The MASA-CUDAlign extension is used with the MASA architecture to align DNA sequences of unrestricted size with the Smith-Waterman and Needleman-Wunsch algorithms combined with Myers-Miller. It uses the NVIDIA CUDA platform to accelerate the computation time. This extension is able to align huge DNA sequences with more than 200 million base pairs (MBP).
Latest Version: masa-cudalign-3.9.1.1024.tar.gz
tar -xvzf masa-cudalign-3.9.1.1024.tar.gz
cd masa-cudalign-3.9.1.1024
./configure
make
./cudalign [options] seq1.fasta seq2.fasta
All the command line arguments can be retrieved using the --help parameter. See the wiki for a list of command line examples.
We have executed MASA-CUDAlign in many different environments. Here we will present the best results in different scenarios. We recommend to read the reference papers in order to understand the feature improvements in each test.
Test Environment (Homogeneous GPU cluster): [CCGRID2014]
Minotauro Cluster - 64 x NVidia Tesla M2090.
| Sequence 1 | Sequence 2 | Len1 | Len2 | Time | GCUPS |
|---|---|---|---|---|---|
| NC_000001.10 | NC_006468.3 | 249M | 228M | 9h09m25s | 1726.47 |
Test Environment (Heterogeneous GPU Nodes): [PPOPP2014]
Laico Labs - 3 Hosts - 1 x NVidia GTX 580 + 2 x NVidia GTX 680.
| Sequence 1 | Sequence 2 | Len1 | Len2 | Time | GCUPS |
|---|---|---|---|---|---|
| NC_000019.9 | NC_006486.3 | 59M | 64M | 7h29m17s | 139.60 |
| NC_000020.10 | NC_006487.3 | 63M | 62M | 7h42m08s | 140.31 |
| NC_000021.8 | NC_006488.2 | 48M | 46M | 4h27m04s | 139.63 |
| NC_000022.10 | NC_006489.3 | 51M | 50M | 5h03m00s | 140.36 |
Test Environment (Heterogeneous GPUs in Single Node): [PPOPP2014]
Panoramix Host - 1 x NVidia Tesla K20c + 2 x NVidia Tesla C2050.
| Sequence 1 | Sequence 2 | Len1 | Len2 | Time | GCUPS |
|---|---|---|---|---|---|
| NC_000019.9 | NC_006486.3 | 59M | 64M | 10h20m52s | 101.02 |
| NC_000020.10 | NC_006487.3 | 63M | 62M | 7h42m08s | 100.96 |
| NC_000021.8 | NC_006488.2 | 48M | 46M | 6h10m38s | 100.62 |
| NC_000022.10 | NC_006489.3 | 51M | 50M | 7h03m36s | 101.38 |
Test Environment (Single GPU): [TPDS2013]
NVIDIA GeForce GTX 560 Ti
| Sequence 1 | Sequence 2 | Len1 | Len2 | Time | GCUPS |
|---|---|---|---|---|---|
| CP000051.1 | CP000051.1 | 1M | 1M | 43s | 25.82 |
| BA000035.2 | BX927147.1 | 3M | 3M | 6m07s | 28.15 |
| AE016879.1 | AE017225.1 | 5M | 5M | 9m18s | 48.98 |
| NC_005027.1 | NC_003997.3 | 7M | 5M | 22m01s | 28.28 |
| NT_033779.4 | NT_037436.3 | 23M | 25M | 5h29m17s | 28.59 |
| NC_000024.9 | NC_006492.2 | 59M | 24M | 13h05m23s | 30.18 |
| BA000046.3 | NC_000021.7 | 33M | 47M | 8h26m09s | 50.70 |
MASA-CUDAlign is an open source project with public license (GPLv3). A copy of the LICENSE is maintained in this repository.
CUDAlign 3.0: Parallel Biological Sequence Comparison in Large GPU Clusters
Retrieving Smith-Waterman Alignments with Optimizations for Megabase Biological Sequences Using GPU