http://www.k-wave.org/forum/topic/hdf5-problems Support for the k-Wave MATLAB toolbox en-US Tue, 12 May 2026 22:28:46 +0000 http://bbpress.org/?v=1.0.2 q http://www.k-wave.org/forum/search.php http://www.k-wave.org/forum/topic/hdf5-problems#post-8736 Fri, 07 Apr 2023 12:27:33 +0000 lschlieder 8736@http://www.k-wave.org/forum/ <p>After a week of fiddeling around, I found out, that there is an environment Variable under linux called HDF5_USE_FILE_LOCKING (<a href="https://docs.hdfgroup.org/hdf5/develop/_h5public_8h.html#a347a82c5915f93e3f03265aac4f7a795" rel="nofollow">https://docs.hdfgroup.org/hdf5/develop/_h5public_8h.html#a347a82c5915f93e3f03265aac4f7a795</a>)</p> <p>You can just:<br /> export HDF5_USE_FILE_LOCKING='FALSE' </p> http://www.k-wave.org/forum/topic/hdf5-problems#post-8735 Wed, 05 Apr 2023 17:33:18 +0000 lschlieder 8735@http://www.k-wave.org/forum/ <p>I posted a similar topic in general, and still have found no solution. I am running into a very weird situation, where kspaceFirstOrder-CUDA fails to open the input h5 file. It seems unable to open or locate the file: </p> <p>me@cluster_node:/clusterpath/KWaveSimulationsCorrect/rng806480170$ kspaceFirstOrder-CUDA -i ./rholo3d_kwave_input.h5 -o test.h5</p> <p>┌───────────────────────────────────────────────────────────────┐<br /> │ kspaceFirstOrder-CUDA v1.3 │<br /> ├───────────────────────────────────────────────────────────────┤<br /> │ Reading simulation configuration: Failed │<br /> └───────────────────────────────────────────────────────────────┘<br /> ┌───────────────────────────────────────────────────────────────┐<br /> │ !!! K-Wave experienced a fatal error !!! │<br /> ├───────────────────────────────────────────────────────────────┤<br /> │ Error: File ./rholo3d_kwave_input.h5 was not found or cannot │<br /> │ be opened.: iostream error │<br /> ├───────────────────────────────────────────────────────────────┤<br /> │ Execution terminated │<br /> └───────────────────────────────────────────────────────────────┘</p> <p>The weird thing is, that the same program can use the same input files and it works, when i start the program on my local pc, instead of the cluster i want to use everything works fine. </p> <p>me@mypc:/cluster_remote_smtp_access/KWaveSimulationsCorrect/rng806480170$ kspaceFirstOrder-CUDA -i rholo3d_kwave_input.h5 -o test.h5</p> <p>┌───────────────────────────────────────────────────────────────┐<br /> │ kspaceFirstOrder-CUDA v1.3 │<br /> ├───────────────────────────────────────────────────────────────┤<br /> │ Reading simulation configuration: Done │<br /> │ Selected GPU device id: 0 │<br /> │ GPU device name: NVIDIA GeForce GTX 1650 Ti │<br /> │ Number of CPU threads: 16 │<br /> │ Processor name: Intel(R) Core(TM) i9-10885H CPU @ 2.40GHz │<br /> ├───────────────────────────────────────────────────────────────┤<br /> │ Simulation details │<br /> ├───────────────────────────────────────────────────────────────┤<br /> │ Domain dimensions: 256 x 256 x 128 │<br /> │ Medium type: 3D │<br /> │ Simulation time steps: 828 │<br /> ├───────────────────────────────────────────────────────────────┤<br /> │ Initialization │<br /> ├───────────────────────────────────────────────────────────────┤<br /> │ Memory allocation: Done │</p> <p>The files are created by Matlab2019b, since newer versions crash in various ways, i.e. 2022a:</p> <p>Error using hdf5lib2<br /> Unable to open the file because of HDF5 Library error. Reason:Unknown</p> <p>Error in H5F.open (line 130)<br /> file_id = H5ML.hdf5lib2('H5Fopen', filename, flags, fapl, is_remote);</p> <p>Error in h5write (line 108)<br /> file_id = H5F.open(Filename,flags,fapl);</p> <p>Error in writeMatrix (line 204)<br /> h5write(filename, ['/' matrix_name], matrix);</p> <p>Error in kspaceFirstOrder_saveToDisk (line 462)<br /> writeMatrix(flags.save_to_disk, eval(variable_list{cast_index}), variable_list{cast_index}, hdf_compression_level);</p> <p>Error in kspaceFirstOrder3D (line 673)<br /> kspaceFirstOrder_saveToDisk;</p> <p>Error in init_kwave_sim (line 169)<br /> sensor_data = kspaceFirstOrder3D(kgrid, medium, source, sensor, input_args{:});</p> <p>Now i do not even know where to start debugging this.<br /> First problem could be, that the file isn't there, but i checked that like 100 times. It could be some weird access stuff, but i never ran into problems before, though i obviously do not have sudo rights on the cluster.</p> <p>I assume, since the binaries are statically linked everything is contained within them, and i do not need to worry about CUDA versions or hdf5 versions. Is that correct? Also does the Card i run it on matter? I assume it just works for all new Nvidia cards, like A100, Tesla V100 etc, correct? </p> <p>Does anyone have any ideas that go beyond "have you checked if the file is really there?" </p>