k-Wave User Forum » Topic: CPU Binaries - Sampled Data Post Processing Fails?

k-Wave User Forum » Topic: CPU Binaries - Sampled Data Post Processing Fails? http://www.k-wave.org/forum/topic/cpu-binaries-sampled-data-post-processing-fails Support for the k-Wave MATLAB toolbox en-US Tue, 12 May 2026 22:24:51 +0000 http://bbpress.org/?v=1.0.2 <![CDATA[Search]]> q http://www.k-wave.org/forum/search.php Jiri Jaros on "CPU Binaries - Sampled Data Post Processing Fails?" http://www.k-wave.org/forum/topic/cpu-binaries-sampled-data-post-processing-fails#post-8311 Tue, 21 Sep 2021 16:32:59 +0000 Jiri Jaros 8311@http://www.k-wave.org/forum/ Hi doguzaif, honestly, I have no idea what can be wrong. I would have to inspect the output file. But looking at the error message, this might be a problem of writing HDF5 attributes. That has no impact on the simulation but attributes such as file description, CPU name, etc. may be missing. Best Jiri doguzaif on "CPU Binaries - Sampled Data Post Processing Fails?" http://www.k-wave.org/forum/topic/cpu-binaries-sampled-data-post-processing-fails#post-8079 Mon, 08 Mar 2021 12:47:13 +0000 doguzaif 8079@http://www.k-wave.org/forum/ Hi Jiri, Thank you for your response. I'm attaching 1) My bash script, where you can see the modules I'm uploading, and 2) the output log. 1) My script file ' #!/bin/bash #SBATCH --nodes=1 #SBATCH --ntasks-per-node=24 #SBATCH --mem=60000 #SBATCH --time=6:00:00 #SBATCH --job-name=position1 #SBATCH --account=free #SBATCH --partition=batch-sky #SBATCH --mail-user=dz322@bath.ac.uk #SBATCH --output=StdOut.o.%j #SBATCH --error=StdErr.e.%j module purge module load slurm module load matlab module load hdf5/intel module load intel/compiler/64/18.5.274 module load intel/mkl/64/18.5.274 module load fftw3/intel/avx/3.3.4 module load gcc/9.2.0 export OMP_NUM_THREADS=24 export OMP_PLACES=cores export OMP_PROC_BIND=true ../kwave/kspaceFirstOrder-OMP/skylake/kspaceFirstOrder-OMP -i position1.h5 -o pos1_out_sky.h5 --checkpoint_file check_pos1_sky --checkpoint_interval 20000 ' 2) Log This first one is the error report. ' ┌───────────────────────────────────────────────────────────────┐ │ !!! K-Wave experienced a fatal error !!! │ ├───────────────────────────────────────────────────────────────┤ │ basic_string::erase: __pos (which is 18446744073709551615) > │ │ this->size() (which is 14) │ ├───────────────────────────────────────────────────────────────┤ │ Execution terminated │ └───────────────────────────────────────────────────────────────┘ ' And this is the output report. I used the university's HPC system, called "Balena". Also, this is the second leg of the computation, and the checkpoint file has been deleted since the task was completed. '[dz322@balena-01 execute2.1]$ cat StdOut.o.4015071 ┌───────────────────────────────────────────────────────────────┐ │ kspaceFirstOrder-OMP v1.3 │ ├───────────────────────────────────────────────────────────────┤ │ Reading simulation configuration: Done │ │ Number of CPU threads: 24 │ │ Processor name: Intel(R) Xeon(R) Gold 6126 CPU @ 2.60GHz │ ├───────────────────────────────────────────────────────────────┤ │ Simulation details │ ├───────────────────────────────────────────────────────────────┤ │ Domain dimensions: 7500 x 7500 │ │ Medium type: 2D │ │ Simulation time steps: 136000 │ ├───────────────────────────────────────────────────────────────┤ │ Initialization │ ├───────────────────────────────────────────────────────────────┤ │ Memory allocation: Done │ │ Data loading: Done │ │ Elapsed time: 62.30s │ ├───────────────────────────────────────────────────────────────┤ │ Recovered from time step: 98504 │ ├───────────────────────────────────────────────────────────────┤ │ FFT plans creation: Done │ │ Pre-processing phase: Done │ │ Elapsed time: 0.11s │ ├───────────────────────────────────────────────────────────────┤ │ Computational resources │ ├───────────────────────────────────────────────────────────────┤ │ Current host memory in use: 4181MB │ │ Expected output file size: 389MB │ ├───────────────────────────────────────────────────────────────┤ │ Simulation │ ├──────────┬────────────────┬──────────────┬────────────────────┤ │ Progress │ Elapsed time │ Time to go │ Est. finish time │ ├──────────┼────────────────┼──────────────┼────────────────────┤ │ 72% │ 0.331s │ 7609.713s │ 07/03/21 18:16:37 │ │ 77% │ 1270.113s │ 6350.353s │ 07/03/21 18:16:48 │ │ 82% │ 2656.418s │ 4971.005s │ 07/03/21 18:16:55 │ │ 87% │ 4038.188s │ 3590.181s │ 07/03/21 18:16:56 │ │ 92% │ 5421.730s │ 2209.407s │ 07/03/21 18:16:59 │ │ 97% │ 6805.662s │ 828.360s │ 07/03/21 18:17:02 │ ├──────────┴────────────────┴──────────────┴────────────────────┤ │ Elapsed time: 7642.89s │ ├───────────────────────────────────────────────────────────────┤ │ Sampled data post-processing: Failed │ └───────────────────────────────────────────────────────────────┘ ######################################################################## ----------------------! Balena Job Details !---------------------------- JobID : 4015071 No. of nodes : 1 No. of CPUs : 24 Timelimit : 06:00:00 Elapsed time : 02:08:30 Nodelist : node-sky-001 Energy Used : 2665375.56 Joules ######################################################################## ' It still does give a final output file, and the results look fine. I'm just not sure what the "sampled data post-processing" step does to the results at the end? Many thanks, Dogu Jiri Jaros on "CPU Binaries - Sampled Data Post Processing Fails?" http://www.k-wave.org/forum/topic/cpu-binaries-sampled-data-post-processing-fails#post-8076 Wed, 03 Mar 2021 18:28:55 +0000 Jiri Jaros 8076@http://www.k-wave.org/forum/ Hi Dogu, I've never seen this error before. Could you be more specific? 1. Did you compile the binary by yourself? If so, what compiler and library versions did you use 2. Could you share the whole log with me? Best wishes Jiri doguzaif on "CPU Binaries - Sampled Data Post Processing Fails?" http://www.k-wave.org/forum/topic/cpu-binaries-sampled-data-post-processing-fails#post-8075 Wed, 03 Mar 2021 13:38:02 +0000 doguzaif 8075@http://www.k-wave.org/forum/ Hi all, So when I run a k-Wave simulation using CPU binaries on my uni's HPC, I get this error at the end of the simulation. According to the error and performance reports, all the steps complete successfully, yet at the prior to "sampled data post processing" step, I get this error: │ basic_string::erase: __pos (which is 18446744073709551615) > │ │ this->size() (which is 14) Could anybody offer any help to do with this? Would be much appreciated, many thanks from now. Best wishes, Dogu Zaifoglu PhD Researcher in Mechanical Engineering MEng, University of Bath