You can't make the CPU and GPU do alternating loop iterations, but you can divide the slices of A into two batches, and make the CPU and GPU work asynchronously on their respective batch, as below.
Acpu=A(:,:,1:n/2); %chunk #1 : send to CPU
Agpu=gpuArray(A(:,:,n/2+1:end)); %chunk #2 : send to GPU with device index 1
p=parpool(2);
F(1)=parFeval(p, @deploy,2,Acpu);
F(2)=parFeval(p, @deploy,2,Agpu,1);
[Q,R] = fetchOutputs(F,'UniformOutput',false); % Blocks until complete
Q=cat(3,Q{1},gather(Q{2}));
R=cat(3,R{1},gather(R{2}));
function [q,r]=deploy(a,Id)
if nargin>1, gpuDevice(Id);end
for i=size(a,3):-1:1
[q(:,:,i),r(:,:,i)]=qr(A(:,:,i));
end
end
Naturally, you should pass the gpuDevice ID numbers that are actually assigned to the graphics cards on your machine. Above, I've assumed they are numbered 1,2, etc...
