hi,
i sm trying to use the C++ code in order to run large grid simulations.
I created a h5 input file in local matlab (kwave_input_data_128_64_64.h5), and run the next script:
#!/bin/csh
./kspaceFirstOrder3D-OMP -i kwave_input_data_128_64_64.h5 -o output_data.h5
exit
I get the next error "line 3: ./kspaceFirstOrder3D-OMP: Permission denied"
when running without ./ iget the next error: "kspaceFirstOrder3D-OMP: Command not found."
what is the reason?
Thank you,
benj
Hi Benji,
you've got to add +x permission
chmod +x ./kspaceFirstOrder3D-OMP
the you can run the code by
./kspaceFirstOrder3D-OMP ...
Jiri
thank u, that was a silly question of mine:)
i have a matlab script that creates an input file for the c++ binary.
i am running that script in linux OS on university servers, using PBS (Portable Batch System).
i have created successfully input files for a grid of sizes 128^3,256^3 and 512^3, using 10-15GB.
when trying to create an input file for a 768^3 and larger, MATLAB bring up the next error:
///////////////////////////////////////////
Error using griddedInterpolant/subsref
Out of memory. Type HELP MEMORY for your options.
Error in interpn (line 178)
Vq = F(Xq{:});
Error in kspaceFirstOrder3D (line 556)
rho0_sgy = interpn(kgrid.x, kgrid.y, kgrid.z, rho0, kgrid.x, kgrid.y + kgrid.dy/2, kgrid.z, '*linear');
Error in create_input_1024_1024_1024 (line 51)
kspaceFirstOrder3D(kgrid, medium, source, sensor, input_args{:},'SaveToDisk',filename);
////////////////////////////////////////
i note that i have been trying to run that with up to 48GB of physical memory+48GB of vmem (the maxumum i can be allocated at the moment). i believe 48GB shoukd be much more than inough to create a 678X678X678 or 1024X1024X1024 grid input file (using wsave to disc').
what could be the reason for that and how can it be solved?
thank u very much,
benji
Hi benji,
Unfortunately this is a common problem using MATLAB's inbuilt interpolation function. One way to save some memory is to save to disk in parts. There is an example in the k-Wave MATLAB help covering how to do this, although I think this currently skips calculating the density on a staggered grid (it probably shouldn't).
For larger input files, we always save to disk in parts, and get around the MATLAB interp problem by using a C++ mex function to perform the interpolation. I'd be happy to send it to you if that's helpful.
Brad.
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