FaaST: Public Demo Version

System requirements

• JDK 11 (necessary)
• Gradle > 7.4 (tested with 7.4)

Short description

This repository contains a version of FaaST, which runs without requiring the whole AFCL tech-stack. While the full version utilizes a database server, to retrieve metadata information about the available function types (FT), its correspoding deployments (FD) and important scheduling information like average round trip time (avgRTT), this version is configured to retrieve this information from static files located in metadata.

The used setup provides you with an environment which is easy to set up (without requiring a separate DB) and is able to deliver reproducable results.

The class ScheduleInvoker represents the Main of this Java program and can be used to further customize input and output files. By default, the input file is BWAfaast4_afcl.yaml, the output file BWAfaast4_cfcl.yaml and as Scheduler the proposed FaaST is chosen. The loop is assumed to have 60 iterations. Note, that by changing the field ALGRORITHM in ScheduleInvoker to Random, a random scheduler is chosen.

Installation and Execution

git clone https://github.com/pgritsch/faast_public.git && cd faast_public

gradle clean build

java -jar build/libs/afcl_published-1.0-IEEE.jar

Example Workflow - BWA

For BWA see https://doi.org/10.1093/bioinformatics/btp698

Input file (full file see BWAfaast4_afcl.yaml)

Note that no resource is defined, on where to execute the given function, but just the function type (FT) splitType

Yaml Representation

parallelBody:
   - section:
       - function:
           name: "split0"
           type: "splitType"
           dataIns:
             - name: "fastaFolder"
               type: "string"
               source: "pSample/fastaFolder"
             ### further inputs omitted for brevity ###
             - name: "chunks"
               type: "number"
               source: "pSample/chunks"
           dataOuts:
             - name: "fasta"
               type: "string"

Graphical Representation (created with http://fceditor.dps.uibk.ac.at:8180/#/editor)

Output file

Yaml Representation

Note that after scheduling the resource property is filled with an IBM cloud function.

Additionally, the name has an appended subscript. This is because the inner parallel is splitted again to allow for each segment to be executed on different resources. (see the graphical depiction with 4 separate branches, where each of the branches runs on a different resource configuration).

parallelBody:
  - section:
    - function:
        name: "split0_0"
        type: "splitType"
        dataIns:
        - name: "fastaFolder"
          type: "string"
          source: "pSample_0/fastaFolder"
        ### further inputs omitted for brevity ###
        - name: "chunks"
          type: "number"
          source: "pSample_0/chunks"
        dataOuts:
        - name: "fasta"
          type: "string"
        properties:
        - name: "resource"
          value: "https://eu-gb.functions.appdomain.cloud/api/v1/web/office%40dps.uibk.ac.at_dev/bwa/split.json"

Graphical Representation