# \#hdf5

**URL:** https://discourse.julialang.org/tag/hdf5/84.md

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## [Implementing HDF5.jl REPL tab completion, private REPL.REPLCompletions.find\_dict\_matches](https://discourse.julialang.org/t/implementing-hdf5-jl-repl-tab-completion-private-repl-replcompletions-find-dict-matches/139505)

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**Author:** [@mkitti](https://discourse.julialang.org/u/mkitti)\
**Replies:** 1\
**Last updated:** [September 17, 2026, 2:57pm UTC](https://discourse.julialang.org/t/implementing-hdf5-jl-repl-tab-completion-private-repl-replcompletions-find-dict-matches/139505 "2026-09-17T14:57:36Z")

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I am implementing multi-level REPL path completion in HDF5.jl. The only way I have figured out how to implement multi-level completion is by overloading REPL.REPLCompletions.find\_dict\_matches which is not public. This AP…

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## [HDF5.jl with vector of tuples of strings](https://discourse.julialang.org/t/hdf5-jl-with-vector-of-tuples-of-strings/139148)

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**Author:** [@BambOoxX](https://discourse.julialang.org/u/BambOoxX)\
**Replies:** 4\
**Last updated:** [September 2, 2026, 7:25am UTC](https://discourse.julialang.org/t/hdf5-jl-with-vector-of-tuples-of-strings/139148 "2026-09-02T07:25:32Z")

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@mkitti I just stumbled on another similar string related issue. If one tries to write a Vector{@NamedTuple...} where at least one type is a string, the writing fails. This is on v0.17.3. using HDF5 arr = \[ (;A…

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## [HDF5.jl variable length string](https://discourse.julialang.org/t/hdf5-jl-variable-length-string/98808)

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**Author:** [@thomaskroi1996](https://discourse.julialang.org/u/thomaskroi1996)\
**Replies:** 10\
**Last updated:** [April 4, 2024, 10:38pm UTC](https://discourse.julialang.org/t/hdf5-jl-variable-length-string/98808 "2024-04-04T22:38:46Z")

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Hello everyone! I am currently trying to translate i python code to julia! What i am trying to do, broken down, is creating a dataset where dtype=“String”. I know that to do that in python you have to declare a special …

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## [Interpolate over large HDF5 arrays](https://discourse.julialang.org/t/interpolate-over-large-hdf5-arrays/127079)

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**Author:** [@henry2004y](https://discourse.julialang.org/u/henry2004y)\
**Replies:** 18\
**Last updated:** [December 3, 2025, 5:52pm UTC](https://discourse.julialang.org/t/interpolate-over-large-hdf5-arrays/127079 "2025-12-03T17:52:48Z")

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Hi, I have a extremely large standard HDF5 file (2 TB) which saves a 3D array, let’s say B. With HDF5.jl, I can access individual elements of the array in the same way as this thread shows: load-hdf5-file-larger-than-me…

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## [MPI library mismatch erro HDF5, Netcdf with Oceananigans](https://discourse.julialang.org/t/mpi-library-mismatch-erro-hdf5-netcdf-with-oceananigans/131579)

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**Author:** [@farolap](https://discourse.julialang.org/u/farolap)\
**Replies:** 2\
**Last updated:** [September 1, 2025, 6:17am UTC](https://discourse.julialang.org/t/mpi-library-mismatch-erro-hdf5-netcdf-with-oceananigans/131579 "2025-09-01T06:17:17Z")

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Dear all, Im having strong issues with a specific package in Julia while trying to run it in MPI. Initially I define the following libraries: export LD\_LIBRARY\_PATH=/sw/spack-levante/netcdf-c-4.8.1-7dq6g2/lib/:$LD\_LIBR…

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## [Read!( ) not working for HDF5 file](https://discourse.julialang.org/t/read-not-working-for-hdf5-file/129722)

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**Author:** [@raman\_kumar](https://discourse.julialang.org/u/raman_kumar)\
**Replies:** 1\
**Last updated:** [June 15, 2025, 11:46am UTC](https://discourse.julialang.org/t/read-not-working-for-hdf5-file/129722 "2025-06-15T11:46:24Z")

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I have an HDF5 file. I want to read or allocate its data in variable r repeatedly instead of allocating in different places :seat: in memory. using HDF5 fname = tempname(); # temporary file fid = h5open(fname, "w") cre…

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## [Out of memory error in \`viz\` of 3D \`RectilinearGrid\` from Meshes.jl](https://discourse.julialang.org/t/out-of-memory-error-in-viz-of-3d-rectilineargrid-from-meshes-jl/128643)

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**Author:** [@raman\_kumar](https://discourse.julialang.org/u/raman_kumar)\
**Replies:** 33\
**Last updated:** [May 31, 2025, 7:30pm UTC](https://discourse.julialang.org/t/out-of-memory-error-in-viz-of-3d-rectilineargrid-from-meshes-jl/128643 "2025-05-31T19:30:03Z")

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I want to plot a grid using Meshes.jl and GLMakie.jl. I am reading the HDF5 data file output of Athena++ astrophysical code using HDF5.jl library. In Athena++ mesh grid is divided into smaller parts called Blocks to use…

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## [Leveraging the GDAL VSI for “raw” access to NetCDF/HDF5 files inside a Zip archive?](https://discourse.julialang.org/t/leveraging-the-gdal-vsi-for-raw-access-to-netcdf-hdf5-files-inside-a-zip-archive/128129)

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**Author:** [@Oblomov](https://discourse.julialang.org/u/Oblomov)\
**Replies:** 9\
**Last updated:** [April 17, 2025, 6:27am UTC](https://discourse.julialang.org/t/leveraging-the-gdal-vsi-for-raw-access-to-netcdf-hdf5-files-inside-a-zip-archive/128129 "2025-04-17T06:27:47Z")

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Hello all, I have an interesting conundrum. My situation is the following: I have some data which is distributed as a zip archive of .nc files. The files are rather large, so I would prefer to not unzip the archive to r…

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## [Is it possible to make \`HDF5\` show progress in \`copy\_object\`?](https://discourse.julialang.org/t/is-it-possible-to-make-hdf5-show-progress-in-copy-object/126860)

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**Author:** [@VinceNeede](https://discourse.julialang.org/u/VinceNeede)\
**Replies:** 0\
**Last updated:** [March 12, 2025, 10:57am UTC](https://discourse.julialang.org/t/is-it-possible-to-make-hdf5-show-progress-in-copy-object/126860 "2025-03-12T10:57:34Z")

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I was copying a big HDF5.Group and I was wondering whether there was a way to make copy\_object show a progress bar or something similar

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## [HDF5 is broken on Windows?](https://discourse.julialang.org/t/hdf5-is-broken-on-windows/125988)

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**Author:** [@joa-quim](https://discourse.julialang.org/u/joa-quim)\
**Replies:** 2\
**Last updated:** [February 17, 2025, 6:57pm UTC](https://discourse.julialang.org/t/hdf5-is-broken-on-windows/125988 "2025-02-17T18:57:50Z")

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Since yesterday I started to see failures in building GMT in CI (and locally) due to ERROR: LoadError: InitError: could not load library "C:\\Users\\j\\.julia\\artifacts\\a0f65aec92810567654b7ca3b29b0786088806a6\\bin\\libnetcd…

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## [Invalid memory operation in delete\_object in HDF5](https://discourse.julialang.org/t/invalid-memory-operation-in-delete-object-in-hdf5/124093)

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**Author:** [@0samuraiE](https://discourse.julialang.org/u/0samuraiE)\
**Replies:** 4\
**Last updated:** [December 22, 2024, 4:45pm UTC](https://discourse.julialang.org/t/invalid-memory-operation-in-delete-object-in-hdf5/124093 "2024-12-22T16:45:52Z")

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Hi. As title suggests, my application crashes occasionally when call delete\_object. Every time I try, the error message changes. Sometimes free(): invalid pointer malloc(): unaligned tcache chunk detected Aborted (core…

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## [HDF5 error: MPIExt cannot find libmpi\_usempif08.40.dylib](https://discourse.julialang.org/t/hdf5-error-mpiext-cannot-find-libmpi-usempif08-40-dylib/115900)

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**Author:** [@PetrKryslUCSD](https://discourse.julialang.org/u/PetrKryslUCSD)\
**Replies:** 8\
**Last updated:** [November 9, 2024, 8:27pm UTC](https://discourse.julialang.org/t/hdf5-error-mpiext-cannot-find-libmpi-usempif08-40-dylib/115900 "2024-11-09T20:27:26Z")

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Missing /.julia/artifacts/69e85a392db842d919cf5759941f8f3e8a0e569e/lib/libhdf5\_fortran.so" libmpi\_usempif08.so.40: cannot open shared object file: No such file or directory ? Any idea what that is about?

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## [Write a String with parallel HDF5](https://discourse.julialang.org/t/write-a-string-with-parallel-hdf5/121025)

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**Author:** [@johnomotani](https://discourse.julialang.org/u/johnomotani)\
**Replies:** 1\
**Last updated:** [October 16, 2024, 6:09am UTC](https://discourse.julialang.org/t/write-a-string-with-parallel-hdf5/121025 "2024-10-16T06:09:21Z")

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Does anyone know the ‘correct’ way to write a scalar variable (especially a String) using parallel HDF5? I think I have a way of doing it, but it’s so ugly I’m hoping there’s a better way! The problem: suppose I have a …

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## [Reading hdf5 files with ascii headers](https://discourse.julialang.org/t/reading-hdf5-files-with-ascii-headers/117632)

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**Author:** [@Tim\_Hultberg](https://discourse.julialang.org/u/Tim_Hultberg)\
**Replies:** 0\
**Last updated:** [July 30, 2024, 2:25pm UTC](https://discourse.julialang.org/t/reading-hdf5-files-with-ascii-headers/117632 "2024-07-30T14:25:07Z")

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In my program I have to read data from a large number of hdf5 files with a fixed size (3307) ascii header added. For now, I loop through the files and write a temporary file to disk without the disturbing ascii header a…

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## [Reading multiple files and also one file containg limits to read other file's content upto](https://discourse.julialang.org/t/reading-multiple-files-and-also-one-file-containg-limits-to-read-other-files-content-upto/115060)

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**Author:** [@raman\_kumar](https://discourse.julialang.org/u/raman_kumar)\
**Replies:** 8\
**Last updated:** [June 17, 2024, 3:32pm UTC](https://discourse.julialang.org/t/reading-multiple-files-and-also-one-file-containg-limits-to-read-other-files-content-upto/115060 "2024-06-17T15:32:42Z")

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I have python code like: from pyfiles import \* runname='./' #define start dir and file, uncomment below sane = 1#0 for MAD98, 1 for SANE00 if sane == 1: inputfile=runname+'sane00.athinput' datafile='sane00.prim…

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## [Python function cis.read\_data() equivalent in Julia](https://discourse.julialang.org/t/python-function-cis-read-data-equivalent-in-julia/115361)

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**Author:** [@raman\_kumar](https://discourse.julialang.org/u/raman_kumar)\
**Replies:** 10\
**Last updated:** [June 11, 2024, 6:34am UTC](https://discourse.julialang.org/t/python-function-cis-read-data-equivalent-in-julia/115361 "2024-06-11T06:34:11Z")

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I want to write Python function cis.read\_data() equivalent in Julia. def read\_data(data\_list, read\_function): """ Wrapper for calling an HDF reading function for each dataset, and then concatenating the result. …

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## [Plotting using \`Trixi2Vtk\` of \`.h5\` files](https://discourse.julialang.org/t/plotting-using-trixi2vtk-of-h5-files/115337)

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**Author:** [@Devansh1106](https://discourse.julialang.org/u/Devansh1106)\
**Replies:** 2\
**Last updated:** [June 9, 2024, 2:20pm UTC](https://discourse.julialang.org/t/plotting-using-trixi2vtk-of-h5-files/115337 "2024-06-09T14:20:30Z")

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I am plotting some .h5 solution files that are generated from running code similar to Trixi package. I am using Trixi2Vtk package for plotting. Command given in Trixi docs is: julia\> trixi2vtk(joinpath("out", "solution…

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## [Storing lots of time series](https://discourse.julialang.org/t/storing-lots-of-time-series/115169)

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**Author:** [@alemelis](https://discourse.julialang.org/u/alemelis)\
**Replies:** 12\
**Last updated:** [June 5, 2024, 7:35pm UTC](https://discourse.julialang.org/t/storing-lots-of-time-series/115169 "2024-06-05T19:35:46Z")

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Hello, I’ve a large number of time series as result of my simulations. As today the dataset is made of ~1e7 time series (100 points each), stored on disk in .csv files (each one containing 5 of them). I’ll have more (1…

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## [How to open sub-directory of HDF5 file in Julia?](https://discourse.julialang.org/t/how-to-open-sub-directory-of-hdf5-file-in-julia/115010)

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**Author:** [@raman\_kumar](https://discourse.julialang.org/u/raman_kumar)\
**Replies:** 5\
**Last updated:** [May 31, 2024, 3:27pm UTC](https://discourse.julialang.org/t/how-to-open-sub-directory-of-hdf5-file-in-julia/115010 "2024-05-31T15:27:38Z")

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I want to open sub-directory of HDF5 file in Julia? For example- how can i open "Coordinates" folder using HDF5.jl?

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## [Question on Loading HDF Data Saved in Python](https://discourse.julialang.org/t/question-on-loading-hdf-data-saved-in-python/114562)

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**Author:** [@TI36XPro](https://discourse.julialang.org/u/TI36XPro)\
**Replies:** 19\
**Last updated:** [May 28, 2024, 12:35am UTC](https://discourse.julialang.org/t/question-on-loading-hdf-data-saved-in-python/114562 "2024-05-28T00:35:15Z")

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Hello, Does anyone have experience with this? My colleague has some large data saved on our cluster in the .h5 file format. He saved it in python using the h5py package. I’d like to now open and analyze the same data …

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## [Saving and updating in-memory HDF5 files?](https://discourse.julialang.org/t/saving-and-updating-in-memory-hdf5-files/112395)

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**Author:** [@Ahmed\_Salih](https://discourse.julialang.org/u/Ahmed_Salih)\
**Replies:** 3\
**Last updated:** [April 2, 2024, 4:52pm UTC](https://discourse.julialang.org/t/saving-and-updating-in-memory-hdf5-files/112395 "2024-04-02T16:52:46Z")

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Hello! Reading the documentation of HDF5.jl (Home · HDF5.jl) I see how it is possible to have an in-memory hdf5 file. I was wondering if; Can I update a dataset in an hdf in place? Can I save a copy of the current in-…

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## [HDF5 high-level wrapper for nested Dicts](https://discourse.julialang.org/t/hdf5-high-level-wrapper-for-nested-dicts/111588)

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**Author:** [@baptnz](https://discourse.julialang.org/u/baptnz)\
**Replies:** 3\
**Last updated:** [March 14, 2024, 4:58am UTC](https://discourse.julialang.org/t/hdf5-high-level-wrapper-for-nested-dicts/111588 "2024-03-14T04:58:01Z")

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I’m storing some data in hdf5 format to use in a multilanguage environment (others will use Python, R, C, etc. to access those files). I’ve implemented the export using HDF5.jl without much trouble, but it’s not very wel…

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## [Windows users, test my new HDF5\_jll 1.14.3 builds!](https://discourse.julialang.org/t/windows-users-test-my-new-hdf5-jll-1-14-3-builds/108459)

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**Author:** [@mkitti](https://discourse.julialang.org/u/mkitti)\
**Replies:** 8\
**Last updated:** [January 7, 2024, 5:55pm UTC](https://discourse.julialang.org/t/windows-users-test-my-new-hdf5-jll-1-14-3-builds/108459 "2024-01-07T17:55:28Z")

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As part of the effort to update the HDF5 libraries to version 1.14.3, I have built a series of test packages for Windows located here: If you run Windows, I would appreciate if you could try running the following short…

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## [Load HDF5 file larger than memory](https://discourse.julialang.org/t/load-hdf5-file-larger-than-memory/107412)

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**Author:** [@jisutich](https://discourse.julialang.org/u/jisutich)\
**Replies:** 6\
**Last updated:** [December 12, 2023, 7:27am UTC](https://discourse.julialang.org/t/load-hdf5-file-larger-than-memory/107412 "2023-12-12T07:27:27Z")

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Hi, I am trying to read data from a HDF5 file which is larger than the memory of my computer. I think every time I just need part of data in the file. Is there a way to get part of groups/dataset in the file without loa…

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## [Is there a Julia function that returns h5 group structures à la h5dump?](https://discourse.julialang.org/t/is-there-a-julia-function-that-returns-h5-group-structures-a-la-h5dump/102778)

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**Author:** [@alex-s-gardner](https://discourse.julialang.org/u/alex-s-gardner)\
**Replies:** 10\
**Last updated:** [September 6, 2023, 8:18am UTC](https://discourse.julialang.org/t/is-there-a-julia-function-that-returns-h5-group-structures-a-la-h5dump/102778 "2023-09-06T08:18:21Z")

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I’m looking for a function that maps h5 data structures, i.e. variable paths, names and Types, and attribute paths, names and Types. This would be similar to h5dump.

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## [HDF5 variable length Array](https://discourse.julialang.org/t/hdf5-variable-length-array/101971)

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**Author:** [@thomaskroi1996](https://discourse.julialang.org/u/thomaskroi1996)\
**Replies:** 0\
**Last updated:** [July 23, 2023, 5:20pm UTC](https://discourse.julialang.org/t/hdf5-variable-length-array/101971 "2023-07-23T17:20:33Z")

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Hello! I was wondering what the cleanest way to write variable length arrays to HDF5 format in Julia, using HDF5.jl. In python this can be easily done with create\_dataset('StepNumbers', data=\[\], dtype=np.dtype('uint32…

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## [HDF5 utilising only a fraction of available system resources](https://discourse.julialang.org/t/hdf5-utilising-only-a-fraction-of-available-system-resources/98481)

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**Author:** [@silkskier](https://discourse.julialang.org/u/silkskier)\
**Replies:** 5\
**Last updated:** [May 8, 2023, 10:41pm UTC](https://discourse.julialang.org/t/hdf5-utilising-only-a-fraction-of-available-system-resources/98481 "2023-05-08T22:41:37Z")

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I’ve recently written a simple script converting the OCVS (OGLE Collection of Variable Stars) database (which is basically a single text file containing a list of attributes of every star in the collection) and a large a…

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## [Reading and writing HDF5 compound-typed array datasets](https://discourse.julialang.org/t/reading-and-writing-hdf5-compound-typed-array-datasets/97516)

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**Author:** [@airpmb](https://discourse.julialang.org/u/airpmb)\
**Replies:** 3\
**Last updated:** [April 16, 2023, 2:33am UTC](https://discourse.julialang.org/t/reading-and-writing-hdf5-compound-typed-array-datasets/97516 "2023-04-16T02:33:46Z")

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I wanted to write vectors of LabelledArrays to HDF5 files, preserving the labels, and be able to read these back and reconstruct the original data. My data is pretty much entirely numeric. I’ve found it hard to find any…

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## [Datatype when save matrices in HDF5 file](https://discourse.julialang.org/t/datatype-when-save-matrices-in-hdf5-file/95364)

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**Author:** [@jisutich](https://discourse.julialang.org/u/jisutich)\
**Replies:** 2\
**Last updated:** [March 1, 2023, 8:18pm UTC](https://discourse.julialang.org/t/datatype-when-save-matrices-in-hdf5-file/95364 "2023-03-01T20:18:28Z")

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Hi, I am trying to write a HDF5 file in Julia. Now suppose I want to create a dataset mydataset which contains a matrix A in the group mygroup, what datatype should I use in the function create\_dataset? (In the documen…

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## [Using large NTuples makes Julia hang](https://discourse.julialang.org/t/using-large-ntuples-makes-julia-hang/78900)

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**Author:** [@Maurizio\_Tomasi](https://discourse.julialang.org/u/Maurizio_Tomasi)\
**Replies:** 23\
**Last updated:** [February 10, 2023, 10:40am UTC](https://discourse.julialang.org/t/using-large-ntuples-makes-julia-hang/78900 "2023-02-10T10:40:10Z")

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Julia 1.7.2 on Linux x86\_64 seems to hang when instantiating structures containing large NTuple types, as the following code shows: struct Foo id:: UInt64 tag::NTuple{32, UInt8} start\_comment::NTuple{4096, U…

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