Parthenon developer guide

(Kokkos) programming model

The following list contains a few overall design decision that are useful to keep in mind

  • Kokkos never hides copies, i.e., there are no hidden deep copies and all data transfer needs to be explicit.

  • Kernel launches (e.g., a parallel region) are non-blocking, i.e., the CPU continues to execute code following a kernel that is executed on a GPU.

Kokkos wrappers/abstractions

  • par_for wrappers use inclusive bounds, i.e., the loop will include the last index given

  • ParArrayND arrays by default allocate on the device using default precision configured

  • To create an array on the host with identical layout to the device array either use

    • auto arr_host = Kokkos::create_mirror(arr_dev); to always create a new array even if the device is associated with the host (e.g., OpenMP) or

    • auto arr_host = Kokkos::create_mirror_view(arr_dev); to create an array on the host if the HostSpace != DeviceSpace or get another reference to arr_dev through arr_host if HostSpace == DeviceSpace

  • par_for and Kokkos::deep_copy by default use the standard stream (on Cuda devices) and are discouraged from use. Use mb->par_for and mb->deep_copy instead where mb is a MeshBlock (explanation: each MeshBlock has an ExecutionSpace, which may be changed at runtime, e.g., to a different stream, and the wrapper within a MeshBlock offer transparent access to the parallel region/copy where the MeshBlock’s ExecutionSpace is automatically used).

  • The default loop pattern for the mb->par_for wrappers is defined at compile time through the PAR_LOOP_LAYOUT and PAR_LOOP_INNER_LAYOUT CMake variables Note, that the 1D and 2D abstractions currently only wrap Kokkos::RangePolicy and Kokkos::MDRangePolicy, respectively, and, thus, are indepdent of the PAR_LOOP_LAYOUT and PAR_LOOP_INNER_LAYOUT configuration.

  • DeviceAllocate and DeviceCopy return a unique_ptr to an object allocated on device memory; the latter also copies data from a provided object in host memory. These unique_ptrs automatically free the device memory when they go out of scope. This is especially useful for inheritance, but note that these allocation and deallocation calls are not performant and should be used minimally.

An arbitrary-dimensional wrapper for Kokkos::Views is available as ParArrayND. See documentation here.

The wrappers par_for_outer and par_for_inner provide a nested parallelism interface that is needed for managing memory cached in tightly nested loops. The wrappers are documented here.

View of Views

Special care needs to be taken when working with a View of View.

To repeat the Kokkos documenation: Don’t use them

But if you have to (which is the case in some places inside Parthenon) then follow this pattern:

Kokkos::View<ParArray1D<Real> *> view_of_pararrays(parthenon::ViewOfViewAlloc("myname"), 10);

The ViewOfViewAlloc ensures that the Kokkos::SequentialHostInit property is added, which results in the (inner View ) deallocators being called on the host (rather than on the device by default).

Similarly, when you create a host mirror of said View of View add the additional property for the same reason.

auto view_of_pararrays_h =
     Kokkos::create_mirror_view(Kokkos::view_alloc(Kokkos::SequentialHostInit), view_of_pararrays);

Note that the SequentialHostInit was only added in Kokkos 4.4.1 (which is now the default in Parthenon).

The need for reductions within function handling MeshBlock data

A task (often a function associated with a MeshBlock) in the original Athena++ code was guaranteed to only being executed using a single CPU thread at any time. Thus, a reduction within a single MeshBlock(e.g., finding a minimum value in the MeshBlock data or filling a buffer using an incremented offset pointer) did not require special care. This is not true in Parthenon any more as a parallel region may be handled by many (GPU/…) threads in parallel. Therefore, a parallel_reduce needs to be used instead of a parallel_for.

A strong hint where this is in order are places where a single variable is incremented within a kernel or where another reduction over MPI processes follows the preceding computations.

Parthenon provides abstractions that provide the ability to perform reductions. In particular, reductions are available for loops from 1D to 5D, but do not include any nested parallel patterns. The interface for the abstracted parallel_for and parallel_reduce executions are nearly identical, with calls to par_reduce having one additional final argument compared to par_for. The additional argument should be a Kokkos Reducer, for example one of the built-in Reducers that ship with Kokkos.

Examples can be found in the advection example

-  Real vmin = 1.0;
-  Real vmax = 0.0;
-  for (int k = kb.s; k <= kb.e; k++) {
-    for (int j = jb.s; j <= jb.e; j++) {
-      for (int i = ib.s; i <= ib.e; i++) {
-        vmin = (v(k, j, i) < vmin ? v(k, j, i) : vmin);
-        vmax = (v(k, j, i) > vmax ? v(k, j, i) : vmax);
-      }
-    }
-  }
+ typename Kokkos::MinMax<Real>::value_type minmax;
+ pmb->par_reduce(
+     "advection check refinement", kb.s, kb.e, jb.s, jb.e, ib.s, ib.e,
+     KOKKOS_LAMBDA(int k, int j, int i,
+                   typename Kokkos::MinMax<Real>::value_type &lminmax) {
+       lminmax.min_val = (v(k, j, i) < lminmax.min_val ? v(k, j, i) : lminmax.min_val);
+       lminmax.max_val = (v(k, j, i) > lminmax.max_val ? v(k, j, i) : lminmax.max_val);
+     },
+     Kokkos::MinMax<Real>(minmax));

or in the buffer packing functions

-void PackData(ParArrayND<T> &src, T *buf, int sn, int en, int si, int ei, int sj, int ej,
-              int sk, int ek, int &offset) {
-  for (int n = sn; n <= en; ++n) {
-    for (int k = sk; k <= ek; k++) {
-      for (int j = sj; j <= ej; j++) {
-#pragma omp simd
-        for (int i = si; i <= ei; i++)
-          buf[offset++] = src(n, k, j, i);
-      }
-    }
-  }
+void PackData(ParArray4D<T> &src, ParArray1D<T> &buf, int sn, int en, int si, int ei,
+              int sj, int ej, int sk, int ek, int &offset, MeshBlock *pmb) {
+  int ni = ei + 1 - si;
+  int nj = ej + 1 - sj;
+  int nk = ek + 1 - sk;
+  int nn = en + 1 - sn;
+
+  pmb->par_for(
+      "PackData 4D", sn, en, sk, ek, sj, ej, si, ei,
+      KOKKOS_LAMBDA(const int n, const int k, const int j, const int i) {
+        buf(offset + i - si + ni * (j - sj + nj * (k - sk + nk * (n - sn)))) =
+            src(n, k, j, i);
+      });
+  offset += nn * nk * nj * ni;
+  return;

Note the explicit calculation of the offset within the kernel and the explicit increment of the offset by the full extent after the kernel.

FAQ

  • What’s the difference between GetDim and extent?

ParArrayND offer GetDim to access the underlying array dimension. Here, GetDim(0) refers to the “first” dimension (e.g., x-direction). ParArray#Ds (with # being 1, 2, 3, …) are direct typedefs to Kokkos::Views. Thus, a call to extent(0) returns the dimension along the first index. Given that ParArray#Ds are constructed using reverse indices (note the k,j,i order in accessing elements), extent and GetDim using the same number usually have different meaning.

auto myarr_nd = ParArrayND<Real>("myarr",nx4,nx3,nx2,nx1); // is logically a 6D array under the hood
ParArray4D<Real> myarr_fd = myarr_nd.Get<4>(); // extracts a 4D View with fixed dimensions

myarr_nd.GetDim(4); // = nx4
myarr_nd.GetDim(1); // = nx1
myarr_fd.extent(0); // = nx4
myarr_fd.extent(3); // = nx1

  • Where to allocate scratch pad memory (e.g., for temporary arrays that are shared between multiple function calls within a nested parallel region)?

Scratch pad memory is unique to each team can will be reused from a larger pool of memory available for all teams. However, this allocation tracking only works if the ScratchPadViews are constructed within the outer parallel regions. Therefore, allocating/constructing ScratchPadViews within functions that are called in the outer parallel region will lead to an overallocation of memory (and likely result in a segfault or out of memory exceptions).

  • Where to use barriers/fences?

As mentioned above, kernel launches are non-blocking and kernel executions are asynchronous (potentially handles by the execution space scheduler). Thus, barriers are required where the following code requires the successful execution of all kernels scheduled. There are three obvious places where this applies: 1. Around MPI calls, e.g., sending a buffer should first be done when the kernel filling the buffer has finished. In order for the parallel execution to continue (e.g., multiple MeshBlocks in multiple device streams) the fence function of the corresponding execution space needs to be used, i.e., pmb->exec_space.fence(); and not the global fence (Kokkos::fence();). 2. Within a nested parallel regions when using scratch space. The threads within a team are independent and thus a member.team_barrier() is required between filling the scratch space and (re)using it. 3. When collecting the results of a parallel reduction on a View. Usually parallel_reduce regions are blocking if the result of the reduction is a host variable (more precisely, of scalar type), e.g., a simple double (or here a Real). If the result of the reduction is a View then the region is non-blocking and other places in the code should ensure that all reductions are finished (e.g., calculating the minimum timestep over all MeshBlocks of a single process. This also applies to hierarchical parallelism, i.e., when an inner parallel_reduce reduces to a ScratchPadView then a team_barrier() is required.

  • Why do I need to redefine variables preceding a parallel region?

The KOKKOS_LAMBDA macro expands into a capture by value [=] (plus host/device annotations). Thus, class member variables are not captured directly, but rather this is, see also a related issue on GitHub. A redefinition, e.g., auto coarse_coords = this->coarse_coords; ensures that the desired object is properly captured and available within the kernel(/parallel region).

  • What does "error: The enclosing parent function ("...") for an extended __host__ __device__ lambda cannot have private or protected access within its class" mean?

This is a current Cuda limitation for extended device lambdas, see Cuda programming guide, and can be “fixed”/addressed by making the function public.