Segemantaion Fault (core dumped)

[vaghasiyautsav]

vaxine@VaxineGPU3:~/BioInfoSoft/Vina-GPU-2.1-main/AutoDock-Vina-GPU-2.1$ ./AutoDock-Vina-GPU-2-1 --config ./input_file_example/2bm2_config.txt
#################################################################
# If you used AutoDockVina-GPU 2.1 in your work, please cite:   #
#                                                               #
# Ding, Ji, et al. Vina-GPU 2.0: Further Accelerating AutoDock  #
# Vina and Its Derivatives with Graphics Processing Units.      #
# Journal of Chemical Information and Modeling (2023).          #
#                                                               #
# DOI https://doi.org/10.1021/acs.jcim.2c01504                  #
#                                                               #
# Shidi, Tang, Chen Ruiqi, Lin Mengru, Lin Qingde,              #
# Zhu Yanxiang, Wu Jiansheng, Hu Haifeng, and Ling Ming.        #
# Accelerating AutoDock Vina with GPUs.                         #
# Molecules 27.9 (2022): 3041.                                  #
#                                                               #
# DOI https://doi.org/10.3390/molecules27093041                 #
#                                                               #
# And also the origin AutoDock Vina paper:                      #
# O. Trott, A. J. Olson,                                        #
# AutoDock Vina: improving the speed and accuracy of docking    #
# with a new scoring function, efficient optimization and       #
# multithreading, Journal of Computational Chemistry 31 (2010)  #
# 455-461                                                       #
#                                                               #
# DOI 10.1002/jcc.21334                                         #
#                                                               #
#################################################################

Using virtual sreening mode

Output will be in the directory ./test_out
Reading input ... done.
Setting up the scoring function ... done.
Using heuristic search_depth
Analyzing the binding site ... done.
GPU Platform: NVIDIA CUDA
GPU Device: NVIDIA GeForce GTX 1650
Using random seed: 2071502842

Build kernel 1 from source
OpenCL version: 2.0
1 warning generated.

Build kernel 2 from source
OpenCL version: 2.0
Segmentation fault (core dumped)

getting this error while initial example run. Can anybody help here ?

[OH-AU]

Running into same (looking) issue but for QuickVina2-GPU-2.1 (using OpenCL 3.0) on an Nvidia Tesla P100 and H100. cuda driver: 535.104.05 cuda: 12.2.2 gcc: 12.3 OS: SLES SP3 (P100) and SP4 (H100)

I then attempted to run AutoDock-Vina-GPU-2.1 since that's what this ticket is about and ran into the same error:

Using virtual sreening mode

Output will be in the directory ./test_out Reading input ... done. Setting up the scoring function ... done. Using heuristic search_depth Analyzing the binding site ... done. GPU Platform: NVIDIA CUDA GPU Device: NVIDIA H100 80GB HBM3 Using random seed: -1919286168

Build kernel 1 from source OpenCL version: 3.0

Build kernel 2 from source OpenCL version: 3.0 Segmentation fault (core dumped)

[Glinttsd]

Hi, many issues may lead to Segmentation fault. You can refer to our previous site here to find any solution. You can also try to set a smaller thread or update your GPU driver to see if it works.

[vaghasiyautsav]

Hi Sir,

The issue was with config file as default address was yours file location. I edited with this and it worked well.

opencl_binary_path = /home/vaxine/BioInfoSoft/Vina-GPU-2.1-main/AutoDock-Vina-GPU-2.1

Thank you for the help. :) Looking forward for great advancement on Vina-GPU.