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MFDn Case Study

Description of MFDn

Many-Fermion Dynamics---nuclear, or MFDn, is a configuration interaction (CI) code for nuclear structure calculations. It is a platform independent Fortran 90 code using a hybrid MPI/ OpenMP programming model,and is being used on current supercomputers, such as Edison at NERSC, for ab initio calculations of atomic nuclei using realistic nucleon-nucleons and three-nucleon forces. A calculation consists of generating a many-body basis space, constructing the many-body Hamiltonian matrix in this basis, obtaining the lowest eigenpairs, and calculating a set of observables from those eigenpairs. Key computational challenges for MFDn include effectively using the available aggregate memory, efficient construction of the matrix, and efficient sparse matrix--vector products used in the solution of the eigenvalue problem.

In principle an infinite-dimensional basis space is needed for an exact representation of the many-body wavefuctions. However, in practice the basis space is truncated and observables are studied as a function of the truncation parameters. Typical basis space dimensions for large-scale production runs are of the order of several billion. The corresponding many-body matrix is extremely sparse, with tens of trillion nonzero matrix elements, which are stored in core. This defines one of the key computational challenges for this code---effectively using the aggregate memory available in a cluster.

To accurately capture this need we developed a test code which uses representative data for production calculations on 5,000 Knights Landing (KNL) nodes (approximately half the size of Cori at NERSC) using over 80~GB of memory per node. In such a production run, half of the symmetric matrix is distributed in a two-dimensional fashion over the available MPI ranks. Each MPI rank constructs and stores its own sparse submatrix. The test code performs nearly all the computational work a single node would do in the production run but with the communication removed.

MFDn performance

MFDn has excellent thread scaling, but is not NUMA aware. So typically the application is best run with 1 MPI process per NUMA domain. This also minimizes memory overheads from data duplicated across MPI ranks such as lookup tables for matrix element computation.

openmp scale

OpenMP thread scaling of kernels on KNL B0 with 64 physical cores and up to 4 logical threads per core. Speedup is measured against wall time with 8 threads.


Improving the performance of MFDn linear algebra operations

The lowest few eigenvalues and eigenvectors of the very large real sparse symmetric Hamiltonian matrix are found with iterative solvers Lanczos or LOBPCG. The key kernels in the iterative eigensolver are Sparse Matrix--Vector (SpMV) and Sparse transposed Matrix--Vector (SpMVT) products, as only half of the symmetric matrix is stored in order to save memory. The sparse matrix is stored in a CSB_Coo format, which allows for efficient linear algebra operations on very sparse matrices, improved cache reuse on multicore architectures and thread scaling even when the same structure is used for both SpMV and SpMVT (as is the case in this application).

In a production run on 5,000 KNL nodes over 80 GB of memory per node is required for a calculation. The nonzero matrix elements and corresponding indices account for 64 GB of the memory and the input/ output vectors account for up to 16 GB depending on the specific problem and on the eigensolver that is used. To improve data reuse and allow for vectorization, in LOBPCG we replace SpMV with SpMM operations on a block of vectors. To fully utilize AVX-512 instructions on KNL up to 16 vectors could be used, however due to memory requirements and the need to balance traffic on MCDRAM and DDR controllers we limit to 8 simultaneous vectors. To access more memory bandwidth we explicitly place the input/ output vectors in MCDRAM using the memkind library and FASTMEM directives. 

To analyze the performance we measure the arithmetic intensity (AI, the ratio of FLOPs to data movement) of the SpMM operation.  We used the dynamic instruction tracing capabilities of Intel's Software Development Emulator (SDE) to count the number of floating point operations. Due to the size of the matrices and vectors the most relevant measure for data movement are the main memory counters. To access the data movement at DDR and MCDRAM controllers we use Intel's VTune Amplifier XE.

spmm on HAswell (2 MPI ranks & 16 threads each)
n vectors  Arithmetic Intensity GLOP/s   DDR Bandwidth (GB/s)
1 0.26  23 122
4 0.62  57 125 
8 0.80  68  125 



KNL B0 1 mpi rank with 256 threads
1 0.20 0.33 0.13 83 55 17
4 0.80 0.36 0.25 81 180 62
8 1.57 0.37 0.30 71 300 109

On KNL we will use data from both DDR and MCDRAM. In this case two factors, the total data movement and the ratio of data movement on MCDRAM to DDR, are important. For optimal performance the ratio of data moved on each controller should match the ratio of available bandwidth (R = MCDRAM / DDR ~ 4.7) in order to fully utilize each memory system. For m=1,4,8 the ratio of data moved on each controller is R=0.6, 2.2, 4.2, respectively. We estimate that if enough MCDRAM was available the ratio for m=16 would be approximately 8, which would result in the DDR being under-utilized. Increasing m reduces the traffic on DDR and reduces the total data moved on both controllers, resulting in increased total arithmetic intensity. Assuming that it is possible to simultaneously fully utilize both memory systems the expected performance is given by min[ B_drr * AI_drr, B_mcdram * AI_mcdram ]. B_i is the maximum available bandwidth on i. Where the AI for MCDRAM remains mostly constant due to the cache aware matrix format and L2 cache sizes and the AI for DDR increases proportionally since the number of times the full matrix must be streamed from DDR decreases.


performance model for SPMV where matrix is on DDR and vectors are on MCDRAM. M is the number of simultaneous vectors. Red dots are measured on B0 KNL with 256 threads.

MFDn summary

spmm time

Haswell times taken with 2 MPI ranks (1 per socket) and 16 threads per rank. KNL timings were taken with 256 threads and 1 MPI rank on a B0 white box.

Increasing the number of simultaneous vectors helps performance on all architectures, resulting in speedups of 2-5x. On KNL utilizing cache mode results in speedups of 1.3-2.8x over running out of DDR only and using memkind to explicitly place vectors on MCDRAM and the matrix data on DDR results in speedups of 1.3-3.6x over DDR only.

speedup from multiple vectors
  1 4 8
Haswell 1.0  2.5 2.9 
KNL (DDR) 1.0  2.1 2.3 
KNL (cache) 1.0  3.2 5.2 
KNL (memkind) 1.0  3.7 6.4 

We found that utilizing the MCDRAM in combination with increasing the number of vectors was needed to get better performance than on Haswell. Cache mode is faster than KNL only when operating on blocks of 8 vectors, but this mode also reduced the total addressable memory by 16 GB. Explicitly placing the vectors into MCDRAM gave the best performance and with 8 vectors is 60% faster than a single Haswell node.

KNL Speedup over haswell
  1 4 8
Haswell 1.0 1.0 1.0
KNL (DDR) 0.6 0.5 0.5
KNL (cache) 0.7 0.9 1.3
KNL (memkind) 0.7 1.1 1.6