packages/pypi/files/c31df048ca7e28b073b35aded20ecf92dcc622b2196db07678cfed25b8f6b08c/py_beta_common-1.26.1-py3-none-any.whl (from https://gitlab.beta.team/api/v4/projects/beta%2Fpypi/packages/pypi/simple/py-beta-common/)> (42 kB)
pdm.termui:   Adding requirement cerberus>=1.3.4(from py-beta-common 1.26.1)
pdm.termui:   Adding requirement concurrent-log-handler(from py-beta-common 1.26.1)
pdm.termui:   Adding requirement deprecation(from py-beta-common 1.26.1)
pdm.termui:   Adding requirement fsspec(from py-beta-common 1.26.1)
pdm.termui:   Adding requirement json-schema-for-humans(from py-beta-common 1.26.1)
pdm.termui:   Adding requirement jsonschema>=4.17.3(from py-beta-common 1.26.1)
pdm.termui:   Adding requirement numpy>=1.26.3(from py-beta-common 1.26.1)
pdm.termui:   Adding requirement pydantic>=2.7.1(from py-beta-common 1.26.1)
pdm.termui:   Adding requirement toml>=0.10.2(from py-beta-common 1.26.1)
pdm.termui:   Adding requirement hatchling>=1.1.0(from hatch-vcs 0.4.0)
pdm.termui:   Adding requirement setuptools-scm>=6.4.0(from hatch-vcs 0.4.0)
pdm.termui:   Adding requirement packaging>=24.2(from hatchling 1.27.0)
pdm.termui:   Adding requirement pathspec>=0.10.1(from hatchling 1.27.0)
pdm.termui:   Adding requirement pluggy>=1.0.0(from hatchling 1.27.0)
pdm.termui:   Adding requirement trove-classifiers(from hatchling 1.27.0)
pdm.termui:   Adding requirement attrs>=22.2.0(from jsonschema 4.23.0)
pdm.termui:   Adding requirement jsonschema-specifications>=2023.03.6(from jsonschema 4.23.0)
pdm.termui:   Adding requirement referencing>=0.28.4(from jsonschema 4.23.0)
pdm.termui:   Adding requirement rpds-py>=0.7.1(from jsonschema 4.23.0)
pdm.termui:   Adding requirement referencing>=0.31.0(from jsonschema-specifications 2024.10.1)
pdm.termui:   Adding requirement attrs>=22.2.0(from referencing 0.36.2)
pdm.termui:   Adding requirement rpds-py>=0.7.0(from referencing 0.36.2)
pdm.termui:   Adding requirement typing-extensions>=4.4.0; python_version < "3.13"(from referencing 0.36.2)
pdm.termui:   Adding requirement annotated-types>=0.6.0(from pydantic 2.10.6)
pdm.termui:   Adding requirement pydantic-core==2.27.2(from pydantic 2.10.6)
pdm.termui:   Adding requirement typing-extensions>=4.12.2(from pydantic 2.10.6)
pdm.termui:   Adding requirement typing-extensions!=4.7.0,>=4.6.0(from pydantic-core 2.27.2)
pdm.termui:   Adding requirement packaging>=20(from setuptools-scm 8.1.0)
pdm.termui:   Adding requirement setuptools(from setuptools-scm 8.1.0)
pdm.termui:   Adding requirement portalocker>=1.6.0(from concurrent-log-handler 0.9.25)
pdm.termui:   Adding requirement packaging(from deprecation 2.1.0)
pdm.termui:   Adding requirement Jinja2>3(from json-schema-for-humans 1.3.4)
pdm.termui:   Adding requirement PyYAML<7.0.0,>=6.0.2(from json-schema-for-humans 1.3.4)
pdm.termui:   Adding requirement Pygments<3.0.0,>=2.18.0(from json-schema-for-humans 1.3.4)
pdm.termui:   Adding requirement click<9.0.0,>=8.0.1(from json-schema-for-humans 1.3.4)
pdm.termui:   Adding requirement dataclasses-json<0.7.0,>=0.6.7(from json-schema-for-humans 1.3.4)
pdm.termui:   Adding requirement markdown2<3.0.0,>=2.5.0(from json-schema-for-humans 1.3.4)
pdm.termui:   Adding requirement pytz(from json-schema-for-humans 1.3.4)
pdm.termui:   Adding requirement requests<3.0.0,>=2.32.3(from json-schema-for-humans 1.3.4)
pdm.termui:   Adding requirement marshmallow<4.0.0,>=3.18.0(from dataclasses-json 0.6.7)
pdm.termui:   Adding requirement typing-inspect<1,>=0.4.0(from dataclasses-json 0.6.7)
pdm.termui:   Adding requirement packaging>=17.0(from marshmallow 3.26.1)
pdm.termui:   Adding requirement charset-normalizer<4,>=2(from requests 2.32.3)
pdm.termui:   Adding requirement idna<4,>=2.5(from requests 2.32.3)
pdm.termui:   Adding requirement urllib3<3,>=1.21.1(from requests 2.32.3)
pdm.termui:   Adding requirement certifi>=2017.4.17(from requests 2.32.3)
pdm.termui:   Adding requirement mypy-extensions>=0.3.0(from typing-inspect 0.9.0)
pdm.termui:   Adding requirement typing-extensions>=3.7.4(from typing-inspect 0.9.0)
pdm.termui:   Adding requirement MarkupSafe>=2.0(from Jinja2 3.1.5)
pdm.termui: ======== Resolution Result ========
pdm.termui:                      python None
pdm.termui:              py-beta-common 1.26.1
pdm.termui:                   hatch-vcs 0.4.0
pdm.termui:                   hatchling 1.27.0
pdm.termui:                    cerberus 1.3.7
pdm.termui:                  jsonschema 4.23.0
pdm.termui:                       attrs 25.1.0
pdm.termui:   jsonschema-specifications 2024.10.1
pdm.termui:                 referencing 0.36.2
pdm.termui:                     rpds-py 0.22.3
pdm.termui:                       numpy 2.2.3
pdm.termui:                   packaging 24.2
pdm.termui:                    pathspec 0.12.1
pdm.termui:                      pluggy 1.5.0
pdm.termui:                    pydantic 2.10.6
pdm.termui:               pydantic-core 2.27.2
pdm.termui:           typing-extensions 4.12.2
pdm.termui:             annotated-types 0.7.0
pdm.termui:              setuptools-scm 8.1.0
pdm.termui:                        toml 0.10.2
pdm.termui:      concurrent-log-handler 0.9.25
pdm.termui:                 portalocker 3.1.1
pdm.termui:                 deprecation 2.1.0
pdm.termui:                      fsspec 2025.2.0
pdm.termui:      json-schema-for-humans 1.3.4
pdm.termui:                       click 8.1.8
pdm.termui:            dataclasses-json 0.6.7
pdm.termui:                   markdown2 2.5.3
pdm.termui:                 marshmallow 3.26.1
pdm.termui:                    pygments 2.19.1
pdm.termui:                      pyyaml 6.0.2
pdm.termui:                    requests 2.32.3
pdm.termui:          charset-normalizer 3.4.1
pdm.termui:                        idna 3.10
pdm.termui:              typing-inspect 0.9.0
pdm.termui:                     urllib3 2.3.0
pdm.termui:                     certifi 2025.1.31
pdm.termui:                      jinja2 3.1.5
pdm.termui:                  markupsafe 3.0.2
pdm.termui:             mypy-extensions 1.0.0
pdm.termui:                        pytz 2025.1
pdm.termui:                  setuptools 75.8.0
pdm.termui:           trove-classifiers 2025.2.18.16
pdm.termui: Fetching hashes for typing-extensions@4.12.2
pdm.termui: Fetching hashes for jsonschema@4.23.0
pdm.termui: Fetching hashes for annotated-types@0.7.0
pdm.termui: Fetching hashes for portalocker@3.1.1
double free or corruption (!prev)
/usr/bin/bash: line 282:   190 Aborted                 (core dumped) pdm sync --no-editable -v