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DeltaGroupNJUPT / Vina-GPU

A heterogeneous OpenCL implementation of AutoDock Vina
Apache License 2.0
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Segmentation fault (core dumped) #5

Closed ZeroDesigner closed 2 years ago

ZeroDesigner commented 2 years ago

When I install the software ,I meet the problem

Reading input ... done.
Setting up the scoring function ... done.
Analyzing the binding site ... done.
Using random seed: -181661601

Platform: NVIDIA CUDA
Platform 0 device name:Tesla V100-SXM2-16GB

Platform 0 global memory size:16.945512 GB

Platform 0 local memory size:49.152000 KB

Search depth is set to 5
Segmentation fault (core dumped)

Have you tested your program in the A100 (Ampere Architecture) + Linux ?If did ,could you tell me the version of CUDA, GCC , boost, OS .

debanjansen48 commented 2 years ago

################################################################

If you used Vina-GPU in your work, please cite:

Shidi, Tang, Chen Ruiqi, Lin Mengru, Lin Qingde,

Zhu Yanxiang, Wu Jiansheng, Hu Haifeng, and Ling Ming.

Accelerating AutoDock VINA with GPUs. ChemRxiv (2021).Print.

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

#################################################################

Reading input ... done. Setting up the scoring function ... done. Analyzing the binding site ... done. Using random seed: -1748224053 Segmentation fault (core dumped)

ZeroDesigner commented 2 years ago

################################################################

If you used Vina-GPU in your work, please cite:

Shidi, Tang, Chen Ruiqi, Lin Mengru, Lin Qingde, # #Zhu Yanxiang, Wu Jiansheng, Hu Haifeng, and Ling Ming. # #Accelerating AutoDock VINA with GPUs. ChemRxiv (2021).Print.

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

#################################################################

Reading input ... done. Setting up the scoring function ... done. Analyzing the binding site ... done. Using random seed: -1748224053 Segmentation fault (core dumped)

... What do you want to tell ?

debanjansen48 commented 2 years ago

When I run the tutorial file for testing it returned above error. Segmentation error. Only ./Vina-gpu working. If ./Vina-gpu --config file_name.txt returns segmentation fault erroe

sameer73 commented 2 years ago

same error im also getting, did you find solution?

Glinttsd commented 2 years ago

Hi, Vina-GPU has been tested on the 3090 (the same Ampere architecture with A100) + linux (ubuntu 21.04), GCC version: 10.3.0, CUDA version: 11.5, BOOST version: 1.77.0

Thank you for your feedback, we've upgraded our code, and provided more error information during the running. Please check out the new commits, hope these work : )

debanjansen48 commented 2 years ago

Downloaded the new version and able to compile it. Still return same error

./Vina-GPU --config 2bm2_config.txt ################################################################# # If you used Vina-GPU in your work, please cite: # #Shidi, Tang, Chen Ruiqi, Lin Mengru, Lin Qingde, # #Zhu Yanxiang, Wu Jiansheng, Hu Haifeng, and Ling Ming. # #Accelerating AutoDock VINA with GPUs. ChemRxiv (2021).Print. # # 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 # #################################################################

Reading input ... done. Setting up the scoring function ... done. Analyzing the binding site ... done. Using random seed: -1098921832 Segmentation fault (core dumped)

Glinttsd commented 2 years ago

This might be caused by a stack overflow, check your stack size by ulimit -s and try to change the stack size to 8MB (or large) by ulimit -s 8192

debanjansen48 commented 2 years ago

FL-MC$ ulimit -s unlimited

debanjansen48 commented 2 years ago

after using ulimit -s 8192 it returns following

Reading input ... done. Setting up the scoring function ... done. Analyzing the binding site ... done. Using random seed: -788124577

Platform: NVIDIA CUDA Device: NVIDIA GeForce RTX 2070 SUPER

Build kernels from sourceError: failed to open file : ./OpenCL/src/kernels/code_head.cppError: failed to open file : ./OpenCL/src/kernels/mutate_conf.cppError: failed to open file : ./OpenCL/src/kernels/matrix.cppError: failed to open file : ./OpenCL/src/kernels/quasi_newton.cppError: failed to open file Segmentation fault (core dumped)

Glinttsd commented 2 years ago

You should make sure that the binary file Vina-GPU is in the ./Vina-GPU dir which includes ./OpenCL dir if you compiled it with make source command

debanjansen48 commented 2 years ago

Yes it works now.... Reading input ... done. Setting up the scoring function ... done. Analyzing the binding site ... done. Using random seed: 1716094900

Platform: NVIDIA CUDA Device: NVIDIA GeForce RTX 2070 SUPER

Build kernels from source OpenCL version: 3.0 Search depth is set to 6 Perform docking|================done=================| GPU monte carlo runtime: 1.721 s Refining results ... done.

mode | affinity | dist from best mode | (kcal/mol) | rmsd l.b.| rmsd u.b. -----+------------+----------+---------- 1 -8.8 0.000 0.000 2 -8.4 4.052 6.595 3 -8.3 1.762 2.483 4 -8.0 4.602 7.499 5 -8.0 2.704 3.624 6 -7.9 5.740 8.929 7 -7.8 4.751 6.904 8 -7.8 2.353 5.154 9 -7.8 2.975 4.039 Writing output ... done. Vina-GPU total runtime: 28.161 s

Plz consider few quarries from my end

  1. How to setup Virtual screening of a ultra large chemical libery?
  2. Covalent docking and ZN-protein docking based virtual screening possible?
Glinttsd commented 2 years ago

After your first run, you should see the Kernel2_Opt.bin file in the dir. Type make clean and make, you can use the boosted Vina-GPU for your docking, all you need are the Vina-GPU and Kernel2_Opt.bin binary file (See README for more information) Answers to your inquiries:

  1. virtual screening with Vina-GPU can be performed by script (shell, python etc.) for now, but we are working on an integrated availability to perform virtual screening on our GUI
  2. we have not tested covalent docking and ZN-protein docking yet, we suggest to give it a try
debanjansen48 commented 2 years ago

prepared one script, can I implement gnu parallel?? I will be grateful if you share your email id.

Glinttsd commented 2 years ago

gnu parallel might not be working if you have only one GPU card my email: 1020173019@njupt.edu.cn