Enzo v2.0 documentation

Parallel Root Grid IO

Parallel Root Grid IO (PRGIO) is a set of Enzo behaviors that allow the user to run problems that has a root grid larger than the available memory on a single node.

This page is intended for developers that need to write new problem generators that will be run at extremely large scale. Large problem size will need to utilize the PRGIO machinery in Enzo. As this brings a significant amount of added complexity, it isn’t recommended for smaller problems. It is also recommended that you write the problem generator without this machinery first, and test on smaller problems, before adding the additional complexity. If you don’t intend to write your own problem generator, this page is basically irrelevant.

Background: why it is how it is

PRGIO is an essential component of doing any simulations at large scale. In its initial inception, Enzo worked on shared memory machines. This meant that the total computer memory available dictated the problem size. Enzo would allocate the root grid on the root processor, then distribute spatially decomposed parts of the root grid to the other processors. When it came time to write the data, the root grid was collected back to the root processor, and written in a single file.

This worked fine until distributed computers were deployed in response to the limitations of a shared memory computer. This coincided with a growth of the desired root grid size for the Enzo simulation. Now, the total aggregate memory of a single shared memory computer and the memory required were vastly different. The old model broke down because you simply can’t fit the 15x5123arrays you need in 512 Mb of RAM, but you can on 64 nodes if the memory is taken as an aggregate total. So out of necessity, PRGIO was born.

Short version

Essentially, PRGIO has three components (though not called in this order)

Input and Restarting

During initialization, the root grid is partitioned into tiles, and each processor reads the part, i.e. a HDF5 hyperslab, of the initial data files. For restarts, each grid is read by one processor that owns the data (ProcessorNumber == MyProcessorNumber) from the HDF5 file containing it.

Output

Unlike early versions of Enzo that collected all the grid data on one processor before writing to disk, with PRGIO each processor writes an HDF5 file for each grid it owns. In the packed AMR output mode, each processor writes one HDF5 file, and in it go all the grids it owns.

Initialization

This is the part that needs attention, because the details are not obvious from the code itself.

Initialization BEFORE PRGIO happens in three steps:

  • Set up grid
  • Allocate Data on the TopGrid object, on the Root Processor
  • Partition TopGrid across processors.

WITH PRGIO, the order is different:

  • Set up grid
  • Partition TopGrid
  • Allocate Data on the working grids.

Setup and Allocation

This is pretty straightforward in principle, but the implementation is a little confusing.

First grids need to be set up. There aren’t very many things you need to do. See MyProblemInitializeGrid for a more comprehensive overview. Simplified, a count of the NumberOfBaryonFields is made and a record of which field is which goes in the FieldType array.

After the Partition (next section), you need to allocate the data.

The confusing bits are in the implementation. We’ll describe this by way of example, using Cosmology simulations as our descriptor. CosmologySimulationInitialize.C contains two routines: CosmologySimulationInitialize() (CSI) and CosmologySimulationReInitialize() (CSRI). These are both called in InitializeNew(). The job of the first routine is to set up the hierarchy of grids and subgrids you’ll need for your cosmology simulation, and call CosmologySimulationInitializeGrid (CSIG). Both CSI and CSIG are called whether or not PRGIO is on. CSRI is called from InitializeNew() after the Top Grid is partitioned. It is only called when PRGIO is on.

Stated a different way:

  1. InitializeNew: reads the parameter file, then calls
  2. CosmologySimulationInitialize: sets up the grid hierarchy. On each of those grids gets called
  3. CosmologySimulationInitializeGrid: which sets NumberOfBaryonFields, and may allocate data.
  4. PartitionGrid: breaks the root grid into parts, and sends those parts to the other processors.
  5. CosmologySimulationReInitialize: If PRGIO is on, this is called. It loops over grids and calls CosmologySimulationInitializeGrid again, which allocates and defines the data.

CSI passes a flag, TotalRefinement to CSIG for each grid you initialize. This is equal to (refinement factor)(refinement level of this grid). So for the Top grid, this is equal to 1, and something that is greater than 1 on all other grids.

Inside of CSIG: if PRGIO is on and TotalRefinement == 1, then statements relating to reading data from disk, allocating memory, and accessing memory are skipped. (this is done by setting ReadData = FALSE) In all other cases, it’s left on. (So if PRGIO is off, or this grid is not on the root level.) Thus at the first pass at initialization, the TopGrid doesn’t get it’s BaryonFields allocated.

The same procedure is done on the nested initial grids if PartitionNestedGrids == 1. If not, the root processor will read the entire nested grid, partition it into smaller subgrids, and finally send the data to different processors if LoadBalancing > 0. Regardless of the value of PartitionNestedGrids, the partitions of the static nested grids will never be re-combined for I/O, unlike the behavior of the root grid when PRGIO is off.

CSRI is called AFTER the root grid has been partitioned and sent off to the other processors. It does very little except call CSIG again. This time when CSIG is called, TotalRefinement = -1. This allows the data to be allocated.

Partition TopGrid and /* bad kludge */

The other confusing part the partition, specifically a line in ExternalBoundary::Prepare().

if (ParallelRootGridIO == TRUE)
    TopGrid->NumberOfBaryonFields = 0; /* bad kludge! */

More on that in a moment.

CommunicationPartitionGrid() is the routine that takes the TopGrid (or, any grid) and breaks it across the processors. It first sorts out the layout of the processors with MPI\_Dims\_create(). It then evenly splits the initial grid over those processors by first creating a new grid on each tile, linking them to the Hierarchy linked list. It then (and here’s the tricky part) allocates each grid on the Root processor and copies data from the Initial Grid to the new tile. Finally, it take these freshly created root grid tiles and sends them to their new processor home.

Here’s where the bad kludge! comes in. You’ll note that in the above description, there’s an allocate on each of the newly created tiles on the root processor, which will allocate more than the root grid data. This is the problem we were trying to avoid. So ExternalBoundary::Prepare() sets NumberOfBaryonFields to zero, so when the allocate comes around it’s allocating Zero fields.

Why is it in ExternalBoundary::Prepare()? A look at the lines immediately preceding the ‘kludge’ help:

BoundaryRank = TopGrid->GridRank;
NumberOfBaryonFields = TopGrid->NumberOfBaryonFields;
if (ParallelRootGridIO == TRUE)
  TopGrid->NumberOfBaryonFields = 0; /* bad kludge! */

In order to do its job properly, the ExternalBoundary objects need to know how many BaryonFields there are in the simulation. So ExternalBoundary::Prepare() records the data, and because that’s the last place NumberOfBaryonFields is needed, sets it to zero.

When CommunicationPartitionGrid() gets to the point where it allocates the data, NumberOfBaryonFields is now zero, so it allocates no data. These empty root grid tiles are then distributed to the other processors.

Finally, CosmologyReInitialize() is called, which calls CosmologyInitializeGrid(). This code then resets NumberOfBaryonFields to its proper value, and since TotalRefinement = -1 allocates all the data.

Then the simulation continues on, only aware of PRGIO when it comes time to not collect the data again.