Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/broadinstitute/beast2-beagle-cuda

assets for creating Docker images containing beagle/cuda-accelerated beast2, suitable for execution on GCE via dsub

https://github.com/broadinstitute/beast2-beagle-cuda

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.7%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

assets for creating Docker images containing beagle/cuda-accelerated beast2, suitable for execution on GCE via dsub

Basic Info
  • Host: GitHub
  • Owner: broadinstitute
  • License: mit
  • Language: Shell
  • Default Branch: master
  • Size: 11.7 KB
Statistics
  • Stars: 3
  • Watchers: 12
  • Forks: 2
  • Open Issues: 1
  • Releases: 0
Created over 6 years ago · Last pushed 10 months ago
Metadata Files
Readme License

README.md

beast2-beagle-cuda

GPU-accelerated Docker images containing BEAST2 and BEAGLE, compiled with NVIDIA CUDA support

Note: BEAST2 is separate and different from BEAST. If you're looking for Dockerized BEAST with BEAGLE, see this repo: https://github.com/broadinstitute/beast-beagle-cuda

IMPORTANT: The XML file provided to BEAST2 will need to be generated by a version of BEAUTi2 compatible with the version of BEAST2 distributed within the Docker image (currently v2.5.0)

Instructions

  • (Follow the dsub instructions to Get Started on Google Cloud)
  • Install dsub
  • Create an input XML for BEAST (via BEAUTi)
  • Transfer the XML file to a GS bucket
  • Call dsub_beast.sh: ``` Usage: dsubbeast2.sh gs://path/to/in.xml gcp-project-name numgpus [beagle_order]

Note: The version of BEAST2 used should match the version of BEAUTi2 used to generate the input xml file.

    Docker images have been built for several versions of BEAST2.
    The Docker image to be used can be selected by the BEAST_VERSION environment variable.
    For example:
      BEAST_VERSION='2.5.0' dsub_beast.sh gs://path/to/in.xml gcp-project-name num_gpus [beagle_order]
    For available versions of BEAST2, see the tags on Quay.io:
      https://quay.io/repository/broadinstitute/beast2-beagle-cuda?tab=tags
    If BEAST_VERSION is not specified the 'latest' tag will be used.

    The GPU type can be set via the BEAST_GPU_MODEL environment variable.
    For example:
      BEAST_GPU_MODEL='nvidia-tesla-v100' dsub_beast.sh gs://path/to/in.xml gcp-project-name num_gpus beagle_order
    For available GPU models, see:
      https://cloud.google.com/compute/docs/gpus/

    Extra arguments for BEAST2 may be passed via the BEAST_EXTRA_ARGS environment variable.
    For example:
      BEAST_EXTRA_ARGS='-beagle_instances 4' dsub_beast.sh gs://path/to/in.xml gcp-project-name num_gpus [beagle_order]

```

Owner

  • Name: Broad Institute
  • Login: broadinstitute
  • Kind: organization
  • Location: Cambridge, MA

Broad Institute of MIT and Harvard

GitHub Events

Total
  • Pull request review event: 1
  • Pull request review comment event: 1
  • Pull request event: 1
  • Create event: 1
Last Year
  • Pull request review event: 1
  • Pull request review comment event: 1
  • Pull request event: 1
  • Create event: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • tomkinsc (1)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

Dockerfile docker
  • nvidia/cuda 9.2-devel-ubuntu18.04 build