search

DeltaGroupNJUPT / Vina-GPU-2.1

Vina-GPU 2.1, an improved docking toolkit for faster speed and higher accuracy on the virtual screening
Apache License 2.0
42 stars 12 forks source link

'Err-4:CL_MEM_OBJECT_ALLOCATION_FAILURE' When test D-LARGE format with AutoDock-Vina-GPU-2.1 #34

Open marramWang opened 3 weeks ago

marramWang commented 3 weeks ago

Thanks for your great efforts on enlarging the atom num and size of grid boxes. However I encountered errors

' Err-4:CL_MEM_OBJECT_ALLOCATION_FAILURE'

when using AutoDock-GPU-Vina-2.1 run the test data in format of D-LARGE format (MAKEFILE).The same test data works well in the D-SMALL format. this.

Full Running page:

{CITE Infomation} 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 RTX 3080 Using random seed: -1345958431 Err-4:CL_MEM_OBJECT_ALLOCATION_FAILURE

my revised part in Makefile Listed below:

WORK_DIR=/home/wr/softwares/Vina-GPU-2.1-main/AutoDock-Vina-GPU-2.1 BOOST_LIB_PATH=/home/wr/softwares/boost_1_77_0 OPENCL_LIB_PATH=/usr/local/cuda OPENCL_VERSION=-DOPENCL_3_0 GPU_PLATFORM=-DNVIDIA_PLATFORM DOCKING_BOX_SIZE=-DLARGE_BOX

I unlimited the Stack size as 'unlimited', actually, 8192,81920 and 100000 have been tried as well but still,the same error before. ulimit -a

core file size (blocks, -c) unlimited data seg size (kbytes, -d) unlimited scheduling priority (-e) 0 file size (blocks, -f) unlimited pending signals (-i) 1029981 max locked memory (kbytes, -l) 32968648 max memory size (kbytes, -m) unlimited open files (-n) 1024 pipe size (512 bytes, -p) 8 POSIX message queues (bytes, -q) 819200 real-time priority (-r) 0 stack size (kbytes, -s) unlimited cpu time (seconds, -t) unlimited max user processes (-u) 1029981 virtual memory (kbytes, -v) unlimited file locks (-x) unlimited

clinfo `Number of platforms 1 Platform Name NVIDIA CUDA Platform Vendor NVIDIA Corporation Platform Version OpenCL 3.0 CUDA 12.2.79 Platform Profile FULL_PROFILE Platform Extensions cl_khr_global_int32_base_atomics cl_khr_global_int32_extended_atomics cl_khr_local_int32_base_atomics cl_khr_local_int32_extended_atomics cl_khr_fp64 cl_khr_3d_image_writes cl_khr_byte_addressable_store cl_khr_icd cl_khr_gl_sharing cl_nv_compiler_options cl_nv_device_attribute_query cl_nv_pragma_unroll cl_nv_copy_opts cl_nv_create_buffer cl_khr_int64_base_atomics cl_khr_int64_extended_atomics cl_khr_device_uuid cl_khr_pci_bus_info cl_khr_external_semaphore cl_khr_external_memory cl_khr_external_semaphore_opaque_fd cl_khr_external_memory_opaque_fd Platform Extensions with Version cl_khr_global_int32_base_atomics 0x400000 (1.0.0) cl_khr_global_int32_extended_atomics 0x400000 (1.0.0) cl_khr_local_int32_base_atomics 0x400000 (1.0.0) cl_khr_local_int32_extended_atomics 0x400000 (1.0.0) cl_khr_fp64 0x400000 (1.0.0) cl_khr_3d_image_writes 0x400000 (1.0.0) cl_khr_byte_addressable_store 0x400000 (1.0.0) cl_khr_icd 0x400000 (1.0.0) cl_khr_gl_sharing 0x400000 (1.0.0) cl_nv_compiler_options 0x400000 (1.0.0) cl_nv_device_attribute_query 0x400000 (1.0.0) cl_nv_pragma_unroll 0x400000 (1.0.0) cl_nv_copy_opts 0x400000 (1.0.0) cl_nv_create_buffer 0x400000 (1.0.0) cl_khr_int64_base_atomics 0x400000 (1.0.0) cl_khr_int64_extended_atomics 0x400000 (1.0.0) cl_khr_device_uuid 0x400000 (1.0.0) cl_khr_pci_bus_info 0x400000 (1.0.0) cl_khr_external_semaphore 0x9000 (0.9.0) cl_khr_external_memory 0x9000 (0.9.0) cl_khr_external_semaphore_opaque_fd 0x9000 (0.9.0) cl_khr_external_memory_opaque_fd 0x9000 (0.9.0) Platform Numeric Version 0xc00000 (3.0.0) Platform Extensions function suffix NV Platform Host timer resolution 0ns

Platform Name NVIDIA CUDA Number of devices 1 Device Name NVIDIA GeForce RTX 3080 Device Vendor NVIDIA Corporation Device Vendor ID 0x10de Device Version OpenCL 3.0 CUDA Device UUID fa4cf603-d831-d614-c6b1-8ad9933a48e5 Driver UUID fa4cf603-d831-d614-c6b1-8ad9933a48e5 Valid Device LUID No Device LUID 6d69-637300000000 Device Node Mask 0 Device Numeric Version 0xc00000 (3.0.0) Driver Version 535.54.03 Device OpenCL C Version OpenCL C 1.2 Device OpenCL C all versions OpenCL C 0x400000 (1.0.0) OpenCL C 0x401000 (1.1.0) OpenCL C 0x402000 (1.2.0) OpenCL C 0xc00000 (3.0.0) Device OpenCL C features opencl_c_fp64 0xc00000 (3.0.0) opencl_c_images 0xc00000 (3.0.0) opencl_c_int64 0xc00000 (3.0.0) opencl_c_3d_image_writes 0xc00000 (3.0.0) Latest comfornace test passed v2022-10-05-00 Device Type GPU Device Topology (NV) PCI-E, 0000:73:00.0 Device Profile FULL_PROFILE Device Available Yes Compiler Available Yes Linker Available Yes Max compute units 68 Max clock frequency 1710MHz Compute Capability (NV) 8.6 Device Partition (core) Max number of sub-devices 1 Supported partition types None Supported affinity domains (n/a) Max work item dimensions 3 Max work item sizes 1024x1024x64 Max work group size 1024 Preferred work group size multiple (device) 32 Preferred work group size multiple (kernel) 32 Warp size (NV) 32 Max sub-groups per work group 0 Preferred / native vector sizes char 1 / 1 short 1 / 1 int 1 / 1 long 1 / 1 half 0 / 0 (n/a) float 1 / 1 double 1 / 1 (cl_khr_fp64) Half-precision Floating-point support (n/a) Single-precision Floating-point support (core) Denormals Yes Infinity and NANs Yes Round to nearest Yes Round to zero Yes Round to infinity Yes IEEE754-2008 fused multiply-add Yes Support is emulated in software No Correctly-rounded divide and sqrt operations Yes Double-precision Floating-point support (cl_khr_fp64) Denormals Yes Infinity and NANs Yes Round to nearest Yes Round to zero Yes Round to infinity Yes IEEE754-2008 fused multiply-add Yes Support is emulated in software No Address bits 64, Little-Endian Global memory size 10487529472 (9.767GiB) Error Correction support No Max memory allocation 2621882368 (2.442GiB) Unified memory for Host and Device No Integrated memory (NV) No Shared Virtual Memory (SVM) capabilities (core) Coarse-grained buffer sharing Yes Fine-grained buffer sharing No Fine-grained system sharing No Atomics No Minimum alignment for any data type 128 bytes Alignment of base address 4096 bits (512 bytes) Preferred alignment for atomics SVM 0 bytes Global 0 bytes Local 0 bytes Atomic memory capabilities relaxed, work-group scope Atomic fence capabilities relaxed, acquire/release, work-group scope Max size for global variable 0 Preferred total size of global vars 0 Global Memory cache type Read/Write Global Memory cache size 1949696 (1.859MiB) Global Memory cache line size 128 bytes Image support Yes Max number of samplers per kernel 32 Max size for 1D images from buffer 268435456 pixels Max 1D or 2D image array size 2048 images Max 2D image size 32768x32768 pixels Max 3D image size 16384x16384x16384 pixels Max number of read image args 256 Max number of write image args 32 Max number of read/write image args 0 Pipe support No Max number of pipe args 0 Max active pipe reservations 0 Max pipe packet size 0 Local memory type Local Local memory size 49152 (48KiB) Registers per block (NV) 65536 Max number of constant args 9 Max constant buffer size 65536 (64KiB) Generic address space support No Max size of kernel argument 32764 (32KiB) Queue properties (on host) Out-of-order execution Yes Profiling Yes Device enqueue capabilities (n/a) Queue properties (on device) Out-of-order execution No Profiling No Preferred size 0 Max size 0 Max queues on device 0 Max events on device 0 Prefer user sync for interop No Profiling timer resolution 1000ns Execution capabilities Run OpenCL kernels Yes Run native kernels No Non-uniform work-groups No Work-group collective functions No Sub-group independent forward progress No Kernel execution timeout (NV) No Concurrent copy and kernel execution (NV) Yes Number of async copy engines 2 IL version (n/a) ILs with version <printDeviceInfo:186: get CL_DEVICE_ILS_WITH_VERSION : error -30> printf() buffer size 1048576 (1024KiB) Built-in kernels (n/a) Built-in kernels with version <printDeviceInfo:190: get CL_DEVICE_BUILT_IN_KERNELS_WITH_VERSION : error -30> Device Extensions cl_khr_global_int32_base_atomics cl_khr_global_int32_extended_atomics cl_khr_local_int32_base_atomics cl_khr_local_int32_extended_atomics cl_khr_fp64 cl_khr_3d_image_writes cl_khr_byte_addressable_store cl_khr_icd cl_khr_gl_sharing cl_nv_compiler_options cl_nv_device_attribute_query cl_nv_pragma_unroll cl_nv_copy_opts cl_nv_create_buffer cl_khr_int64_base_atomics cl_khr_int64_extended_atomics cl_khr_device_uuid cl_khr_pci_bus_info cl_khr_external_semaphore cl_khr_external_memory cl_khr_external_semaphore_opaque_fd cl_khr_external_memory_opaque_fd Device Extensions with Version cl_khr_global_int32_base_atomics 0x400000 (1.0.0) cl_khr_global_int32_extended_atomics 0x400000 (1.0.0) cl_khr_local_int32_base_atomics 0x400000 (1.0.0) cl_khr_local_int32_extended_atomics 0x400000 (1.0.0) cl_khr_fp64 0x400000 (1.0.0) cl_khr_3d_image_writes 0x400000 (1.0.0) cl_khr_byte_addressable_store 0x400000 (1.0.0) cl_khr_icd 0x400000 (1.0.0) cl_khr_gl_sharing 0x400000 (1.0.0) cl_nv_compiler_options 0x400000 (1.0.0) cl_nv_device_attribute_query 0x400000 (1.0.0) cl_nv_pragma_unroll 0x400000 (1.0.0) cl_nv_copy_opts 0x400000 (1.0.0) cl_nv_create_buffer 0x400000 (1.0.0) cl_khr_int64_base_atomics 0x400000 (1.0.0) cl_khr_int64_extended_atomics 0x400000 (1.0.0) cl_khr_device_uuid 0x400000 (1.0.0) cl_khr_pci_bus_info 0x400000 (1.0.0) cl_khr_external_semaphore 0x9000 (0.9.0) cl_khr_external_memory 0x9000 (0.9.0) cl_khr_external_semaphore_opaque_fd 0x9000 (0.9.0) cl_khr_external_memory_opaque_fd 0x9000 (0.9.0)

NULL platform behavior clGetPlatformInfo(NULL, CL_PLATFORM_NAME, ...) No platform clGetDeviceIDs(NULL, CL_DEVICE_TYPE_ALL, ...) No platform clCreateContext(NULL, ...) [default] No platform clCreateContext(NULL, ...) [other] Success [NV] clCreateContextFromType(NULL, CL_DEVICE_TYPE_DEFAULT) No platform clCreateContextFromType(NULL, CL_DEVICE_TYPE_CPU) No devices found in platform clCreateContextFromType(NULL, CL_DEVICE_TYPE_GPU) No platform clCreateContextFromType(NULL, CL_DEVICE_TYPE_ACCELERATOR) No devices found in platform clCreateContextFromType(NULL, CL_DEVICE_TYPE_CUSTOM) Invalid device type for platform clCreateContextFromType(NULL, CL_DEVICE_TYPE_ALL) No platform

I have been struggled with this for quite a time, it will be great helpful if anyone figures out what is going on here?

Glinttsd commented 3 weeks ago

Hi, can you offer the memory capacity of the GPU? Larger box requires larger memory, which maybe your problem.

marramWang commented 3 weeks ago

Hi, can you offer the memory capacity of the GPU? Larger box requires larger memory, which maybe your problem.

nvidia-smi

Tue Jun 11 10:25:47 2024 +---------------------------------------------------------------------------------------+ | NVIDIA-SMI 535.54.03 Driver Version: 535.54.03 CUDA Version: 12.2 | |-----------------------------------------+----------------------+----------------------+ | GPU Name Persistence-M | Bus-Id Disp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. | | | | MIG M. | |=========================================+======================+======================| | 0 NVIDIA GeForce RTX 3080 Off | 00000000:73:00.0 On | N/A | | 0% 55C P8 17W / 320W | 2MiB / 10240MiB | 0% Default | | | | N/A | +-----------------------------------------+----------------------+----------------------+

+---------------------------------------------------------------------------------------+ | Processes: | | GPU GI CI PID Type Process name GPU Memory | | ID ID Usage | |=======================================================================================| | No running processes found | +---------------------------------------------------------------------------------------+

marramWang commented 3 weeks ago

Hi, can you offer the memory capacity of the GPU? Larger box requires larger memory, which maybe your problem.

Hi again, thanks for your kind response before. thanks to your helpful reminder, i checked the GPU capacity again: nvidia-smi shows 'Memory-Usage' stay 2MiB/10240MiB, and according to clinfo, my 'Global memory size' is 10487529472 (9.767GiB) and 'Max memory allocation' is 2621882368 (2.442GiB), (other information listed on the primary issue https://github.com/DeltaGroupNJUPT/Vina-GPU-2.1/issues/34#issue-2343533312)

is that enough for large boxes? how much memory required under D-LARGE format? Or it would be helpful if it is convenient for you to tell me which script i should check to find the required GPU capacity for larger boxes?

Since I have changed the stack size into 'unlimited', with ulimit -s unlimited ,which still cannot solve the problem.

Sincerely waiting for your replying, Thanks a lot.

Glinttsd commented 3 weeks ago

Hi, the large box is tested in the enviroment of V100 GPU with 32 GB memory. I don't think 10GB is enough for such a large box.

But you can adjust the maximum box size by modifying MAX_NUM_OF_GRID_MI/MAX_NUM_OF_GRID_MJ/MAX_NUM_OF_GRID_MK and MAX_NUM_OF_ATOM_RELATION_COUNT in the kernel2.h file according to your device.

neru1234 commented 1 week ago

Hi @Glinttsd, What is the size limit of small box? My box is 56, 46, 52. It can't dock with "An error occurred: Relation too large! Define a large box (see readme) would help". Now large box can't work on PC. Is there any way to dock my size? my gpu

+---------------------------------------------------------------------------------------+
| NVIDIA-SMI 535.113.01             Driver Version: 535.113.01   CUDA Version: 12.2     |
|-----------------------------------------+----------------------+----------------------+
| GPU  Name                 Persistence-M | Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp   Perf          Pwr:Usage/Cap |         Memory-Usage | GPU-Util  Compute M. |
|                                         |                      |               MIG M. |
|=========================================+======================+======================|
|   0  NVIDIA GeForce RTX 4060 Ti     Off | 00000000:01:00.0  On |                  N/A |
|  0%   37C    P5               9W / 165W |    940MiB / 16380MiB |     26%      Default |
|                                         |                      |                  N/A |
+-----------------------------------------+----------------------+----------------------+