Release Notes
- Colored builds use far less memory at low and moderate thread counts. On
149,998 Salmonella assemblies at 16 threads, peak RSS falls from 22.4 GB to
8.9 GB (C++ Cuttlefish 3: 11.5 GB), with wall time unchanged; at 64 threads
it falls from 25.5 GB to 18.0 GB. Colored partition buckets are now written
as they fill instead of being staged for a 12 GiB source window. The window
is kept only as the fallback for a source too large to stage whole, which it
still regroups exactly. Output is unchanged.
- The maximal-unitig coordinate map holds smaller per-bucket writer buffers
(128 KiB instead of 1 MiB), and colored worker batches flush when any of
their streams fills. This removes about 3 GB from the colored map-phase peak
and about 1.2 GB from uncolored builds.
- Local contraction workers reuse their per-subgraph output buffers instead of
allocating and freeing them for every one of the 16,384 subgraphs, which
removes about a third of the phase's page faults, and the unitig walk no
longer builds error values it then has to drop. Together these keep colored
local contraction at 3.0.2's speed; end to end, 150k-assembly colored builds
are as fast as 3.0.2 at 16 threads and 8.5% faster at 256.
Install cuttlefish-rs-cli 3.0.3
Install prebuilt binaries via shell script
curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/cuttlefish/releases/download/v3.0.3/cuttlefish-rs-cli-installer.sh | sh
Download cuttlefish-rs-cli 3.0.3
