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Fixing broken links to results files

Last edited by Eric Franz

1. Fixing broken links to results files

AweSim apps currently have been storing absolute paths to files in the database. The currently home directory paths are prefixed with /users/$PROJECT/$USER (i.e. /users/PZS0562/efranz/awesim_data/awe0011/container_fill_sim/containers/1) whereas previously the paths were prefixed with /nfs/$NFS_SERVER_NUMBER/$USER (i.e. /nfs/17/efranz/awesim_data/awe0011/container_fill_sim/containers/1).

Apps running now have their AweSim dataroot set to the value of $HOME, which uses the new path. For AweSim apps, we have symlinks so the old paths still work.

On Resolving-the-url-to-a-results-file-of-a-simulation I recommended adding a method to get the relative path to the staged directory of a job, so that you could use this to build the URL to access results:

def staged_dir_relative_path
  Pathname.new(staged_dir).relative_path_from(AwesimRails.dataroot)
end

The problem is that when

  1. staged_dir is /nfs/17/efranz/awesim_data/awe0011/container_fill_sim/containers/1 and
  2. AwesimRails.dataroot is /users/PZS0562/efranz/awesim_data/awe0011/container_fill_sim

instead of the method staged_dir_relative_path returning a path containers/1 it returns ../../../../../../nfs/17/efranz/awesim_data/awe0011/container_fill_sim/containers/1

A solution is to avoid using relative_path_from between 2 different paths. I updated Resolving-the-url-to-a-results-file-of-a-simulation to reflect this:

def staged_dir_relative_path
  Pathname.new(staging_target_dir_name).join(Pathname.new(staged_dir).basename)
end

2. Another approach

If a staged directory of a simulation is always 2 levels below the dataroot in your app, you can do this:

def staged_dir_relative_path
  Pathname.new(staged_dir).relative_path_from(Pathname.new(staged_dir).parent.parent)
end

3. Fixing links to output and error files

Also, our current recommendation for accessing output and error files is to set the name of the output and error file in the PBS headers of the job so that you know which file to look for: Accessing-Output-and-Error-files

But if you followed my original recommendation (pre appkit-1.0) to add some methods to the Job class to get the output and error files, there might be similar problem that needs to be fixed. You can see the changes we made to Container Fill Sim to fix this: https://github.com/AweSim-OSC/containerfillsim/commit/bf8cad61755d2020a9b4f343308deec981e4a650