# Hdf-forum archives **URL:** https://forum.hdfgroup.org/c/hdf-forum/11.md [Latest](https://forum.hdfgroup.org/latest.md) · [Categories](https://forum.hdfgroup.org/categories.md) --- ## [About the Hdf-forum archives category](https://forum.hdfgroup.org/t/about-the-hdf-forum-archives-category/908)
**Author:** [@system](https://forum.hdfgroup.org/u/system)\ **Replies:** 0\ **Last updated:** [March 11, 2018, 8:27pm UTC](https://forum.hdfgroup.org/t/about-the-hdf-forum-archives-category/908 "2018-03-11T20:27:47Z")
Messages from the previous HDF-Forum. These will be sorted into product categories as The HDF Group staff time allows. --- ## [HDF Project for storing Time-Series storage of Physiological Waveforms - ECG etc](https://forum.hdfgroup.org/t/hdf-project-for-storing-time-series-storage-of-physiological-waveforms-ecg-etc/3441)
**Author:** [@Rajah\_Tim\_NIH\_CC\_SUR](https://forum.hdfgroup.org/u/Rajah_Tim_NIH_CC_SUR)\ **Replies:** 4\ **Last updated:** [April 11, 2025, 3:39pm UTC](https://forum.hdfgroup.org/t/hdf-project-for-storing-time-series-storage-of-physiological-waveforms-ecg-etc/3441 "2025-04-11T15:39:17Z")
Hello Everyone, I had posted earlier ago requesting any information on HDF based projects that were developed for Time-Series based storage of Physiological waveforms such as ECG etc. I would really appreciate your hel… --- ## [Working with JPEG](https://forum.hdfgroup.org/t/working-with-jpeg/1041)
**Author:** [@White\_Robert](https://forum.hdfgroup.org/u/White_Robert)\ **Replies:** 2\ **Last updated:** [October 9, 2024, 10:54am UTC](https://forum.hdfgroup.org/t/working-with-jpeg/1041 "2024-10-09T10:54:32Z")
Hello, I am new to the HDF system and the documentation is about opaque on how to go about taking a .jpg or jpeg file and placing it into an HDF file. Does anyone have an example (in C or C++) on this process and any … --- ## [Configuring 1.8.18 on macOS Sierra with GFortran 6.3.0](https://forum.hdfgroup.org/t/configuring-1-8-18-on-macos-sierra-with-gfortran-6-3-0/3999)
**Author:** [@mike.jackson](https://forum.hdfgroup.org/u/mike.jackson)\ **Replies:** 1\ **Last updated:** [February 19, 2024, 3:34pm UTC](https://forum.hdfgroup.org/t/configuring-1-8-18-on-macos-sierra-with-gfortran-6-3-0/3999 "2024-02-19T15:34:21Z")
I am having issues configuring HDF5 1.8.18 with CMake on macOS Sierra using GFortran 6.3.0 and the normal Xcode tooling. The following is the error that I get during cmake configuration: -- Detecting Fortran/C Interface … --- ## [Mixing use of ZLib and SZip compression](https://forum.hdfgroup.org/t/mixing-use-of-zlib-and-szip-compression/3643)
**Author:** [@houssen](https://forum.hdfgroup.org/u/houssen)\ **Replies:** 3\ **Last updated:** [January 20, 2024, 7:52pm UTC](https://forum.hdfgroup.org/t/mixing-use-of-zlib-and-szip-compression/3643 "2024-01-20T19:52:10Z")
When using HDF5, is it possible to mix ZLib and SZip compression ? If yes how ? My understanding is that: 1. ZLib can compress any data (char \*, int, double, ...) 2. SZip is dedicated to number compression only (float… --- ## [make check hangs on iopipe](https://forum.hdfgroup.org/t/make-check-hangs-on-iopipe/2469)
**Author:** [@mkb789](https://forum.hdfgroup.org/u/mkb789)\ **Replies:** 2\ **Last updated:** [December 30, 2022, 5:21pm UTC](https://forum.hdfgroup.org/t/make-check-hangs-on-iopipe/2469 "2022-12-30T17:21:29Z")
Hello, I'm trying to install hdf5-1.8.7 on Mac OSX 10.6.8. Following the instructions in the INSTALL file, I type: sudo ./configure --prefix=/usr/local/hdf5 sudo make sudo make check from within the hdf5-1.8.7 sub… --- ## [C++ Read Compound dataset without taking static structure for fieldname](https://forum.hdfgroup.org/t/c-read-compound-dataset-without-taking-static-structure-for-fieldname/10116)
**Author:** [@er\_akhilesh15](https://forum.hdfgroup.org/u/er_akhilesh15)\ **Replies:** 0\ **Last updated:** [August 22, 2022, 8:45am UTC](https://forum.hdfgroup.org/t/c-read-compound-dataset-without-taking-static-structure-for-fieldname/10116 "2022-08-22T08:45:01Z")
I have multiple H5 files and i am creating a generic code where i need to read specific field defined in input whether it will be an array or double or int. i can’t take like fixed struct s1\_t like below because it has d… --- ## [compound attribute with Java HDF Object package](https://forum.hdfgroup.org/t/compound-attribute-with-java-hdf-object-package/1622)
**Author:** [@Brian\_Walsh](https://forum.hdfgroup.org/u/Brian_Walsh)\ **Replies:** 2\ **Last updated:** [December 3, 2021, 12:07pm UTC](https://forum.hdfgroup.org/t/compound-attribute-with-java-hdf-object-package/1622 "2021-12-03T12:07:05Z")
Is it possible to create a compound attribute using the java HDF object package? I am trying to create a simple compound type that holds two 32-bit unsigned integers. (An array would be trivial, but an existing impleme… --- ## [H5Dread get data incompletely](https://forum.hdfgroup.org/t/h5dread-get-data-incompletely/9205)
**Author:** [@lei.zheng](https://forum.hdfgroup.org/u/lei.zheng)\ **Replies:** 0\ **Last updated:** [November 27, 2021, 3:52pm UTC](https://forum.hdfgroup.org/t/h5dread-get-data-incompletely/9205 "2021-11-27T15:52:58Z")
I want to read h5 file in C. Here is my code to read a compound dataset. I have 7 members in structure “Boundary”, which are floats or integers. However i can’t get the last member from H5Dread. The other 6 members have … --- ## [H5Eset\_auto for all threads?](https://forum.hdfgroup.org/t/h5eset-auto-for-all-threads/1501)
**Author:** [@andrew.collette](https://forum.hdfgroup.org/u/andrew.collette)\ **Replies:** 5\ **Last updated:** [October 12, 2021, 7:01pm UTC](https://forum.hdfgroup.org/t/h5eset-auto-for-all-threads/1501 "2021-10-12T19:01:10Z")
Hi, I am using H5Eset\_auto to register a custom error callback function. However, it seems I need to call H5Eset\_auto again from each new thread I create; the callback which prints to stderr is used by default. Is t… --- ## [H5Import and 1 dimensional data](https://forum.hdfgroup.org/t/h5import-and-1-dimensional-data/9039)
**Author:** [@dnessett](https://forum.hdfgroup.org/u/dnessett)\ **Replies:** 0\ **Last updated:** [October 11, 2021, 6:41pm UTC](https://forum.hdfgroup.org/t/h5import-and-1-dimensional-data/9039 "2021-10-11T18:41:31Z")
Hi. I am trying to open an HDF5 file in Python using vaex\_open() that was created using H5Import. It appears there is no way to create the HDF5 file as a one-dimensional vector. For example, if I use (for a binary file c… --- ## [Issues with parallel HDF5 build on Mac](https://forum.hdfgroup.org/t/issues-with-parallel-hdf5-build-on-mac/9031)
**Author:** [@18659209056](https://forum.hdfgroup.org/u/18659209056)\ **Replies:** 0\ **Last updated:** [October 7, 2021, 3:04pm UTC](https://forum.hdfgroup.org/t/issues-with-parallel-hdf5-build-on-mac/9031 "2021-10-07T15:04:47Z")
Hi there, I’m not quite familiar with hdf5, but my research work requires for building Parallel HDF5, during configuration, error occurs compliant that libmpio.a was not found, and could not find a simple mpi I/o program… --- ## [Writing large data using parallel HDF5 ](https://forum.hdfgroup.org/t/writing-large-data-using-parallel-hdf5/8942)
**Author:** [@soorena.parthian](https://forum.hdfgroup.org/u/soorena.parthian)\ **Replies:** 0\ **Last updated:** [September 4, 2021, 9:34pm UTC](https://forum.hdfgroup.org/t/writing-large-data-using-parallel-hdf5/8942 "2021-09-04T21:34:26Z")
Hi, I have problem writing large data using parallel HDF5. I watched “Parallel HDF5 quick start and tuning knobs” by Quincey Koziol on youtube and followed his examples, which are nicely available on https://github.com… --- ## [Zstandard compression plug-in](https://forum.hdfgroup.org/t/zstandard-compression-plug-in/3922)
**Author:** [@paramon](https://forum.hdfgroup.org/u/paramon)\ **Replies:** 1\ **Last updated:** [August 31, 2021, 7:15am UTC](https://forum.hdfgroup.org/t/zstandard-compression-plug-in/3922 "2021-08-31T07:15:11Z")
Hello HDF5 group! Zstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression / speed trade-off, while being backed by a very fast decoder. Zstandard lib… --- ## [Irregular access time to datasets in subgroups (h5py)](https://forum.hdfgroup.org/t/irregular-access-time-to-datasets-in-subgroups-h5py/7934)
**Author:** [@djdematties](https://forum.hdfgroup.org/u/djdematties)\ **Replies:** 1\ **Last updated:** [December 29, 2020, 3:09pm UTC](https://forum.hdfgroup.org/t/irregular-access-time-to-datasets-in-subgroups-h5py/7934 "2020-12-29T15:09:37Z")
Hi, I am a bit disorientated, I am using h5py to read datasets from a hierarchical multi group h5 file First I implemented a NN using jupyter-notebook on google colab, then I decided to move most of the stuff inside cus… --- ## [File keeps being updated long after the dataset is closed](https://forum.hdfgroup.org/t/file-keeps-being-updated-long-after-the-dataset-is-closed/3403)
**Author:** [@Maxime\_Boissonneault](https://forum.hdfgroup.org/u/Maxime_Boissonneault)\ **Replies:** 9\ **Last updated:** [December 28, 2020, 7:34am UTC](https://forum.hdfgroup.org/t/file-keeps-being-updated-long-after-the-dataset-is-closed/3403 "2020-12-28T07:34:54Z")
Hi, I am writing a very large (572GB) file with HDF5, on a Lustre filesystem, using 960 MPI processes spread over 120 nodes. I am monitoring the IO that is going on the filesystem at this time. I see a very large peak,… --- ## [H5LTfind\_dataset matches strings or substrings?](https://forum.hdfgroup.org/t/h5ltfind-dataset-matches-strings-or-substrings/3663)
**Author:** [@borreguero](https://forum.hdfgroup.org/u/borreguero)\ **Replies:** 1\ **Last updated:** [December 3, 2020, 5:37pm UTC](https://forum.hdfgroup.org/t/h5ltfind-dataset-matches-strings-or-substrings/3663 "2020-12-03T17:37:30Z")
Dear all, I am querying for the existence of dataset with name "fq" in a file containing a dataset with name "fqt", but no dataset with name "fq": H5LTfind\_dataset(h5file, "fqt"); //returns 1 as expected H5LTfind\_dat… --- ## [make install under OSX creates error](https://forum.hdfgroup.org/t/make-install-under-osx-creates-error/2948)
**Author:** [@Philipp\_Kraus](https://forum.hdfgroup.org/u/Philipp_Kraus)\ **Replies:** 2\ **Last updated:** [July 20, 2020, 4:27pm UTC](https://forum.hdfgroup.org/t/make-install-under-osx-creates-error/2948 "2020-07-20T16:27:32Z")
Hello, I try to build under OSX with cmake & make the HDF 1.8.11 lib, but on the make install call I get this error: CMake Error at cmake\_install.cmake:78 (FILE): file INSTALL cannot find "/hdf5-1.8.11/release\_d… --- ## [windows opens hdf5 in ASCII mode ](https://forum.hdfgroup.org/t/windows-opens-hdf5-in-ascii-mode/7290)
**Author:** [@hdf3](https://forum.hdfgroup.org/u/hdf3)\ **Replies:** 1\ **Last updated:** [July 19, 2020, 12:13pm UTC](https://forum.hdfgroup.org/t/windows-opens-hdf5-in-ascii-mode/7290 "2020-07-19T12:13:02Z")
Hello, I have successfully compiled and used hdf5 (v 1.12.0) under Linux. Compiling under Windows using MinGW also succeeded. However, it seems that opening a file under Windows is done in ASCII mode instead of binary… --- ## [C4251 Warning at C++ Example](https://forum.hdfgroup.org/t/c4251-warning-at-c-example/3919)
**Author:** [@Dennis\_Zimmermann](https://forum.hdfgroup.org/u/Dennis_Zimmermann)\ **Replies:** 2\ **Last updated:** [May 20, 2020, 2:37pm UTC](https://forum.hdfgroup.org/t/c4251-warning-at-c-example/3919 "2020-05-20T14:37:13Z")
Hello, I am using VS 2015 Community Edition and used the installer to get HDF5-1.8.18: Windows 64-bit \[1\] Compilers: CMake VS 2015 C, C++, IVF 16 I tried to run this example: #include \ #include \ … --- ## [ANN: HDF5 for Python (h5py) 1.2](https://forum.hdfgroup.org/t/ann-hdf5-for-python-h5py-1-2/1320)
**Author:** [@andrew.collette](https://forum.hdfgroup.org/u/andrew.collette)\ **Replies:** 3\ **Last updated:** [March 31, 2020, 6:41am UTC](https://forum.hdfgroup.org/t/ann-hdf5-for-python-h5py-1-2/1320 "2020-03-31T06:41:10Z")
Announcing HDF5 for Python (h5py) 1.2 ▶ ··· --- ## [Problems installing h5py on Mac OS X 10.8](https://forum.hdfgroup.org/t/problems-installing-h5py-on-mac-os-x-10-8/2694)
**Author:** [@Axel\_Perschmann](https://forum.hdfgroup.org/u/Axel_Perschmann)\ **Replies:** 5\ **Last updated:** [February 3, 2020, 3:36pm UTC](https://forum.hdfgroup.org/t/problems-installing-h5py-on-mac-os-x-10-8/2694 "2020-02-03T15:36:27Z")
Hello, I finally managed to install HDF5 following this tutorial: http://cdx.jpl.nasa.gov/documents/technical-design/accessing-hdf-data-from-python-on-mac-os-x/ But now I'm stuck with h5py ... Here I tried to follow … --- ## [Installation of hdf5-1.10.5 with parallel mode with openmpi-4.0.2](https://forum.hdfgroup.org/t/installation-of-hdf5-1-10-5-with-parallel-mode-with-openmpi-4-0-2/6450)
**Author:** [@guidogranda](https://forum.hdfgroup.org/u/guidogranda)\ **Replies:** 0\ **Last updated:** [December 6, 2019, 1:04am UTC](https://forum.hdfgroup.org/t/installation-of-hdf5-1-10-5-with-parallel-mode-with-openmpi-4-0-2/6450 "2019-12-06T01:04:39Z")
Hello, I’m trying to install hdf5-1.10.5 with parallel mode enabled using openmpi-4.0.2 like this: CC= /home/guido/libraries/compiled\_with\_gcc-7.3.0/openmpi-4.0.2/bin/mpicc FC=/home/guido/libraries/compiled\_with\_gcc-7… --- ## [H5Pset\_virtual\_source\_path](https://forum.hdfgroup.org/t/h5pset-virtual-source-path/3820)
**Author:** [@nelson99](https://forum.hdfgroup.org/u/nelson99)\ **Replies:** 5\ **Last updated:** [September 17, 2019, 1:29pm UTC](https://forum.hdfgroup.org/t/h5pset-virtual-source-path/3820 "2019-09-17T13:29:08Z")
The RFC for the virtual datasets indicates that you can set a path in which to search for the source files referenced in the virtual datasets, using the H5Pset\_virtual\_source\_path function. It doesn't appear that this wa… --- ## [HDF installation ](https://forum.hdfgroup.org/t/hdf-installation/6158)
**Author:** [@mfuplasma](https://forum.hdfgroup.org/u/mfuplasma)\ **Replies:** 0\ **Last updated:** [September 16, 2019, 2:46pm UTC](https://forum.hdfgroup.org/t/hdf-installation/6158 "2019-09-16T14:46:00Z")
I am new a about to start using HDF. I have downloaded the modis data files in hdf extension and want to extract data to analyin ms excal. For this i want to install HDF on my laptop. i have windows environment. Please … --- ## [Recommendations for improving python skills](https://forum.hdfgroup.org/t/recommendations-for-improving-python-skills/4144)
**Author:** [@friedhelm.matten](https://forum.hdfgroup.org/u/friedhelm.matten)\ **Replies:** 1\ **Last updated:** [January 17, 2018, 3:56pm UTC](https://forum.hdfgroup.org/t/recommendations-for-improving-python-skills/4144 "2018-01-17T15:56:21Z")
Hi John, I ' m an Java developer for 20 years and relative new to python. But I would like to help for a better effort. How and where could I start and help? Thanks and regards Friedhelm ▶ ··· --- ## [provide more details on limitations for H5Dget\_offset in documentation](https://forum.hdfgroup.org/t/provide-more-details-on-limitations-for-h5dget-offset-in-documentation/3270)
**Author:** [@Stohr\_Alexander](https://forum.hdfgroup.org/u/Stohr_Alexander)\ **Replies:** 1\ **Last updated:** [June 28, 2019, 5:06am UTC](https://forum.hdfgroup.org/t/provide-more-details-on-limitations-for-h5dget-offset-in-documentation/3270 "2019-06-28T05:06:12Z")
Hello, referring to and quoting from: http://www.hdfgroup.org/HDF5/doc/RM/RM\_H5D.html#Dataset-GetOffset Purpose: Returns dataset address in file. Description: H5Dget\_offset returns the address in the… --- ## [Issue while using compound datatype with an array element (and h5dump output)](https://forum.hdfgroup.org/t/issue-while-using-compound-datatype-with-an-array-element-and-h5dump-output/3461)
**Author:** [@Pramod\_Kumbhar](https://forum.hdfgroup.org/u/Pramod_Kumbhar)\ **Replies:** 2\ **Last updated:** [June 10, 2019, 11:10pm UTC](https://forum.hdfgroup.org/t/issue-while-using-compound-datatype-with-an-array-element-and-h5dump-output/3461 "2019-06-10T23:10:51Z")
Dear All, I am using parallel hdf5 to write compound dataset from biological simulations. I am trying to use compound datatype with an array element whose size is known at runtime (I see similar question which is not … --- ## [Error message using H5AOpen](https://forum.hdfgroup.org/t/error-message-using-h5aopen/5821)
**Author:** [@jaume.sagues](https://forum.hdfgroup.org/u/jaume.sagues)\ **Replies:** 0\ **Last updated:** [May 29, 2019, 5:54pm UTC](https://forum.hdfgroup.org/t/error-message-using-h5aopen/5821 "2019-05-29T17:54:25Z")
I am using H5AOpen to open an attribute that some times exists but other times it does not. I understand that when the attribute does not exist, then H5AOpen returns a negative number. It does so, but it writes this mess… --- ## [H5Fcreate and H5Fopen with chinese filename (wide char)](https://forum.hdfgroup.org/t/h5fcreate-and-h5fopen-with-chinese-filename-wide-char/1450)
**Author:** [@ALLAN\_MC](https://forum.hdfgroup.org/u/ALLAN_MC)\ **Replies:** 9\ **Last updated:** [March 3, 2019, 9:25pm UTC](https://forum.hdfgroup.org/t/h5fcreate-and-h5fopen-with-chinese-filename-wide-char/1450 "2019-03-03T21:25:35Z")
Hi, On windows, i want to create a hdf5 filename with Chinese characters. Filename is a wide string (wchar\_t \*wcfilename) H5Fcreate and H5Fopen seems to accept only ansi characters. How to do you ? Thanks you ··· [Next page](https://forum.hdfgroup.org/c/hdf-forum/11.md?page=1)