/osg_tutorial

Tutorial for AMNH open science grid (OSG)

Primary LanguageShell

Table of Contents
  1. To start
  2. Prepare to submit jobs
  3. Submit jobs
  4. Cheat sheet
  5. To cite OSG

To start

Ask David Zurek for an OSG account. Other questions related to the OSG can be directed to Sajesh Singh (ssingh@amnh.org), who is the IT person who knows everything about OSG.

Prepare to submit jobs

  1. Create a folder with all the following files (assuming you are running python): fib.sub, wrapper.sh, and python_build.tgz.

  2. wrapper.sh is the shell scrip to run your code, which typically contains the following:

    • tar xzf python_build.tgz to unzip the python folder
    • python_build/bin/python3 <your script>.py $1 to run the python script on $1, which $1 will be obtained from the fib.sub file.

  3. fib.sub is the submission file, the main things to change are:

    • This part is typically at the end of the fib.sub file. It indicates the arguments to pass down into the shell script.
    queue fib from <filename>

    this will execute wrapper.sh on every node with each line in <filename> as argument.

    E.g., if <filename> includes 3 lines that are:
    aaa
    bbb
    ccc

    It will execute ./wrapper.sh aaa, ./wrapper.sh bbb, ./wrapper.sh ccc, on different nodes. This is very good for repeating jobs, e.g., if each line is a light curve file you want to process.

    • This part is typically at the end of the fib.sub file. It indicates the arguments and files to pass down into the shell script.
    executable = wrapper.sh
arguments = $(fib)
transfer_input_files = ztf_download.py, python_build.tgz, hotstars.csv

    Define the the executable shell script: executable = wrapper.sh.
    Arguments passed to the shell script: arguments = $(fib). e.g., this is the same as the argument $1 we see in the shell script earlier. fib is typically taken from the text file you passed down (<filename> in this case).
    The last line represents the files you want to transfer to the node, it will typically include all the files you need to run the code besides the wrapper.sh and fib.sub file.

    • This part is typically in the middle of the file, it will indicate whether you want to transfer the output data to your home where you submit the script.
    should_transfer_files = YES
when_to_transfer_output = ON_EXIT

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Submit jobs

Note: make sure your file has less than 5000 lines since you can only submit 5000 jobs at once.

condor_submit fib.sub

Cheat sheet

  1. To check your jobs: condor_q <username>
  2. If your job is on hold and you want to know the reason: condor_q -better-analyze <job_ID>
  3. If you fixed the problem that holds your job and you want to release them: condor_release <username>
  4. To install new packages in your python:
    • Extract the tgz file for python_build tar xzvf python_build.tgz
    • Run the following command: python_build/bin/pip3 install <PACKAGE NAME>
    • Recreate the tgz file tar czvf python_build.tgz python_build

To cite OSG

"This research was done using services provided by the OSG Consortium \citep{OSG1,OSG2}, which is supported by the National Science Foundation awards #2030508 and #1836650."

  • .bib citations:
  title  = {The open science grid},
  author = {
    Pordes, Ruth 
    and Petravick, Don 
    and Kramer, Bill 
    and Olson, Doug 
    and Livny, Miron 
    and Roy, Alain 
    and Avery, Paul 
    and Blackburn, Kent 
    and Wenaus, Torre 
    and W{\"u}rthwein, Frank 
    and Foster, Ian
    and Gardner, Rob
    and Wilde, Mike
    and Blatecky, Alan
    and McGee, John
    and Quick, Rob
  },
  doi       = {10.1088/1742-6596/78/1/012057},
  booktitle = {J. Phys. Conf. Ser.},
  volume    = {78},
  series    = {78},
  pages     = {012057},
  year      = {2007},
}

@inproceedings{OSG2,
  title        = {The pilot way to grid resources using glideinWMS},
  author       = {
    Sfiligoi, Igor    
    and Bradley, Daniel C 
    and Holzman, Burt     
    and Mhashilkar, Parag 
    and Padhi, Sanjay     
    and Wurthwein, Frank
  },
  doi          = {10.1109/CSIE.2009.950},
  booktitle    = {2009 WRI World Congress on Computer Science and Information Engineering},
  volume       = {2},
  series       = {2},
  pages        = {428--432},
  year         = {2009},
}

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