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Juan Alvarado, 04/22/2023 07:49 PM

1 1 Alexandre Camsonne
h1. Wiki
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To run PARTONS on the farm we need to do is to create a singularity container, follow these steps
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* Set the environment and load the appropriate modules
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source /site/env/syscshrc
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module load singularity/3.9.5
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* Build the container:
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singularity build --sandbox partons_singularity docker://partons/partons
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* The previous command with create a new folder called "partons_singularity". To run the container do: 
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singularity shell --writable partons_singularity
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* Now your terminal has changed. You can find PARTONS' folders in /root/workspace/
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* For instance, to run an example inside the container you can do:
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cd /root/workspace/partons-example/
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./bin/PARTONS_example data/examples/gpd/computeSingleKinematicsForGPD.xml
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* To run partons using a .xml outside the container (I am using computeSingleKinematicsForGPD.xml), we need to bind the folder on host to a folder on the container.
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 1. I create a folder where the xml files are going to be linked on the container.
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 mkdir partons_singularity/root/workspace/partons-example/input
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 2. Create a script with the commands to run. I call it "order". The content of my file named "order" is:
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   cd /root/workspace/partons-example/
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   ./bin/PARTONS_example "path_to_xml_file"
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 The script will change working directory on the container and will execute PARTONS. 
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 This script has to be located in your home directory (or any other mounted location e.g. input folder) and you need to give permissions using chmod 755 ~/order
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 3. Then, execute PARTONS binding the folder containing the .xml file (on host) to the folder you have have just created (I created the folder input in the current location):
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 singularity exec --writable --bind ./input/:/root/workspace/partons-example/input/ partons_singularity/ ./order
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 where the "path_to_xml_file" will be "input/computeSingleKinematicsForGPD.xml"
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 For completeness, notice that the "order" file contains the following lines:
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 cd /root/workspace/partons-example/
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 ./bin/PARTONS_example input/computeSingleKinematicsForGPD.xml
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 If you need to re-build the container and get the error "no space left on device", you just need to delete the folder .apptainer and .singularity in your home directory
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To run EpIC, just copy the file epic_partons.tar.xz to the desired location and extract it with tar -xf
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* singularity shell --writable --containall epic_partons (to enter the container)
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* singularity exec --writable --containall --bind ./test/:/work/workspace/epic/test/ epic_partons run.sh (to bind a folder and use it as executable)
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*Some important links*
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https://partons.cea.fr
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https://pawelsznajder.github.io/epic/
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https://docs.sylabs.io/guides/3.0/user-guide/build_a_container.html
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https://docs.sylabs.io/guides/2.6/user-guide/singularity_and_docker.html
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https://singularity-tutorial.github.io/02-basic-usage/