alembic: use threadsafe hdf5 (#30682)

* hdf5: introduce hdf5-threadsafe variant

Compiled with thread safe support and without the High Level library
which is incompatible with thread safety.

* alembic: clean buildInputs to nativeBuildInputs

* alembic: use hdf5-threadsafe

pkgs/development/libraries/alembic/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, unzip, cmake, openexr, hdf5 }:
+{ stdenv, fetchFromGitHub, unzip, cmake, openexr, hdf5-threadsafe }:
 
 stdenv.mkDerivation rec
 {
@@ -14,7 +14,8 @@ stdenv.mkDerivation rec
 
   outputs = [ "bin" "dev" "out" "lib" ];
 
-  buildInputs = [ unzip cmake openexr hdf5 ];
+  nativeBuildInputs = [ unzip cmake ];
+  buildInputs = [ openexr hdf5-threadsafe ];
 
   enableParallelBuilding = true;
 

pkgs/top-level/all-packages.nix

@@ -2688,6 +2688,13 @@ with pkgs;
     inherit gfortran;
   });
 
+  hdf5-threadsafe = appendToName "threadsafe" (hdf5.overrideAttrs (oldAttrs: {
+      # Threadsafe hdf5
+      # However, hdf5 hl (High Level) library is not considered stable
+      # with thread safety and should be disabled.
+      configureFlags = oldAttrs.configureFlags ++ ["--enable-threadsafe" "--disable-hl" ];
+  }));
+
   hdfview = callPackage ../tools/misc/hdfview {
     javac = jdk;
   };