DSpace at VNU: Acceleration of fast multipole method using special-purpose computer GRAPE

1 ACCELERATION OF FAST MULTIPOLE METHOD USING SPECIAL-PURPOSE COMPUTER GRAPE Nguyen Hai Chau Atsushi Kawai Toshikazu Ebisuzaki Abstract We have implemented the fast multipole method (FMM) on a special-purpose computer GRAPE (GRAvity piPE) The FMM is one of the fastest approximate algorithms to calculate forces among particles Its calculation cost scales as O(N), while the naive algorithm scales as O(N2) Here, N is the number of particles in the system GRAPE is hardware dedicated to the calculation of Coulombic or gravitational forces among particles GRAPE’s calculation speed is 100–1000 times faster than that of conventional computers of the same price, though it cannot handle anything but force calculation We can expect significant speedup by the combination of the fast algorithm and the fast hardware However, a straightforward implementation of the algorithm actually runs on GRAPE at rather modest speed This is because of the limited functionality of the hardware Since GRAPE can handle particle forces only, just a small fraction of the overall calculation procedure can be put on it The remaining part must be performed on a conventional computer connected to GRAPE In order to take full advantage of the dedicated hardware, we modified the FMM using the pseudoparticle multipole method and Anderson’s method In the modified algorithm, multipole and local expansions are expressed by distribution of a small number of imaginary particles (pseudoparticles), and thus they can be evaluated by GRAPE Results of numerical experiments on ordinary GRAPE systems show that, for large-N systems (N ≥ 105), GRAPE accelerates the FMM by a factor ranging from for low accuracy (RMS relative force error ~10–2) to 60 for high accuracy (RMS relative force error ~10–5) Performance of the FMM on GRAPE exceeds that of Barnes–Hut treecode on GRAPE at high accuracy, in case of close-to-uniform distribution of particles However, in the same experimental environment the treecode outperforms the FMM for inhomogeneous distribution of particles Key words: molecular dynamics, numerical simulation, fast multipole method, tree algorithm, Anderson’s method, pseudoparticle multipole method, special-purpose computer Introduction Molecular dynamics (MD) simulations are highly compute intensive The most expensive part of MD is calculation of Coulombic forces among particles (i.e., atoms and ions) In a naive direct-summation algorithm, cost of the force calculation scales as O(N2), where N is the number of particles This is because Coulombic force is a long-range interaction In order to reduce the cost of force calculation, fast algorithms such as the Barnes–Hut treecode (Barnes and Hut 1986) and the fast multipole method (FMM; Greengard and Rokhlin 1987) have been developed In the treecode, particles are grouped and forces from them are approximated by multipole expansions of the group Particles that are more distant are organized into larger groups, and thus the calculation cost scales as O(NlogN) In the FMM, the force is also approximated by a multipole expansion Then the multipole expansion is converted to a local expansion at each observation point The force on each particle is obtained by evaluating the local expansion The calculation cost of this scheme scales as O(N) These fast algorithms are widely used in the field of MD simulation (Lakshminarasimhulu and Madura 2002; Lupo et al 2002) There exists another approach to accelerate the force calculation It is to use hardware dedicated to the calculation of inter-particle forces GRAPE (GRAvity PipE; Sugimoto et al 1990; Makino and Taiji 1998) is one of the most widely used pieces of special-purpose hardware of this kind Figure shows the basic structure of a GRAPE system It consists of a GRAPE processor board and a general-purpose computer (hereafter the host computer) The host computer sends positions and charges of parti- Fig Basic structure of a GRAPE system COLLEGE OF TECHNOLOGY, VIETNAM NATIONAL UNIVERSITY, 144 XUAN THUY, CAU GIAY, HANOI, VIETNAM (CHAUNH@VNU.EDU.VN; NHCHAU@GMAIL.COM) K&F COMPUTING RESEARCH CO., 1-21-6-407, KOJIMA-CHO, CHOFU, TOKYO, JAPAN 182-0026 The International Journal of High Performance Computing Applications, Volume 22, No 2, Summer 2008, pp 194–205 DOI: 10.1177/1094342008090912 © 2008 SAGE Publications Los Angeles, London, New Delhi and Singapore 194 COMPUTATIONAL ASTROPHYSICS LABORATORY, INSTITUTE OF PHYSICAL AND CHEMICAL RESEARCH, (RIKEN), HIROSAWA 2-1, WAKO-SHI, SAITAMA, JAPAN 351-0198 COMPUTING APPLICATIONS Downloaded from hpc.sagepub.com at SETON HALL UNIV on March 30, 2015 cles to GRAPE GRAPE then calculates the forces, and sends results back to the host computer Using hardwired pipelines, a typical GRAPE system performs the force calculation 100–1000 times faster than conventional computers of the same price For small5 N (say N < ∼ 10 ) particle systems, therefore, the combination of a simple direct-summation algorithm and GRAPE is the fastest calculation scheme Fast algorithms are not very effective at such a small N For large-N particle systems, however, O(N2) directsummation becomes expensive, even with GRAPE If we successfully combine one of the fast algorithms and the fast hardware, significant speed up for large-N particle systems would be expected As for the tree algorithm, Makino (1991) has successfully implemented a modified treecode (Barnes 1990) on GRAPE, and achieved a factor of 30–50 speedup For the FMM, on the other hand, no implementation on GRAPE so far exists The FMM’s implementation on dedicated hardware of a similar kind is reported, but its performance is rather modest (Amisaki et al 2003) This is mainly because of the limited functionality of the hardware Since dedicated hardware can calculate the particle force only, it cannot handle multipole and local expansions Therefore, only a small fraction of the FMM’s calculation can be performed on such hardware, and the speedup gain remains rather modest In order to take full advantage of GRAPE, we modified the FMM using the pseudoparticle multipole method (Makino 1999) and Anderson’s (1992) method Using these methods, we can express the multipole and local expansion by a distribution of a small number of imaginary particles (pseudoparticles) With the modification, we can use GRAPE to evaluate the expansions Therefore, a significant fraction of the modified FMM can be handled on GRAPE In this paper we describe the implementation and performance of the modified FMM on GRAPE The paper is organized as follows Section gives a summary of the FMM and related algorithms In Section 3, a brief overview of GRAPE system is given In Section 4, we describe the implementation of our FMM code, which is modified so that it runs on GRAPE Results of numerical tests of the code are shown in Section Section is devoted to discussion and Section summarizes FMM and Related Algorithms Here we give a brief description of the FMM (Section 2.1), and two related algorithms, namely, the Anderson’s method (Section 2.2) and the pseudoparticle multipole method (Section 2.3) As will be seen in Section 4, the latter two algorithms are used to implement the FMM on GRAPE Fig 2.1 Schematic idea of force approximation in FMM FMM The FMM is an approximate algorithm to calculate forces among particles In case of close-to-uniform distribution of particles, the FMM’s calculation cost scales as O(N) This scaling is achieved by approximation of the forces using the multipole and local expansion technique Figure shows a schematic idea of force approximation in the FMM The force from a group of distant particles are approximated by a multipole expansion At an observation point, the multipole expansion is converted to local expansion The local expansion is evaluated by each particle around the observation point A hierarchical tree structure is used for grouping of the particles The algorithm is applicable for two-dimensional (Greengard and Rokhlin 1987) and three-dimensional (Greengard and Rokhlin 1997) particle systems In the following, we review the calculation procedure of the algorithm for the three-dimensional case 2.1.1 Tree construction Assume we have an isolated particle system Initially, we define a large enough cube (root cell) to cover all particles in the system We construct an oct-tree structure by hierarchical subdivision of the cube into eight smaller cubes (child cells) The subdivision procedure starts from the root cell at refinement level l = The subdivision is then repeated recursively for all sub cells, and stopped when l reaches an optimal refinement level lmax The optimal level lmax is determined so that it optimizes the calculation speed 2.1.2 M2M transition Next, we form multipole expansions for each leaf cell by calculating contributions from all particles inside the cell Then we ascend the tree structure to form multipole expansions of all non-leaf cells in all coarser levels The procedure starts from parents of the leaf cells For each cell, the multipole expansions of its children are shifted to the geometric center of the cell (M2M transition) and summed This procedure is continued until it reaches the root cell ACCELERATION OF FMM USING GRAPE Downloaded from hpc.sagepub.com at SETON HALL UNIV on March 30, 2015 195 2.2 Anderson’s Method Anderson (1992) proposed a variant of the FMM using a new formulation of the multipole and local expansions The advantage of his method is its simplicity Anderson’s method makes the implementation of the FMM significantly simpler Here we briefly describe his method Anderson’s method is based on the Poisson’s formula This formula gives the solution of the boundary value problem of the Laplace equation When the potential on the surface of a sphere of radius a is given, the potential Φ at position → r = (r, φ, θ) is expressed as a n+1 ∞ s→⋅ → r → → ( 2n + )  - P n  -  Φ ( as )ds (1) Φ ( r ) = -   r 4π S n = r  ∫∑ Fig Neighbour and interaction list of the hatched cell 2.1.3 M2L conversion Then we evaluate the multipole expansions In order to describe this part, here we define the terminology “neighbor list” and “interaction list.” The neighbor list of a cell is a set of cells in the same level of refinement which have contact with the cell The interaction list of a cell is a set of cells which are children of the neighbors of the cell’s parent and which are not neighbors of the cell itself Figure shows the neighbor and interaction list of a cell for the two-dimensional case For each cell we evaluate the multipole expansion of all cells in its interaction list We convert the multipole expansion to the local expansion at the geometric center of the cell in question (M2L conversion), and sum them 2.1.4 L2L transition In the next step, we descend the tree structure We sum the local expansions at different refinement levels to obtain the total potential field at leaf cells For each cell in level l we shift the center of the local expansion of its parent at level l – (L2L transition), and then add it to the local expansion of the cell By this procedure, all cells in level l will have the local expansion of the total potential field except for the contribution of the neighbor cells By repeating this procedure for all levels, we obtain the potential field for all leaf cells 2.1.5 Force evaluation Finally, we calculate the force on each particle in all leaf cells by summing the contributions of far field and near field forces The near field contribution is directly calculated by evaluating the particle– particle force The far field contribution is calculated by evaluating local expansion of the leaf cell at position of the particle 196 for r ≥ a, and → → r n ∞ s⋅r → → ( 2n + )  - P n  -  Φ ( as Φ ( r ) = -)ds  a  r  4π S n = ∫∑ (2) for r ≤ a Note that here we use a spherical coordinate system Here, Φ(a→ s ) is the given potential on the sphere surface The area of the integration S covers the surface of the unit sphere centered at the origin The function Pn denotes the nth Legendre polynomial In order to use these formulae as replacements of the multipole and local expansions, Anderson proposed a discrete version of them, i.e., he truncated the right-hand side of the equations (1)–(2) at a finite n, and replaced the integrations over S with numerical ones using a spherical t-design Hardin and Sloane (1996) define the spherical tdesign as follows A set of K points = {P1, …, PK} on the unit sphere Ωd = Sd – = {x = (x1, …, xd) ∈ Rd : x · x = 1} forms a spherical t-design if the identity ∫ f ( x ) dµ ( x ) Ωd K f ( Pi ) = -Ki = ∑ (3) (where µ is a uniform measure on Ωd normalized to have a total measure 1) holds for all polynomials f of degree ≤ t (Hardin and Sloane 1996) Note that the optimal set, i.e., the smallest set of the spherical t-design is not known so far for general t In practice we use spherical t-designs as empirically found by Hardin and Sloane Examples of such t-designs are available at http://www.research.att.com/~njas/ sphdesigns/ Using the spherical t-design, Anderson obtained the discrete versions of (1) and (2) as follows: COMPUTING APPLICATIONS Downloaded from hpc.sagepub.com at SETON HALL UNIV on March 30, 2015 → Φ( r ) ≈ p K ∑∑ i = 1n = a ( 2n + )  -  r n+1 s→i ⋅ → r - Φ ( as→i )w i (4) P n   r  for r ≥ a (outer expansion) and → Φ( r ) ≈ p ∑∑ n → Qj = (5) for r ≤ a (inner expansion) Here wi is constant weight value and p is the number of untruncated terms Hereafter we refer to p as the expansion order Anderson’s method uses equations (4) and (5) for M2M and L2L transitions, respectively The procedures of other stages are the same as that of the original FMM 2.3 p N → i s ⋅r r → ( 2n + )  - P n   Φ ( as i )w i  a  r  i = 1n = K assigned to each pseudoparticle is then reduced from four to one Makino’s approach systematically gives the solution of the inversion formula as follows: i i=1 l ij ), (6) l=0 where Qj is the charge of the pseudoparticle, → r i = (ri, φ, θ) is the position of the physical particle, γ is the angle ij → between → r i and the position vector R j of the jth pseudoparticle For the derivation procedure of equation (6), see Makino (1999) Equation (6) gives the solution for outer expansion We found that following a similar approach, we can obtain the solution for inner expansion: Pseudoparticle Multipole Method Makino (1999) proposed the pseudoparticle multipole method (P2M2) – yet another formulation of the multipole expansion The advantage of his method is that the expansions can be evaluated using GRAPE 2 The basic idea of P M is to use a small number of pseudoparticles to express the multipole expansions In other words, this method approximates the potential field of physical particles by the field generated by a small number of pseudoparticles This idea is very similar to that of Anderson’s method Both methods use discrete quantities to approximate the potential field of the original distribution of the particles The difference is that P2M2 uses the distribution of point charges, while Ander2 son’s method uses potential values In the case of P M , the potential is expressed by point charges, and thus it can be evaluated using GRAPE In the following, we describe the formulation procedure of P2M2 The distribution of pseudoparticles is determined so that it correctly describes the coefficients of a multipole expansion A naive approach to obtain the distribution is to directly invert the multipole expansion formula For a relatively small expansion order, say p ≤ 2, we can solve the inversion formula, and obtain the optimal distribution with minimum number of pseudoparticles (Kawai and Makino 2001) However, it is rather difficult to solve the inversion formula for higher p, since the formula is nonlinear For p > 2, we adopted Makino’s (1999) approach which is more general In his approach, pseudoparticles are fixed at the positions given by the spherical t-design (Hardin and Sloane 1996), and only their charges can change This makes the formula linear, although the necessary number of pseudoparticles increases This is because we can adjust only the charges of pseudoparticles, since we fixed the positions of them The degree of freedom l 2l + r i -  - P ( cos γ ∑ q ∑ K  a p N Qj = -  - ∑ q ∑ K r  2l + a l+1 i i=1 P l ( cos γ ij ) (7) i l=0 For the derivation procedure of equation (7), see Appendix A Function of GRAPE The primary function of GRAPE is to calculate the force → f (→ i at position → r i) exerted on particle r i, and potential → → → φ( r i) associated with f ( r i) Although there are several variants of GRAPE for different applications such as astrophysics and MD, the basic functions of these hardware devices→are substantially the same → The force f ( → r i) and the potential φ( r i) are expressed as → → i f(r ) = → → qj ( ri – rj ) rs j=1 N ∑ (8) and → φ ( ri ) = N qj ∑ -r-, j=1 s (9) where N is the number of particles to handle, → r j and qj are the position and the charge of particle j, and rs is the softened distance between particle i and j defined as 2 → rs ≡ |→ r i – r j| + e , where e is →the softening parameter In order to calculate force f ( → r i), relevant data, → r i, → r j, qj, e, and N are sent from→the host computer to GRAPE GRAPE then calculates f ( → r i) for every i, and sends it back to the host The potential φ( → r i) is calculated in the same manner Implementation of the FMM on GRAPE The FMM consists of five stages (see Section 2.1), namely, the tree construction, M2M transition, M2L con- ACCELERATION OF FMM USING GRAPE Downloaded from hpc.sagepub.com at SETON HALL UNIV on March 30, 2015 197 Table Mathematical expressions and operations used in different implementations of the FMM Underlined parts run on GRAPE Original (Greengard and Rokhlin 1997) M2M Multipole expansion M2L M2L conversion formula L2L Local expansion Near field force Evaluation of physical-particle force Far field force Evaluation of local expansion PM Code B (Section 5) P2M2 Evaluation of pseudoparticle potential Evaluation of pseudoparticle potential Anderson’s method P M2 Evaluation of physical-particle force Evaluation of physical-particle force Equation (10) Evaluation of pseudo particles force version, L2L transition, and the force evaluation The force evaluation stage consists of near field and far field evaluation parts In the case of the original FMM, only the near field part of the force evaluation stage can be performed on GRAPE At this stage, GRAPE directly evaluates force from each particle expressed in the form of equation (8) At all other stages, mathematical operations not in the form of equation (8) or equation (9) are required GRAPE cannot handle these operations In our implementation (hereafter code A), we modified the original FMM so that GRAPE could handle the M2L conversion stage, which is the most time consuming For 2 this purpose, we used P M to express the multipole expansions With this modification GRAPE can handle the M2L stage by evaluating potential values from the pseudoparticles At the L2L stage, potential values are locally expanded and shifted using Anderson’s method Table summarizes mathematical expressions and operations used at each calculation stage In the following, we describe the detail of our implementation reaches the root cell This process is performed completely on the host computer 4.1 Tree Construction 4.6 The tree construction stage has no change It is performed in the same way as in the original FMM Using equation (5), the far field potential on a particle at position → r can be calculated from the set of potential values of the leaf cell which contains the particle Meanwhile the far field force is calculated using a derivative of equation (5): 4.2 M2M Transition At the M2M transition stage, we compute positions and charges of pseudoparticles, instead of forming multipole expansion as in the original FMM The procedure starts from the leaf cells Positions and charges of the leaf cells are calculated from positions and charges of physical particles Then, those of non-leaf cells are calculated from positions and charges of pseudoparticles of their child cells This procedure is continued until it 198 Code A (Section 4) 4.3 M2L Conversion The M2L conversion stage is done on GRAPE In contrast to the original FMM we not use the formula to convert the multipole expansion to a local expansion We directly calculate potential values due to pseudoparticles in the interaction list of each cell 4.4 L2L Transition The L2L transition is done in the same manner as Anderson We use equation (5) to convert the local expansion of each cell to that of its children 4.5 Force Evaluation (Near Field) The near field contribution is directly calculated by evaluating the particle–particle force GRAPE can handle this part without any modification of the algorithm Force Evaluation (Far Field) → – ∇Φ ( r ) ≈ ur→ – → si r →  nrP  n ( u ) + ∇P n ( u )   i = 1n = 1–u K p ∑∑ r n – -2 → g ( as i )w i, × ( 2n + ) -an where u = → si · → r /r COMPUTING APPLICATIONS Downloaded from hpc.sagepub.com at SETON HALL UNIV on March 30, 2015 (10) All the calculation at this stage is done on the host computer Further Improved Implementation With the modification described in Section 4, we have successfully put the bottleneck, namely, the M2L conversion stage, on GRAPE The overall calculation of the FMM is significantly accelerated However, we still have room for improvement The M2L stage is put on GRAPE and is no longer a bottleneck Now the most expensive part is the far field force evaluation Equation (10) is complicated and evaluation of it would take rather a large fraction of the overall calculation time (Chau, Kawai, and Ebisuzaki 2002) If we can convert a set of potential values into a set of pseudoparticles at marginal calculation cost, the force from those pseudoparticles can be evaluated on GRAPE, and the bottleneck would disappear In order to facilitate this conversion, we have developed a new systematic procedure (hereafter A2P conversion) Using the A2P conversion, we have implemented yet another version of FMM (hereafter code B) In code B, we use A2P conversion to obtain a distribution of pseudoparticles that reproduces the potential field given by Anderson’s inner expansion Once the distribution of pseudoparticles is obtained, the L2L stage can be performed using inner-P2M2 formula (equation (7)), and then the force evaluation stage is totally done on GRAPE (the final column of Table 1) In the following, we show the procedure of A2P conversion For the first step, we distribute pseudoparticles on the surface of a sphere with radius b using the spherical tdesign Here, b should be larger than the radius of the sphere a on which Anderson’s potential values g(a→ s i) are defined According to equation (7), it is guaranteed that we can adjust the charge of the pseudoparticles so that g(a→ s i) are reproduced Therefore, the relation K Qj ∑ -→ j=1 → i = Φ ( as→i ) R j – as (11) should be satisfied for all i →= … K Using a matrix = → → → T {1/| R j – a s i|} and vectors Q = [Q1, Q2, …, QK] and P = T [Φ(a→ s 1), Φ(a→ s 2), …, Φ(a→ s K)], we can rewrite equation (11) as → → 1Q = P (12) In the next step, we solve the linear equation (12) to obtain charges Qj By numerical experiment we found that appropriate value of radius b is about 6.0 for particles inside a cell with side length 1.0 Anderson (1992) specified that a should be about 0.4 Because of large difference between a and b, equation (12) becomes nearly singular for high order expansions In this case, Gaussian elimination and LU decomposition not give a numerically accurate enough solution Therefore, we applied singular values decomposition (SVD; Press et al 1992) to solve the equation, and obtained better accuracy The additional cost for SVD is negligible Numerical Tests We performed numerical tests on accuracy and performance of our hardware-accelerated FMM Here we show the results 6.1 Accuracy of Inner-P2M2 and the A2P Conversion Here we show the result of a test on accuracy of the A2P conversion (Section 5) and inner-P2M2 (equation (7)) We performed the test in the following steps: Locate a particle q at (r, π, π/2) (spherical coordinate) Here r runs from to 10 Evaluate potential values due to q at positions defined by spherical t-design on the surface of a sphere radius a = 0.4 centered at the origin The number and position of the evaluation points depends on the expansion order p Apply A2P conversion to the local expansion obtained in the previous step, i.e., solve equation (12) to obtain charges of pseudoparticles Qj on the surface of a sphere radius b = centered at the origin The number and position of the pseudoparticles depend on p Evaluate the force and potential due to the pseudoparticles at observation point L : (0.5, π, π/2) Compare the result with exact force and potential The exact values are obtained by direct evaluation Figure depicts the test process Figures and show the results of the test The potential error and the force error are shown in Figures and 6, respectively In both cases, the error for p = to behaves as theoretically expected, i.e., the potential error scales as r–(p + 2), and the force error scales as r–(p + 1) For p = 6, the error stops decreasing at r ≥ This is because of the singularity of the matrix in equation (12) Since a large number of pseudoparticles are used, the solution of equation (12) suffers large computational error ACCELERATION OF FMM USING GRAPE Downloaded from hpc.sagepub.com at SETON HALL UNIV on March 30, 2015 199 Fig Fig Description of the test for accuracy of innerP2M2 and the A2P conversion Numbers on the figure are steps in the test Fig Error of the potential calculated with inner2 P M and the A2P conversion From top to bottom, six dashed curves are plotted with expansion order p = 1, 2, 3, 4, and 6, respectively 6.2 Performance on MDGRAPE-2 Here we show the performance of the FMM code B (Section 5) measured on MDGRAPE-2 (Susukita et al 2003) MDGRAPE-2 is one of the latest devices in the GRAPE series It is developed for MD simulation and has additional function to the original GRAPEs, so that it can handle forces that not decay as 1/r , such as Van der Waals force However, in our test we use MDGRAPE-2 only to calculate Coulombic force and potential The additional functions are not used in our tests 200 Force error: details as in Figure For the measurement, we used two GRAPE systems The first one consists of one MDGRAPE-2 board (64 pipelines, 192 Gflop/s) and a host computer COMPAQ DS20E (Alpha 21264/667 MHz) The second one consists of one MDGRAPE-2 board (16 pipelines, 48 Gflop/s) and a self-assembled host computer (Pentium 4/2.2 GHz, Intel D850 motherboard) We refer the former system as “system I,” and the latter as “system II.” In the test, we distributed particles uniformly within a unit cube centered at the origin, and evaluated the force on all particles The number of particles is from 128K to 4M Notations K and M are 1024 and 1024 × 1024, respectively We measured the calculation time at both high (p = 5) and low (p = 1) accuracy, with and without GRAPE The finest refinement level lmax is set to lmax = and 5, for runs with and without GRAPE, respectively These values are experimentally chosen so that the overall calculation time is minimized (see Section 2.1) In this paper we not present in detail our experiments in the case of inhomogeneous distribution of particles since inhomogeneity is not as important as homogeneity or closeto-uniformity in molecular dynamics simulations However, our experiments in the two GRAPE systems show that the treecode runs faster than the FMM in the inhomogeneous case Results for close-to-uniform distribution cases are shown in Figures 7–10 and Tables 2–3 Figures and are results of system I Figures and 10 and Tables 2–3 are of system II In Figures and 8, calculation time of the code B is plotted against the number of particles N Results shown in Figures and are measured on system I and II, respectively Results of the direct-summation algorithm are also shown for comparison Our code scales as O(N) while direct method scales as O(N ) On system I, runs COMPUTING APPLICATIONS Downloaded from hpc.sagepub.com at SETON HALL UNIV on March 30, 2015 Fig Force calculation time of FMM and direct-summation algorithm on system I Circles denote performance of FMM on MDGRAPE-2 Pentagons denote that on the host computer Open and filled symbols are for low (p = 1) and high accuracy (p = 5), respectively Solid and dashed curves without symbols are performance of direct method on MDGRAPE-2 and the host computer, respectively Fig Comparison of force calculation time for FMM and treecode on MDGRAPE-2 on system I Circles are performance of FMM on MDGRAPE-2 Triangles are that of the treecode on MDGRAPE-2 Open and filled symbols are for low and high accuracy, respectively Parameter pairs (p, θ) to obtain low and high accuracy of the treecode are (1, 1.0) and (2, 0.33), respectively Fig Force calculation time of FMM and direct-summation algorithm on system II Symbols as in Figure Fig 10 Comparison of force calculation time for FMM and treecode on MDGRAPE-2 on system II Details as in Figure with GRAPE are faster than those without GRAPE by a factor of and 60 for low (RMS relative force error ~10–2) and high accuracy (RMS relative force error ~10–5), respectively On system II, the speedup factors are and 14.5 Since the amount of calculation for the M2L stage becomes more significant at higher p (Table 2), the speedup factor is larger for higher accuracy Table shows the breakdown of the calculation time for 1M-particle runs We can see GRAPE significantly accelerates the M2L part and force evaluation part The overall performance of our implementation is limited by the speed of the communication bus between the host and GRAPE, rather than the speed of GRAPE itself For fur- ACCELERATION OF FMM USING GRAPE Downloaded from hpc.sagepub.com at SETON HALL UNIV on March 30, 2015 201 Table Pairwise interaction count for 1M particle run With GRAPE (lmax = 4) Without GRAPE (lmax = 5) Low High Low High Accuracy M2L 6.8 × 10 2.8 × 10 7.7 × 10 3.2 × 109 Force evaluation far field 1.6 × 108 9.1 × 109 1.8 × 108 5.6 × 109 near field 6.1 × 109 6.1 × 109 8.2 × 108 8.2 × 108 Table Time breakdown for 1M particles run on system II With GRAPE (lmax = 4) Without GRAPE (lmax = 5) Low High Low High Tree construction 1.05 1.03 1.02 1.06 Building neighbor and interaction lists 0.06 0.08 1.89 2.31 M2M 0.22 5.92 0.26 5.97 0.01 0.21 0.36 133.88 0.16 4.78 0 0.0004 0.18 0 _ _ _ 0.17 5.17 0.36 133.88 0.01 0.34 0.05 4.11 Host 0.78 0.97 54.35 330.99 Data transfer 8.57 17.37 0 Accuracy M2L Host Data transfer GRAPE _ L2L _ Force evaluation GRAPE _ Total 3.92 9.48 0 _ _ _ _ 13.27 27.82 54.35 330.99 14.78 40.36 57.93 478.32 ther acceleration, we need to switch from the legacy PCI bus (32 bit/33 MHz) to the faster buses, such as PCI-X, or PCI Express Figure shows the calculation time of our FMM code and the treecode (Kawai, Makino, and Ebisuzaki 2004), both running on GRAPE The order of the multipole expansion p and the opening angle θ for the treecode is set to (p, θ) = (1, 1.0) and (2, 0.33) for low and high accuracy, respectively These values are chosen so that the treecode gives roughly the same RMS force error as that 202 of the FMM The RMS force errors at low and high accu–2 –5 racy are ~5 × 10 and ~2 × 10 , respectively We can see that the performance of our FMM code and the treecode is almost the same The FMM is better than the treecode at high accuracy, and worse at low accuracy In a particular GRAPE system, parameters tuning for optimal performance of the modified FMM can be defined by experiments One should measure the code B’s performance on a randomly generated particles system with COMPUTING APPLICATIONS Downloaded from hpc.sagepub.com at SETON HALL UNIV on March 30, 2015 Table Performance comparison with Wrankin’s code N Wrankin’s code Our code with GRAPE without GRAPE 98,304 33.2 2.9 34.1 393,216 190.2 16.4 196.5 1,572,864 629.6 64.0 878.8 different values of the finest refinement level lmax for each expansion order p from to For example, if the number of particles in the system is from 128K to 4M and the GRAPE’s peak performance is either 48 Gflop/s or 192 Gflop/s then the values of lmax that should be tested are 3, and 7.1 Discussion Comparison with Other Implementations We compared the performance of our FMM implementation (the code B) with Wrankin’s distributed parallel multipole tree algorithm (DPMTA; Wrankin and Board 1995) We measured the performance of Wrankin’s code on system II, using the serial version of DPMTA 3.1.3 available at http://www.ee.duke.edu/~wrankin/Dpmta/ For the measurement, particles are distributed in a unit cube The expansion order and other parameters of each code are chosen so that relatively high accuracy (~10–5) is achieved, and the performance is optimized Table summarizes the comparison Using GRAPE, our code outperforms Wrankin’s codes by tenfold Without GRAPE, our code is slower than Wrankin’s code by a factor of 1.1–1.4, mainly because our code requires a larger number of operation counts, so that it takes full advantage of GRAPE 7.2 Kawai 2005) We can follow a similar approach to parallelize our FMM code Parallelization on GRAPE Cluster Parallelization of the FMM on a cluster of GRAPEs requires no special techniques Algorithms used for parallelization on a cluster of general-purpose computers (Hu and Johnsson 1996) can be applied without modification In our modified FMM, GRAPE is used for the M2L and force evaluation stages The presence of GRAPE has no effect to parallelization of the tree construction, building neighbor and interaction lists In the case of the treecode, several versions of parallel codes have been developed so far These codes are used for productive runs in the field of astrophysics (Fukushige, Kawai, and Makino 2004; Fukushige, Makino, and Summary Using special-purpose hardware GRAPE, we have successfully accelerated the FMM In order to take full advantage of the hardware, we have modified the original FMM using Anderson’s method, the pseudoparticle multipole method, and two conversion techniques we have newly invented The experimental results show that GRAPE accelerates the FMM by a factor of to 60, and the factor increases as the required accuracy becomes higher Comparison with the treecode shows that in the case of close-to-uniform distribution of particles, our FMM is faster at high accuracy, while the treecode is faster at low accuracy In case of inhomogeneous distribution of particles, the treecode is faster than the FMM It is suggested that one should use the code B for large scale molecular dynamics simulations and where high accuracy is demanded Acknowledgments Thanks are due to Dr T Iitaka at the Institute of Physical and Chemical Research (RIKEN) for the suggestion of using the SVD method We are grateful to Prof J A Smith from Bridge to Asia and Prof D E Keyes from Columbia University for refining the manuscript This work is supported by the Advanced Computing Center, RIKEN and the College of Technology, Vietnam National University, Hanoi Part of this work was carried out while N H Chau was a contract researcher of RIKEN and A Kawai was a special postdoctoral researcher of RIKEN Appendix A In this appendix, we describe the derivation procedure of 2 equation (7), inner expansion of P M The local expansion of the potential Φ( → r ) is expressed as → p Φ ( r ) = 4π l ∑∑β r Y l ( θ, φ ) m l l m (13) l = m = –l Here, Y l (θ, φ) is the spherical harmonics and β l is the expansion coefficient In order to approximate the potential field due to the distribution of N particles, the coefficients should satisfy m m N m* m - Y ( θ i, φ i ), β l = q i -2l + i = r li + l ∑ (14) ACCELERATION OF FMM USING GRAPE Downloaded from hpc.sagepub.com at SETON HALL UNIV on March 30, 2015 203 where qi and → r i = (ri, θ, φ) are the charges and positions of the particles, and * denotes the complex conjugate In order to reproduce the expansion→Φ( → r ) up to pth order, the charges Qj and the positions R j = (Rj, θj, φj) of pseudoparticles must satisfy In practice, we can directly calculate Qj from the charges qi and the positions → r i of physical particles Combining equations (14) and (19), Qj is expressed as 4π Q j = -K p N l ∑ ∑ ∑ q  r - b i l = m = –l i = i l+1 Y l ( θ j, φ j )Y l ( θ i, φ i ) (20) m m* K 1 m* m - Y ( θ j, φ j ) β l = Q j 2l + j = R lj + l ∑ (15) for all (p + 1) combinations of l and m in the range of ≤ l ≤ p and –l ≤ m ≤ l Here K is the number of pseudoparticles Following Makino’s (1999) approach, we restrict the distribution of pseudoparticles to the surface of a sphere centered at the origin With this restriction, the coefficients of local expansion generated by the pseudoparticles are expressed as K m - Q j Y m* β l = -l ( θ j, φ j ), l+1 ( 2l + )b j = ∑ (16) where b is the radius of the sphere If we consider the limit of infinite K, equation (16) is replaced by - ρ ( a, θ, φ )Y m* β = -l ( θ, φ )ds l–1 ( 2l + )b S ∫ m l (17) Here S is the surface of a unit sphere, and ρ is the continuous charge representation of pseudoparticle In this limit, the charge distribution is obtained by the inverse transform of spherical harmonics expansion as follows: p ρ ( a, θ, φ ) = l ∑ ∑ ( 2l + )b l–1 m β l Y l ( θ, φ ) m (18) l = m = –l We can discretize ρ using the spherical t-design In other words, the spherical t-design gives a distribution of pseudoparticles over which numerical integration retains the orthogonality of spherical harmonics up to pth order The charges of the pseudoparticles are then obtained as Using the addition theorem of spherical harmonics, we can simplify this equation and obtain the formula to give Qj from qj and → r i: p N Qj = -  - ∑ ∑ K r  qi i=1 2l + b l=0 i l+1 P l ( cos γ ij ) (21) Author Biographies Nguyen Hai Chau, has a Ph.D and his present position is head of the Information Systems Department, Faculty of Information Technology, College of Technology, Vietnam National University, Hanoi, Vietnam (http:// www.coltech.vnu.edu.vn) Nguyen Hai Chau obtained his PhD degree in computer science from Vietnam National University in 1999 His research interests are fast algorithms for force calculation in molecular dynamics simulations and fuzzy reasoning methods Atsushi Kawai has a Ph.D and is currently chief technical officer of K&F Computing Research Co (http:// www.kfcr.jp/index-e.html) Atsushi Kawai obtained his PhD degree in computer science from Tokyo University in 2000 His research interests are the development of special-purpose computers and software dedicated to scientific simulations Toshikazu Ebisuzaki has a Ph.D and is currently chief scientist of the Computational Astrophysics Laboratory, RIKEN (http://www.riken.jp) Toshikazu Ebisuzaki obtained his PhD degree in astrophysics from Tokyo University in 1986 His research interests are: ultra-high energy cosmic-rays; development of super-high speed special-purpose computers; dynamics of biomolecules; computational materials science; science of the earth and planets; application of computers to education References 4π Q j = -K p l ∑ ∑ ( 2l + )b l+1 m β l Y l ( θ j, φ j ) m (19) l = m = –l This equation gives the charges Qj of pseudoparticles m from the expansion coefficients of physical particles β l 204 Amisaki, T., Toyoda, S., Miyagawa, H., and Kitamura, K (2003) Development of hardware accelerator for molecular dynamics simulations: A computation board that calculates nonbonded interactions in cooperation with fast multipole method, Journal of Computational Chemistry 24: 582–592 COMPUTING APPLICATIONS Downloaded from hpc.sagepub.com at SETON HALL UNIV on March 30, 2015 Anderson, C R (1992) An 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(2002) A cell multipole based domain decomposition algorithm for molecular dynamics simulation of systems of arbitrary shape, Computer Physics Communications 144: 141–153 Lupo, J A., Wang, Z Q., McKenney, A M., Pachter, R., and Mattson, W (2002) A large scale molecular dynamics simulation code using the fast multipole algorithm (FMD): Performance and application, Journal of Molecular Graphics and Modelling 21: 89–99 Makino, J (1991) Treecode with a special-purpose processor, Publications of the Astronomical Society of Japan 43: 621–638 Makino, J (1999) Yet another fast multipole method without multipoles – Pseudoparticle multipole method, Journal of Computational Physics 151: 910–920 Makino, J and Taiji, M (1998) Scientific simulations with special-purpose computers – The GRAPE systems, Chichester: John Wiley and Sons Press, W H., Teukolsky, S A., Vetterling, W T., and Flannery, B P (1992) Numerical recipes in C – The art of scientific computing, 2nd edition, Cambridge University Press, New York, NY Sugimoto, D., Chikada, Y., Makino, J., Ito, T., Ebisuzaki, T., and Umemura, M (1990) A special-purpose computer for gravitational many-body problems, Nature 345: 33–35 Susukita, R., Ebisuzaki, T., Elmegreen, B G., Furusawa, H., Kato, K., Kawai, A., Kobayashi, Y et al (2003) Hardware accelerator for molecular dynamics: MDGRAPE-2, Computer Physics Communications 155: 115–131 Wrankin, W T and Board, J A (1995) A portable distributed implementation of the parallel multipole tree algorithm In Proceedings of the Fourth IEEE International Symposium on High Performance Distributed Computing 1995 (HPDC 95), The Ritz Carlton Pentagon City, Virginia, ACCELERATION OF FMM USING GRAPE Downloaded from hpc.sagepub.com at SETON HALL UNIV on March 30, 2015 205 ... the form of equation (8) At all other stages, mathematical operations not in the form of equation (8) or equation (9) are required GRAPE cannot handle these operations In our implementation (hereafter... development of super-high speed special-purpose computers; dynamics of biomolecules; computational materials science; science of the earth and planets; application of computers to education References... hardware accelerator for molecular dynamics simulations: A computation board that calculates nonbonded interactions in cooperation with fast multipole method, Journal of Computational Chemistry