You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Hi,
I have compiled from the sources the latest version of AutoDock-GPU on the Leonardo cluster.
I have compiled two versions.
The first with DEVICE= CUDA and NUMWI=256 and the second with DEVICE=OCLGPU and NUMWI=256.
I have used the following commands:
module load cuda
module load python
and
module list returns:
Currently Loaded Modulefiles:
Key:
default-version
Then
export GPU_INCLUDE_PATH=/leonardo/prod/opt/compilers/cuda/11.8/none/include
export GPU_LIBRARY_PATH=/leonardo/prod/opt/compilers/cuda/11.8/none/lib64
make DEVICE= ............................
If I run both the executables without any arguments there is no problem.
I have made a test with only one ligand with the compiled versions and I receive errors.
First I use prepare_gpf4.py and ADFR's autogrid4 and then the AutoDock executables.
For the CUDA version I run:
$ python3 test_ad4gpu.py
sh: line 1: 3637611 Aborted (core dumped) /leonardo/home/userexternal/slemme00/sources/AutoDock-GPU/bin_256wi/autodock_gpu_256wi -x 0 --ffile receptor.maps.fld --lfile DB16260.pdbqt --nrun 100 -N ./docking_res/DB16260.pdbqt_docking_res --gbest 1 > ./docking_res/DB16260.pdbqt_docking_res.log 2>&1
$ less docking_res/DB16260.pdbqt_docking_res.log
autodock_gpu_256wi: ./host/src/performdocking.cpp:128: void setup_gpu_for_docking(GpuData&, GpuTempData&): Assertion `0' failed.
I also have used previous python script with slurm directives and 40 ligands but I receive the same problems.
For the OCLGPU version I run:
$ python3 test_ad4gpu_ocl.py
$ less docking_res_ocl/DB16260.pdbqt_docking_res.log
AutoDock-GPU version: v1.5.3-54-g41083c5e1224d54ad043b62ca53f6618d5e8325d-dirty
Running 1 docking calculation
Kernel source used for development: ./device/calcenergy.cl
Kernel string used for building: ./host/inc/stringify.h
Kernel compilation flags: -I ./device -I ./common -DN256WI -cl-mad-enable
Error: clGetPlatformIDs(): -1001
For the system I use at login I have:
Atos Bull Sequana XH21355 "Da Vinci" Blade -
Red Hat Enterprise Linux 8.6 (Ootpa)
3456 compute nodes with:
- 32 cores Ice Lake at 2.60 GHz
- 4 x NVIDIA Ampere A100 GPUs, 64GB
- 512 GB RAM
@xavgit The Cuda runtime error should get resolved compiling with TARGETS="80" (plus other desired compute capabilities if there are other architectures). The OpenCL error you are seeing usually means the OpenCL platform isn't registered (installed) on the system.
Hi,
I have compiled from the sources the latest version of AutoDock-GPU on the Leonardo cluster.
I have compiled two versions.
The first with DEVICE= CUDA and NUMWI=256 and the second with DEVICE=OCLGPU and NUMWI=256.
I have used the following commands:
module load cuda
module load python
and
module list returns:
Currently Loaded Modulefiles:
Key:
default-version
Then
export GPU_INCLUDE_PATH=/leonardo/prod/opt/compilers/cuda/11.8/none/include
export GPU_LIBRARY_PATH=/leonardo/prod/opt/compilers/cuda/11.8/none/lib64
make DEVICE= ............................
If I run both the executables without any arguments there is no problem.
I have made a test with only one ligand with the compiled versions and I receive errors.
First I use prepare_gpf4.py and ADFR's autogrid4 and then the AutoDock executables.
For the CUDA version I run:
$ python3 test_ad4gpu.py
sh: line 1: 3637611 Aborted (core dumped) /leonardo/home/userexternal/slemme00/sources/AutoDock-GPU/bin_256wi/autodock_gpu_256wi -x 0 --ffile receptor.maps.fld --lfile DB16260.pdbqt --nrun 100 -N ./docking_res/DB16260.pdbqt_docking_res --gbest 1 > ./docking_res/DB16260.pdbqt_docking_res.log 2>&1
$ less docking_res/DB16260.pdbqt_docking_res.log
autodock_gpu_256wi: ./host/src/performdocking.cpp:128: void setup_gpu_for_docking(GpuData&, GpuTempData&): Assertion `0' failed.
I also have used previous python script with slurm directives and 40 ligands but I receive the same problems.
For the OCLGPU version I run:
$ python3 test_ad4gpu_ocl.py
$ less docking_res_ocl/DB16260.pdbqt_docking_res.log
AutoDock-GPU version: v1.5.3-54-g41083c5e1224d54ad043b62ca53f6618d5e8325d-dirty
Running 1 docking calculation
Kernel source used for development: ./device/calcenergy.cl
Kernel string used for building: ./host/inc/stringify.h
Kernel compilation flags: -I ./device -I ./common -DN256WI -cl-mad-enable
Error: clGetPlatformIDs(): -1001
For the system I use at login I have:
Atos Bull Sequana XH21355 "Da Vinci" Blade -
Red Hat Enterprise Linux 8.6 (Ootpa)
3456 compute nodes with:
- 32 cores Ice Lake at 2.60 GHz
- 4 x NVIDIA Ampere A100 GPUs, 64GB
- 512 GB RAM
Internal Network: Nvidia Mellanox HDR DragonFly++
SLURM 22.05.7
test_ad4gpu.py
import os
os.system( '/leonardo/home/userexternal/slemme00/sources/AutoDock-GPU/bin_256wi/autodock_gpu_256wi -x 0 --ffile receptor.maps.fld --lfile ' + 'DB16260.pdbqt' + ' --nrun 100 -N ' + './docking_res/' + 'DB16260.pdbqt' + '_docking_res --gbest 1 > ./docking_res/' + 'DB16260.pdbqt' + '_docking_res.log 2>&1' )
test_ad4gpu_ocl.py
import os
os.system( '/leonardo/home/userexternal/slemme00/sources/AutoDock-GPU/bin_oclgpu_256/autodock_gpu_256wi -x 0 --ffile receptor.maps.fld --lfile ' + 'DB16260.pdbqt' + ' --nrun 100 -N ' + './docking_res_ocl/' + 'DB16260.pdbqt' + '_docking_res --gbest 1 > ./docking_res_ocl/' + 'DB16260.pdbqt' + '_docking_res.log 2>&1' )
The previous python scripts were modified from a working code on a PC with only one RTX 2080Ti.
What I can do?
Thanks.
Saverio
The text was updated successfully, but these errors were encountered: