Julia on Raspberry Pi: error building HDF5 package

General Usage
1

I’ve installed Julia language on Raspberry Pi as mentioned here:

But then trying to ]add HDF5 the following error appears:

(v1.2) pkg> add HDF5
 Resolving package versions...
 Installed CMakeWrapper ─────── v0.2.3
 Installed OrderedCollections ─ v1.1.0
 Installed Blosc ────────────── v0.5.1
 Installed BinDeps ──────────── v0.8.10
 Installed Parameters ───────── v0.12.0
 Installed BinaryProvider ───── v0.5.6
 Installed Compat ───────────── v2.2.0
 Installed HDF5 ─────────────── v0.12.4
 Installed CMake ────────────── v1.1.2
 Installed URIParser ────────── v0.4.0
  Updating ~/.julia/environments/v1.2/Project.toml
  [f67ccb44] + HDF5 v0.12.4
  Updating ~/.julia/environments/v1.2/Manifest.toml
  [9e28174c] + BinDeps v0.8.10
  [b99e7846] + BinaryProvider v0.5.6
  [a74b3585] + Blosc v0.5.1
  [631607c0] + CMake v1.1.2
  [d5fb7624] + CMakeWrapper v0.2.3
  [34da2185] + Compat v2.2.0
  [f67ccb44] + HDF5 v0.12.4
  [bac558e1] + OrderedCollections v1.1.0
  [d96e819e] + Parameters v0.12.0
  [30578b45] + URIParser v0.4.0
  [2a0f44e3] + Base64 
  [ade2ca70] + Dates 
  [8bb1440f] + DelimitedFiles 
  [8ba89e20] + Distributed 
  [b77e0a4c] + InteractiveUtils 
  [76f85450] + LibGit2 
  [8f399da3] + Libdl 
  [37e2e46d] + LinearAlgebra 
  [56ddb016] + Logging 
  [d6f4376e] + Markdown 
  [a63ad114] + Mmap 
  [44cfe95a] + Pkg 
  [de0858da] + Printf 
  [3fa0cd96] + REPL 
  [9a3f8284] + Random 
  [ea8e919c] + SHA 
  [9e88b42a] + Serialization 
  [1a1011a3] + SharedArrays 
  [6462fe0b] + Sockets 
  [2f01184e] + SparseArrays 
  [10745b16] + Statistics 
  [8dfed614] + Test 
  [cf7118a7] + UUIDs 
  [4ec0a83e] + Unicode 
  Building CMake → ~/.julia/packages/CMake/nSK2r/deps/build.log
  Building Blosc → ~/.julia/packages/Blosc/lzFr0/deps/build.log
  Building HDF5 ─→ ~/.julia/packages/HDF5/rF1Fe/deps/build.log
┌ Error: Error building HDF5: 
│ [ Info: Downloading https://github.com/bicycle1885/ZlibBuilder/releases/download/v1.0.4/Zlib.v1.2.11.arm-linux-gnueabihf.tar.gz to /home/pi/.julia/packages/HDF5/rF1Fe/deps/usr/downloads/Zlib.v1.2.11.arm-linux-gnueabihf.tar.gz...
│ ERROR: LoadError: LoadError: MethodError: no method matching iterate(::Nothing)
│ Closest candidates are:
│   iterate(!Matched::Core.SimpleVector) at essentials.jl:604
│   iterate(!Matched::Core.SimpleVector, !Matched::Any) at essentials.jl:604
│   iterate(!Matched::ExponentialBackOff) at error.jl:214
│   ...
│ Stacktrace:
│  [1] append_any(::Any, ::Vararg{Any,N} where N) at ./essentials.jl:722
│  [2] top-level scope at /home/pi/.julia/packages/HDF5/rF1Fe/deps/build_HDF5.v1.10.5.jl:40
│  [3] include at ./boot.jl:328 [inlined]
│  [4] include_relative(::Module, ::String) at ./loading.jl:1094
│  [5] include(::Module, ::String) at ./Base.jl:31
│  [6] include(::String) at ./client.jl:431
│  [7] top-level scope at /home/pi/.julia/packages/HDF5/rF1Fe/deps/build.jl:2
│  [8] include at ./boot.jl:328 [inlined]
│  [9] include_relative(::Module, ::String) at ./loading.jl:1094
│  [10] include(::Module, ::String) at ./Base.jl:31
│  [11] include(::String) at ./client.jl:431
│  [12] top-level scope at none:5
│ in expression starting at /home/pi/.julia/packages/HDF5/rF1Fe/deps/build_HDF5.v1.10.5.jl:40
│ in expression starting at /home/pi/.julia/packages/HDF5/rF1Fe/deps/build.jl:2
2

Can you file an issue on the HDF5.jl repository? It sounds like the zlib dependency might not have been built for the RPi’s processor.

3

But it should be https://github.com/bicycle1885/ZlibBuilder/releases/tag/v1.0.4, no? :thinking:

4

Isn’t in libhdf5 itself that is not built for ARM:

https://github.com/JuliaPackaging/Yggdrasil/blob/b883454778587adaad49277870ca65585f109880/H/HDF5/build_tarballs.jl#L78-L84

5

Added issue to HDF5.jl:

https://github.com/JuliaIO/HDF5.jl/issues/588

6

We will need some help to get HDF5 builds for ARM.

7

What kind of help you’ll need?

8

I had a look to the work to do, it doesn’t seem too hard. But I need time, I definitely don’t have this week.

9

Great. Would love your help on this. Please message me if you need building for the Windows platform. The patches we require are available on the msys2 repo, shoot me a message on slack for them.

10

Ok, I think I’ll give up as it clearly doesn’t support cross-compilation: HDF5 FAQ - Compile Issues

11

That was from 4 years ago. I think the situation is improved now?

Mustafa M

12

No, I found that page after crashing my head for a few minutes to skip all those AC_TRY_RUN, that are still there. I couldn’t even finish ./configure. If what they say about the make stage is still true, there is no work around that.

13

Maybe this can help?

https://archlinuxarm.org/packages/armv7h/hdf5

https://developer.arm.com/tools-and-software/server-and-hpc/arm-architecture-tools/resources/porting-and-tuning/building-hdf5-with-arm-compiler

14

No, it doesn’t. I actually started from the Arch Linux ARM page.

The problem is that BinaryBuilder.jl does cross-compilation, but HDF5 specifically cannot work with it.

Currently, the only way to provide a package for the Rasperry Pi is to find a pre-built binary for this platform and use it, which is actually what we do for the few supported platforms.

15

So, how can I tell HDF5.jl to use prebuilt binary (or more generally, for any other package that usually build 3rd-party binaries from source)?

16

This is not something that you can easily do on your side without a lot of manual work. This should be rather done in HDF5.jl if we find a pre-built package that can be easily used in our framework.

17

Found an instructuin for cross-compilation from here: https://github.com/HDFGroup/armed-hdf5/wiki
The link is broken, so I found another copy of that page: http://hdf-forum.184993.n3.nabble.com/Cross-compiling-HDF5-for-a-ARM-platform-td4026501.html

18

I found that page too, but it’s super old, I’m not sure the instruction still apply.

19

Hi

I ran into this problem this week and would like to know if you managed to find a solution yet?

I’m almost certain I had used MAT.jl which depends on HDF5.jl on Julia v0.6 in Jul-Sep 2017.

Anyway, my problem seems to be that CMake.jl doesn’t want to build due to compiler versions and/or compiler flags. I logged a issue https://github.com/JuliaPackaging/CMake.jl/issues/24 but wanted to check here if anyone else is seeing similar problems.

20

HDF5 library does not support cross-compilation, so the only solution is to compile it on RPi and link your cross-compiled code to already compiled libraries. That’s how we did it in our cpp projects. However, I don’t know, how to do that in HDF5.jl