http://www.k-wave.org/forum/topic/optimised-codes-using-checkpoints Support for the k-Wave MATLAB toolbox en-US Tue, 12 May 2026 22:24:52 +0000 http://bbpress.org/?v=1.0.2 q http://www.k-wave.org/forum/search.php http://www.k-wave.org/forum/topic/optimised-codes-using-checkpoints#post-8078 Mon, 08 Mar 2021 12:40:05 +0000 doguzaif 8078@http://www.k-wave.org/forum/ <p>Hi Jiri,</p> <p>Thank you for your response - it was indeed as simple as running the code again! </p> <p>And thank you for your tips regarding the script; I'll look into automating the process.</p> <p>Kind regards,<br /> Dogu </p> http://www.k-wave.org/forum/topic/optimised-codes-using-checkpoints#post-8077 Wed, 03 Mar 2021 18:36:29 +0000 Jiri Jaros 8077@http://www.k-wave.org/forum/ <p>Hi Dogu,<br /> it's really simple, just start it again with the same parameters. If the binary finds the checkpoint file, it will continue from the point where it was interrupted. If not, it will start from the beginning!</p> <p>In order to automate the whole process, I check the output file and compare datasets t_index and Nt. If they are equal, the simulation has finished. If not, I resubmit the same job (you can do it as the last command in your bash script). You can use, e.g., h5dump to read the data, or use pyh5 (<a href="https://docs.h5py.org/en/stable/high/dataset.html" rel="nofollow">https://docs.h5py.org/en/stable/high/dataset.html</a>)</p> <p>Best wishes<br /> Jiri </p> http://www.k-wave.org/forum/topic/optimised-codes-using-checkpoints#post-8073 Mon, 01 Mar 2021 22:39:01 +0000 doguzaif 8073@http://www.k-wave.org/forum/ <p>Hi all,</p> <p>I have a simulation at hand that looks like it will take ~8 hours on the cluster machine I have access to, yet I can run simulations for only 6 hours in one job submission. Using a bash script, I have managed to create a checkpoint file for the first leg of the simulation. However, at the moment I am not sure how to make the second leg start from where the checkpoint file was created. Does this just happen automatically when I run the same simulation script? Here is my code:</p> <p>#!/bin/bash</p> <p>#SBATCH --nodes=1<br /> #SBATCH --ntasks-per-node=24</p> <p>#SBATCH --mem=60000</p> <p>#SBATCH --time=6:00:00</p> <p>#SBATCH --job-name=position1<br /> #SBATCH --account=free<br /> #SBATCH --partition=batch-sky</p> <p>#SBATCH --mail-user=dz322@bath.ac.uk</p> <p>#SBATCH --output=StdOut.o.%j<br /> #SBATCH --error=StdErr.e.%j</p> <p>module purge<br /> module load slurm<br /> module load matlab<br /> module load hdf5/intel<br /> module load intel/compiler/64/18.5.274<br /> module load intel/mkl/64/18.5.274<br /> module load fftw3/intel/avx/3.3.4<br /> module load gcc/9.2.0</p> <p>export OMP_NUM_THREADS=24<br /> export OMP_PLACES=cores<br /> export OMP_PROC_BIND=true</p> <p>../kwave/kspaceFirstOrder-OMP/skylake/kspaceFirstOrder-OMP -i position1.h5 -o pos1_out_sky_2.h5 --checkpoint_file check_pos5_sky --checkpoint_interval 20000</p> <p>The manual is talking about putting a loop in the bash script, yet I am unsure as to how I can implement this. Any help to do with this would be greatly appreciated. Many thanks!</p> <p>Best wishes,<br /> Dogu Zaifoglu<br /> PhD candidate in Mechanical Engineering<br /> MEng, University of Bath </p>