The Lustre file system provides high aggregated I/O bandwidth and is in widespread use throughout the HPC community. Here we report on work (1) developing a model for understanding collective parallel MPI write operations on Lustre, and (2) producing a library that optimizes parallel write performance in a user-friendly way. We note that a system's default stripe count is rarely a good choice for parallel I/O, and that performance depends on a delicate balance between the number of stripes and the actual (not requested) number of collective writers. Unfortunate combinations of these parameters may degrade performance considerably. For the programmer, however, it's all about the stripe count: an informed choice of this single parameter allows MPI to assign writers in a way that achieves near-optimal performance. We offer recommendations for those who wish to tune performance manually and describe the easy-to-use T3PIO library that manages the tuning automatically.

SUMMARY: New sequence data useful for phylogenetic and evolutionary analyses continues to be added to public databases. The construction of multiple sequence alignments and inference of huge phylogenies comprising large taxonomic groups are expensive tasks, both in terms of man hours and computational resources. Therefore, maintaining comprehensive phylogenies, based on representative and up-to-date molecular sequences, is challenging. PUmPER is a framework that can perpetually construct multi-gene alignments (with PHLAWD) and phylogenetic trees (with ExaML or RAxML-Light) for a given NCBI taxonomic group. When sufficient numbers of new gene sequences for the selected taxonomic group have accumulated in GenBank, PUmPER automatically extends the alignment and infers extended phylogenetic trees by using previously inferred smaller trees as starting topologies. Using our framework, large phylogenetic trees can be perpetually updated without human intervention. Importantly, resulting phylogenies are not statistically significantly worse than trees inferred from scratch. AVAILABILITY AND IMPLEMENTATION: PUmPER can run in stand-alone mode on a single server, or offload the computationally expensive phylogenetic searches to a parallel computing cluster. Source code, documentation, and tutorials are available at https://github.com/fizquierdo/perpetually-updated-trees. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary Material is available at Bioinformatics online.