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public:docker [2017-02-09 09:01] – [LOFAR Pipeline Software] Jan David Mol | public:docker [2018-02-05 10:31] – [Development (extending the software)] Jan David Mol | ||
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We offer the LOFAR software as Docker images, allowing anyone to run our software using the same configuration, | We offer the LOFAR software as Docker images, allowing anyone to run our software using the same configuration, | ||
- | ====== LOFAR Pipeline | + | ====== LOFAR Interferometry Post-Processing |
To run the lofar pipeline software, you need to: | To run the lofar pipeline software, you need to: | ||
- | | + | |
- | | + | |
docker run -it --rm -u $UID -e USER -e HOME -v $HOME:$HOME lofar/ | docker run -it --rm -u $UID -e USER -e HOME -v $HOME:$HOME lofar/ | ||
</ | </ | ||
- | | + | |
you@3617438dfc63:/ | you@3617438dfc63:/ | ||
Usage: DPPP [-v] [parsetfile] [parsetkeys...] | Usage: DPPP [-v] [parsetfile] [parsetkeys...] | ||
Line 33: | Line 33: | ||
</ | </ | ||
- | Once you have the above up and running, you will need some data to work on, and likely a parset with configuration settings. If you've put both in your home directory, they' | + | ====== LOFAR Pulsar Post-Processing Software ====== |
- | ===== Q&A ===== | + | To run the lofar pipeline software, you need to: |
+ | - Install and configure [[https:// | ||
+ | - Download and start the LOFAR image by running: < | ||
+ | docker run -it --rm -u $UID -e USER -e HOME -v $HOME:$HOME lofar/ | ||
+ | </ | ||
+ | - You now have the LOFAR pulp software available at your finger tips, and your home directory available. You can run for example: < | ||
+ | you@3617438dfc63:/ | ||
+ | Usage: pulp.py <--id ObsID> [-h|--help] [OPTIONS] | ||
+ | </ | ||
+ | |||
+ | ====== Q& | ||
+ | |||
+ | ===== Installation | ||
=== Q: Where can I find a list of available LOFAR software versions? === | === Q: Where can I find a list of available LOFAR software versions? === | ||
- | A: [[https:// | + | A: For '' |
- | === Q: I get " | + | === Q: What is included in the image? === |
+ | |||
+ | We put the following in our '' | ||
+ | |||
+ | * LOFAR Pipeline Framework & Recipes | ||
+ | * NDPPP | ||
+ | * AWImager | ||
+ | * AOFlagger | ||
+ | * DAL2 | ||
+ | * Casacore + casarest + python-casacore | ||
+ | |||
+ | ===== Running the software ===== | ||
+ | |||
+ | === Q: I can't see my data or parset? === | ||
+ | |||
+ | Once you have the Docker image up and running, you will need some data to work on, and likely a parset with configuration settings. If you've put both in your home directory, they' | ||
+ | |||
+ | === Q: I get " | ||
A: The LOFAR software is compiled for a 2015-era processor (Intel Xeon E5-2603v3 to be exact) for performance reasons, and uses CPU instructions not available on older machines. Please run our images on a newer machine. | A: The LOFAR software is compiled for a 2015-era processor (Intel Xeon E5-2603v3 to be exact) for performance reasons, and uses CPU instructions not available on older machines. Please run our images on a newer machine. | ||
+ | |||
+ | ===== Development (extending the software) ===== | ||
+ | |||
+ | === Q: How do I obtain your Dockerfiles? | ||
+ | |||
+ | A: By running: | ||
+ | |||
+ | < | ||
+ | svn co -N https:// | ||
+ | cd LOFAR-Release-2_19 | ||
+ | mkdir -p build/ | ||
+ | |||
+ | cmake ../.. -DBUILD_PACKAGES=Docker -DUSE_LOG4CPLUS=OFF -DUSE_CASACORE=OFF && make -j 16 install | ||
+ | </ | ||
+ | |||
+ | which will put the Dockerfiles in subdirectories in '' | ||
+ | |||
+ | === Q: How do I build your Docker images from scratch? === | ||
+ | |||
+ | A: By obtaining the Dockerfiles (see above), and running: | ||
+ | |||
+ | < | ||
+ | # load LOFAR environment variables, used to determine tags etc | ||
+ | source installed/ | ||
+ | # build all LOFAR images, in the order required by their interdependencies | ||
+ | docker-build-all.sh | ||
+ | </ | ||
+ | |||
+ | === Q: How do I add files/ | ||
+ | |||
+ | A: The best way to add stuff to our images is by creating a new image based on ours. To do so, create a directory containing the files you want to add. Add to this directory a '' | ||
+ | |||
+ | < | ||
+ | FROM lofar-pipeline: | ||
+ | |||
+ | COPY my_extension / | ||
+ | </ | ||
+ | |||
+ | Finally, you run < | ||
+ | |||
+ | === Q: How do I add initialisation stuff? (PYTHONPATH, | ||
+ | |||
+ | A: Our Docker images execute ''/ | ||
+ | |||
+ | Note: if you add eggs to the image, you need to put the egg // |