Commit ed0515c8 authored by James Clark's avatar James Clark

Merge branch 'master' into 'master'

Container cleanup

See merge request !58
parents b5359b23 f6466b3a
Pipeline #46740 passed with stages
in 2 minutes and 7 seconds
...@@ -19,7 +19,7 @@ test:master: ...@@ -19,7 +19,7 @@ test:master:
- master - master
stage: test stage: test
script: script:
- docker run -u $(id -u):$(id -g) $CI_REGISTRY_IMAGE:latest "/opt/bayeswave/test/test-bayeswave.sh" - docker run -u $(id -u):$(id -g) $CI_REGISTRY_IMAGE:latest "/opt/lscsoft/bayeswave/test/test-bayeswave.sh"
docker:production: docker:production:
only: only:
...@@ -34,7 +34,7 @@ test:production: ...@@ -34,7 +34,7 @@ test:production:
- stable - stable
stage: test stage: test
script: script:
- docker run -u $(id -u):$(id -g) $CI_REGISTRY_IMAGE:production "/opt/bayeswave/test/test-bayeswave.sh" - docker run -u $(id -u):$(id -g) $CI_REGISTRY_IMAGE:production "/opt/lscsoft/bayeswave/test/test-bayeswave.sh"
docker:testing: docker:testing:
only: only:
...@@ -49,4 +49,4 @@ test:testing: ...@@ -49,4 +49,4 @@ test:testing:
- testing - testing
stage: test stage: test
script: script:
- docker run -u $(id -u):$(id -g) $CI_REGISTRY_IMAGE:testing "/opt/bayeswave/test/test-bayeswave.sh" - docker run -u $(id -u):$(id -g) $CI_REGISTRY_IMAGE:testing "/opt/lscsoft/bayeswave/test/test-bayeswave.sh"
...@@ -4,14 +4,12 @@ RUN echo "Building bayeswave" ...@@ -4,14 +4,12 @@ RUN echo "Building bayeswave"
MAINTAINER James Alexander Clark <james.clark@ligo.org> MAINTAINER James Alexander Clark <james.clark@ligo.org>
# Dependencies # Dependencies
USER root
RUN apt-get update && apt-get install --assume-yes \ RUN apt-get update && apt-get install --assume-yes \
build-essential \ build-essential \
pkg-config \ pkg-config \
python-pip \ python-pip \
git git
RUN python -m pip install --upgrade setuptools
RUN python -m pip install --upgrade setuptools pip acor
# Copy and build BayesWave # Copy and build BayesWave
WORKDIR / WORKDIR /
...@@ -21,15 +19,15 @@ COPY install.sh / ...@@ -21,15 +19,15 @@ COPY install.sh /
COPY src /src COPY src /src
copy etc/bayeswave-user-env.sh /etc/bayeswave-user-env.sh copy etc/bayeswave-user-env.sh /etc/bayeswave-user-env.sh
COPY BayesWaveUtils /BayesWaveUtils COPY BayesWaveUtils /BayesWaveUtils
RUN sh install.sh /opt/bayeswave RUN sh install.sh /opt/lscsoft/bayeswave
COPY test /opt/bayeswave/test COPY test /opt/lscsoft/bayeswave/test
RUN rm -rf .git install.sh /src /BayesWaveUtils /etc/bayeswave-user-env.sh RUN rm -rf .git install.sh /src /BayesWaveUtils /etc/bayeswave-user-env.sh
RUN mkdir -p /cvmfs /hdfs /hadoop RUN mkdir -p /cvmfs /hdfs /hadoop
# BayesWave env # BayesWave env
ENV PATH /opt/bayeswave/bin:${PATH} ENV PATH /opt/lscsoft/bayeswave/bin:${PATH}
ENV LD_LIBRARY_PATH /opt/bayeswave/lib:${LD_LIBRARY_PATH} ENV LD_LIBRARY_PATH /opt/lscsoft/bayeswave/lib:${LD_LIBRARY_PATH}
ENV PYTHONPATH /opt/bayeswave/lib/python2.7/site-packages:${PYTHONPATH} ENV PYTHONPATH /opt/lscsoft/bayeswave/lib/python2.7/site-packages:${PYTHONPATH}
ENTRYPOINT ["/bin/bash"] ENTRYPOINT ["/bin/bash"]
......
...@@ -136,11 +136,6 @@ set your environment accordingly. Note that there is an environment script ...@@ -136,11 +136,6 @@ set your environment accordingly. Note that there is an environment script
## BayesWaveUtils ## BayesWaveUtils
**Requirements** **Requirements**
* acor: a python port of a fast autocorrelation routine is required by
`megasky.py`. This is not part of the LSC software stack and must be
installed manually. Details can be found at
[PyPi](https://pypi.org/project/acor/). The quick and dirty solution is
simply: `pip install acor --user`
* Swig-wrapped LALSuite: provides an easy interface for reading `sim-inspiral` * Swig-wrapped LALSuite: provides an easy interface for reading `sim-inspiral`
tables from XML tables from XML
* Glue: provides tools for segment generation and HTCondor workflows management. * Glue: provides tools for segment generation and HTCondor workflows management.
......
...@@ -146,7 +146,7 @@ utils=/opt/bayeswave/utils ...@@ -146,7 +146,7 @@ utils=/opt/bayeswave/utils
* The container can see your `/home`: you are free to point to your own * The container can see your `/home`: you are free to point to your own
versions of the bayeswave executables for e.g., code development. versions of the bayeswave executables for e.g., code development.
* No bayeswave installation required (You do still need BayesWavePipe, though) * No bayeswave installation required (You do still need BayesWavePipe, though)
* All dependencies, including `acor`, are baked into the image * All dependencies are baked into the image
* You are guarenteed to find exactly the same image on all clusters (with * You are guarenteed to find exactly the same image on all clusters (with
CVMFS) when you use that image path: no need to maintain multiple CVMFS) when you use that image path: no need to maintain multiple
BayesWave installations at different sites! BayesWave installations at different sites!
......
#!/bin/bash #!/bin/bash
# single ifo example with trivial MCMC iterations # single ifo example with trivial MCMC iterations
BayesWave \ BayesWave \
--ifo H1 --H1-flow 32 \ --ifo H1 --H1-flow 32 \
......
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