Get undefined symbol: sqlite3_deserialize when running docking #151
Description
Describe the problem.
Hi. I followed the docking documentation to create docking environment and tried to run docking with parsl executor. Then I got the undefined symbol: sqlite3_trace_v2 error as mentioned in the documentation so I installed libsqlite accordingly. But then I got another error:
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/work/cse-zhousc/webs/taps/run/__main__.py", line 3, in <module>
from taps.run.main import main
File "/work/cse-zhousc/webs/taps/run/main.py", line 17, in <module>
from taps.run.config import Config
File "/work/cse-zhousc/webs/taps/run/config.py", line 25, in <module>
from taps.engine import EngineConfig
File "/work/cse-zhousc/webs/taps/engine/__init__.py", line 3, in <module>
from taps.engine._config import EngineConfig
File "/work/cse-zhousc/webs/taps/engine/_config.py", line 11, in <module>
from taps.executor import ExecutorConfig
File "/work/cse-zhousc/webs/taps/executor/__init__.py", line 7, in <module>
from taps.executor.globus import GlobusComputeConfig
File "/work/cse-zhousc/webs/taps/executor/globus.py", line 5, in <module>
import globus_compute_sdk
File "/work/cse-zhousc/miniconda3/envs/taps-docking/lib/python3.11/site-packages/globus_compute_sdk/__init__.py", line 10, in <module>
from globus_compute_sdk.sdk.client import Client
File "/work/cse-zhousc/miniconda3/envs/taps-docking/lib/python3.11/site-packages/globus_compute_sdk/sdk/client.py", line 28, in <module>
from .login_manager import LoginManager, LoginManagerProtocol, requires_login
File "/work/cse-zhousc/miniconda3/envs/taps-docking/lib/python3.11/site-packages/globus_compute_sdk/sdk/login_manager/__init__.py", line 1, in <module>
from .authorizer_login_manager import AuthorizerLoginManager
File "/work/cse-zhousc/miniconda3/envs/taps-docking/lib/python3.11/site-packages/globus_compute_sdk/sdk/login_manager/authorizer_login_manager.py", line 6, in <module>
from globus_compute_sdk.sdk.login_manager.manager import LoginManager
File "/work/cse-zhousc/miniconda3/envs/taps-docking/lib/python3.11/site-packages/globus_compute_sdk/sdk/login_manager/manager.py", line 16, in <module>
from .tokenstore import get_token_storage_adapter
File "/work/cse-zhousc/miniconda3/envs/taps-docking/lib/python3.11/site-packages/globus_compute_sdk/sdk/login_manager/tokenstore.py", line 6, in <module>
from globus_sdk.tokenstorage import SQLiteAdapter
File "/work/cse-zhousc/miniconda3/envs/taps-docking/lib/python3.11/site-packages/globus_sdk/tokenstorage/__init__.py", line 4, in <module>
from globus_sdk.tokenstorage.sqlite_adapter import SQLiteAdapter
File "/work/cse-zhousc/miniconda3/envs/taps-docking/lib/python3.11/site-packages/globus_sdk/tokenstorage/sqlite_adapter.py", line 5, in <module>
import sqlite3
File "/work/cse-zhousc/miniconda3/envs/taps-docking/lib/python3.11/sqlite3/__init__.py", line 57, in <module>
from sqlite3.dbapi2 import *
File "/work/cse-zhousc/miniconda3/envs/taps-docking/lib/python3.11/sqlite3/dbapi2.py", line 27, in <module>
from _sqlite3 import *
ImportError: /work/cse-zhousc/miniconda3/envs/taps-docking/lib/python3.11/lib-dynload/_sqlite3.cpython-311-x86_64-linux-gnu.so: undefined symbol: sqlite3_deserializeI searched solution for this error and found this, so I tried to remove these files:
~/miniconda3/envs/taps-docking/include/sqlite3ext.h
~/miniconda3/envs/taps-docking/include/sqlite3.h
~/miniconda3/envs/taps-docking/lib/libsqlite3.a
~/miniconda3/envs/taps-docking/lib/libsqlite3.so
~/miniconda3/envs/taps-docking/lib/libsqlite3.so.0
~/miniconda3/envs/taps-docking/lib/libsqlite3.so.0.8.6Then I got undefined symbol: sqlite3_trace_v2 again.
I would appreciate it if you could help me to solve this.
How did you install TaPS?
$ git clone [email protected]:ClaudiaCumberbatch/webs.git
Then switch to the for_PR branch which is synchronized with the newest version of taps in this repo.
Then followed the docking documentation to configure the environment.TaPS Version
Python Version
3.11
OS and Platform
x86 linux