Can't install on macbook M1 - Enabled feature "threadsafe" but the HDF5 library was not built with HDF5_ENABLE_THREADSAFE

[nleroy917]

I am having some trouble installing SnapATAC2 on my MacBook. I had the exact same issue described in #140, but I was able to solve it by attempting to install from source after patching the hdf5 and hdf5-sys crates.

However, I hit another roadblock. When trying to install, I got an error indicating that usage of the features = ["threadsafe"] was causing problems:

--- stderr
  thread 'main' panicked at ~/.cargo/git/checkouts/hdf5-rust-c1072d7a2617f7d8/26046fb/hdf5-sys/build.rs:697:17:
  Enabled feature "threadsafe" but the HDF5 library was not built with HDF5_ENABLE_THREADSAFE
  stack backtrace:
     0: rust_begin_unwind
               at /rustc/cc66ad468955717ab92600c770da8c1601a4ff33/library/std/src/panicking.rs:595:5
     1: core::panicking::panic_fmt
               at /rustc/cc66ad468955717ab92600c770da8c1601a4ff33/library/core/src/panicking.rs:67:14
     2: build_script_build::Config::check_against_features_required
     3: build_script_build::LibrarySearcher::finalize
     4: build_script_build::main
     5: core::ops::function::FnOnce::call_once

I recognize that this is a problem with my own hdf5 installation, but it seems like installing threadsafe hdf5 is not an easy thing to do very common. I had to custom edit some homebrew formulas to get even close to that. Moreover, the people over at hdf5 suggested just using the static feature over the threadsafe feature.

update: I even tried pulling one of their binaries, but that didn't work either since it seems like those weren't build with --enable-threadsafe

Any thoughts? Whats a good way to get this going locally I am eager to try it out and very excited about this project!

[kaizhang]

I believe this problem may be caused by a locally installed HDF5 library. Either uninstalling the HDF5 library installed by homebrew or unsetting the "HDF5_DIR" environmental variable may solve this problem.

The patch is unnecessary as I've successfully installed it on my M1 macbook without patch. Just try the following:

unset HDF5_DIR
pip install snapatac2

[nleroy917]

Wow, that was it... so simple. Thank you so much for the help. Hopefully, my suggestion in the other issue thread solves things for the other user.