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casa:install [2020/10/30 12:54] – bemmelcasa:install [2020/11/05 08:20] (current) – janssen
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 ===== Jupyter CASA ===== ===== Jupyter CASA =====
  
-=== Install instructions for Jupyter CASA === +==== Install instructions for Jupyter CASA ====
- +
-__Installing the infrastructure to run the Jupyter Notebooks is optional.__+
  
 For parts of the tutorials we have developed Jupyter Notebooks based on the Jupyter CASA environment. This requires singularity or a docker container to run. For MacOS there is only a beta-version of singularity available, so the instructions below are based on docker. This installation is optional, all tutorials can also be done using the stand-alone version of CASA. For parts of the tutorials we have developed Jupyter Notebooks based on the Jupyter CASA environment. This requires singularity or a docker container to run. For MacOS there is only a beta-version of singularity available, so the instructions below are based on docker. This installation is optional, all tutorials can also be done using the stand-alone version of CASA.
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   - If you downloaded the tutorial notebook you should see it in the list on your browser and can launch it by clicking on the link once.   - If you downloaded the tutorial notebook you should see it in the list on your browser and can launch it by clicking on the link once.
  
-=== Notes ===+==== Notes ====
  
 There is a known issue with X11-forwarding on MacOS. The workaround for this is to slightly modify step 6 above. You first launch the docker, inside the docker you launch the notebook. You can than proceed with step 7 above. There is a known issue with X11-forwarding on MacOS. The workaround for this is to slightly modify step 6 above. You first launch the docker, inside the docker you launch the notebook. You can than proceed with step 7 above.
  
-  - Start the docker with ''docker run -p 8888:8888 -i -t -e DISPLAY=$DISPLAY -v <absolute path to your data processing directory>:/home/jupyter/data penngwyn/jupytercasa'' +  - Start the docker with ''docker run -p 8888:8888 -i -t -e DISPLAY=$DISPLAY -v <absolute path to your data processing directory>:/home/jupyter/data penngwyn/jupytercasa bash'' 
   - Inside the same terminal window launch the notebook ''xvfb-run jupyter notebook''   - Inside the same terminal window launch the notebook ''xvfb-run jupyter notebook''
  
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 The notebook runs CASA5.6, but this should not impact the basic functionality used in the tutorials.\\ The notebook runs CASA5.6, but this should not impact the basic functionality used in the tutorials.\\
  
-=== Available Jupyter notebooks ===+==== Available Jupyter notebooks ====
  
 For the VLA tutorial there is a version of the notebook available in the [[https://github.com/aardk/jupyter-casa/tree/master/examples|examples]]. To get this to your laptop, in a terminal type ''wget https://github.com/aardk/jupyter-casa/raw/master/examples/vla-cont-tutorial.ipynb'' For the VLA tutorial there is a version of the notebook available in the [[https://github.com/aardk/jupyter-casa/tree/master/examples|examples]]. To get this to your laptop, in a terminal type ''wget https://github.com/aardk/jupyter-casa/raw/master/examples/vla-cont-tutorial.ipynb''
  
-There is a beta version of the [[https://code.jive.eu/bemmel/EVN_CASA_pipeline/raw/branch/master/EVN_continuum_pyp.ipynb|EVN pipeline notebook]] and an example notebook based on the DARA and EVN tutorials. These will be linked here later.+There is a beta version of the [[https://code.jive.eu/bemmel/EVN_CASA_pipeline/raw/branch/master/EVN_continuum_pyp.ipynb|EVN pipeline notebook]] and an [[https://www.dropbox.com/s/5tbdj90mzihggpr/n14c3_pipe.ipynb?dl=0|example notebook]] based on the DARA and EVN tutorials. Both contain all calibration steps up to the imaging.
  
  
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 1) $ docker pull mjanssen2308/casavlbi:latest\\ 1) $ docker pull mjanssen2308/casavlbi:latest\\
 2) $ docker run --name picard.cont -it --init --env HOME=/data --user $(id -u) -v /etc/passwd:/etc/passwd --network=host -v /tmp/.X11-unix:/tmp/.X11-unix:ro -e DISPLAY=$DISPLAY -v /full/path/to/your/working/dir:/data mjanssen2308/casavlbi:latest\\ 2) $ docker run --name picard.cont -it --init --env HOME=/data --user $(id -u) -v /etc/passwd:/etc/passwd --network=host -v /tmp/.X11-unix:/tmp/.X11-unix:ro -e DISPLAY=$DISPLAY -v /full/path/to/your/working/dir:/data mjanssen2308/casavlbi:latest\\
 +!! It seems like the wiki page messes up double dashes in the above command. See the README of https://bitbucket.org/M_Janssen/picard for the correct version of that command which works for copy/paste.\\
 (you will have to fill in the correct path for /full/path/to/your/working/dir here)\\ (you will have to fill in the correct path for /full/path/to/your/working/dir here)\\
 3) $ cd /data\\ 3) $ cd /data\\
casa/install.1604062482.txt.gz · Last modified: 2020/10/30 12:54 by bemmel