Segemantaion Fault (core dumped)
Closed this issue · 3 comments
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 #
# #
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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 ?
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)
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.
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.