William Jannen

Cooperation and security isolation of library OSes for multi-process applications

Library OSes are a promising approach for applications to efficiently obtain the benefits of virtual machines, including security isolation, host platform compatibility, and migration. Library OSes refactor a traditional OS kernel into an application library, avoiding overheads incurred by duplicate functionality. When compared to running a single application on an OS kernel in a VM, recent library OSes reduce the memory footprint by an order-of-magnitude. Previous library OS (libOS) research has focused on single-process applications, yet many Unix applications, such as network servers and shell scripts, span multiple processes. Key design challenges for a multi-process libOS include management of shared state and minimal expansion of the security isolation boundary. This paper presents Graphene, a library OS that seamlessly and efficiently executes both single and multi-process applications, generally with low memory and performance overheads. Graphene broadens the libOS paradigm to support secure, multi-process APIs, such as copy-on-write fork, signals, and System V IPC. Multiple libOS instances coordinate over pipe-like byte streams to implement a consistent, distributed POSIX abstraction. These coordination streams provide a simple vantage point to enforce security isolation.

BetrFS: Write-Optimization in a Kernel File System

The Be-tree File System, or BetrFS (pronounced “better eff ess”), is the first in-kernel file system to use a write-optimized data structure (WODS). WODS are promising building blocks for storage systems because they support both microwrites and large scans efficiently. Previous WODS-based file systems have shown promise but have been hampered in several ways, which BetrFS mitigates or eliminates altogether. For example, previous WODS-based file systems were implemented in user space using FUSE, which superimposes many reads on a write-intensive workload, reducing the effectiveness of the WODS. This article also contributes several techniques for exploiting write-optimization within existing kernel infrastructure. BetrFS dramatically improves performance of certain types of large scans, such as recursive directory traversals, as well as performance of arbitrary microdata operations, such as file creates, metadata updates, and small writes to files. BetrFS can make small, random updates within a large file 2 orders of magnitude faster than other local file systems. BetrFS is an ongoing prototype effort and requires additional data-structure tuning to match current general-purpose file systems on some operations, including deletes, directory renames, and large sequential writes. Nonetheless, many applications realize significant performance improvements on BetrFS. For instance, an in-place rsync of the Linux kernel source sees roughly 1.6--22 × speedup over commodity file systems.

Visualizing RNA base-pairing probabilities with RNAbow diagrams

There are many effective ways to represent a minimum free energy RNA secondary structure that make it easy to locate its helices and loops. It is a greater challenge to visualize the thermal average probabilities of all folds in a partition function sum; dot plot representations are often puzzling. Therefore, we introduce the RNAbows visualization tool for RNA base pair probabilities. RNAbows represent base pair probabilities with line thickness and shading, yielding intuitive diagrams. RNAbows aid in disentangling incompatible structures, allow comparisons between clusters of folds, highlight differences between wild-type and mutant folds, and are also rather beautiful.

Writes Wrought Right, and Other Adventures in File System Optimization

File systems that employ write-optimized dictionaries (WODs) can perform random-writes, metadata updates, and recursive directory traversals orders of magnitude faster than conventional file systems. However, previous WOD-based file systems have not obtained all of these performance gains without sacrificing performance on other operations, such as file deletion, file or directory renaming, or sequential writes. Using three techniques, late-binding journaling, zoning, and range deletion, we show that there is no fundamental trade-off in write-optimization. These dramatic improvements can be retained while matching conventional file systems on all other operations. BetrFS 0.2 delivers order-of-magnitude better performance than conventional file systems on directory scans and small random writes and matches the performance of conventional file systems on rename, delete, and sequential I/O. For example, BetrFS 0.2 performs directory scans 2.2 × faster, and small random writes over two orders of magnitude faster, than the fastest conventional file system. But unlike BetrFS 0.1, it renames and deletes files commensurate with conventional file systems and performs large sequential I/O at nearly disk bandwidth. The performance benefits of these techniques extend to applications as well. BetrFS 0.2 continues to outperform conventional file systems on many applications, such as as rsync, git-diff, and tar, but improves git-clone performance by 35% over BetrFS 0.1, yielding performance comparable to other file systems.