CUDA Runtime Error when running Uni-Dock about uni-dock HOT 11 OPEN

Add：
root@DESKTOP-1IV2ND2:~/screening# nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2023 NVIDIA Corporation
Built on Fri_Jan__6_16:45:21_PST_2023
Cuda compilation tools, release 12.0, V12.0.140
Build cuda_12.0.r12.0/compiler.32267302_0

from uni-dock.

Hi @hotwa ,
Looks like you and @XingyuLiao in #12 are facing the same problem.
We are trying to build a WSL environment and further investigate this issue.

from uni-dock.

execute in docker images：
I use this images: nvidia/cuda:latest.
root@fa5ddca634eb:/# ./unidock --receptor ./input_file_example/2bm2_protein.pdbqt --gpu_batch ./input_file_example/2bm2_
ligand.pdbqt --search_mode balance --scoring vina --center_x 40.415 --center_y 110.986 --center_z 82.673 --size_x 25 --size_y 25 --size_z 25 --num_modes 20 --dir ./input_file_example/
Uni-Dock v0.1.0

If you used Uni-Dock in your work, please cite:

Yu, Y., Cai, C., Wang, J., Bo, Z., Zhu, Z., & Zheng, H. (2023).
Uni-Dock: GPU-Accelerated Docking Enables Ultralarge Virtual Screening.
Journal of Chemical Theory and Computation.
https://doi.org/10.1021/acs.jctc.2c01145

Tang, S., Chen, R., Lin, M., Lin, Q., Zhu, Y., Ding, J., ... & Wu, J. (2022).
Accelerating autodock vina with gpus. Molecules, 27(9), 3041.
DOI 10.3390/molecules27093041

J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force
Field, and Python Bindings, J. Chem. Inf. Model. (2021)
DOI 10.1021/acs.jcim.1c00203

O. Trott, A. J. Olson,
AutoDock Vina: improving the speed and accuracy of docking
with a new scoring function, efficient optimization and
multithreading, J. Comp. Chem. (2010)
DOI 10.1002/jcc.21334

Please refer to https://github.com/dptech-corp/Uni-Dock/ for
bug reporting, license agreements, and more information.

Scoring function : vina
Rigid receptor: ./input_file_example/2bm2_protein.pdbqt
Grid center: X 40.415 Y 110.986 Z 82.673
Grid size : X 25 Y 25 Z 25
Grid space : 0.375
Exhaustiveness: 384
CPU: 0
Verbosity: 1

Computing Vina grid ... entering done
done.
exiting done
Total ligands: 1
Avaliable Memory = 23006MiB Total Memory = 24563MiB
Batch 1 size: 1
Performing docking (random seed: -1212963753) ... CUDA error at /root/code/Uni-Dock-private/src/cuda/monte_carlo.cu:1719 code=2(cudaErrorMemoryAllocation) "cudaMallocHost(&p_data, sizeof(p_m_data_cuda_t) * MAX_P_DATA_M_DATA_SIZE)"

An error occurred: CUDA Runtime Error.

Please report bugs through the Issue Tracker on GitHub
(https://github.com/dptech-corp/Uni-Dock/issues)., so
that this problem can be resolved. The reproducibility of the
error may be vital, so please remember to include the following in
your problem report:

• the EXACT error message,
• your version of the program,
• the type of computer system you are running it on,
• all command line options,
• configuration file (if used),
• ligand file as PDBQT,
• receptor file as PDBQT,
• flexible side chains file as PDBQT (if used),
• output file as PDBQT (if any),
• input (if possible),
• random seed the program used (this is printed when the program starts).

Thank you!

from uni-dock.

I encountered an issue while using Uni-Dock for molecular docking. When I ran the command ./unidock --receptor ./input_file_example/2bm2_protein.pdbqt --gpu_batch ./input_file_example/2bm2_ligand.pdbqt --search_mode balance --scoring vina --center_x 40.415 --center_y 110.986 --center_z 82.673 --size_x 25 --size_y 25 --size_z 25 --num_modes 20 --dir ./input_file_example, the output showed "Total ligands: 1," but then I received an error message saying "ERROR: Empty ligand list."

Here is my environment information:

Operating System: Ubuntu 20.04
GPU: NVIDIA Titan V
Driver Version: 530.30.02
CUDA Version: 12.1
I have confirmed that the ligand file exists and the correct path is specified. I have tried other command and parameter combinations in the same environment, but I still encounter the same issue.

I would like to understand why this error occurs and find a solution. Any help or insights would be greatly appreciated. Thank you!

./unidock --receptor ./input_file_example/2bm2_protein.pdbqt --gpu_batch ./input_file_example/2bm2_ligand.pdbqt --search_mode balance --scoring vina --center_x 40.415 --center_y 110.986 --center_z 82.673 --size_x 25 --size_y 25 --size_z 25 --num_modes 20 --dir ./input_file_example
Uni-Dock v0.1.0

If you used Uni-Dock in your work, please cite:               
 
Yu, Y., Cai, C., Wang, J., Bo, Z., Zhu, Z., & Zheng, H. (2023). 
Uni-Dock: GPU-Accelerated Docking Enables Ultralarge Virtual Screening. 
Journal of Chemical Theory and Computation.                    
https://doi.org/10.1021/acs.jctc.2c01145                       

Tang, S., Chen, R., Lin, M., Lin, Q., Zhu, Y., Ding, J., ... & Wu, J. (2022). 
Accelerating autodock vina with gpus. Molecules, 27(9), 3041. 
DOI 10.3390/molecules27093041                                 

J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli  
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force      
Field, and Python Bindings, J. Chem. Inf. Model. (2021)       
DOI 10.1021/acs.jcim.1c00203                                  

O. Trott, A. J. Olson,                                        
AutoDock Vina: improving the speed and accuracy of docking    
with a new scoring function, efficient optimization and        
multithreading, J. Comp. Chem. (2010)                         
DOI 10.1002/jcc.21334                                         

Please refer to https://github.com/dptech-corp/Uni-Dock/ for  
bug reporting, license agreements, and more information.      

Scoring function : vina
Rigid receptor: ./input_file_example/2bm2_protein.pdbqt
Grid center: X 40.415 Y 110.986 Z 82.673
Grid size  : X 25 Y 25 Z 25
Grid space : 0.375
Exhaustiveness: 384
CPU: 0
Verbosity: 1

Computing Vina grid ... entering done
done.
exiting done
Total ligands: 1
Avaliable Memory = 4450MiB   Total Memory = 12054MiB
Batch 1 size: 0
ERROR: Empty ligand list.

from uni-dock.

Hi @hotwa ,
Sorry for the late reply. It seems that your GPU memory size is insufficient for Uni-Dock to launch. We are working on the compatibility on multiple GPUs.

from uni-dock.

I need at least 24GB of GPU memory for Uni-Dock to launch？

from uni-dock.

I need at least 24GB of GPU memory for Uni-Dock to launch？

@hotwa 12GB is recommended. Please see #9 (comment)

from uni-dock.

Hi @hotwa ,

I compiled Uni-Dock from source code and successfully finished the task under examples/screening_test. I use ubuntu 22.04 with WSL2, on my 3070 Ti 8GB GPU. It seems that Uni-Dock works smoothly on WSL2 systems.

You could compiling from source code and try again.

from uni-dock.

I use binary file，before. Maybe is the compiled problem.

from uni-dock.

When compiled it, I have some trouble. if unidock runing in anaconda, will be great.

from uni-dock.

When compiled it, I have some trouble. if unidock runing in anaconda, will be great.

Please try:
conda install -c https://conda.mlops.dp.tech/caic -c conda-forge unidock

from uni-dock.