accel-oil

Hardware accelerator for OIL algorithm

Files

bioinformatics/ is the folder with testing case data. It holds programs and samples which the algorithm will be evaluated against to.

bioinformatics/FullChangeOrders.json and bioinformatics/ExportedData.json are ProteinTagger files that were used to get sampling data.

bioinformatics/oil/ contains the PC program using the shared C implementation of OIL, this is reusing the files under src/

bioinformatics/sampler contains the program used to preprocess data to feed OIL implementation, it emits JSON formatted sample sets.

The flow was the following:

1. First query uniprot for potyviridae sequences.
2. Export full search result dataset in XML format (uniprot-taxonomy-potyviridae.xml).
3. Use ProteinTagger to match and unify protein tag names for annotated segments.
4. Export tagged dataset (ExportedData.json).
5. Use sampler script generate_samples.cmd to gather final samples into an special data structure to handle the highly repetitive data with efficiency, it uses ExportedData.json and uniprot-taxonomy-potyviridae.xml to generate sampleset.json.
6. Use resulting data structure with oil.

Knowledge base

HDL generation is broken on Vivado HLS (at least 2014.1). Entities matching *_async_fifo.vhdl will be bad wired by missing of if_write_ce signal.

For EDK simulation ensure that ModelSIM libraries are compiled. You can use COMPXLIB to compile them, compile all for your devices.

Sometimes XPS may refuse to build your simulation files because of microblaze IP libraries not found, to solve just try COMPXLIB with other options

solution_virtex5_plb is the prefered solution currently working on. It has PLB buses only. impl/impl_test_single is the XPS system implementation for test using one instance. This system is the simulation targeted design. impl/impl_test_pcie is the XPS system implementation targeted to ML505 Virtex 5 board instancing multiple accelerators and PCIe bridge.