Comments (6)
Hi,
Please make sure more than 12 GB memory is available. Or you can try --max_gpu_memory
option. If it doesn't work, I'm afraid Titan-V GPU is not supported so far. Please use GPUs with larger global memory such as T4 and V100.
from uni-dock.
Hi,
I have same a problem when I run the example code which is described unidock folder.
My gpu enviromnent is Tesla V100 (16G)
And out put is below. I tried to add --max_gpu_memory option but nothing is improved.
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: ./indata/mmp13.pdbqt
Grid center: X -6.93 Y 26.58 Z 54.14
Grid size : X 22 Y 22 Z 22
Grid space : 0.375
Exhaustiveness: 128
CPU: 0
Verbosity: 1
Computing Vina grid ... entering done
done.
exiting done
Total ligands: 4
Avaliable Memory = 15852MiB Total Memory = 16160MiB
Batch 1 size: 4
Performing docking (random seed: 5) ... Kernel running time: 1
entering done
exiting done
WARNING: Could not find any conformations completely within the search space.
WARNING: Check that it is large enough for all movable atoms, including those in the flexible side chains.
WARNING: Or could not successfully parse PDBQT input file of ligand #0
WARNING: Could not find any conformations completely within the search space.
WARNING: Check that it is large enough for all movable atoms, including those in the flexible side chains.
WARNING: Or could not successfully parse PDBQT input file of ligand #1
WARNING: Could not find any conformations completely within the search space.
WARNING: Check that it is large enough for all movable atoms, including those in the flexible side chains.
WARNING: Or could not successfully parse PDBQT input file of ligand #2
WARNING: Could not find any conformations completely within the search space.
WARNING: Check that it is large enough for all movable atoms, including those in the flexible side chains.
WARNING: Or could not successfully parse PDBQT input file of ligand #3
WARNING: Could not find any poses. No poses were written.
WARNING: Could not find any poses. No poses were written.
WARNING: Could not find any poses. No poses were written.
WARNING: Could not find any poses. No poses were written.
I'll be happy if you could give me any suggestions or comments
Thanks,
Taka
from uni-dock.
Hi @iwatobipen ,
Checking whether the main calculation process is exited normally on GPU is lacked. This will help locating the failure. We'll add it ASAP.
from uni-dock.
Hi @caic99,
Thanks for your prompt reply.
I tried following command and the calculation worked but took long time.
Thanks,
Taka
$ unidock --receptor ./indata/mmp13.pdbqt --ligand ./indata/ligands_unique/decoys1944.pdbqt --center_x -6.93 --center_y 26.58 --center_z 54.14 --size_x 22 --size_y 22 --size_z 22 --dir ./result/mmp13 --exhaustiveness 128 --max_step 20 --num_modes 9 --scoring vina --refine_step 3 --seed 5 --cpu 16
Output will be ./indata/ligands_unique/decoys1944_out.pdbqt
Scoring function : vina
Rigid receptor: ./indata/mmp13.pdbqt
Ligand: ./indata/ligands_unique/decoys1944.pdbqt
Grid center: X -6.93 Y 26.58 Z 54.14
Grid size : X 22 Y 22 Z 22
Grid space : 0.375
Exhaustiveness: 128
CPU: 16
Verbosity: 1
Computing Vina grid ... entering done
done.
exiting done
Performing docking (random seed: 5) ...
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 -8.772 0 0
2 -8.283 3.446 6.89
3 -8.215 3.859 6.28
4 -8.106 4.486 8.667
5 -8.061 3.712 8.493
6 -7.837 4.068 8.525
7 -7.836 3.738 8.755
8 -7.835 4.01 8.391
9 -7.761 2.931 7.912
from uni-dock.
Hi @iwatobipen ,
Uni-Dock features in docking numerous ligands to one pocket. If the number of ligand is not sufficient to fully utilize GPU, the overhead would be large enough affecting docking speed.
from uni-dock.
Hi @caic99
I build unidcok with DEBBUG mode and run unidock. Then I got following message.
Available Memory = 15800MiB Total Memory = 16160MiB
Batch 1 size: 1
Performing docking (random seed: 1936787721) ...
Thread 1 "unidock" hit Breakpoint 1, monte_carlo::operator() (this=0x7ffffffd0900, m_gpu=..., out_gpu=..., p_gpu=..., m_data_list_gpu=0x7ffffffe70e8, ig=..., corner1=..., corner2=..., generator=..., verbosity=1,
seed=0, bias_batch_list=...) at /home/hoge/Uni-Dock/unidock/src/cuda/monte_carlo.cu:1591
1591 kernel<<<thread / 32 + 1, 32>>>(m_cuda_gpu, ig_cuda_gpu, p_cuda_gpu, rand_molec_struc_gpu,
(cuda-gdb) next
warning: Cuda API error detected: cudaLaunchKernel returned (0x2)
Cuda API error (0x2) means OOM but my environment has V100 16GB GPUs.
I will be happy if you have any comments or suggestions to solve the issue.
Thanks,
from uni-dock.
Related Issues (20)
- 1.1.1 source release contains version string 1.1.0 HOT 1
- Error in vina score HOT 2
- typo in examples HOT 1
- missing installation instruction in unidock_tools
- How to dock
- WARNING: Could not find any conformations
- run unidock, report segmentation fault while using file index
- OOM using ad4 scoring function
- CUDA Runtime Error when using ad4 maps HOT 4
- Fail on screening test case mmp13 on version v1.1.x HOT 2
- Unidock pipeline fails to read ligand index HOT 1
- target_compile_features no known features for CXX compiler HOT 6
- Unknown order of ligands in the output HOT 2
- in ligand index, unable to find mol file, only first without others. HOT 1
- Seed doesn't seem to be working properly. HOT 3
- Cuda runtime error =
- Segmentation Fault (Core Dumped)
- v1.1.2 randomly changes its output without any valid cause HOT 1
- cmake -B build -D FETCH_BOOST=ON does not fetch boost HOT 6
- Compiling error on CUDA 11
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