k-Wave User Forum » Topic: Error reading h5 files when using binaries (MATLAB 2020a)

k-Wave User Forum » Topic: Error reading h5 files when using binaries (MATLAB 2020a) http://www.k-wave.org/forum/topic/error-reading-h5-files-when-using-binaries Support for the k-Wave MATLAB toolbox en-US Sat, 23 May 2026 20:28:33 +0000 http://bbpress.org/?v=1.0.2 <![CDATA[Search]]> q http://www.k-wave.org/forum/search.php Bradley Treeby on "Error reading h5 files when using binaries (MATLAB 2020a)" http://www.k-wave.org/forum/topic/error-reading-h5-files-when-using-binaries#post-8650 Tue, 08 Nov 2022 10:27:51 +0000 Bradley Treeby 8650@http://www.k-wave.org/forum/ Noting this bug has been addressed in k-Wave v1.4 janee11 on "Error reading h5 files when using binaries (MATLAB 2020a)" http://www.k-wave.org/forum/topic/error-reading-h5-files-when-using-binaries#post-8586 Wed, 20 Jul 2022 09:33:57 +0000 janee11 8586@http://www.k-wave.org/forum/ using R2022a, still works perfectly, did not need to download the patch saturnnan on "Error reading h5 files when using binaries (MATLAB 2020a)" http://www.k-wave.org/forum/topic/error-reading-h5-files-when-using-binaries#post-8437 Wed, 26 Jan 2022 09:38:51 +0000 saturnnan 8437@http://www.k-wave.org/forum/ The above error（Error: Invalid format of the input file: iostream error） will also appear in Matlab R2021a. It can be solved according to the method （So in short, the work around is: 1. Open acousticFieldPropagator, writeAttributes, and writeMatrix in k-Wave...） provided by Treeby. Thanks a lot. Audrey Ntad on "Error reading h5 files when using binaries (MATLAB 2020a)" http://www.k-wave.org/forum/topic/error-reading-h5-files-when-using-binaries#post-8131 Tue, 20 Apr 2021 13:11:35 +0000 Audrey Ntad 8131@http://www.k-wave.org/forum/ Hello, I am glad to find this discussion, I am actually using the k-wave toolbox with Matlab 2021a and have been encountering many issues such as errors in reading h5 files and some executables (kspaceFirstOrder3D-OMP.exe) stopping to work. Has anyone tried to solve these issues on the 2021a Mtlab version (I have the 1.2version of the toolbox). Thank you satchit24 on "Error reading h5 files when using binaries (MATLAB 2020a)" http://www.k-wave.org/forum/topic/error-reading-h5-files-when-using-binaries#post-8111 Fri, 02 Apr 2021 06:04:21 +0000 satchit24 8111@http://www.k-wave.org/forum/ Hello, I have 2020b Version in windows 10. I tried to follow the steps as Bradley has mentioned but while writing those files it gives an error 'Access is Denied'. How to go about this error. Kindly let me know. marjanbn on "Error reading h5 files when using binaries (MATLAB 2020a)" http://www.k-wave.org/forum/topic/error-reading-h5-files-when-using-binaries#post-8072 Mon, 01 Mar 2021 19:09:47 +0000 marjanbn 8072@http://www.k-wave.org/forum/ Hello, I could resolve my problem by changing the permission of the codes in the binaries folder. Since I am using a Linux system, I could do that by using the eclipse app, then through properties/permissions of the e.g., kspaceFirstOrder-CUDA file, I clicked on Execute for User. Hope it helps and thanks for your fantastic toolbox. SamPichardo on "Error reading h5 files when using binaries (MATLAB 2020a)" http://www.k-wave.org/forum/topic/error-reading-h5-files-when-using-binaries#post-8067 Wed, 24 Feb 2021 18:37:04 +0000 SamPichardo 8067@http://www.k-wave.org/forum/ Just to say that these latest versions of Matlab have become a nightmare to read HDF5 files, files generated in Python-based libraries (h5py) make now crash Matlab completely, when before it was completely ok. MATLAB crash file:C:\Users\samme\AppData\Local\Temp\matlab_crash_dump.31768-1: -------------------------------------------------------------------------------- Access violation detected at 2021-02-24 10:34:28 -0700 -------------------------------------------------------------------------------- Configuration: Crash Decoding : Disabled - No sandbox or build area path Crash Mode : continue (default) Default Encoding : windows-1252 Deployed : false Graphics Driver : Unknown hardware Graphics card 1 : Intel Corporation ( 0x8086 ) Intel(R) UHD Graphics 630 Version 30.20.100.9314 (2021-2-12) Graphics card 2 : NVIDIA ( 0x10de ) NVIDIA GeForce RTX 2080 SUPER Version 27.21.14.6542 (2021-1-23) Java Version : Java 1.8.0_202-b08 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode MATLAB Architecture : win64 MATLAB Entitlement ID : 3294103 MATLAB Root : C:\Program Files\MATLAB\R2020b MATLAB Version : 9.9.0.1592791 (R2020b) Update 5 OpenGL : hardware Operating System : Microsoft Windows 10 Home Insider Preview Process ID : 31768 Processor ID : x86 Family 6 Model 158 Stepping 13, GenuineIntel Session Key : 018388dd-f82e-4a1d-8d88-162c6fc40c86 Window System : Version 10.0 (Build 21318) Fault Count: 1 Abnormal termination: Access violation Current Thread: 'MCR 0 interpreter thread' id 3300 Register State (from fault): RAX = 0000000000000001 RBX = 0000000000000000 RCX = 000001e13c124280 RDX = 0000000000000000 RSP = 0000006b37bf81f0 RBP = 0000000000000001 RSI = 000001e12f2a2140 RDI = 000000000300013c R8 = 0000000000000001 R9 = 000001e12a8b3ca0 R10 = 00000000000001e0 R11 = 000001e135b897a0 R12 = 0000000004000003 R13 = 0000000000000002 R14 = 000001e127d9b280 R15 = 0000000000000008 RIP = 00007ffb68c417a3 EFL = 00010256 CS = 0033 FS = 0053 GS = 002b Stack Trace (from fault): [ 0] 0x00007ffb68c417a3 C:\Program Files\MATLAB\R2020b\toolbox\matlab\imagesci\private\hdf5infoc.mexw64+00071587 mexfilerequiredapiversion+00018067 [ 1] 0x00007ffb68c3c07e C:\Program Files\MATLAB\R2020b\toolbox\matlab\imagesci\private\hdf5infoc.mexw64+00049278 [ 2] 0x00007ffb68c3c380 C:\Program Files\MATLAB\R2020b\toolbox\matlab\imagesci\private\hdf5infoc.mexw64+00050048 [ 3] 0x00007ffb68c38c2c C:\Program Files\MATLAB\R2020b\toolbox\matlab\imagesci\private\hdf5infoc.mexw64+00035884 [ 4] 0x00007ffb68c39ec9 C:\Program Files\MATLAB\R2020b\toolbox\matlab\imagesci\private\hdf5infoc.mexw64+00040649 [ 5] 0x00007ffb68c3d08f C:\Program Files\MATLAB\R2020b\toolbox\matlab\imagesci\private\hdf5infoc.mexw64+00053391 mexFunction+00000335 [ 6] 0x00007ffb8bf2a289 C:\Program Files\MATLAB\R2020b\bin\win64\libmex.dll+00565897 mexfile::Inspector::needs_upgrade+00015977 [ 7] 0x00007ffb8bf2b67b C:\Program Files\MATLAB\R2020b\bin\win64\libmex.dll+00571003 MexRetrieveVersion+00003579 [ 8] 0x00007ffb8bf2b9b4 C:\Program Files\MATLAB\R2020b\bin\win64\libmex.dll+00571828 MexRetrieveVersion+00004404 [ 9] 0x00007ffb8bf0c209 C:\Program Files\MATLAB\R2020b\bin\win64\libmex.dll+00442889 mexUnlock_800+00023993 [ 10] 0x00007ffb8c5626c1 bin\win64\pgo\m_dispatcher.dll+00665281 Mfh_file::dispatch_file_common+00000165 [ 11] 0x00007ffb8c561d62 bin\win64\pgo\m_dispatcher.dll+00662882 Mfh_error::lookup+00006498 [ 12] 0x00007ffb8c562615 bin\win64\pgo\m_dispatcher.dll+00665109 Mfh_file::dispatch+00000045 [ 13] 0x00007ffb8953c08f bin\win64\pgo\m_lxe.dll+00770191 CGGBuiltinImpl+00361103 [ 14] 0x00007ffb89627d92 bin\win64\pgo\m_lxe.dll+01736082 MathWorks::lxe::ShutdownLxeEngine+00090818 [ 15] 0x00007ffb89627bff bin\win64\pgo\m_lxe.dll+01735679 MathWorks::lxe::ShutdownLxeEngine+00090415 [ 16] 0x00007ffb895156b4 bin\win64\pgo\m_lxe.dll+00612020 CGGBuiltinImpl+00202932 [ 17] 0x00007ffb8964173d bin\win64\pgo\m_lxe.dll+01840957 mwboost::archive::detail::oserializer<mwboost::archive::binaryTerm_oarchive,MathWorks::lxe::ClosedAbstractionFunctionDescriptorOwningIrTree>::oserializer<mwboost::archive::binaryTerm_oarchive,MathWorks::lxe::ClosedAbstractionFunctionDescriptorOwningIrTree>+00033337 [ 18] 0x00007ffb8951944d bin\win64\pgo\m_lxe.dll+00627789 CGGBuiltinImpl+00218701 [ 19] 0x00007ffb8951871d bin\win64\pgo\m_lxe.dll+00624413 CGGBuiltinImpl+00215325 [ 20] 0x00007ffb895069b7 bin\win64\pgo\m_lxe.dll+00551351 CGGBuiltinImpl+00142263 [ 21] 0x00007ffb895065bf bin\win64\pgo\m_lxe.dll+00550335 CGGBuiltinImpl+00141247 [ 22] 0x00007ffb89512d65 bin\win64\pgo\m_lxe.dll+00601445 CGGBuiltinImpl+00192357 [ 23] 0x00007ffb895173c5 bin\win64\pgo\m_lxe.dll+00619461 CGGBuiltinImpl+00210373 [ 24] 0x00007ffb895163cc bin\win64\pgo\m_lxe.dll+00615372 CGGBuiltinImpl+00206284 [ 25] 0x00007ffb895ec163 bin\win64\pgo\m_lxe.dll+01491299 CGGBuiltinImpl+01082211 [ 26] 0x00007ffb895ec04b bin\win64\pgo\m_lxe.dll+01491019 CGGBuiltinImpl+01081931 [ 27] 0x00007ffb895ebf5a bin\win64\pgo\m_lxe.dll+01490778 CGGBuiltinImpl+01081690 [ 28] 0x00007ffb89626174 bin\win64\pgo\m_lxe.dll+01728884 MathWorks::lxe::ShutdownLxeEngine+00083620 [ 29] 0x00007ffb89626122 bin\win64\pgo\m_lxe.dll+01728802 MathWorks::lxe::ShutdownLxeEngine+00083538 [ 30] 0x00007ffb8afd6dba bin\win64\pgo\m_lxe.dll+28667322 MathWorks::lxe::profiler::IMexProfilingSupport::~IMexProfilingSupport+00058926 [ 31] 0x00007ffb8bfdb609 C:\Program Files\MATLAB\R2020b\bin\win64\libmwbridge.dll+00177673 mnGetPrompt+00031273 [ 32] 0x00007ffb8c8511ff C:\Program Files\MATLAB\R2020b\bin\win64\iqm.dll+00463359 iqm::Iqm::instance+00001023 [ 33] 0x00007ffb8c8c38b7 C:\Program Files\MATLAB\R2020b\bin\win64\iqm.dll+00932023 iqm::UserEvalPlugin::execute+00001351 [ 34] 0x00007ffb7feb80be C:\Program Files\MATLAB\R2020b\bin\win64\nativejmi.dll+00360638 nativejmi::JmiIIP::serializeExplicit+00013438 [ 35] 0x00007ffb8c877a3f C:\Program Files\MATLAB\R2020b\bin\win64\iqm.dll+00621119 iqm::Iqm::setupIqmFcnPtrs+00113615 [ 36] 0x00007ffb8c8831b0 C:\Program Files\MATLAB\R2020b\bin\win64\iqm.dll+00668080 iqm::Iqm::setupIqmFcnPtrs+00160576 [ 37] 0x00007ffb8c846fc3 C:\Program Files\MATLAB\R2020b\bin\win64\iqm.dll+00421827 iqm::Iqm::create+00007235 [ 38] 0x00007ffb8bfc7a3e C:\Program Files\MATLAB\R2020b\bin\win64\libmwbridge.dll+00096830 ioReadLine+00000478 [ 39] 0x00007ffb8bfc781c C:\Program Files\MATLAB\R2020b\bin\win64\libmwbridge.dll+00096284 ioReadLine+00000188 [ 40] 0x00007ffb8bfdba50 C:\Program Files\MATLAB\R2020b\bin\win64\libmwbridge.dll+00178768 mnGetCommandLineBuffer+00000304 [ 41] 0x00007ffb8bfdbeda C:\Program Files\MATLAB\R2020b\bin\win64\libmwbridge.dll+00179930 mnParser+00000506 [ 42] 0x00007ffb8c6862f4 C:\Program Files\MATLAB\R2020b\bin\win64\mcr.dll+00549620 mcr_set_enableReadingFromStdin+00016084 [ 43] 0x00007ffb8c61e7ad C:\Program Files\MATLAB\R2020b\bin\win64\mcr.dll+00124845 mcrFunctionSignature::set_signature+00103437 [ 44] 0x00007ffb8c63baea C:\Program Files\MATLAB\R2020b\bin\win64\mcr.dll+00244458 mcrFunctionSignature::set_signature+00223050 [ 45] 0x00007ffb8c8a4504 C:\Program Files\MATLAB\R2020b\bin\win64\iqm.dll+00804100 iqm::PackagedTaskPlugin::execute+00000084 [ 46] 0x00007ffb8c6803ce C:\Program Files\MATLAB\R2020b\bin\win64\mcr.dll+00525262 services::lmgr::exception::LicensingStartupException::~LicensingStartupException+00009822 [ 47] 0x00007ffb8c877a3f C:\Program Files\MATLAB\R2020b\bin\win64\iqm.dll+00621119 iqm::Iqm::setupIqmFcnPtrs+00113615 [ 48] 0x00007ffb8c847c42 C:\Program Files\MATLAB\R2020b\bin\win64\iqm.dll+00425026 iqm::Iqm::create+00010434 [ 49] 0x00007ffb8c847421 C:\Program Files\MATLAB\R2020b\bin\win64\iqm.dll+00422945 iqm::Iqm::create+00008353 [ 50] 0x00007ffb8c6560dc C:\Program Files\MATLAB\R2020b\bin\win64\mcr.dll+00352476 mcrInstantiationError::operator=+00011756 [ 51] 0x00007ffb8c656a3c C:\Program Files\MATLAB\R2020b\bin\win64\mcr.dll+00354876 mcrInstantiationError::operator=+00014156 [ 52] 0x00007ffb8c6543cc C:\Program Files\MATLAB\R2020b\bin\win64\mcr.dll+00345036 mcrInstantiationError::operator=+00004316 [ 53] 0x00007ffc1ff3a2a3 C:\Program Files\MATLAB\R2020b\bin\win64\mwboost_thread-vc141-mt-x64-1_70.dll+00041635 mwboost::thread::swap+00000083 [ 54] 0x00007ffc43466bcc C:\WINDOWS\System32\ucrtbase.dll+00158668 recalloc+00000092 [ 55] 0x00007ffc444654ee C:\WINDOWS\System32\KERNEL32.DLL+00087278 BaseThreadInitThunk+00000030 [ 56] 0x00007ffc45abc81b C:\WINDOWS\SYSTEM32\ntdll.dll+00509979 RtlUserThreadStart+00000043 This error was detected while a MEX-file was running. If the MEX-file is not an official MathWorks function, please examine its source code for errors. Please consult the External Interfaces Guide for information on debugging MEX-files. dgiraud on "Error reading h5 files when using binaries (MATLAB 2020a)" http://www.k-wave.org/forum/topic/error-reading-h5-files-when-using-binaries#post-8066 Mon, 22 Feb 2021 19:25:14 +0000 dgiraud 8066@http://www.k-wave.org/forum/ Using k-Wave 1.3 and MATLAB 2020b on Windows 10 with precompiled binaries, I was able successfully use kspaceFirstOrder3DC (within example_us_beam_patterns.m) following steps 1 and 2 of Brad's instructions. Step 3 appears unnecessary, as christianbaker noted. It looks like R2020b has been updated with the patch Brad provided; R2020b h5writeatt.m is essentially the same as the patch file. However, when trying kspaceFirstOrder3DG (again, within example_us_beam_patterns.m), the code produces an error similar to what marjanbn posted: --- Error using h5readc Unable to open 'C:\Users\giraud\AppData\Local\Temp\1\kwave_output_data22-Feb-2021-09-38-19.h5'. File or folder not found. Error in h5read (line 93) [data,var_class] = h5readc(Filename,Dataset,start,count,stride); Error in kspaceFirstOrder3DC (line 569) Nx = h5read(output_filename, '/Nx'); Error in kspaceFirstOrder3DG (line 69) sensor_data = kspaceFirstOrder3DC(varargin{:}); Error in dg_example_us_beam_patterns (line 182) sensor_data = kspaceFirstOrder3DG(kgrid, medium, transducer, sensor, input_args{:}); --- Is a work-around possible for this error? Looking in the k-Wave m files, I couldn't find any additional calls to h5writeatt where I could specify 'TextEncoding'. Big thank you to the k-Wave team for making this code available! I'm very grateful to be able use your work. marjanbn on "Error reading h5 files when using binaries (MATLAB 2020a)" http://www.k-wave.org/forum/topic/error-reading-h5-files-when-using-binaries#post-8057 Mon, 08 Feb 2021 22:53:16 +0000 marjanbn 8057@http://www.k-wave.org/forum/ Hello, I am using MATLAB R2020b and I couldn't fix the problem as explained by Brad. The error I am getting is ---------------------------------------------- Error using h5readc Unable to open '/tmp/kwave_output_data08-Feb-2021-16-43-56.h5'. File or folder not found. Error in h5read (line 93) [data,var_class] = h5readc(Filename,Dataset,start,count,stride); Error in kspaceFirstOrder3DC (line 569) Nx = h5read(output_filename, '/Nx'); ----------------------------------- I appreciate it if you clarify if the error I am getting is the same as in this thread and if not, how should I fix it? Mengjie_shi on "Error reading h5 files when using binaries (MATLAB 2020a)" http://www.k-wave.org/forum/topic/error-reading-h5-files-when-using-binaries#post-8027 Tue, 26 Jan 2021 10:33:42 +0000 Mengjie_shi 8027@http://www.k-wave.org/forum/ I don't think 2020b has fixed the bug. I tried to update my MATLAB2020b to the latest version but still has the same error. Anyway, the solution provided by Brad works, Thank you! Bradley Treeby on "Error reading h5 files when using binaries (MATLAB 2020a)" http://www.k-wave.org/forum/topic/error-reading-h5-files-when-using-binaries#post-7973 Thu, 03 Dec 2020 10:01:48 +0000 Bradley Treeby 7973@http://www.k-wave.org/forum/ Thanks Christian, that's good to know! christianbaker on "Error reading h5 files when using binaries (MATLAB 2020a)" http://www.k-wave.org/forum/topic/error-reading-h5-files-when-using-binaries#post-7969 Mon, 30 Nov 2020 10:18:43 +0000 christianbaker 7969@http://www.k-wave.org/forum/ Just tested this in 2020b and all works fine without downloading the patched <code>h5writeatt</code>, so it seems Mathworks have fixed the issue since 2020a. samantp on "Error reading h5 files when using binaries (MATLAB 2020a)" http://www.k-wave.org/forum/topic/error-reading-h5-files-when-using-binaries#post-7685 Fri, 03 Jul 2020 12:52:50 +0000 samantp 7685@http://www.k-wave.org/forum/ Ah, that seems to have resolved the issue. Thanks! Bradley Treeby on "Error reading h5 files when using binaries (MATLAB 2020a)" http://www.k-wave.org/forum/topic/error-reading-h5-files-when-using-binaries#post-7657 Sat, 27 Jun 2020 13:37:01 +0000 Bradley Treeby 7657@http://www.k-wave.org/forum/ Hi samantp, Are you using k-Wave V1.3? This function should be in the private folder, which should be accessible to writeAttributes if the root k-Wave folder is on the MATLAB path. Brad. samantp on "Error reading h5 files when using binaries (MATLAB 2020a)" http://www.k-wave.org/forum/topic/error-reading-h5-files-when-using-binaries#post-7645 Thu, 25 Jun 2020 15:48:21 +0000 samantp 7645@http://www.k-wave.org/forum/ Hi, I tried this solution but now I get the error "Unrecognized function or variable 'getH5Literals'. Error in writeAttributes (line 45) getH5Literals; " anubhav on "Error reading h5 files when using binaries (MATLAB 2020a)" http://www.k-wave.org/forum/topic/error-reading-h5-files-when-using-binaries#post-7479 Tue, 05 May 2020 04:09:09 +0000 anubhav 7479@http://www.k-wave.org/forum/ That worked like a charm. Thanks a lot for the quick reply on this one and the speedups are amazing. Bradley Treeby on "Error reading h5 files when using binaries (MATLAB 2020a)" http://www.k-wave.org/forum/topic/error-reading-h5-files-when-using-binaries#post-7477 Mon, 04 May 2020 16:21:55 +0000 Bradley Treeby 7477@http://www.k-wave.org/forum/ Due to a change in <code>h5writeatt</code> in MATLAB 2020a (it changed the default value of <code>'TextEncoding'</code> from <code>'system'</code> to <code>'UTF-8'</code>), this version of MATLAB isn't compatible with k-Wave (any version). This doesn't affect the MATLAB-only version of k-Wave, just the functions writing HDF5 input files to use with the C++ codes. I wrote a bug-fix by adding the lines <code>'TextEncoding', 'system'</code> to all calls to <code>h5writeatt</code>, but then discovered a MATLAB bug in <code>h5writeatt</code> which doesn't allow the text encoding to be changed back. After liaising with Mathworks, they confirmed this is a known issue, and helpfully sent me a patch for <code>h5writeatt</code> which you can download <a href="http://www.k-wave.org/downloads/h5writeatt.m">here</a>. They've given me permission to share this with k-Wave users. So in short, the work around is: 1. Open <code>acousticFieldPropagator</code>, <code>writeAttributes</code>, and <code>writeMatrix</code> in k-Wave. 2. For all calls to <code>h5writeatt</code>, add the option <code>'TextEncoding', 'system'</code> to the end. For example: <code>h5writeatt(save_to_disk, '/', FILE_MAJOR_VER_ATT_NAME, FBP_FILE_MAJOR_VERSION);</code> becomes: <code>h5writeatt(save_to_disk, '/', FILE_MAJOR_VER_ATT_NAME, FBP_FILE_MAJOR_VERSION, 'TextEncoding', 'system');</code> 3. Download the <a href="http://www.k-wave.org/downloads/h5writeatt.m">patch</a> for <code>h5writeatt</code> and either replace the version in MATLAB 2020a, or place it somewhere on the MATLAB path. You can find where <code>h5writeatt</code> is stored by typing: <code>which h5writeatt</code> It should be something like: <code>C:\Program Files\MATLAB\R2020a\toolbox\matlab\imagesci\</code>. Let me know any problems. I've put a link to this thread on the downloads page. Brad. anubhav on "Error reading h5 files when using binaries (MATLAB 2020a)" http://www.k-wave.org/forum/topic/error-reading-h5-files-when-using-binaries#post-7472 Sun, 03 May 2020 23:43:24 +0000 anubhav 7472@http://www.k-wave.org/forum/ I have tried this with downloading the executables provided and by compiling from source but it seems like when using the C++ and GPU binaries there is an issue in reading the h5 files. Here is the error I get ./kspaceFirstOrder-CUDA -i /tmp/example_input.h5 -o /tmp/example_output.h5 --p_final --p_max --verbose 2 ┌───────────────────────────────────────────────────────────────┐ │ kspaceFirstOrder-CUDA v1.3 │ ├───────────────────────────────────────────────────────────────┤ │ Git hash: 468dc31c2842a7df5f2a07c3a13c16c9b0b2b770 │ ├───────────────────────────────────────────────────────────────┤ │ Reading simulation configuration: Failed │ └───────────────────────────────────────────────────────────────┘ ┌───────────────────────────────────────────────────────────────┐ │ !!! K-Wave experienced a fatal error !!! │ ├───────────────────────────────────────────────────────────────┤ │ Error: Invalid format of the input file: iostream error │ ├───────────────────────────────────────────────────────────────┤ │ Execution terminated │ └───────────────────────────────────────────────────────────────┘ My findings and process: I am comiling from source using hdf5 v1.8.12 ( this seems to be the same version used by Matlab R2020a to write the file) >> a = hdf5info('/tmp/example_input.h5') a = struct with fields: Filename: 'example_input.h5' LibVersion: '1.8.12' Offset: 0 FileSize: 42880070 GroupHierarchy: [1×1 struct] On digging deeper into and doing console logs in the Hdf5/Hdf5File.cpp library to see the values of attributes fetched, it looks like there is an issue when attempting to read it. string Hdf5File::readStringAttribute Added : std::cout << " ****** readStringAttr ******* " << attributeName.c_str() << " ::: " << string(value) << "\n"; Output : ****** readStringAttr ******* file_type ::: �� Please let me know how to resolve this error and I can use the CUDA library for optimizing the simulations