Lattice QCD Applications on QPACE

Lattice QCD Applications on QPACE

Y. Nakamura A. Nobile D. Pleiter H. Simma T. Streuer T. Wettig F. Winter Center for Computational Sciences, University of Tsukuba, Ibaraki 305-8577, Japan Department of Physics, University of Regensburg, 93040 Regensburg, Germany Deutsches Elektronen-Synchrotron DESY, 15738 Zeuthen, Germany School of Physics, University of Edinburgh, Edinburgh EH9 3JZ, UK
Abstract

QPACE is a novel massively parallel architecture optimized for lattice QCD simulations. A single QPACE node is based on the IBM PowerXCell 8i processor. The nodes are interconnected by a custom 3-dimensional torus network implemented on an FPGA. The compute power of the processor is provided by 8 Synergistic Processing Units. Making efficient use of these accelerator cores in scientific applications is challenging. In this paper we describe our strategies for porting applications to the QPACE architecture and report on performance numbers.

keywords:
Parallel architectures, network architecture and design, computer applications
Pacs:
12.38.Gc

1 Introduction

Improving our understanding of the fundamental forces in nature by means of numerical simulations has become an important approach in elementary particle physics. In particular, computer simulations are required to investigate the strong interactions because of their non-perturbative nature. The theory which is supposed to describe the strong interactions is Quantum Chromodynamics (QCD). The formulation of the theory on a discrete space-time lattice is called lattice QCD (LQCD) and has opened the path to numerical calculations. Results from such calculations are key input for the interpretation of data obtained from experiments performed at existing and planned particle accelerators. The enormous cost of such experiments amply justifies the numerical efforts undertaken in LQCD.

Since the availability of computing resources has been and continues to be a limiting factor for making progress in this research field, several projects have been carried out in the past aiming at the development and deployment of massively parallel computers optimized for LQCD applications. Until the previous generation such special purpose computers were typically based on a custom design including a custom-designed processor, see, e.g., apeNEXT apenext () and QCDOC qcdoc (). In QPACE, however, each node comprises a commodity processor: An IBM PowerXCell 8i, one of the most powerful processors available at project start.

From an architectural point of view QPACE may be considered to be a cluster of (not particularly powerful) PowerPC cores with an attached accelerator. Heterogeneous node architectures have recently become more common among the most powerful supercomputers, which can be seen from the top positions of the Top500 list, see Roadrunner (Los Alamos, USA) or more recently Tianhe-1A (Tianjin, China). Such more complex hardware architectures pose significant challenges to the application programmers who want to make efficient use of such powerful machines.

When porting applications to QPACE we applied two strategies. First, highly optimized versions of kernels which dominate the overall performance have been implemented aiming for a significant speed-up of these kernels. Second, the implementation of software interfaces has been explored which allow one to use the accelerator cores while completely hiding the architectural details from the application programmer when implementing the remaining part of the code. This allows one to increase the fraction of code which is accelerated.

The performance can furthermore be improved by choosing an algorithm which is optimal for a given architecture. However, on heterogeneous architectures it is often much more difficult to assess the interplay between machine performance and algorithmic performance. The machine performance can be defined as a set of relevant performance numbers which can be measured during execution of a computational task in terms of a hardware related metric, e.g., number of floating-point operations per time unit executed by a particular set of hardware units. The algorithmic performance refers to the number of atomic sub-tasks, e.g., matrix-vector multiplications, to solve a particular problem, e.g., to compute the solution of a system of linear equations.

After an overview of the QPACE architecture we will discuss in section 3 the requirements of the application for which this machine has been designed. In sections 4 and 5 we will discuss two independent approaches to the porting of application codes to QPACE. In sections 6 and 7 we report on performance results.

2 QPACE architecture

The main building block of the QPACE architecture is the node card, see Fig. 1 (left). The commodity part of the node consists of a PowerXCell 8i processor and 4 GBytes of main memory. To realize a custom network a Field Programmable Gate Array (FPGA) and six physical transceivers (PHY) have been added. The FPGA implements the Network Processor (NWP), a custom I/O fabric which is directly connected to the processor and which furthermore includes 6 links through which the node is connected to its nearest neighbors within a 3-dimensional torus. The PHYs implement the physical layer of the torus network links.

Figure 1: QPACE node-card (left) and simplified block diagram of the PowerXCell 8i processor (right).

The PowerXCell 8i processor is an enhanced version of the Cell processor which has been developed by Sony, Toshiba, and IBM, with Sony’s PlayStation 3 as the first major commercial application. The PowerXCell 8i is the second implementation of the Cell Broadband Engine Architecture cbea (), which unfortunately has been discontinued. The most important enhancements are the support for high-performance double precision operations and IEEE-compliant rounding. The processor comprises multiple cores, see Fig. 1 (right), including the Power Processing Element (PPE), which is a standard PowerPC core. On this core Linux is running and the execution of applications is started. To make full use of the processor’s compute power the application has to start threads on the 8 Synergistic Processing Elements (SPE). All 9 cores, the memory interface as well as the I/O interface are interconnected via a ring-bus. This bus has a very high bandwidth of up to 200 GBytes/sec.

The SPEs have a non-standard architecture, which, however, is very suitable for LQCD applications. Each of them consists of a Synergistic Processing Unit (SPU) and a Memory Flow Controller (MFC). In each clock cycle the SPU can perform a multiply-add operation on a vector of 4 (2) single (double) precision floating-point numbers. With a clock frequency of 3.2 GHz this gives a peak floating-point performance per SPU of 25.6 or 12.8 GFlops in single or double precision, respectively. The memory hierarchy of the processor is non-trivial. Each of the SPUs has its own Local Store (LS), a 256 kBytes on-chip memory. Loading and storing data from and to other devices attached to the ring-bus is handled by the Direct Memory Access (DMA) engine in the MFC. The interface to the external memory provides a bandwidth of 25.6 GBytes/sec. This interface is shared by all SPEs, thus reducing the bandwidth per clock cycle and SPE to 1 Byte peak.

Thanks to an innovative water-cooling system a QPACE rack can host up to 256 nodes, i.e., the aggregate peak performance per rack is 52 or 26 TFlops in single or double precision, respectively. For further details of the QPACE hardware see Baier:2009yq (); qpace-enahpc ().

The custom torus network Pivanti:2011hd () has been optimized for LQCD applications. Since the communication patterns in these applications are typically homogeneous and symmetric a two-sided communication model has been adopted. When node initiates transmission of a message to node it has to rely on node initiating a corresponding receive operation. This communication model minimizes the protocol overhead since it avoids handshake between transmitter and receiver. However, it leaves the responsibility to the programmer to keep the order of the communication operations and the parameters (e.g., message size) on transmitter and receiver side consistent.

When a processor wants to inject data into the network it has to write the data to the corresponding link in the NWP. The typical use case is that the transmit buffer resides in the LS and the DMA engine of the attached MFC is used for moving the data to the FPGA. On the receiving side the processor has to provide a credit to the NWP which defines how many data packets can be written to the receive buffers. These buffers can either be located on-chip (i.e., in LS) or off-chip (i.e., in main memory). The packets have a fixed length and consist of a 4 Byte header, a 128 Byte payload, and a 4 Byte checksum. When a packet arrives at the destination link and a matching credit is available a DMA engine in the NWP will write the payload into the receive buffer. Once a credit has been consumed a notification is generated and the transfer is completed. The network supports virtual channels to allow different pairs of cores to use the same physical link.

3 Application requirements

Simulations in lattice QCD can be split in multiple stages:

  1. Generation of gauge field configurations

  2. Measurement of physical observables on these gauge field configurations, e.g., computation of correlation functions

  3. Analysis of the measurements

The first two stages are by far the most compute intensive. For instance, the generation of a typical ensemble of gauge field configurations may require dozens of sustained TFlops years. We have ported two application programs which can be used for these first stages of simulation to the Cell processor or QPACE:

  • BQCD Nakamura:2010qh () is a program for generating gauge configurations with or flavors of different types of Wilson fermions. It is extensively used on various massively parallel machines, including machines with x86-based nodes, IBM BlueGene, and QPACE.

  • Chroma Edwards:2004sx () is a LQCD software system which consists of several applications including a program to compute various physical observables. It is implemented on top of the QCD Data Parallel (QDP++) library.

In both applications a large fraction of the execution time is spent on solving a system of linear equations of type

(1)

The exact form of the matrix may vary in different calculations. This reflects the fact that there is no unique way of formulating the physical theory, which is defined in a space-time continuum, on a discrete lattice. In the following we will only consider the case of Wilson or Clover fermions, where is not Hermitian. All formulations have in common that is a huge but sparse complex matrix. Therefore, iterative algorithms are used to compute a solution for the system of linear equations. Conjugate Gradient is probably the best known (although not necessarily the most efficient) algorithm used for this kind of problems.

Any of the iterative algorithms can be split into a sequence of computational tasks which involves matrix-vector multiplications. From a computational point of view the latter is the most demanding step since it is compute intensive and involves communication of data between the nodes. On most architectures the performance of this task is limited by the amount of data which can be transferred within the node and between the nodes. It is therefore instructive to consider the information flow function which defines the amount of data that have to be transferred between two storage devices and (e.g., main memory and register file) for a certain subtask and subtask size . The link or processing device which connects the storage devices can be characterized by the bandwidth and start-up latency . An estimate of the time needed to execute the subtask is given by

(2)

If we assume that in first approximation several subtasks, e.g., transfer between main memory and processor as well as floating-point computations, can run concurrently, an optimistic estimate of the execution time is obtained taking

(3)

Let us denote by the minimal compute time for the floating-point operations of a task that could be achieved with an ideal implementation. The floating point efficiency for a given task is then defined as .

As an example let us consider the operation

(4)

where , , are arrays (of length ) of double precision complex matrices, and . These SU(3) matrices occur at different places in LQCD applications. We will assume to be large such that the arrays cannot be kept in the LS of the PowerXCell 8i processor and have to be stored in main memory (MM). The register file is, however, large enough to guarantee full data re-use during the matrix multiplications. Therefore, for each we have to load and store  Bytes, i.e., . For the ideal case of full memory bandwidth saturation (and negligible or hidden latency) we find ns. For each we furthermore have to perform 108 fused vector multiply-adds. Ignoring data dependencies and shuffle operations the time for this subtask is ns. The sustained performance of this operation is thus dominated by the memory bandwidth.

4 Optimized software interfaces

In LQCD applications a large fraction of the computational effort is spent in a few kernel routines. But once the accelerator cores provide a significant speed-up of these routines, the remaining part starts to dominate the overall execution time. This is a well-known result of Amdahl’s law which tells us that the total speed-up is limited by the fraction which can be accelerated by a factor :

(5)

Let us assume that is the fraction spent for solving the system of linear equations described in the previous section. In this case strongly depends on the simulation parameters but is in practice .

If is large it may become more efficient (or, in fact, necessary) to increase in order to improve . Our strategy to increase was to port a software interface to the PowerXCell 8i processor to hide the hardware details from the application programmer. This strategy has been extensively used for the Chroma application suite which is implemented on top of QDP++, which provides a data-parallel programming environment suitable for implementing LQCD applications. Porting Chroma to another architecture basically reduces to a port of QDP++.

QDP++ is a C++ library which can be considered to be an active library, i.e., a library which takes an active role in generating code and interacts with programming tools veldhuizen (). This leads to particular challenges when porting this code since, e.g., the list of instantiated functions will only be known after compilation.

To port this library to the PowerXCell 8i processor the following approach has been chosen winter-phd ():

  1. Identification of all QDP++ functions involved in a particular run of the main application by performing a test run.

  2. Automated generation of SPE code for each of the individual functions.

  3. Re-generation of the main executable now including the SPE code and call-outs to the SPE threads from the PPE.

The resulting application build process is shown in Fig. 2.

Figure 2: The build process of Chroma for the PowerXCell 8i processor: Starting from the left first an executable for the PPE is generated. During a test execution of this executable a list of instantiated functions is retrieved. This is used by a code generator which generates SPE code. This code and a library is used to produce a new executable.

The list of instantiated functions is obtained during the test run, i.e., the PPE-only version of the executable is run and so-called pretty-functions are streamed into the meta-code database. A pretty-function is a C-style string variable available at run time containing the function’s name, return type, and arguments. The meta code collected during this test run is processed by an SPE code generator which constructs for each of the pretty-functions a C++ function restoring the original mathematical semantics but this time with additional support for the accelerator architecture. The mathematical function is implemented using the lattice-wide data types and operations provided by QDP++. Support for the accelerator architecture was integrated by implementing a light-weight version of QDP++ for this type of processor cores. In order to keep the size of all instructions which will be loaded into the LS at the same time small it is mandatory to use the code overlay feature provided by the IBM Cell development tools.

Most functions operate on vectors such that the elements are processed independently of each other, see the example in Eq. (4). To parallelize such an operation on multiple cores the vector is split into disjoint parts and no further dependencies need to be taken into account.

Since most of the operations are limited in performance by the time needed to transfer data from MM to LS and back using explicit DMA operations, special care is needed to optimize the bandwidth usage and to hide latencies. The latter is achieved by employing multi-buffering techniques. The required memory in the LS is managed by a custom pool-based memory allocator. The software needs to determine the transfer sizes, which depend on the size of the input/output vector elements, the pool size, and memory address alignment requirements. The pool size is fixed before compile time while the size of the vector elements has to be determined at compile time. The vector length typically is a run-time parameter.

In QDP++ data types are constructed in a nested manner leveraging template programming techniques. It is therefore possible to manually override the generic construction of types at any level of type construction by means of class template specializations. This technique is exploited in particular to improve the floating-point performance, e.g., by transforming scalar operations into vector operations which make use of the full width of the floating-point unit in the SPE (and as a by-product eliminate shuffle operations).

The strategy outlined above has been successfully implemented and tested on a single PowerXCell 8i processor. Performance results are reported in section 6. The work to extend this to a parallelized version on QPACE is ongoing.

5 Highly optimized application kernel

In the following we consider two algorithms for solving the equations given in 1. One is the Conjugate Gradient (CG), which exploits the symmetry and positive definiteness of the normal operator , and the other is based on a domain decomposition strategy.

CG gained its popularity due to good convergence properties, simplicity, and robustness. The most intensive numerical task in the CG algorithm is the matrix-vector product.Almost all of the optimization effort is usually spent on this particular task. In the case of Wilson-like fermions assuming an optimal implementation of the multiplication by the matrix (i.e., maximum data reuse and minimum traffic on the memory bus) it was found that the performance is bounded by the main memory bandwidth to assuming the peak value for Belletti:2007pp (). For a real implementation has been measured andrea-phd (), which is in good agreement with the upper limit given by this simple model. The considered implementation is subject to a lattice-size constraint in order to achieve maximum data reuse. The maximum local lattice size for a single- (double-) precision computation is limited to (), where , the temporal extent of the lattice, is not constrained. This limitation comes from the size of the local store. This optimal implementation is also able to tolerate a network latency of a few microseconds, i.e., clock cycles.

It is, however, common to use CG to solve the Schur complement equation arising from the even-odd decomposition of the matrix operator. In this case both memory and network accesses become more problematic. During the application of the operator, the vectors on the borders of the local lattice must be communicated twice, since this operator couples next-to-nearest-neighbor lattice points. A practical implementation requires two sweeps of the lattice, each of which requires all of the so-called link variables to be loaded while doing half of the needed floating-point operations. The memory bandwidth limitation thus becomes more critical and the estimated performance on a single node, taking into account the efficiency of the memory, goes below .

In order to circumvent these problems, including the restrictions on the choice of the local lattice sizes, we consider the SAP-FGCR algorithm proposed by Lüscher Luscher:2003qa (), who also demonstrated the algorithmic speed-up in realistic use-cases. The Schwarz Alternating Procedure (SAP) belongs to the class of domain decomposition methods. The lattice is divided into non-overlapping blocks which are checkerboard-colored. One iteration (cycle) of the SAP proceeds as follows: first the Wilson-Dirac equation is solved on all the white blocks, then the residue is updated both on the white blocks and on the internal border of the black blocks, then the equation is solved on the black blocks, with the source being the updated residue, and finally the residue is updated on the black blocks and on the internal border of the white blocks. The blocks are solved with a fixed number of iterations using a simple iterative solver (MR) and Dirichlet boundary conditions. In this procedure the only step which requires network communications is the update of the residue on neighboring blocks. (We assume that individual blocks do not extend beyond a single processor.) Since the updated residue is needed only after half of the blocks are solved, it is possible to completely overlap communication and computation. The procedure is thus able to tolerate very high network latencies without performance loss. The network bandwidth requirement is a fraction of the requirement of the equivalent Wilson-Dirac operator on the whole lattice, where is the number of iterations used in the block solver.

The SAP procedure is used as a preconditioner inside an FGCR iteration. The outer FGCR iteration is able to tolerate variations in the preconditioner since the preconditioner is obtained with an iterative method and thus is not a stationary operator. FGCR is mathematically equivalent to FGMRES saad () and requires one to store two vectors per iteration. This requirement translates in the practical need to restart the FGCR recursion. Mixed precision is implemented through iterative refinement itref (). All operations can proceed in single precision, and only when the FGCR recursion is restarted, the residue is computed in double precision and the double-precision solution is updated by adding the single-precision correction. The most time-consuming task in the SAP is the solution of the Wilson-Dirac equation on the blocks. Since the block size can be chosen such that all the data necessary for a block solve fit in the local store, SAP is able to achieve a high sustained performance by making efficient use of the local store. The local lattice size is only constrained to be a multiple of the block size.

In order to allow for the maximum possible block size and to have the flexibility to scale the algorithm to a large number of nodes, we choose to parallelize the block solver over the 8 SPEs. The block is divided along the temporal direction across the 8 SPEs. This constrains the block size in this direction to be a multiple of 8, which in practice is not a severe restriction. Our implementation overlaps communication and computation also for on-chip parallelization.

All the floating-point intensive code was written using vector intrinsics, and different data layouts were analyzed theoretically before implementing the code. The data layout has a strong impact on the performance, and trade-offs may be necessary to simplify programming. Lattice points are ordered such that points belonging to the same block are contiguous. Inside the blocks, lattice points are divided into two sets, even and odd. In this way DMA operations performed to move block fields between main memory and local store are greatly simplified and the performance is maximized. For the spinor layout, different possibilities were analyzed by counting the floating-point and shuffle instructions involved in the application of the Wilson-Dirac operator for the different layouts. The final choice is such that the indices, from the slowest to the fastest, are color, spinor, complex. The SU(3) matrices, consisting of 72-Byte arrays in single precision, do not satisfy the basic 16-Byte alignment constraint coming from the size of the registers. We have thus chosen to pad the corresponding data structures to 80 Bytes. While this choice introduces an overhead by wasting a fraction of the memory bandwidth, it greatly simplifies the code by avoiding the manual alignment operations that would otherwise be necessary.

Complete overlap of memory accesses with computation can in principle be achieved for sufficiently large on-chip memory. We, however, have chosen to use the maximum possible block size in order to maximize the block solver performance. This limits the amount of data that can be prefetched.

Denoting the SAP operator by , a simple but effective estimation of its performance is given by

(6)

where is the time spent in iterations of the block solver assuming peak floating-point performance, the factor takes into account the operations needed for the even-odd preconditioning on the blocks, is the actual time spent in the block solver for iterations, is the time spent moving data between main memory and local store assuming peak main-memory bandwidth, is a coefficient that models the efficiency of the memory subsystem, and is the time needed for network communication. It is assumed here that there is no overlap between computation and main-memory accesses while there is complete overlap between computation and network communication. The coefficient was determined in micro-benchmarks to be about 0.8.

block size (m) (e) (m) (1.5) (3.0)
8484 458 145 128 64
8266 258 89 128 64
82210 172 52 94 47
Table 1: Performance numbers for the SAP preconditioner as explained in the text.

Table 1 shows the performance of the block solver, , and of the whole preconditioner, , for different block sizes. The measured performance (m) agrees very well with the estimated one (e), which is obtained from expression (6) assuming 4 block-solver iterations. , , (1.5), and (3.0) are, respectively, the time spent doing floating-point operations, moving data between local store and main memory, and performing network communications assuming 1.5 GB/s and 3.0 GB/s bandwidth. Times are expressed in thousands of clock cycles per block.

The structure of the SAP algorithm fits nicely the features of the network. After one block is solved, the data necessary for the update of the residue on neighboring blocks residing on remote nodes are available and sent via a DMA put to the remote nodes directly from the SPEs. Communications are either between two cores of the same node or between two nodes. This difference is, however, hidden in the SPE code because it is controlled by the addresses provided by the thread running on the PPE. All the complexity associated with the network is thus handled by the PPE control code which is also responsible for issuing network receive commands. This simplifies coding significantly.

6 Application performance: QDP++/Chroma

We start our investigation of the performance of our QDP++ port by considering the case of no computation, i.e., only memory transfer operations are performed. This is sensible because we expect the performance of a large portion of the functions to be limited by the bandwidth between MM and LS. Fig. 3 (left pane) shows, for a large set of QDP++ functions , the memory bandwidth saturation , where each of the functions has been assigned an index . The explicit mathematical form of the individual functions cannot easily be recovered due to their construction via the expression template technique. We observe that for most of the functions a good memory bandwidth saturation of about 80% is achieved. Only for a few functions the memory bandwidth is small. It turned out that in these particular cases the load or store operations could not be organized in an efficient way, e.g., because only a few Bytes per vector element have to be transferred. However, the impact on the overall performance of functions with only a few Bytes to transfer is small. The pool size seems to have little impact on the memory bandwidth saturation for most of the functions.

Figure 3: The left pane shows the memory bandwidth saturation for all investigated QDP++ functions with SPE computations being switched off. The different lines correspond to results for different pool sizes . The right pane shows the relative change in memory bandwidth saturation with and without template specializations (values are due to small fluctuations in the execution times).

Next we consider the relative change of the memory bandwidth saturation when computations are switched on:

(7)

In the right pane of Fig. 3 is shown for two cases, using either generic code or template specializations. At this stage we have only executed an optimized version of the complex multiplication. The benchmark result shows the impact of using this optimized version instead of the scalar version of complex multiplication, which requires many more shuffle, load, and store operations. We also observe that more than half of the functions do not require further optimization in terms of the number of floating-point operations since they already execute with .

However, for the other functions can be increased by supplying further optimized code via template specializations. For instance, the function corresponds to the operation defined in Eq. (4), which is memory-bandwidth limited. Here the relative memory-bandwidth saturation is reduced by 20% when computation is enabled due to generic code for the matrix multiplication. We expect that for an optimized implementation of the matrix multiplications could be achieved.

To test the performance of our QDP++ port in a full LQCD application we measure the execution time for a particular application in Chroma (which computes the hadron spectrum). This part does not involve calls to optimized kernel routines and would thus usually not make use of the accelerator cores. On a dual-core 2.0 GHz Intel Xeon processor 5130 we measured an execution time of 83.5 sec. On an IBM QS22 blade using a single 3.2 GHz PowerXCell 8i processor we measured 617.9 sec for a PPE-only version of Chroma. Using our light-weight version of QDP++ for the accelerator cores, the execution time on the same system goes down to 142.4 sec. Thus, although the performance on the PowerXCell 8i processor is significantly smaller compared to the Xeon processor, a speed-up of over 4x is obtained from the PPE-only to the accelerated version. In practice this speed-up is sufficient because only a relatively small fraction of the compute time is spent on this part of the program.

7 Application performance: BQCD

BQCD implements the Hybrid Monte Carlo algorithm for generating gauge field configurations. The fraction of time spent for solving the linear system of equations strongly depends on the simulation parameters. For the most expensive runs currently performed by the QCDSF collaboration (i.e., runs with and a spatial lattice extent ) the BlueGene/P and QPACE versions of BQCD spend about 95% and 75% of the total execution time in the solver, respectively. On QPACE we use the SAP-based solvers described in section 5. These solvers have been ported to the SPEs where they reach a performance of of the single-precision peak. Also some of the other most time-consuming kernels of BQCD have been ported to the SPEs. However, the rest of the code runs on the PPE which explains (at least partially) why a significantly larger fraction of time is spent in this part compared to the BlueGene/P version.

In Fig. 4 (left pane) we show the scaling up to 256 nodes of the SAP preconditioner using an 8484 block size, compared with the ideal scaling slope based on the performance measured on a single node. We observe an excellent scaling behavior.

Figure 4: The left pane shows the scaling of the SAP preconditioner performance as a function of the number of nodes, up to 256 nodes (i.e., 2048 cores), using an 8844 block size. The right pane shows different convergence rates of SAP-FGCR as the Krylov subspace dimension is changed (32, 70, and 100), and the convergence achieved with SAP-FGMRES-DR with 10 deflated vectors and maximum Krylov subspace dimension of 70 (including the deflated vectors).

The condition number of the matrix depends on the simulation parameters and can become very large. The convergence of SAP-FGCR and SAP-FGMRES then tends to become highly sensitive to the dimension of the Krylov subspace. This can be intuitively understood by noticing that the solution of the Dirac equation in this regime is rich in low modes that are not efficiently inverted by the SAP preconditioner. The outer FGMRES iteration then has to reduce the norm of the residue associated with those modes.

In order to improve the convergence properties of FGMRES we implemented deflation in the form of deflated restart (FGMRES-DR) morgan (). This algorithmic trick allows one to preserve some of the information about the Krylov subspace when restarting by reinserting approximate eigenvectors into the Krylov subspace between restarts. We note that in these cases the performance of the algorithm severely depends on the dimension of the Krylov subspace, which is limited by the amount of available memory. This dependence is softer in case of FGMRES-DR. In Fig. 4 (right pane) the convergence rate for solving the same problem is compared using the two algorithms and different Krylov subspace dimensions. It would be interesting, but beyond the scope of the present paper, to study the isoefficiency Kumar:1987 () of our application taking into account both algorithmic and machine performance. From Fig. 4 (right pane) we can deduce a (somewhat counter-intuitive) example where increasing the number of nodes at fixed problem size can increase the algorithmic efficiency since more memory becomes available for the Krylov subspace.

8 Summary and conclusions

In this paper we presented the strategies we applied to achieve high-performance implementations of the most relevant kernel routines on QPACE and to increase the fraction of code which leverages the compute power of the accelerator cores of the PowerXCell 8i processor.

In an exploratory study it has been successfully shown that it is possible to port a library which implements an application-specific software interface to the Cell processor. This enables application programmers to use the accelerator cores while the hardware details are completely hidden. This goal has been accomplished by using advanced template programming techniques and a code generator which generates code for the SPEs. On top of this software interface the Chroma application suite has been successfully built and tested.

When porting BQCD, an application for generating gauge configurations, to QPACE we focused on an efficient solver for a linear set of equations. This is the computationally most demanding part of the program. A high machine performance has been obtained when using SAP-based solvers. These algorithms allow us to perform a large number of operations on the data stored in the on-chip memory, thus minimizing the amount of data that is moved in or out of the processor. Furthermore, large latencies for node-to-node communications can be hidden.

The number of iterations needed by the SAP-based solvers strongly depends on the dimension of the Krylov subspace, which is limited by the main memory size. While hardware parameters typically impact the machine performance, this is an interesting example where the algorithmic performance is affected. This needs to be taken into account when defining optimal machine parameters for a given algorithm.

In the summer of 2009 eight QPACE racks with an aggregate peak performance of 200 TFlops (double precision) have been deployed and are now used for scientific applications, mainly from LQCD. The set of applications running on QPACE also includes a fluid dynamics code based on the discretized Boltzmann approach lbe ().

In the future we plan to apply the strategies we pursued for using the accelerator cores of the PowerXCell 8i processor also to other architectures with accelerator devices. For GP-GPUs highly optimized implementations of relevant LQCD kernels are already available which, however, still lack scalability to a large number of nodes (see, e.g., Babich:2010mu ()). The implementation of software interfaces as described in this paper will be more challenging due to the non-uniform memory and the relatively slow bus connecting host processor and accelerator device.

Acknowledgments

We thank all members of the QPACE team for their hard and creative work that laid the groundwork for the studies reported on in this paper. For the implementation of the SAP-based solvers the availability of a reference implementation by M. Lüscher at http://luscher.web.cern.ch/luscher/DD-HMC is gratefully acknowledged. We also acknowledge the funding of the QPACE project provided by the Deutsche Forschungsgemeinschaft (DFG) in the framework of SFB/TR-55 and by IBM. We furthermore thank the following companies who contributed significantly to the project in financial and/or technical terms: Axe Motors (Italy), Eurotech (Italy), IBM, Knürr (Germany), Xilinx (USA), and Zollner (Germany). This work was supported in part by the European Union (grants 238353/ITN STRONGnet and 227431/HadronPhysics2).

We dedicate this paper to the memory of Gottfried Goldrian, who played a key role in the development of the QPACE architecture. He passed away in January 2011.

References

  • (1) F. Belletti et al., Computing for LQCD: apeNEXT, Computing in Science and Engineering 8 (2006) 18–29. doi:10.1109/MCSE.2006.4.
  • (2) P. A. Boyle et al., Overview of the QCDSP and QCDOC computers, IBM J. Res. Dev. 49 (2005) 351–365. doi:10.1147/rd.492.0351.
  • (3) H. P. Hofstee, A. K. Nanda, eds., Cell Broadband Engine Technology and Systems, IBM J. Res. Dev. 51 (2007) 501.
  • (4) H. Baier et al., QPACE: A QCD parallel computer based on Cell processors, PoS LAT2009 (2009) 001. arXiv:0911.2174.
  • (5) H. Baier et al., QPACE: power-efficient parallel architecture based on IBM PowerXCell 8i, Computer Science - R&D 25 (2010) 149–154. doi:10.1007/s00450-010-0122-4.
  • (6) M. Pivanti, S. F. Schifano, H. Simma, An FPGA-based Torus Communication Network, PoS LAT2010 (2010) 038. arXiv:1102.2346.
  • (7) Y. Nakamura, H. Stüben, BQCD - Berlin Quantum Chromodynamics program, PoS LAT2010 (2010) 040. arXiv:1011.0199.
  • (8) R. G. Edwards, B. Joo, The Chroma software system for lattice QCD, Nucl.Phys.Proc.Suppl. 140 (2005) 832. arXiv:hep-lat/0409003, doi:10.1016/j.nuclphysbps.2004.11.254.
  • (9) T. L. Veldhuizen, D. Gannon, Active Libraries: Rethinking the roles of compilers and libraries, in: In Proceedings of the SIAM Workshop OO’98, SIAM Press, 1998. arXiv:math.NA/9810022.
  • (10) F. Winter, Investigation of Hadron Matter using Lattice QCD and Implementation of Lattice QCD Applications on Heterogeneous Multicore Acceleration Processors, Ph.D. thesis, Regensburg University (2011).
  • (11) F. Belletti et al., QCD on the Cell Broadband Engine, PoS LAT2007 (2007) 039. arXiv:0710.2442.
  • (12) A. Nobile, Performance Analysis and Optimization of LQCD Kernels on the Cell BE Processor, Ph.D. thesis, University Milano-Bicocca (2008).
  • (13) M. Lüscher, Solution of the Dirac equation in lattice QCD using a domain decomposition method, Comput.Phys.Commun. 156 (2004) 209–220. arXiv:hep-lat/0310048, doi:10.1016/S0010-4655(03)00486-7.
  • (14) Y. Saad, Iterative methods for sparse linear systems, 2nd Edition, SIAM, 2003.
  • (15) C. B. Moler, Iterative Refinement in Floating Point, J. ACM 14 (1967) 316–321. doi:10.1145/321386.321394.
  • (16) R. B. Morgan, GMRES with deflated restarting, SIAM Journal on Scientific Computing 24 (2002) 20–37. doi:10.1137/S1064827599364659.
  • (17) V. Kumar, V. N. Rao, Parallel depth first search. Part II. Analysis, International Journal of Parallel Programming 16 (1987) 501–519. doi:10.1007/BF01389001.
  • (18) L. Biferale, F. Mantovani, M. Sbragaglia, A. Scagliarini, F. Toschi, R. Tripiccione, High resolution numerical study of Rayleigh-Taylor turbulence using a thermal lattice Boltzmann scheme, Physics of Fluids 22 (2010) 115112. arXiv:1009.5483, doi:10.1063/1.3517295.
  • (19) R. Babich, M. A. Clark, B. Joo, Parallelizing the QUDA Library for Multi-GPU Calculations in Lattice Quantum Chromodynamics, Proceedings of Supercomputing 2010. arXiv:1011.0024, doi:10.1109/SC.2010.40.
Comments 0
Request Comment
You are adding the first comment!
How to quickly get a good reply:
  • Give credit where it’s due by listing out the positive aspects of a paper before getting into which changes should be made.
  • Be specific in your critique, and provide supporting evidence with appropriate references to substantiate general statements.
  • Your comment should inspire ideas to flow and help the author improves the paper.

The better we are at sharing our knowledge with each other, the faster we move forward.
""
The feedback must be of minimum 40 characters and the title a minimum of 5 characters
   
Add comment
Cancel
Loading ...
138454
This is a comment super asjknd jkasnjk adsnkj
Upvote
Downvote
""
The feedback must be of minumum 40 characters
The feedback must be of minumum 40 characters
Submit
Cancel

You are asking your first question!
How to quickly get a good answer:
  • Keep your question short and to the point
  • Check for grammar or spelling errors.
  • Phrase it like a question
Test
Test description