Scholarly article on topic 'Optimal Temporal Blocking for Stencil Computation'

Optimal Temporal Blocking for Stencil Computation Academic research paper on "Computer and information sciences"

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Procedia Computer Science
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{"Parallel computation" / "Stencil computation" / Optimization}

Abstract of research paper on Computer and information sciences, author of scientific article — Takayuki Muranushi, Junichiro Makino

Abstract Temporal blocking is a class of algorithms which reduces the required memory bandwidth (B/F ratio) of a given stencil computation, by “blocking” multiple time steps. In this paper, we prove that a lower limit exists for the reduction of the B/F attainable by temporal blocking, under certain conditions. We introduce the PiTCH tiling, an example of temporal blocking method that achieves the optimal B/F ratio. We estimate the performance of PiTCH tiling for various stencil applications on several modern CPUs. We show that PiTCH tiling achieves 1.5<2 times better B/F reduction in three-dimensional applications, compared to other temporal blocking schemes. We also show that PiTCH tiling can remove the bandwidth bottleneck from most of the stencil applications considered.

Academic research paper on topic "Optimal Temporal Blocking for Stencil Computation"

Procedia Computer Science

Volume 51, 2015, Pages 1303-1312

ICCS 2015 International Conference On Computational Science

Optimal Temporal Blocking for Stencil Computation

Takayuki Muranushi1 and Junichiro Makino2

1 RIKEN AICS, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan


Temporal blocking is a class of algorithms which reduces the required memory bandwidth (B/F ratio) of a given stencil computation, by "blocking" multiple time steps. In this paper, we prove that a lower limit exists for the reduction of the B/F attainable by temporal blocking, under certain conditions. We introduce the PiTCH tiling, an example of temporal blocking method that achieves the optimal B/F ratio. We estimate the performance of PiTCH tiling for various stencil applications on several modern CPUs. We show that PiTCH tiling achieves 1.5 ~ 2 times better B/F reduction in three-dimensional applications, compared to other temporal blocking schemes. We also show that PiTCH tiling can remove the bandwidth bottleneck from most of the stencil applications considered.

Keywords: Parallel computation,Stencil computation,Optimization

1 Introduction

Many important applications in computational science are based on stencil computation. Its optimization has been an important topic, particularly on machines with deep memory hierarchy, since one of the characteristics of stencil computation is that it requires relatively high memory bandwidth. We measure the requirement for memory bandwidth by B/F (bytes-perflop ratio, or simply B-over-F), the amount of the data transferred between the main memory and CPU per one floating point operation.

The dependence of the B/F ratios of numerical algorithms on the cache size N can be classified into two categories; constant B/F algorithms whose B/F ratios are independent of N, and cache-dependent B/F algorithms whose B/F depends on N. Stencil computation has been considered to be a constant B/F algorithm. In traditional implementations, the entire solution at one time step is calculated before moving on to the next time step. For this kind of schemes, we have

B/F > Arad =2He / Ce (1)

Selection and peer-review under responsibility of the Scientific Programme Committee of ICCS 2015 1303 (gi The Authors. Published by Elsevier B.V.


(a) Orthotope tiling

(b) Parallelotope tiling (c) Trapezoidal tiling

Figure 1: The state-of-the-art temporal blocking methods.

where He is the size of the stencil cell and Ce is the computation per cell update. Examples of cache-dependent B/F algorithms include direct-N-body simulations and matrix-matrix multiplications, whose B/F ratios as functions of N are O(N-1) and O(N5), respectively.

The actual B/F ratio possible on high-performance computing (HPC) platforms has been decreasing. Traditional vector processors had B/F ~ 4, while the B/F of the K computer is approximately 0.5. The exascale systems planned in Japan, US and China will have B/F of 0.1 ^ 0.2. As a result, the efficiency of stencil applications on modern HPC platforms has been decreasing. Thus, if we can reduce the B/F requirement of stencil computation beyond ^trad, that would have a very large impact.

In general, B/F requirement can be decreased by exploiting the data locality [11, 5, 10, 8, 7]. Temporal blocking is such an optimization technique for stencil computation which can reduce the B/F ratio beyond ^trad. The idea of temporal blocking is to decompose the entire computation domain in (d + 1)-dimensional spacetime, into set of regions {R} where each R C Zd+1 contains grid points from multiple time steps. The shape of R is determined so that the calculation for R fits into the cache of the CPU, and thus the required B/F is reduced. Figure 1 illustrates some of the known blocking algorithms for d =1. (for review see [12].)

The orthotope tiling (Figure 1a) is possibly the simplest temporal blocking scheme. It decomposes the set of space-temporal points (t,x) E Zd+1 into regions Rortho(t, X) labeled by as follows:

-N o / f tNf < t < (t + 1)Nf

(t'X) E Rortho(t,x) ^ < xi < (Xi + 1)Nt (2)

It is called the "overlapped tiling" in [12], because in the orthotope tiling, computation of one region includes calculation of the solutions not only at the points in the region but also at some points in its neighboring regions. In order to obtain the solution for the top segment of region 2, we need to start computation from the bottom of the green trapezoid, which contains grid points in regions 1 and 3. On the other hand, by allowing this redundant calculation, all regions in one time slice can be computed in parallel, without the need of inter-region communication.

The parallelotope tiling (Figure 1b):

(tx)e R (t ( N < t < (t + 1)nf (3)

(t,X) E Rpara(T,X) Xint < xi - Nt < (Xi + 1)nt (3)

does not require redundant computations. Parallelotope tilings have also been studied in the context of cache-oblivious computations and have shown excellent performance on multithreaded computations [2, 3, 9]. However, in the parallelotope tiling, regions Rpara located on a temporal plane t have global dependency. In the case of Figure 1b, the computation must go

from right to left. This global dependency makes parallelotope tiling unsuitable for large-scale parallel computation.

The trapezoidal tiling (Figure 1c) and the diamond tiling [6] are examples of temporal blocking schemes that do not suffer from this global dependency. In Figure 1c, we can first calculate regions 2,4, ••• in parallel, and then regions 1, 3, ••• in parallel. However, these tilings can be applied to only one dimension in their original forms. Therefore, it is difficult to apply them on large-scale parallel computers where we would like to decompose the computational domain in all spatial dimensions.

We identify the four conditions which a temporal blocking scheme should satisfy to be usable on large-scale parallel computers.

1. Translational Symmetry. The entire computational domain is filled with a unit lattice, which in turn contains one or more (d + 1)-dimensional polytope regions. The spacetime is filled with only one kind of unit lattice, without gap or overlap, first by creating its spatially-translated copies and then by temporally translating them.

2. Spacelikeness. For any two adjacent regions A and B, either A depends on B or B depends on A. This means that the slope of the facets of a region R must be equal to or shallower than 1/Ns, where NS is the number of grid points in the stencil in one direction.

3. Independence of the unit lattices. Any two regions are causally independent, if they match by spatial translation that maps a unit lattice to another.

4. Finiteness. The scheme should be able to decompose all of the spatial dimensions, so that the size of the unit lattice is finite in all dimensions of spacetime.

Condition 1 allows us to use a simple, SPMD-like programming model. Condition 2 lets us evaluate each region independently, without overlapped computations. Condition 2 and 3 allow us to evaluate unit lattices located on a temporal plane t in any order, or in parallel. Condition 4 is needed to achieve scaling up to thousands and millions of nodes.

There already exists several state-of-the-art temporal blocking methods that satisfy all of the four conditions. One way to achieve such a tiling is to apply the trapezoidal tiling recursively to each spatial dimension [4], which is called "nested splitting." In this method (c.f. Figure 6a of [4]), the unit lattice consists of 2d polytope regions such as hyperfrustums, parallelotopes, and other shapes. Another way to satisfy the four condition is to fill the spacetime with tilted hypercubes [1]. These two approaches are generalizations of trapezoidal tiling and diamond tiling to higher dimensions, respectively.

In this paper, we show that the theoretical limit for the B/F reduction exists. In §2 we show, under certain assumptions, that 2dNS/Ncached is the lower limit for the B/F reduction that can be achieved by temporal blocking. Here NS is the halo size of the stencil, and Ncache is the number of cells that fit into the cache. In §3 we give a temporal blocking method that achieves this lower limit. In §4 we describe its execution model, and then estimate the performance of the proposed method when applied to several typical stencils on present-day CPUs. Finally in §5, we discuss the implications of the limit, and the possibilities of future software and hardware designs to overcome the limitations of the memory bandwidth.

2 Conditions for the Optimal Temporal Blocking

In this paper, we limit the scope of our analysis to variants of temporal blocking where computation within each region proceed in time direction. We have found that the same lower limit

for the B/F reduction exists for variants of the nested splitting where the computation proceed in space direction, and we will discuss it in more detail in the Appendix.

Tile shapes covered by our analysis include the orthotope, the parallelotope, the trapezoid, and the tilted hypercube. We have found that their asymptotic B/F behavior can be expressed in the following common form:

B/F = rptrad (4)

where r = Nf + 2N + (5'

Because typical values for three-dimensional applications are NS = 3 ~ 4, and NT = Ncache1/d — 100, the second term in Equation (5), 2dNS/NT — 0.2 dominates over the first term if Np > 5. As a result, the reduction of B/F is limited by this term even for very large

values of NF .

Of the two terms 1/Np and 2dNS/NT in Equation (5), the former corresponds to the data transfer in time direction through initial and final boundaries, while the latter corresponds to that in space direction through the stencil halo. In Figure 1, they are represented in red and blue line segments, respectively. Using these words our finding can be rephrased as follows. In the large-Np limit, the halo term dominates the main memory bandwidth. The design of optimal temporal blocking, therefore, should be guided by the optimization of the halo term.

To analyze the data transfer within stencil algorithms, we introduce the notion of partition of a region R into batches: {Qi c Zd+1 | Qi c R,i e [1, ••• ,Nq]}. They are cache-fitting batches if and only if:

[Qi] is a set of collectively exhaustive and mutually exclusive subsets of R. yi. #Qi < Ncache, where #A denotes the number of elements of the set A.

• all solutions at grid points [Qi] can be computed depending on solutions at points [Qi, ••• , Qi-1] and points outside R.

Let h : p(Zd+1) ^ P(Zd+1) be the function that maps a set of grid points to its halo (the set of points it directly depends on):

h(Q) = [(t',X') \ (t,x) e Q,t = t - 1, \xi - Xi\<Ns ]. (6)

Given the cache-filling batches, the stencil algorithm proceeds iteratively, by bringing the values of the solutions at positions h(Qi) on-cache and by computing the solutions for positions Qi. This, however, does not mean that all of the grid points in h(Qi) are transferred from the main memory. The transfer can be omitted for grid points in h(Qi) n Qi-1, since they are already on cache from the (i — l)-th iteration. Thus, the set of grid points on cache, and the set of points loaded at iteration i, are

Qcache,i Qi—1, (7)

Qld,i = h(Qi)\Qcache,i = h(Qi)\Qi-1, (8)

respectively, and the amount of load at iteration i is

Hidi = # (h(Qi)\Qi-1) • He. (9)

The total amount of memory transaction, H, is the sum of the initial load, the final store, the halo-loading transactions, and the halo-storing transactions which is the same amount as the loading transactions.

h = He(#Qi + #qNq ) + Hidi (10)

X)Hid,i = 2He^ # (h(Qi)\Qi-i)

i=i i=i

/ Nq Nq

> 2He ]T#h(Qi) #Qi

Compared to the set Qi, the set h(Qi) has extra NS-cells-thick layers of grid points in each of the d spatial dimensions.

Now, for any d-dimensional polytope Q, let V = Vold(Q) be its d-dimensional volume, and S\ = Vold-1(Pi(Q)) be the (d — 1)-dimensional volume of the projection Pi of Q onto (d — 1)-dimensional hyperplane that is perpendicular to «-axis. Then the following inequality holds (the sketch of proof is given in Appendix A):

Ed — 1

Si > d ■ v~.

From this inequality, and from the fact that #Qi < Ncache we obtain

#h(Qi) - #Qi > 2dNs

The equality holds if and only if Qi is a d-dimensional hypercube of size NT where NT = Ncache1/d. By substituting inequality (13) into inequality (11), and by defining 1/Np = (#Qi + #Qnq)/(2J2 =1 #Qi) , we have

CeEN?i #Qi

+ ~nNL) ßtiad>

which gives the lower limit of B/F attainable by temporal blocking.

Now we know that the optimal shape of Qi is a d-dimensional hypercube of size NT and one-cell thick in time direction, the next task is to determine the shape of R = UN=1 Qi,. In order to comply the condition 2 (spacelikeness), the only solutions are to let the d-dimensional hypercube "sweep" the spacetime at slope (±1/NS, ±1/NS, ■ ■■ , ±1/NS). This gives parallelotope regions. Since we have just seen in §1 that parallelotope tiling suffer from global dependency, one might think that the optimal temporal blocking is unattainable.

3 Our Method

We have found that the parallelotope tiling, Equation (3), can be slightly modified so that it satisfies all of the four conditions. The modified decomposition is as follows:

(M) e mr.X) » { N Î ' + Ng * : ,(T VN (15)

I XiNT < Xi - Nst : (Xi + 1)Nt

Figure 2: The PiTCH tiling.

Figure 2a shows the decomposition in d = l. We call this PiTCH (Parallelotopes in Tilted Cube Hierarchy) tiling. PiTCH tiling is similar to parallelotope tiling shown in Figure lb, with the exception that each parallelotope region is deformed and shifted in time direction by multiples of Ng. Because of this modification, PiTCH tiling satisfies independence of the unit lattices, which parallelotope tiling did not. This property is demonstrated in Figure 2a, by the fact that region 1 matches region 6 by spatial translation, not region 5.

In Figure 2a, regions 1 • • • 4 form a unit lattice. This corresponds to regions R'(0, 0), • • • , R'(0, 3) in Figure 2b. Generally speaking, a unit lattice of PiTCH tiling consists of (NF/NG)d regions. The unit lattice fills the entire computational domain first by its spatially-translated copies, then by the temporally-translated copies of the space-filling pattern, in such ways that satisfy the four conditions (Figure 2b).

The parameter NG of PiTCH tiling is constrained by the spacelikeness condition:

ng < Ns ■ (16)

The inequality (16) is used to model the performance of PiTCH tiling.

4 Execution and Performance Models

Figure 3 shows an execution model of the stencil computation with PiTCH tiling on a parallel computer. The computer consists of multiple computing nodes, connected with inter-node communication network. Each node is equipped with NCPU CPUs, and a main memory of size Hmem shared by all CPUs. Each CPU is equipped with its own cache of size Hcache.

The computation is distributed over this machine, so that each node is in charge of computing one or several unit lattice(s). The regions within that unit lattice(s) are computed by the CPUs, in the task-parallel manner.

Although the regions within a single unit lattice have dependencies, they can be evaluated in parallel, as shown in Figure 3. In the figure, node 0 is in charge of computing a unit lattice {R'(0, 0), • • • ,R'(0, 3)}, so © cpu0 is computing the region R'(0, 3) © using its own cache. © It writes the values of the leftmost cells of R' (0, 3) into a buffer on the main memory © from which cpu1 reads. With this data cpu1 can © compute the region R'(0, 2). cpu1 © uses its own cache to compute the region R'(0, 2) and © writes its leftmost cells to another buffer. © Initial conditions for regions {R'(0, 0), • • • ,R'(0, 3)} are stored on the main memory of node 0.

® node 1 is computing the adjacent unit cell {R'(0, 4), ••• , R'(0, 7)} in the same manner, and so on.

It is true that at the very beginning of the computation of a unit lattice there is only one region ready. However, because ^ NF, the time the CPUs remain starved of tasks is only a small portion of the total computation time. Furthermore, we can eliminate the stall by overlapping the computation of one unit lattice with that of the next one.

Under this execution model, the main memory of a node must contain at least all the initial conditions for every regions of the unit lattice assigned to the node. Therefore, the maximal number of regions a unit lattice can contain is NTOd, where

NTO < Ud • (17)

As shown in Figure 2, NF < NGNTO. Thus, NF for PiTCH tiling is upper-limited by the main memory size. Since the reduction ratio r is a decreasing function of NF, we can use inequality

(17) to remove NF from inequality (14):

r > + 2N > i /N^V^ d. NS (18)

- Nt NTO NT - ^ +V NmemJ ) NT

In contrast, most of the other temporal blocking schemes have their NF upper-limited by the cache size, and in some schemes r reaches its minimum at certain NF = NF0, instead of decreasing indefinitely. Given such minima, r = cNS/NT where c is a constant. Examples are the overlapped tiling and the nested splitting, where r = 13.0446Ns/Nt at Nfo = 0.1537Nt/Ns, and r = 9.3246Ns/Nt at Nfo = 0.2599Nt/Ns, respectively, for d = 3.

Compared to these schemes, the upper limit NF0 for PiTCH tiling is much larger, since the main memory is 103 to 104 times larger than the cache in modern computers. From inequality

(18), r = 6.075 - 6.6 • Ns /Nt and r = 4.05 - 4.4 • Ns /Nt , respectively, for d = 2, 3. The values of NF0 are well over 104 for d = 2, and are 30 — 200 for d = 3. The value of r for d = 3 is about 0.65 times that of the nested splitting, and 0.47 times the overlapped tiling.

The PiTCH tiling is superior to the other schemes, since it can make the value of r smaller by utilizing the main memory. Only such schemes can achieve the optimal B/F reduction r = 2dNS/Nt , as the main memory size approaches infinity. PiTCH tiling makes a good

(a) FCPU NCPU Hcache ^mem Hmem

SU 751GFlop/s 32 2MB 20GB/s 128GB

KC 256GFlop/s 1 6MB 64GB/s 16GB

X2 819GFlop/s 2 20MB 136GB/s 256GB

X1 1178GFlop/s 1 40MB 136GB/s 128GB

HA 410GFlop/s 1 128MB 51GB/s 16GB

(b) d He Ce Ns

D2 2 4 7 1

C2 2 64 300 1

D3 3 4 10 1

S3 3 36 262 3

H3 3 20 3381 4

C3 3 80 500 1

Table 1: (a) The computer models, (b) The application models that represent — D2, D3: diffusion equation solvers, C2, C3: CIP-scheme for Navier-Stokes equations, S3: seismic wave equations solver, H3: Godunov-type Navier-Stokes equations solver.

— — — — — — — — — — — — — — — — — — — — — — — — — — — — — — (ZO — -*>(=o — -*>(=o — -*>(=OM-'>(ZO — -*>(=o —

Figure 4: The list of estimated performance.

contrast with diamond tiling [6] on this point; although both methods split the spacetime into diamonds (c.f. Figure 2b), the size of the diamonds is constrained by the main memory in case of the former, and by the cache size in case of the latter.

We estimated the performance of two stencil solvers, for the model computers and applications listed in Tables 1. One solver is traditional (uses no temporal blocking) and the other is equipped with PiTCH tiling. The estimated performance are shown in Figure 4. The y-axis is either ©trad/©FP or ©TB/©FP. The y-value lesser than 1 means that the bottleneck is the main-memory bandwidth, while y-value greater than 1 means that the floating-point operation is the bottleneck.

Figure 4 shows that PiTCH tiling can reduce the B/F by 1/2 ~ 1/17, for three-dimensional applications. It also shows that PiTCH tiling can overcome the main-memory bottleneck for most of the stencil applications.

5 Conclusion and Discussion

Stencil computations have been regarded as constant B/F problems. However, we can transform its B/F requirement to be cache-dependent as O(Ncache-1/d). We have shown the existence of the upper limit for the B/F reduction ratio that can be attained by temporal blocking. We also have introduced the PiTCH tiling, an example of tiling algorithm that achieves this upper limit. Future work will cover concrete implementation and benchmark results on real machines.

The lower limit we found, B/F < 2dNS/NT • (3trad applies to any temporal blocking algorithms that follows the pattern in §4. There exist temporal blocking schemes which break one

or more of the assumptions we have made, but all known (or newly found) schemes so far also obey the same lower limit (see Appendix B).

The lower limit (14) has strong implications on the hardware designs. The only hardware change we can make to reduce the B/F is to increase the cache size, as long as we stay under the model of Figure 3. Note that the cache refers to what resource we can use to calculate the single region R. The "cache" can be extended over multiple cores, or even over multiple nodes, if lowlatency communication between cores or nodes is available. This is one of the hardware designs that allows us to overcome the limit.


The authors thank Drs. Nobu Kishimoto and Masataka Chida of Hakubi Center for Advanced Research, Kyoto University, for the original proof of the inequality (12). The authors thank Kengo Nitadori and Naoto Nakasato for discussions that improved this paper. Part of the research covered in this paper research was funded by MEXT's program for the Development and Improvement for the Next Generation Ultra High-Speed Computer System, under its Subsidies for Operating the Specific Advanced Large Research Facilities. This research used computational resources of the K computer provided by the RIKEN Advanced Institute for Computational Science(AICS).


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A Sketch of Proof for Inequality (12)

Let xv and xSi be characteristic functions for Q and Pi(Q), i.e. xv(x) = 1 x £ Q, xv(x) = 0 x £ Q. Then we have xV (xi, ••• , xd) < nd=i xSi (xi, ••• ,xi, ••• ,xd). By integrating this over Rd

Vol d(V) < 17 xs (xi, ••• ,xi, ••• ,xd)dx i •••dx d (19)

Here x\ denotes the removal of the element xi. Now, we can prove the following inequality for d > 2:

/ TT XSi (xi, ...,Xi, ...,xd)dxi...dxd < TT I / Xsi (xi, ...,Xi, ...,xd)dxi...d,xi...d,xd)

jRd JRd-1 )

The proof uses Holder's inequality and induction over d. By applying (20) to the right hand side of

(19) we have Vold(V) < J]t=i Vold — i (Si)d. By the inequality of arithmetic and geometric means,

d • Vold(V)!Ld1 ^d.=i Vold—i(Si). □

B Extension to Assumptions Made in This Paper

There are other ways of using the cache than that assumed in §2. At iteration i — 1, we can choose to keep data in h(Qi—i) on cache, in addition to those in Qi—i. Also, if we break the conditions for cache-filling batches and allow h(Qi) n Qi = 0, we can further reduce the amount of loads by using computational results for some of the points in Qi to compute other points in Qi. Under these modifications, the set of grid points that are kept on cache and that are loaded are

Qcache,i = h(Qi) n (Qi—i U h(Qi— i)), (21)

Qid,i = h(Qi)\(Qi U Qi—i U h(Qi—i)), (22)

respectively (c.f. Equations (7),(8)).

We have found many kinds of temporal blocking schemes that under Equations (21) and (22) show the same asymptotic B/F behavior (14) as PiTCH decomposition. Although they share drawback of having dependent computation within each Qi, they might show advantage to PiTCH decomposition in other points.

So far we have not found any algorithm that achieves B/F lower than (14) even under Equations (21) and (22). We believe that the lower limit (14) holds even under the extensions, but we have not proven it yet.