Matrix Factorization at Scale: a Comparison of Scientific Data Analytics in Spark and C+MPI Using Three Case Studies

We explore the trade-offs of performing linear algebra using Apache Spark, compared to traditional C and MPI implementations on HPC platforms. Spark is designed for data analytics on cluster computing platforms with access to local disks and is optimized for data-parallel tasks. We examine three widely-used and important matrix factorizations: NMF (for physical plausability), PCA (for its ubiquity) and CX (for data interpretability). We apply these methods to TB-sized problems in particle physics, climate modeling and bioimaging. The data matrices are tall-and-skinny which enable the algorithms to map conveniently into Spark's data-parallel model. We perform scaling experiments on up to 1600 Cray XC40 nodes, describe the sources of slowdowns, and provide tuning guidance to obtain high performance

Malleable Scheduling Beyond Identical Machines

In malleable job scheduling, jobs can be executed simultaneously on multiple machines with the processing time depending on the number of allocated machines. Jobs are required to be executed non-preemptively and in unison, in the sense that they occupy, during their execution, the same time interval over all the machines of the allocated set. In this work, we study generalizations of malleable job scheduling inspired by standard scheduling on unrelated machines. Specifically, we introduce a general model of malleable job scheduling, where each machine has a (possibly different) speed for each job, and the processing time of a job j on a set of allocated machines S depends on the total speed of S for j. For machines with unrelated speeds, we show that the optimal makespan cannot be approximated within a factor less than e/(e-1), unless P = NP. On the positive side, we present polynomial-time algorithms with approximation ratios 2e/(e-1) for machines with unrelated speeds, 3 for machines with uniform speeds, and 7/3 for restricted assignments on identical machines. Our algorithms are based on deterministic LP rounding and result in sparse schedules, in the sense that each machine shares at most one job with other machines. We also prove lower bounds on the integrality gap of 1+phi for unrelated speeds (phi is the golden ratio) and 2 for uniform speeds and restricted assignments. To indicate the generality of our approach, we show that it also yields constant factor approximation algorithms (i) for minimizing the sum of weighted completion times; and (ii) a variant where we determine the effective speed of a set of allocated machines based on the L_p norm of their speeds