http://www.k-wave.org/forum/topic/running-k-wave-simulation-in-linux-terminal Support for the k-Wave MATLAB toolbox en-US Tue, 12 May 2026 23:01:41 +0000 http://bbpress.org/?v=1.0.2 q http://www.k-wave.org/forum/search.php http://www.k-wave.org/forum/topic/running-k-wave-simulation-in-linux-terminal#post-5528 Wed, 08 Jun 2016 21:18:39 +0000 Bradley Treeby 5528@http://www.k-wave.org/forum/ <p>Hi benji,</p> <p>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).</p> <p>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.</p> <p>Brad. </p> http://www.k-wave.org/forum/topic/running-k-wave-simulation-in-linux-terminal#post-5522 Sun, 05 Jun 2016 21:46:19 +0000 benji 5522@http://www.k-wave.org/forum/ <p>thank u, that was a silly question of mine:)</p> <p>i have a matlab script that creates an input file for the c++ binary.<br /> i am running that script in linux OS on university servers, using PBS (Portable Batch System).</p> <p>i have created successfully input files for a grid of sizes 128^3,256^3 and 512^3, using 10-15GB.<br /> when trying to create an input file for a 768^3 and larger, MATLAB bring up the next error:</p> <p>///////////////////////////////////////////<br /> Error using griddedInterpolant/subsref<br /> Out of memory. Type HELP MEMORY for your options.</p> <p>Error in interpn (line 178)<br /> Vq = F(Xq{:});</p> <p>Error in kspaceFirstOrder3D (line 556)<br /> rho0_sgy = interpn(kgrid.x, kgrid.y, kgrid.z, rho0, kgrid.x, kgrid.y + kgrid.dy/2, kgrid.z, '*linear');</p> <p>Error in create_input_1024_1024_1024 (line 51)<br /> kspaceFirstOrder3D(kgrid, medium, source, sensor, input_args{:},'SaveToDisk',filename);</p> <p>////////////////////////////////////////</p> <p>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').</p> <p>what could be the reason for that and how can it be solved?</p> <p>thank u very much,<br /> benji </p> http://www.k-wave.org/forum/topic/running-k-wave-simulation-in-linux-terminal#post-5501 Fri, 13 May 2016 23:57:16 +0000 Jiri Jaros 5501@http://www.k-wave.org/forum/ <p>Hi Benji,<br /> you've got to add +x permission </p> <p>chmod +x ./kspaceFirstOrder3D-OMP</p> <p>the you can run the code by<br /> ./kspaceFirstOrder3D-OMP ...</p> <p>Jiri </p> http://www.k-wave.org/forum/topic/running-k-wave-simulation-in-linux-terminal#post-5491 Wed, 04 May 2016 21:55:14 +0000 benji 5491@http://www.k-wave.org/forum/ <p>hi,<br /> i sm trying to use the C++ code in order to run large grid simulations.<br /> I created a h5 input file in local matlab (kwave_input_data_128_64_64.h5), and run the next script:</p> <p>#!/bin/csh</p> <p>./kspaceFirstOrder3D-OMP -i kwave_input_data_128_64_64.h5 -o output_data.h5</p> <p>exit</p> <p>I get the next error "line 3: ./kspaceFirstOrder3D-OMP: Permission denied"</p> <p>when running without ./ iget the next error: "kspaceFirstOrder3D-OMP: Command not found."</p> <p>what is the reason?<br /> Thank you,<br /> benj </p>