Bioinformatic Supercomputer Wishlist

Wed, 15 Jun 2016 13:22:28 -0700
bioinformatics, biology, bluewaters

Many bioinformatic problems require large amounts of memory and processor time to complete. For example, running WGCNA across 10⁶ CpG sites requires 10⁶ choose 2 or 10¹³ comparisons, which needs 10 TB to store the resulting matrix. While embarrassingly parallel, the dataset upon which the regressions are calculated is very large, and cannot fit into main memory of most existing supercomputers, which are often tuned for small-data fast-interconnect problems.

Another problem which I am interested in is computing ancestral trees from whole human genomes. This involves running maximum likelihood calculations across 10⁹ bases and thousands of samples. The matrix itself could potentially take 1 TB, and calculating the likelihood across that many positions is computationally expensive. Furthermore, an exhaustive search of trees for 2000 individuals requires 2000!! comparisons, or 10²⁸⁶⁸; even searching a small fraction of that subspace requires lots of computational time.

Some things that a future supercomputer could have that would enable better solutions to bioinformatic problems include:

1. Fast local storage

2. Better hierarchical storage with smarter caching. Data should ideally move easily between local memory, shared memory, local storage, and remote storage.

3. Fault-tolerant, storage affinity aware schedulers.

4. GPUs and/or other coprocessors with larger memory and faster memory interconnects.

5. Larger memory (at least on some nodes)

6. Support for docker (or similar) images.

7. Better bioinformatics software which can actually take advantage of advances in computer architecture.