casa:install
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
casa:install [2020/10/30 12:49] – bemmel | casa:install [2020/11/05 08:20] (current) – janssen | ||
---|---|---|---|
Line 1: | Line 1: | ||
- | ===== CASA VLBI workshop | + | ====== CASA VLBI optional |
- | On this page you find instructions for optional software | + | Note that support during the workshop will be limited. |
===== 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. | ||
Line 24: | Line 22: | ||
- 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 '' | + | - Start the docker with '' |
- Inside the same terminal window launch the notebook '' | - Inside the same terminal window launch the notebook '' | ||
Line 40: | Line 38: | ||
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:// | For the VLA tutorial there is a version of the notebook available in the [[https:// | ||
- | There is a beta version of the [[https:// | + | There is a beta version of the [[https:// |
+ | |||
+ | |||
+ | ===== CASA rPICARD pipeline ===== | ||
+ | The [[https:// | ||
+ | |||
+ | The pipeline can be installed with [[https:// | ||
+ | |||
+ | === Using Singularity === | ||
+ | |||
+ | You will obtain a containerized version of the software, which is great for scientific reproducibility!\\ | ||
+ | 1) Go to your working directory.\\ | ||
+ | 2) $ singularity build casavlbi.pipe [[docker:// | ||
+ | 3) $ singularity run ./ | ||
+ | Your are now inside Singularity, | ||
+ | $ exit | ||
+ | |||
+ | |||
+ | === Using Docker === | ||
+ | |||
+ | Similar to Singularity and just as great for scientific reproducibility. In fact, you will use the same container | ||
+ | 1) $ docker pull mjanssen2308/ | ||
+ | 2) $ docker run --name picard.cont -it --init --env HOME=/data --user $(id -u) -v / | ||
+ | !! It seems like the wiki page messes up double dashes in the above command. See the README of https:// | ||
+ | (you will have to fill in the correct path for / | ||
+ | 3) $ cd /data\\ | ||
+ | Your are now inside Docker in a mirror of your working directory, where you have access to rPICARD. To go back to your old shell, type\\ | ||
+ | $ exit | ||
+ | |||
+ | |||
+ | === Installing from source on Linux === | ||
+ | |||
+ | (Note that rPICARD runs on CASA6. This will not interfere with your CASA5 installation as you can have multiple versions of CASA on your system.)\\ | ||
+ | 1)Go to a directory where you install your software and obtain the correct CASA version for the pipeline: | ||
+ | $ wget https:// | ||
+ | $ tar xvJf casa-CAS-13094-2.tar.xz | ||
+ | 2)Git clone the repository (do not download as tarball because the .git folder is needed): | ||
+ | $ git clone https:// | ||
+ | 3)Link the pipeline to the CASA installation: | ||
+ | $ ./ | ||
+ | The script will walk you through the automatic installation. | ||
+ | 4)Add picard to your path: \\ | ||
+ | $ printf ' | ||
+ | 5)Add picard to your PYTHONPATH: | ||
+ | $ printf ' | ||
+ | $ source ~/.bashrc \\ | ||
+ | 6)Install [[https:// | ||
+ | better and quicker plotting (optional but strongly recommended). | ||
+ | ==== How to use the pipeline ==== | ||
+ | There is a quick start guide in the [[https:// | ||
+ | In a nutshell, you have to\\ | ||
+ | 1) Put all relevant files or links to those files (FITS-IDI visibility data or a MeasurementSet, | ||
+ | 2) Copy a set of input parameters to the working directory ($ cp -r / | ||
+ | 3) Run the pipeline with\\ | ||
+ | $ picard -p -n 4\\ | ||
+ | Here, -p specifies to run rPICARD in the current working directory and -n 4 allows rPICARD to use 4 of your CPU cores for parallel data processing. | ||
+ | ==== Additional information ==== | ||
+ | * [[https:// | ||
+ | * [[https:// |
casa/install.1604062187.txt.gz · Last modified: 2020/10/30 12:49 by bemmel