No abstract

Ab initio approaches in nuclear theory, such as the no-core shell model (NCSM), have been developed for approximately solving finite nuclei with realistic strong interactions. The NCSM and other approaches require an extrapolation of the results obtained in a finite basis space to the infinite basis space limit and assessment of the uncertainty of those extrapolations. Each observable requires a separate extrapolation and many observables have no proven extrapolation method. We propose a feed-forward artificial neural network (ANN) method as an extrapolation tool to obtain the ground-state energy and the ground-state point-proton root-mean-square (rms) radius along with their extrapolation uncertainties. The designed ANNs are sufficient to produce results for these two very different observables in 6 Li from the ab initio NCSM results in small basis spaces that satisfy the following theoretical physics condition: independence of basis space parameters in the limit of extremely large matrices. Comparisons of the ANN results with other extrapolation methods are also provided.

Abstract. The Message Passing Interface (MPI) is commonly used to write parallel programs for distributed memory parallel computers. MPI-CHECK is a tool developed to aid in the debugging of MPI programs that are written in free or fixed format Fortran 90 and Fortran 77. This paper presents the methods used in MPI-CHECK 2.0 to detect many situations where actual and potential deadlocks occur when using blocking and non-blocking point-to-point routines as well as when using collective routines.

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epiSNP is a program for identifying pairwise single nucleotide polymorphism (SNP) interactions (epistasis) in quantitative-trait genome-wide association studies (GWAS). A parallel MPI version (EPISNPmpi) was created in 2008 to address this computationally expensive analysis on large data sets with many quantitative traits and SNP markers. However, the falling cost of genotyping has led to an explosion of large-scale GWAS data sets that challenge EPISNPmpi's ability to compute results in a reasonable amount of time. Therefore, we optimized epiSNP for modern multi-core and highly parallel many-core processors to efficiently handle these large data sets. This paper describes the serial optimizations, dynamic load balancing using MPI-3 RMA operations, and shared-memory parallelization with OpenMP to further enhance load balancing and allow execution on the Intel Xeon Phi coprocessor (MIC). For a large GWAS data set, our optimizations provided a 38.43 3 speedup over EPISNPmpi on 126 nodes using 2 MICs on TACC's Stampede Supercomputer. We also describe a Coarray Fortran (CAF) version that demonstrates the suitability of PGAS languages for problems with this computational pattern. We show that the Coarray version performs competitively with the MPI version on the NERSC Edison Cray XC30 supercomputer. Finally, the performance benefits of hyper-threading for this application on Edison (average 1.35 3 speedup) are demonstrated.