Comments (6)
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RandomiseGroupLevel worked as I expected on my dataset after downsampling spatial maps in the input volume from 256x256x256 (1mm x 1mm x 1mm) to 128x128x128 (2mm x 2mm x 2mm). That significantly reduced the amount of memory needed for loading this data, without sacrificing specificity. The voxel resolution of the original data from diffusion weighted imaging (DWI) was on the order of (2mm x 2mm x 2mm) to begin with. I registered the DWI to FreeSurfer's CVS template which has voxel resolution (1mm x 1mm x 1mm) to enable group analysis, but I don't believe there is much loss of information by downsampling.
Regardless, here is the output from GetOpenCLInfo and RandomiseGroupLevel when using volumes of spatial maps with dimesnionality 256x256x256 (as I did originally and got error with)
GetOpenCLInfo:
Device info
Platform number: 0
Platform vendor: NVIDIA Corporation
Platform name: NVIDIA CUDA
Platform extentions: 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_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
Platform profile: FULL_PROFILE
Device number: 0
Device vendor: NVIDIA Corporation
Device name: Tesla K80
Hardware version: OpenCL 1.2 CUDA
Software version: 375.66
OpenCL C version: OpenCL C 1.2
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_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
Global memory size in MB: 11439
Size of largest memory object in MB: 2859
Global memory cache size in KB: 208
Local memory size in KB: 48
Constant memory size in KB: 64
Parallel compute units: 13
Clock frequency in MHz: 823
Max number of threads per block: 1024
Max number of threads in each dimension: 1024 1024 64
The output of the call to RandomiseGroupLevel (this here is with 500 permutations. But same thing held when running 5000 permutations).
Authored by K.A. Eklund
Data size: 256 x 256 x 256 x 362
Number of permutations: 500
Number of regressors: 8
Number of contrasts: 3
Performing 3 t-tests
Correlation design detected for t-contrast 1
Correlation design detected for t-contrast 2
Correlation design detected for t-contrast 3
Max number of permutations for contrast 1 is inf
Max number of permutations for contrast 2 is inf
Max number of permutations for contrast 3 is inf
Starting permutation 1
Starting permutation 101
Starting permutation 201
Starting permutation 301
Starting permutation 401
Permutation threshold for contrast 1 for a significance level of 0.050000 is 0.000000
Starting permutation 1
Starting permutation 101
Starting permutation 201
Starting permutation 301
Starting permutation 401
Permutation threshold for contrast 2 for a significance level of 0.050000 is 0.000000
Starting permutation 1
Starting permutation 101
Starting permutation 201
Starting permutation 301
Starting permutation 401
Permutation threshold for contrast 3 for a significance level of 0.050000 is 0.000000
Run kernel error for kernel 'CalculateBetaWeightsGLM' is 'CL_MEM_OBJECT_ALLOCATION_FAILURE'
Run kernel error for kernel 'CalculateStatisticalMapsGLMTTest' is 'CL_MEM_OBJECT_ALLOCATION_FAILURE'
Run kernel error for kernel 'CalculateStatisticalMapsGLMTTestSecondLevelPermutation' is 'CL_MEM_OBJECT_ALLOCATION_FAILURE'
Run kernel error for kernel 'TransformData' is 'CL_MEM_OBJECT_ALLOCATION_FAILURE'
from broccoli.
from broccoli.
Thank you. Does Broccoli have a way of using additional memory to augment the RAM of a graphics card, given my graphics card is limited to 11GB of memory (with largest object size capped at 2.8 GB). I have available ~1 TB of Fast SSD memory mounted.
from broccoli.
from broccoli.
from broccoli.
Related Issues (20)
- BROCOLLI crashes without error
- TFCE is currently turned off error in RandomiseGroupLevel HOT 4
- permutations tmaps different from fsl randomize output by a factor of ~470 HOT 4
- GLM: segmentation fault HOT 2
- permutations turned off HOT 1
- Registration Failure HOT 1
- output uncorrected results for RandomiseGroupLevel HOT 2
- TFCE support? HOT 2
- AMD gpu and Docker failed HOT 4
- Roadmap? HOT 9
- Error building kernelBayesian.cpp for GPU on macOS HOT 2
- Elastic net regularization for GLM? HOT 2
- RandomiseGroupLevel for repeated measures HOT 2
- RandomiseGroupLevel crashing HOT 5
- python wrapper compilation HOT 1
- Segmentation fault - Multiple runs per participant still not fixed
- Compiling the matlab wrapper on Mac HOT 1
- nipype: BROCCOLI nodes do not produce any output within workflows HOT 1
- Broccoli in WSL2 - Ubuntu 22.04 - HOT 14
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from broccoli.