How can I render all render passes for all of the frames of an animation in Cycles to different files or a file with multiple layers? I'm going to do the final compositing in another compositing package and I need to have access to the passes.
Render OpenExr Multilayer for Blender, Nuke and Natron. Go to the Scene Tab, enable all passes which key for compositing and set the Output Format in the Render Tab to
Blender automatically writes all enabled passes and layers as single channels to the EXR as expected.
For After Effects and Fusion I'd suggest render
single EXR's. For more information on rendering passes and layers as EXR's, see: Save all render passes to a single EXR image.
Note: If you want to use Index Passes (IndexOB or IndexMA) see this answer: How to use index passes in other compositing packages?
Another alternative is to render out to separate image sequences. This is handy if you want to output to different render formats for each Render Pass. As well it gives you the flexibility to only re-render some passes if need be.
You can do this by piping the Render Pass outputs into a File Output node. You can add additional inputs to the FO node and make different file format settings for each (notice the first four inputs are set to PNG output while the last two are set to 32bit EXR format).