[BUG] : undefined symbol: `EVP_PKEY_base_id` (in `mgclient.cpython-39-x86_64-linux-gnu.so`)

[Tim-K-DFW]

Memgraph version

v2.11.0

Environment

• Linux 20.04 LTS,
• conda with pip, clean environment with the only thing installed being gqlalchemy (using pip install gqlalchemy)
• memgraph running in docker (docker run --name memgraph -p 7687:7687 -p 7444:7444 -p 3000:3000 memgraph/memgraph-platform)

Describe the bug

Fail to import, see log below; same thing happens whether memgraph is running or not.

To Reproduce

import gqlalchemy

Expected behavior

To import.

Logs

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Cell In[4], line 1
----> 1 import gqlalchemy

File ~/miniconda3/envs/memgraph/lib/python3.9/site-packages/gqlalchemy/__init__.py:34
     19 from gqlalchemy.models import (  # noqa F401
     20     MemgraphConstraintExists,
     21     MemgraphConstraintUnique,
   (...)
     31     Field,
     32 )
     33 from gqlalchemy.disk_storage import SQLitePropertyDatabase  # noqa F401
---> 34 from gqlalchemy.instance_runner import (  # noqa F401
     35     DockerImage,
     36     MemgraphInstanceBinary,
     37     MemgraphInstanceDocker,
     38     wait_for_docker_container,
     39     wait_for_port,
     40 )
     41 from gqlalchemy.exceptions import GQLAlchemyError, GQLAlchemyWarning  # noqa F401
     43 from gqlalchemy.query_builders import (  # noqa F401
     44     neo4j_query_builder,
     45     memgraph_query_builder,
     46     memgraph_query_builder as query_builder,
     47 )

File ~/miniconda3/envs/memgraph/lib/python3.9/site-packages/gqlalchemy/instance_runner.py:35
     27 import psutil
     29 from gqlalchemy.exceptions import (
     30     GQLAlchemyWaitForConnectionError,
     31     GQLAlchemyWaitForDockerError,
     32     GQLAlchemyWaitForPortError,
     33     raise_if_not_imported,
     34 )
---> 35 from gqlalchemy.vendors.memgraph import Memgraph
     38 MEMGRAPH_DEFAULT_BINARY_PATH = "/usr/lib/memgraph/memgraph"
     39 MEMGRAPH_DEFAULT_PORT = 7687

File ~/miniconda3/envs/memgraph/lib/python3.9/site-packages/gqlalchemy/vendors/memgraph.py:19
     16 import sqlite3
     17 from typing import List, Optional, Union
---> 19 from gqlalchemy.connection import Connection, MemgraphConnection
     20 from gqlalchemy.disk_storage import OnDiskPropertyDatabase
     21 from gqlalchemy.exceptions import (
     22     GQLAlchemyError,
     23     GQLAlchemyFileNotFoundError,
     24     GQLAlchemyOnDiskPropertyDatabaseNotDefinedError,
     25     GQLAlchemyUniquenessConstraintError,
     26 )

File ~/miniconda3/envs/memgraph/lib/python3.9/site-packages/gqlalchemy/connection.py:18
     15 from abc import ABC, abstractmethod
     16 from typing import Any, Dict, Iterator, Optional
---> 18 import mgclient
     19 from neo4j import GraphDatabase
     20 from neo4j.graph import Node as Neo4jNode

ImportError: /home/t/miniconda3/envs/memgraph/lib/python3.9/site-packages/mgclient.cpython-39-x86_64-linux-gnu.so: undefined symbol: EVP_PKEY_base_id

Additional context Add any other context about the problem here.

[katarinasupe]

Hi @Tim-K-DFW, can you try pip install GQLAlchemy==1.4.1 until we detect if this is a bug related to latest release?
Btw as far as I can see, you're using Python 3.9?

[Tim-K-DFW]

Hi Katarina, thank you for the quick response!

• Same result with 1.4.1
• Yes, python 3.9.16.

[katarinasupe]

Did you experience any issues when installing with pip?
Also when you installed can you confirm installation is okay by running pip show gqlalchemy and provide output?
P.S. I see you are using Linux OS but is this a virtual machine or not? Wondering about your device architecture, is it ARM or AMD?

[Tim-K-DFW]

1. The only issue first time was pip complaining of cmake missing, so I installed that, and then gqlalchemy installed with no problems.

2. pip show gqlalchemy gives:

Python 3.9.16
(memgraph) t@DESKTOP-KHJBONB:~/ro5_wsl/memgraph$ pip show gqlalchemy
Name: gqlalchemy
Version: 1.4.1
Summary: GQLAlchemy is a library developed to assist with writing and running queries in Memgraph.
Home-page: https://github.com/memgraph/gqlalchemy
Author: Bruno Sacaric
Author-email: bruno.sacaric@memgraph.com
License: Apache-2.0
Location: /home/t/miniconda3/envs/memgraph/lib/python3.9/site-packages
Requires: adlfs, dacite, docker, neo4j, networkx, numpy, psutil, pydantic, pymgclient
Required-by:
(memgraph) t@DESKTOP-KHJBONB:~/ro5_wsl/memgraph$

3. This is WSL2 on a Windows 10 machine, standard Intel CPU (AMD architecture as I understand).

[katarinasupe]

Can you remove that installation, install all necessary prerequisites for GQLAlchemy (that is, pymgclient) and then try reinstalling it?

[Tim-K-DFW]

I did:

• new conda env with python 3.9.16
• sudo apt install python3-dev cmake make gcc g++ libssl-dev (from your link)
• pip3 install --user pymgclient (from your link)
• pip install GQLAlchemy==1.4.1

Same result:

$ python
Python 3.9.16 (main, May 15 2023, 23:46:34)
[GCC 11.2.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import gqlalchemy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/t/miniconda3/envs/memgraph/lib/python3.9/site-packages/gqlalchemy/__init__.py", line 34, in <module>
    from gqlalchemy.instance_runner import (  # noqa F401
  File "/home/t/miniconda3/envs/memgraph/lib/python3.9/site-packages/gqlalchemy/instance_runner.py", line 31, in <module>
    from gqlalchemy.vendors.memgraph import Memgraph
  File "/home/t/miniconda3/envs/memgraph/lib/python3.9/site-packages/gqlalchemy/vendors/memgraph.py", line 19, in <module>
    from gqlalchemy.connection import Connection, MemgraphConnection
  File "/home/t/miniconda3/envs/memgraph/lib/python3.9/site-packages/gqlalchemy/connection.py", line 18, in <module>
    import mgclient
ImportError: /home/t/.local/lib/python3.9/site-packages/mgclient.cpython-39-x86_64-linux-gnu.so: undefined symbol: EVP_PKEY_base_id
>>>

[katarinasupe]

I think that might be related to the mismatch of the OpenSSL version. Can you tell me which version you have?

[Tim-K-DFW]

[katarinasupe]

Are you sure that conda env uses that OpenSSL by default? This reminds me of the closed issue on the pymgclient repository.

[Tim-K-DFW]

Do you happen to know how I can check this?

[Tim-K-DFW]

(I mean, pip show openssl in this environment doesn't show any versions of openssl installed).

[katarinasupe]

Can you try installing the pymgclient prerequisites in conda env with pip? The steps in conda env would be:

pip3 install python3-dev cmake make gcc g++ libssl-dev
pip3 install pymgclient
pip3 install gqlalchemy==1.4.1

[Tim-K-DFW]

ERROR: Invalid requirement: 'g++' 😬 I googled a few solution options but not sure what exactly you had in mind.