ERROR 2002 (HY000): Can't connect to local MySQL server

[tomarovsky]

Hello,

I'm trying to run d-Structman on a compute server. The installation via Docker goes through without any problems, but I get the following error on startup:

$ docker exec -it test structman -i structman/input_data/10_proteins_few_hits.smlf
Using structman_data from : /usr/structman_library/sources/structman/lib
Using 79 core(s), verbosity level: 1
Using following config file: /structman/resources/config.txt
Processing file:  /structman/input_data/10_proteins_few_hits.smlf
Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/structman/lib/database/database.py", line 930, in getSessionId
    cursor.execute(sql)
AttributeError: 'NoneType' object has no attribute 'execute'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/bin/structman", line 8, in <module>
    sys.exit(structman_cli())
  File "/usr/local/lib/python3.8/dist-packages/structman/structman_main.py", line 1155, in structman_cli
    main(infiles, outfolder, config)
  File "/usr/local/lib/python3.8/dist-packages/structman/structman_main.py", line 490, in main
    session_id = database.getSessionId(infile, config)
  File "/usr/local/lib/python3.8/dist-packages/structman/lib/database/database.py", line 934, in getSessionId
    raise NameError("Error in getSessionId: %s" % sql)
NameError: Error in getSessionId: SELECT Session_Id FROM Session WHERE Input_File = '/structman/input_data/10_proteins_few_hits.smlf' AND Checksum = 982454239;

Also, I tried to perform a simple run as suggested in the tutorial, but got an error as well:

$ sudo docker exec -it test structman -i Q9Q288
Using structman_data from : /usr/structman_library/sources/structman/lib
Using 79 core(s), verbosity level: 1
Using following config file: /structman/resources/config.txt
Traceback (most recent call last):
  File "/usr/local/bin/structman", line 8, in <module>
    sys.exit(structman_cli())
  File "/usr/local/lib/python3.8/dist-packages/structman/structman_main.py", line 1155, in structman_cli
    main(infiles, outfolder, config)
  File "/usr/local/lib/python3.8/dist-packages/structman/structman_main.py", line 506, in main
    if session_id is None:
UnboundLocalError: local variable 'session_id' referenced before assignment

I checked the container logs (docker-compose.logs) and found the following error (lines 137 and 274):

test  | ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)

I guess the error is caused by incorrect work of mysql-server and I tried to fix it using the suggested solutions (https://stackoverflow.com/questions/11657829/error-2002-hy000-cant-connect-to-local-mysql-server-through-socket-var-run), but it didn't help. I also tried to perform an installation using a Singularity container, but found the same problem.

Specification of my machine:
Operating System: Rocky Linux 8.5 (Green Obsidian)
Kernel: Linux 4.18.0-348.12.2.el8_5.x86_64
Architecture: x86-64
Docker version 20.10.12, build e91ed57

Do you know what the problem could be? Could you help me with that?