Inquiry Regarding Performance Improvement with --local_only Option (Test Results and System Information Included)

[jslee-hits]

Hello,

I have conducted a test using the files provided in the Unidock GitHub test directory. The details are as follows:

Receptor File: 1a30_protein.pdbqt
Ligand File: 1a30_ligand.sdf
→ The path for this ligand file is repeated 10,000 times in the test_sdfs.txt file.

Test Environment

• Operating System: Red Hat Enterprise Linux 9.3 (Plow) (Output from cat /etc/os-release provided)
• CPU: AMD EPYC 7R32 (x86_64) Total cores: 4 (2 threads per core) (Output from lscpu provided)
• Memory: 15Gi total (Output from free -h provided)
• GPU: NVIDIA A10G Driver Version: 535.154.05, CUDA Version: 12.2 (Output from nvidia-smi provided)

Test Details and Execution Commands

Two modes were tested. In both cases, the box size is fixed at 22.50 × 22.50 × 22.50 and the center coordinates are (8.73, 25.62, 4.68).

1. Normal Mode (without --local_only option)

• Execution command:
  unidock --receptor 1a30_protein.pdbqt --ligand_index test_sdfs.txt --center_x 8.73 --center_y 25.62 --center_z 4.68 --size_x 22.50 --size_y 22.50 --size_z 22.50 --seed 1 --num_modes 1 --search_mode fast --verbosity 0 --dir /tmp/result_normal/sdfs
• Total Execution Time: Approximately 368.36 seconds

2. Local Mode (with --local_only option)

• Execution command:
  unidock --receptor 1a30_protein.pdbqt --ligand_index test_sdfs.txt --center_x 8.73 --center_y 25.62 --center_z 4.68 --size_x 22.50 --size_y 22.50 --size_z 22.50 --seed 1 --num_modes 1 --search_mode fast --verbosity 0 --dir /tmp/result_local/sdfs --autobox --local_only
• Total Execution Time: Approximately 252.40 seconds

This shows an improvement of about 115.96 seconds (roughly 31.5%) when using the --local_only option.

Inquiry

Could you please confirm if this level of performance improvement is within the expected range? Additionally, any suggestions for further optimizations or adjustments to my test setup would be greatly appreciated.

Additionally, I would like to ask whether the requirement to explicitly specify all size parameters (i.e., size_x, size_y, and size_z) when using the --autobox option is intended behavior, or if there are plans to simplify this in the future.

Thank you.