g0-merge/ZeroArray: __gc not called

[liangwang0734]

Description of the bug

In the g0-merge, ZeroArray.Array.__gc() is never called.

Impact

This is causing memory leak, but only at the end of a simulation when all the bulk data arrays go out of scope. In other word, it perhaps doesn't affect simulation results.

Possible causes

The cdata being wrapped, struct gkyl_array is created by an external function call gkyl_array_new, not by ffi itself through new. Therefore, no implicit ffi.gc call is automatically done during the creation of an instance. See this post.

https://github.com/ammarhakim/gkyl/blob/a2931e76f0939f6f90ff35a025a55033ffacb57d/DataStruct/ZeroArray.lua#L389

Possible solutions

• Solution 1, Create the instance through ffi.new, then call some init function to initialize it.
  • This new function gkyl_array_init can use codes of the main body of present gkylzero.gkyl_array_new. The latter can then call gkyl_array_init to avoid duplicate codes.
  • How to handle the gpu copy then?
  • This could be generalized to other gkylzero classes, if needed. That is, we may always prefer to have an independent _init method that initializes a given object.
• Solution 2, following Ammar's workaround, by wrapping over the following struct gkyl_array_container rather than directly struct gkyl_array. Then, in the instance creation, allocate a new gkyl_aray_container object using ffi.new, and embed the actual gkyl_array created by gkyl_array_new.
  • This requires wider code changes, including all of ZeroArray member methods, and any code that uses CartField._zero itself (i.e., a struct gkyl_array), needs to be written as CartField._zero.arr.
  • See 5650513f8b1438108021ed3aefa761c02442a494 and 07a1c91c25cce327a22996f799dbde68125ae0a2

    
    struct gkyl_array_container {
    struct gkyl_array *arr;
    };

local array_fn = { copy = function (self, src) return ffiC.gkyl_array_copy(self.arr, src.arr) end, ... }

local array_mt = { __new = function (self, atype, ncomp, size, on_gpu) local container = new(self) container.arr = ffiC.gkyl_array_new(atype, ncomp, size) return container end, gc = function(self) self:release() end, index = array_fn, }

@nmandell @ammarhakim @JunoRavin 

[liangwang0734]

It turns out less intrusive to manually attach a finalizer according to this explanation.

See https://github.com/liangwang0734/gkyl/commit/21e530560d678950ad4e4084ff5e85da04fb35fb

This will be included in a coming PR regarding merging g0 fluid into g2. But one may cherry-pick this commit (or download the commit and sign it off) to avoid possible conflict.

New usage example:

-- old:
-- return ffiC.gkyl_array_new(atype, ncomp, size)
-- new:
return ffi.gc(ffiC.gkyl_array_new(atype, ncomp, size), ffiC.gkyl_array_release)