This short manual walks you through the steps necessary to run a Python script on Noether.

Noether Basics

1. Login to Noether as ssh [your_username]@noether.hep.manchester.ac.uk.
2. Once in, use ls to see what is in your directory. Warning: some newer Noether accounts are not created with this folder (and subsequent ones within it). If you do not have them, please make them (for your sake).
3. cd scripts to go in scripts.
4. scripts has 3 folders (bin, etc, out) which are the launching ground for all of your jobs.

   • bin (for binary) contains your executable scripts, i.e. the scripts you want to run.

   • etc is the submission folder, i.e. where you set up .sub files that send job requests to the cluster. Here is a sample .sub file:

     executable      = bin/jupyter.sh
     request_memory  = 8G
     request_cpus    = 4
     request_disk    = 5G
     initialdir	= $ENV(HOME)/scripts
     output          = out/jupyter/jupyter-$(Process).out
     error           = out/jupyter/jupyter-$(Process).err
     log             = out/jupyter/jupyter-$(Process).log
     arguments = $(Process)
     
     
     should_transfer_files = yes
     when_to_transfer_output = ON_EXIT
     
     queue 1
     

     • executable: the script you want to run.
     • request_memory: how much RAM you want to use for the job
     • request_cpus: how many CPUs you want to use for the job
     • request_disk: how much disk space you want to use for the job
     • initialdir: the directory where your out (as well as bin and etc) is.
     • output error log: tells the cluster where to send the .output, .error, and .log files that are created when you run your job. These are sent into the out folder and are explained below.
     • queue: tells the cluster how many times you want to run your job.

   • out contains

     • .err files which display any errors that occurred.
     • .log files which document the CPU usage of the cluster while the job is running.
     • .out files which display the terminal output of the code.

Running a job on Noether

1. Copy the script you'd like to run into your bin folder by typing the following line in the terminal: scp [local_path]/[your_script].py [your_username]@noether.hep.manchester.ac.uk:/gluster/home/[your_username]/scripts/bin/. You will now be asked to input your password and then the script will be copied into your bin folder in Noether.

2. Once your script has been copied, login to your Noether account and then go into your etc folder by typing: cd scripts/etc.

3. Once in the etc folder type: cp sleep.sub [your_script].sub to create a submissions file in the right template. After that, you should edit the executable, output, error, and log entries in the [your_script].sub as:

   • executable: bin/[your_script].sh
   • output: out/[your_script]-$(ClusterId)-$(Process).out
   • error: out/[your_script]-$(ClusterId)-$(Process).err
   • log: out/[your_script]-$(ClusterId)-$(Process).log

   -$(ClusterId) is used to keep track of multiple runs of the same job. Every time you run a job, you run it with a different ClusterId, by adding that to your output you can keep track of your run history of a specific script.

4. Then go into bin folder (cd ../bin) and create an empty submission file by typing: touch [your_script].sh.

5. In this file you want to add two things:

   • Add a source to a Python environment. You do this by typing: source /gluster/[path_where_python_environment_is].
   • Tell the cluster which file to run. You do this by typing: python3 /gluster/home/[your_username]/scripts/bin/[your_script].py

6. Go back in the scripts folder and type: condor_submit etc/[your_script].sub.

7. This will run your job.

8. You will see the output of the job in the out folder. There will be three new files which have been explained earlier:

   • [your_script]-[ClusterId]-0.out
   • [your_script]-[ClusterId]-0.err
   • [your_script]-[ClusterId]-0.log