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% ATX_SUP_PARTIAL distributed (multiGPU) backprojector that allows to split the full volume into smaller pieces
% this allows to solve datasets much larger than memory of used GPU or
% spread calculations over several GPUs
%
% volData = Atx_sup_partial(projData, cfg, vectors, split, varargin)
%
% Inputs:
% **projData - array Nlayers x width_sinogram x Nangles of back-projected data
% **cfg - config structure generated by ASTRA_initialize
% **vectors - orientation of projections generated by ASTRA_initialize
% **split 3 or 4 elements vector, [split X, split Y, split Z, split angle ]
% **deformation_fields: 3x1 cell contaning 3D arrays of local deformation of the object
% **verbose - verbose <= 0 : quiet, verbose : standard info , verbose = 2: debug
% **use_shared_memory - true - share data between processed by shared memory, false = use matlab parfor distribution
% **max_memory_blocks - maximal size of used share memory memory
% **varargin - for additional parameters see the code and als the astra.Axt_partial function
% *returns*
% ++volData - backprojected volume
%
% recompile commands
% (Linux, GCC 4.8.5) mexcuda -outdir private +astra/ASTRA_GPU_wrapper/ASTRA_GPU_wrapper.cu +astra/ASTRA_GPU_wrapper/util3d.cu +astra/ASTRA_GPU_wrapper/par3d_fp.cu +astra/ASTRA_GPU_wrapper/par3d_bp.cu
% (Windows) mexcuda -outdir private ASTRA_GPU_wrapper\ASTRA_GPU_wrapper.cu ASTRA_GPU_wrapper\util3d.cu ASTRA_GPU_wrapper\par3d_fp.cu ASTRA_GPU_wrapper\par3d_bp.cu
%*-----------------------------------------------------------------------*
%|                                                                       |
%|  Except where otherwise noted, this work is licensed under a          |
%|  Creative Commons Attribution-NonCommercial-ShareAlike 4.0            |
%|  International (CC BY-NC-SA 4.0) license.                             |
%|                                                                       |
%|  Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch)    |
%|                                                                       |
%|      Author: CXS group, PSI  |
%*-----------------------------------------------------------------------*
% You may use this code with the following provisions:
%
% If the code is fully or partially redistributed, or rewritten in another
% computing language this notice should be included in the redistribution.
%
% If this code, or subfunctions or parts of it, is used for research in a
% publication or if it is fully or partially rewritten for another
% computing language the authors and institution should be acknowledged
% in written form in the publication: “Data processing was carried out
% using the “cSAXS matlab package” developed by the CXS group,
% Paul Scherrer Institut, Switzerland.”
% Variations on the latter text can be incorporated upon discussion with
% the CXS group if needed to more specifically reflect the use of the package
% for the published work.
%
% A publication that focuses on describing features, or parameters, that
% are already existing in the code should be first discussed with the
% authors.
%
% This code and subroutines are part of a continuous development, they
% are provided “as they are” without guarantees or liability on part
% of PSI or the authors. It is the user responsibility to ensure its
% proper use and the correctness of the results.
function volData = Atx_sup_partial(projData, cfg, vectors, split, varargin)
import utils.*
import math.*
par = inputParser;
par.addOptional('deformation_fields', {}) % deformation_fields: 3x1 cell contaning 3D arrays of local deformation of the object
par.addOptional('GPU', []) % list of GPUs to be used in reconstruction
par.addOptional('split_sub', 1) % splitting of the sub block on smaller tasks in the Atx_partial method , 1 == no splitting , otherwise [split_x,split_y,split_z,split_angles]
par.addOptional('verbose', 1) % verbose = 0 : quiet, verbose : standard info , verbose = 2: debug
par.addOptional('use_shared_memory', []) % true - share data between processed by shared memory, false = use matlab parfor distribution
par.addOptional('max_memory_blocks', min(50e9, utils.check_available_memory*1e6/4)) % maximal size of used share memory memory
par.parse(varargin{:})
r = par.Results;
if isscalar(split)
split = split .* ones(1,3);
end
split_orig = split;
if isempty(r.use_shared_memory)
r.use_shared_memory = length(r.GPU) > 1;
end
if isscalar(r.split_sub)
r.split_sub = r.split_sub .* ones(1,3);
end
gpu = gpuDevice;
if isempty(r.GPU)
r.GPU = gpu.Index;
end
N_GPU = length(r.GPU);
if ~isempty(r.deformation_fields)
% deformation field splitting not implemneted for split_sub;
split(1:3) = split(1:3) .* r.split_sub(1:3);
r.split_sub = 1;
end
%% if not splitting on this level is requirested, continue to tomo.Atx_partial
if all(split(1:3) == 1) && N_GPU == 1 && gpu.AvailableMemory > 4*(numel(projData)/10+cfg.iVolX*cfg.iVolY*cfg.iVolZ)
volData = astra.Atx_partial(projData, cfg, vectors, r.split_sub, ...
'GPU', r.GPU, 'deformation_fields', r.deformation_fields, 'verbose', r.verbose);
return
elseif all(split(1:2) == 1) && isempty(r.deformation_fields) && ...
utils.check_available_memory*1e6 > 4*(cfg.iVolX*cfg.iVolY*cfg.iVolZ*N_GPU+numel(projData)) && ...
cfg.iVolX*cfg.iVolY*cfg.iVolZ*4 < min(4*double(intmax('int32')),gpu.TotalMemory/2)
%% if no splitting is needed and the volume is small enough then at least split the data on multiple GPUs by angles
volData = Atx_angle_split(projData, cfg, vectors, r.split_sub, r.GPU, r.verbose);
return
end
%% otherwise do proper checking of all inputs before splitting
if ~(isa(projData, 'gpuArray') && strcmp(classUnderlying(projData), 'single')) && ...
~isa(projData, 'single')
error('Only single precision input array supported')
end
projData = gather(projData);
if any(cfg.pixel_scale ~= 1)
error('Non integer pixel size is not implemented, try to use Atx_partial')
end
if cfg.skewness_angle ~= 0
error('Skewness is not working well with sup-split')
end
if length(cfg.pixel_scale) == 2 && cfg.pixel_scale(1) ~= cfg.pixel_scale(2)
error('Variable pixel size for each axis is not implemented')
end
Nvol_orig = [cfg.iVolX,cfg.iVolY,cfg.iVolZ];
split(3) = max(split(3), ceil(split(3) * ( 4*(numel(projData)/5+cfg.iVolX*cfg.iVolY*cfg.iVolZ*(1+any(r.split_sub>1)) ) / gpu.AvailableMemory / prod(split) )));
split(3) = max(split(3), ceil(split(3) * ( ( cfg.iVolX*cfg.iVolY*cfg.iVolZ)/prod(split(1:3)) / double(intmax('int32')) )));
% make it equaly splitable among the GPUs
split(3) = ceil(max(split(3), ceil(prod(split(1:3)) / N_GPU) * N_GPU) / prod(split(1:2)));
split(1:3) = min(split(1:3), Nvol_orig(1:3));
% adjust splitting to make get equal blocks of the volume
for i = 1:100
split(1:3) = ceil(Nvol_orig ./ floor(Nvol_orig ./ split(1:3)));
end
if prod(r.split_sub) > 1
% reduce the split_sub if possible
r.split_sub(3) = ceil(r.split_sub(3) / 2^nextpow2(prod(split) / prod(split_orig)) );
end
if length(split) < 4
split(4) = 1;
end
% initial parameters check
Nvol_sub = Nvol_orig./split(1:3);
Nproj_full = size(projData);
assert(all(mod(Nvol_sub,1)==0), sprintf('Volume array cannot be divided to %i %i %i cubes', split(1:3)))
assert(all(Nproj_full==[cfg.iProjV,cfg.iProjU,cfg.iProjAngles]), 'Wrong inputs size')
assert(all(size(vectors)==[cfg.iProjAngles,12]), 'Wrong vectors size')
% size of the subprojection of single subvolume
Nproj_sub = [ (Nvol_sub(3)* sind(cfg.lamino_angle) + sqrt(sum(Nvol_sub(1:2).^2))*cosd(cfg.lamino_angle)), ...
sqrt(sum(Nvol_sub(1:2).^2))];
% adjust sub projection size to account for inplane rotation of the geometry
if cfg.tilt_angle ~= 0
Nproj_rot = [cosd(cfg.tilt_angle), -sind(cfg.tilt_angle); +sind(cfg.tilt_angle), cosd(cfg.tilt_angle)] * [0,0; Nproj_sub(1:2)];
% calculate projection window size after rotation
Nproj_rot = max(Nproj_rot) - min(Nproj_rot);
% add some extra padding
Nproj_sub(1:2) = 2*(Nproj_rot - Nproj_sub(1:2)) + Nproj_sub(1:2);
end
% provide extra space for subpixel (linear) interpolation at the borders of the split volumes, needed only for noninteger CoR_offset
Nproj_sub = Nproj_sub + 2*([split(3), max(split([1,2]))] - 1);
Nproj_sub = ceil(Nproj_sub/16)*16; % make it easier splitable for ASTRA
if cfg.lamino_angle == 90
Nproj_sub(1) = min(Nproj_sub(1), Nproj_full(1));
end
% only if there is not split in the horizontal dimension
if all(split(1:2) == 1)
% do not take larger than size of the inputs
Nproj_sub = min(Nproj_sub, Nproj_full(1:2));
end
% avoid low RAM issues due to paralelization
split(4) = max(split(4), ceil(4*prod(Nproj_sub)*cfg.iProjAngles/split(4)/(r.max_memory_blocks/N_GPU)));
Nproj_sub(3) = ceil(cfg.iProjAngles/split(4));
cfg_small = cfg;
cfg_small.iVolX = Nvol_sub(1);
cfg_small.iVolY = Nvol_sub(2);
cfg_small.iVolZ = Nvol_sub(3);
% get new size of projections
cfg_small.iProjU = Nproj_sub(2);
cfg_small.iProjV = Nproj_sub(1);
% calculate and store offset of the center of rotation, it will be used later
offset = vectors(:,4:6) +(vectors(:,10:12).*cfg.iProjV/2+vectors(:,7:9).*cfg.iProjU/2 );
CoR_offset = -[dot(offset', vectors(:,10:12)') ./ dot(vectors(:,10:12)', vectors(:,10:12)');
dot(offset', vectors(:,7:9)') ./ dot(vectors(:,7:9)', vectors(:,7:9)')]' ;
% remove centering offset && apply new offset
shift_vec = vectors(:,10:12)*(cfg.iProjV/2-cfg_small.iProjV/2)+vectors(:,7:9)*(cfg.iProjU/2-cfg_small.iProjU/2);
vectors(:,4:6) = vectors(:,4:6) + shift_vec;
%% keep the volume in RAM , transfer only sub-blocks
Nblocks = prod(split);
%% write back to the preallocated shared array
volData = zeros(Nvol_orig, 'single');
if N_GPU > 1
poolobj = gcp('nocreate');
if isempty(poolobj) || poolobj.NumWorkers < N_GPU
delete(poolobj);
poolobj = parpool(N_GPU);
end
poolobj.IdleTimeout = 600; % set idle timeout to 10 hours
end
% when the function is finished, make sure to execute following code
global status
status = true;
if r.use_shared_memory
out = onCleanup(@()myCleanupFun());
end
% run blocks in series
% run sub-blocks on each GPU in parallel
t_total = tic();
clear output
%% START OF OUTER GPU LOOP
outputs_blocks = [];
%% unitialize one solver per GPU
for thread_id = 1:N_GPU
% parse inputs and try to split them if possible
[outputs_blocks, inputs_block{thread_id},cfg_all{thread_id}] = ...
submit_block(thread_id, thread_id, outputs_blocks, projData, cfg, cfg_small, vectors,CoR_offset, split, Nproj_sub,Nvol_sub, r, varargin{:} );
end
unprocessed_blocks = N_GPU+1:Nblocks;
%% merge blocks back from GPUs and write to the shared array volData
for ii = 1:Nblocks
if r.verbose; utils.progressbar(ii, Nblocks); end
% set values from the small blocks to the final output arrays
[thread_id, timing, id] = gather_block( outputs_blocks,volData, cfg_all, split(4) > 1);
if ~isempty(unprocessed_blocks)
block_id = unprocessed_blocks(1);
unprocessed_blocks(1) = [];
if isa(outputs_blocks, 'parallel.FevalFuture') && sum([outputs_blocks.Read]) ~= 1
outputs_blocks
keyboard
end
% submit a new job once the previous is finished
[outputs_blocks, inputs_block{thread_id},cfg_all{block_id}] = ...
submit_block(block_id, thread_id, outputs_blocks, projData, cfg, cfg_small, vectors, CoR_offset, split, Nproj_sub,Nvol_sub, r, varargin{:} );
if isa(outputs_blocks, 'parallel.FevalFuture') && any(cat(1,[outputs_blocks.Read]))
outputs_blocks
keyboard
end
end
end
if r.verbose > 1
fprintf('Timing system: GPU init %3.2gs shared_mem down %3.2gs upload on GPU %3.2gs tomo projection %3.2gs download from GPU %3.2gs shared_mem %3.2gs \n',sum(timing,2) )
if length(r.GPU) > 1
fprintf('Timing local: GPU init %3.2gs shared_mem down %3.2gs upload on GPU %3.2gs tomo projection %3.2gs download from GPU %3.2gs shared_mem %3.2gs \n ',sum(timing,2)/max(1,length(r.GPU)) )
fprintf('Total time %3.2fs, parfor overhead %3.2fs \n', t_total, t_total - sum(sum(timing,2)/max(1,length(r.GPU))) )
end
end
% finish GPU blocks
% everything was fine -> no cleaning needed
status = false;
end
function [outputs_blocks,inputs_block, cfg_out] = submit_block(block_id, thread_id, outputs_blocks, projData, cfg, cfg_small, vectors, CoR_offset,split, Nproj_sub,Nvol_sub, r, varargin )
% prepare blocks for asynchonous processing
try
inputs_block = prepare_block(block_id, projData, cfg, cfg_small, vectors,CoR_offset, split, Nproj_sub,Nvol_sub, r, varargin{:});
catch err
disp(getReport(err))
keyboard
end
N_GPU = length(r.GPU);
if isempty(outputs_blocks); clear outputs_blocks; end
cfg_out = inputs_block{2};
try
%% process preloaded data
% no paralel toolbox
if N_GPU <= 1
[outputs_blocks{thread_id}.volData_small,outputs_blocks{thread_id}.timing, outputs_blocks{thread_id}.id]=...
run_partial_projector(inputs_block, block_id, 1,r.GPU,0);
else
% run it asynchronously
if r.verbose > 3
ticBytes(gcp);
end
outputs_blocks(thread_id) = parfeval(@run_partial_projector, 3, inputs_block,block_id,thread_id, r.GPU,0);
if r.verbose > 3
try; tocBytes(gcp); end
end
end
catch err
disp(getReport(err))
utils.check_available_memory
keyboard
end
end
function myCleanupFun()
% destroy all shared memory that could have been left behind
!ipcs -m | cut -d' ' -f2 | grep '^[0-9]' | while read x; do ipcrm -m $x; done
end
function [thread_id, timing, id] = gather_block(output_package,volData, cfg_all, add_values )
if isa(output_package, 'parallel.FevalFuture')
% gather results from cluster , WAIT FOR CALCULATIONS TO BE FINISHED
% [~, outputs_block, id] = fetchNext(output_package);
%% my version of the fetchNext function, it seems faster
id = [];
assert(any(~[output_package.Read]), 'All blocks are already read')
while true
for thread_id =1:length(output_package)
if strcmpi(output_package(thread_id).State, 'finished') && output_package(thread_id).Read == 0
try
[volData_small,timing,id] = output_package(thread_id).fetchOutputs;
catch err
if strcmpi(err.identifier, 'parallel:fevalqueue:InvalidExecutionResult')
warning('Unknown error, trying to restart parpool')
delete(gcp('nocreate'));
end
if strcmpi(err.identifier, 'parallel:fevalqueue:InvalidExecutionResult')
warning('Unknown error, trying to restart parpool')
delete(gcp('nocreate'));
end
if ~isempty(output_package(thread_id).Diary)
fprintf('============ THREAD %i FAILED, OUTPUT: ============= \n', thread_id)
disp(output_package(thread_id).Diary)
end
fprintf('============ THREAD %i FAILED, ERROR: ============= \n', thread_id)
disp(getReport(output_package(thread_id).Error))
keyboard
output_package.cancel
rethrow(err)
end
break
end
end
if ~isempty(id); break; end
pause(0.01) % wait for the data to be prepared
end
elseif iscell(output_package)
thread_id = 1;
id = output_package{thread_id}.id;
volData_small = output_package{thread_id}.volData_small;
timing = output_package{thread_id}.timing;
else
disp('FAILED ?? ')
keyboard
end
if isempty(volData_small)
warning('ASTRA projection probably failed')
keyboard
end
if isa(volData_small, 'shm')
% load data from shared memory
[s,volData_small] = volData_small.attach;
s.protected = false; % release shared memory
elseif ~isnumeric(volData_small)
keyboard
end
% write back to the full array stored in RAM
positions = zeros(size(volData_small,3),2)+cfg_all{id}.volume_shift(1:2);
indices = (1:size(volData_small,3)) + cfg_all{id}.volume_shift(3);
% use a MEX code to speed it up
utils.add_to_3D_projection(volData_small, volData,positions,indices, true, false);
end
function prepared_block = prepare_block(id, projData, cfg, cfg_small, vectors,CoR_offset, split, Nproj_sub, Nvol_sub ,r, varargin)
[x,y,z,angle_block_id] = ind2sub(split,id);
block_pos = [x,y,z];
shift = zeros(3,1);
for n = 1:3
%% find optimal shift of the subvolume
if mod(split(n),2)==1 %% odd
shift(n) = (block_pos(n) - ceil(split(n)/2))*Nvol_sub(n);
else
shift(n) = (block_pos(n) - split(n)/2-1/2)*Nvol_sub(n);
end
end
Nangle_per_blocks = ceil(cfg.iProjAngles / split(4));
%% for splitting to angular blocks using close angles, it makes ASTRA faster
angle_ids = (1+(angle_block_id-1)*Nangle_per_blocks:min(cfg.iProjAngles, angle_block_id*Nangle_per_blocks));
cfg_small.iProjAngles = length(angle_ids);
Nproj_sub(3) = cfg_small.iProjAngles;
%% find optimal shift of the subvolume
deform_fields_small = get_subdeform_fields(block_pos, r.deformation_fields, split);
CoR_offset = [CoR_offset, zeros(cfg.iProjAngles,1)] ;
% shift the sub-projections off center to create single
% large projection after assembling, if shift == 0 =>
% projections will be rotationally centered
vec = vectors;
% apply optimal shift
projection_shift = cfg.pixel_scale(1)^2.*[vec(:,10:12)*shift, vec(:,7:9)*shift, zeros(cfg.iProjAngles,1)];
projection_shift = bsxfun(@plus, projection_shift, [cfg.iProjV/2-cfg_small.iProjV/2,cfg.iProjU/2-cfg_small.iProjU/2,0] + CoR_offset);
% calculate subpixel shifts
projection_shift_subpix = projection_shift - round(projection_shift) - CoR_offset;
projection_shift = round(projection_shift);
% apply subpixel shifts
vec(:,4:6) = vec(:,4:6) - ...
( bsxfun(@times,vectors(:,7:9),projection_shift_subpix(:,2))+ ...
bsxfun(@times,vectors(:,10:12),projection_shift_subpix(:,1)));
% just store shifts for later
cfg_small.volume_shift = (block_pos-1).*Nvol_sub;
cfg_small.projection_shift = projection_shift;
% move data using custom made MEX routine
% allocate a small sub array
projData_small = zeros(Nproj_sub, 'single');
if r.use_shared_memory
s = shm();
try
s.allocate(projData_small) % attach the shared memory
catch
keyboard
end
[s, projsmall_shm] = s.attach();
% === write data =====
% use self-made MEX OMP function to move the data s
utils.get_from_3D_projection(projsmall_shm, projData, projection_shift(angle_ids,1:2), angle_ids);
% detach the shared memory
projData_small = s;
s.detach;
else
% use custom made MEX OMP function to move the data
utils.get_from_3D_projection(projData_small, projData, projection_shift(angle_ids,1:2), angle_ids);
end
% return only vector for the use angles
vec = vec(angle_ids,:);
prepared_block = {projData_small, cfg_small, vec, r.split_sub, varargin{:}, ...
'deformation_fields', deform_fields_small, 'verbose', 0, 'GPU', []};
end
function [vol, timing,block_id] = run_partial_projector(prepared_block, block_id, thread_id, GPU_list, verbose)
t0 = tic;
gpu_id = GPU_list(thread_id);
% let matlab to choose which GPU use
gpu = gpuDevice();
if ~isempty(GPU_list) && gpu.Index ~= gpu_id
gpuDevice(gpu_id); % avoid unneeded initalization
end
t_init = toc(t0);
timing = [t_init, 0,0,0,0,0];
t = tic;
if isa(prepared_block{1}, 'shm')
% data are attached to shared memory
[s,projData_small] = prepared_block{1}.attach();
else
% data are given directly to the worker
projData_small = prepared_block{1};
end
timing(2) = toc(t);
t = tic;
timing(3) = toc(t);
% call the next level abstraction
t = tic;
is_remote = ~isempty(getCurrentTask());
% call the next level abstraction around ASTRA wrapper
try
for ii = 1:2
try
vol = astra.Atx_partial(projData_small, prepared_block{2:end},'verbose', max(is_remote, verbose));
break
catch err
if ii == 2
rethrow(err)
else
warning('Atx_partial failed, trying again ... ')
end
end
end
catch err
qkeyboard
gpu = gpuDevice
reset(gpu)
fprintf('Error on GPU %i / %i', gpu.Index, gpuDeviceCount)
disp( getReport(err, 'extended', 'hyperlinks', 'on'))
% projData_small = single([]);
rethrow(err)
end
%%%%%%%%%%%
timing(4) = toc(t);
t = tic;
vol = gather(vol); % move to RAM
timing(5) = toc(t);
t = tic;
if isscalar(prepared_block{1})
% data are distributed to shared memory
s.detach();
s = shm(true);
s.upload(vol);
vol = s;
end
timing(6) = toc(t);
end
function deformation_fields_sub = get_subdeform_fields(block_pos, deform_fields, split)
% crop the deformation field only int the region of interest
if isempty(deform_fields)
deformation_fields_sub = {};
return
end
if prod(split)==1
deformation_fields_sub = deform_fields;
return
end
for ii = 1:3
N_full = size(deform_fields{1,ii});
N_small = ceil( N_full ./ reshape(split(1:3),[],1)');
for kk = 1:3
ind_def{kk} = (1+(block_pos(kk)-1)*N_small(kk)) : min(N_full(kk), (split(kk))*N_small(kk));
end
for jj = 1:2
deformation_fields_sub{jj,ii} = deform_fields{jj,ii}(ind_def{:});
end
end
warning('Splitting of deformation field is not supported / recommended')
end
function volData = Atx_angle_split(projData, cfg, vectors, split, GPU, verbose)
%% simplified version for multiGPU reconstruction of volumes that are small enough
% simply split the projections by angles and apply each projection
% block on a separated GPU
Nangles = cfg.iProjAngles;
N_GPU = length(GPU);
Nblocks = ceil(Nangles / N_GPU);
if length(split) == 4
split(4) = max(1, split(4) / N_GPU);
end
if verbose; utils.progressbar(1,4); end
for id = 1:N_GPU
ind{id} = 1+(id-1)*Nblocks:min(id*Nblocks,Nangles);
projData_shm{id} = shm();
projData_shm{id} = tomo.get_from_array(projData, projData_shm{id}, ind{id});
volData_shm{id} = [];
end
if verbose; utils.progressbar(2,4); end
parfor(id = 1:N_GPU, N_GPU)
t = getCurrentTask();
gpu_id = GPU(1+mod(t.ID-1, N_GPU));
% let parfor to choose which GPU use
gpu = gpuDevice();
if ~isempty(GPU) && gpu.Index ~= gpu_id
gpuDevice(gpu_id); % avoid unneeded initalization
end
[s,projData_block] = projData_shm{id}.attach();
volData_block = astra.Atx_partial(projData_block, cfg, vectors(ind{id},:),split, 'keep_on_GPU', true, 'verbose',0);
volData_block = gather(volData_block);
s.upload(volData_block);
s.protected = true;
volData_shm{id} = s;
end
if verbose; utils.progressbar(3,4); end
volData = single(0);
for id = 1:N_GPU
[s,volData_block] = volData_shm{id}.attach();
volData = volData + volData_block;
s.free;
end
if verbose; utils.progressbar(4,4); end
end