http://www.k-wave.org/forum/topic/parallelizing-on-a-hpc Support for the k-Wave MATLAB toolbox en-US Tue, 12 May 2026 23:05:26 +0000 http://bbpress.org/?v=1.0.2 q http://www.k-wave.org/forum/search.php http://www.k-wave.org/forum/topic/parallelizing-on-a-hpc#post-6138 Mon, 25 Sep 2017 08:23:56 +0000 Jiri Jaros 6138@http://www.k-wave.org/forum/ <p>Hi Thomas,<br /> please send me an email address to <a href="mailto:jarosjir@fit.vutbr.cz">jarosjir@fit.vutbr.cz</a> and I'll prepare a code snapshot for you.</p> <p>Cheers,<br /> Jiri </p> http://www.k-wave.org/forum/topic/parallelizing-on-a-hpc#post-6137 Sun, 24 Sep 2017 16:22:44 +0000 ttiennot 6137@http://www.k-wave.org/forum/ <p>Hi Brad,</p> <p>I have some experience and I also have a local IT support that can do this for me.</p> <p>Thomas </p> http://www.k-wave.org/forum/topic/parallelizing-on-a-hpc#post-6135 Sun, 24 Sep 2017 11:00:10 +0000 Bradley Treeby 6135@http://www.k-wave.org/forum/ <p>Hi Thomas,</p> <p>Are you experienced with compiling libraries and source codes on linux-based HPC clusters, or do you have local IT support that can do this for you? </p> <p>Brad. </p> http://www.k-wave.org/forum/topic/parallelizing-on-a-hpc#post-6133 Thu, 21 Sep 2017 09:35:51 +0000 ttiennot 6133@http://www.k-wave.org/forum/ <p>Hi,</p> <p>I used to work with the GPU code but due to memory issues on large simulations I have to use the CPU code now.</p> <p>I am working on a cluster with more than 2000 cores but I need to use openMPI to work on several nodes. Would you agree to send me the code using Open MPI ?</p> <p>Best regards,</p> <p>Thomas </p> http://www.k-wave.org/forum/topic/parallelizing-on-a-hpc#post-6020 Thu, 29 Jun 2017 14:59:11 +0000 Bradley Treeby 6020@http://www.k-wave.org/forum/ <p>Hi samantp,</p> <p>We don't have a problem with other people using the MPI code, however, the reason we haven't released it widely is that it is difficult to support. It's sometimes non-trivial to compile depending on the machine, available modules, compilers, etc. There are also various compatibility problems and bugs with different combinations of libraries that k-Wave relies on. </p> <p>Do you have experience in compiling libraries and codes from source on HPC clusters?</p> <p>Brad. </p> http://www.k-wave.org/forum/topic/parallelizing-on-a-hpc#post-6008 Thu, 22 Jun 2017 17:38:26 +0000 samantp 6008@http://www.k-wave.org/forum/ <p>Hi Jiri,<br /> Do you have any packages that would allow me to compile and install the code onto a Linux based cluster? I'd need to be able to deploy it myself due to access restrictions on my university's HPC.</p> <p>Thank you </p> http://www.k-wave.org/forum/topic/parallelizing-on-a-hpc#post-5441 Fri, 01 Apr 2016 21:52:29 +0000 Jiri Jaros 5441@http://www.k-wave.org/forum/ <p>Hi Kwoolfe2,<br /> We do have such a code but it is highly experimental and before being released some additional work has to be done. The functionality is here, however, the deployment is not trivial. Typically, I'd need access to your cluster to compile the software stack, test all dependencies, find best configurations, prepare job scripts and the give the bunde to you. </p> <p>Considering you have a node with 32 cores, you'd need at least 4 nodes (128 cores) to get any resonable speed-up. On the other hand, the code is able to scale up to thousands of cores.</p> <p>Please send an email to <a href="mailto:jarosjir@fit.vutbr.cz">jarosjir@fit.vutbr.cz</a> and we can discuss details. </p> <p>Jiri </p> http://www.k-wave.org/forum/topic/parallelizing-on-a-hpc#post-5439 Mon, 28 Mar 2016 15:49:45 +0000 kwoolfe2 5439@http://www.k-wave.org/forum/ <p>I am trying to run the 3-D C++ k-wave code on a HPC. The HPC has hundreds of nodes, and each node only has 32 processors. I have found that OpenMP can't parallelize the code over nodes, but it can parallelize over the 32 processors in a single node. Is there any way to parallelize the code over multiple nodes? Is it even worth it to try, or would the gains made by parallelizing over, say, 100 processors be negated by increased overhead time? </p>