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How do I transfer files between massdata and my local machine?

Please note that massdata is not designed for small files. Attempting to store or retrieve files less than a few megabytes will result in extremely poor performance for all users. If you wish to store lots of small files to massdata, please use a utility such as tar to combine them into a single, larger file.

To transfer files between massdata and your local machine, we recommend the use of rsync. With appropriate options, rsync is resumable should the connection drop mid-transfer. The recommended command line to use on your local machine is

Code Block
languagebash
rsync -avPS [src] [dst]

this two-step workflow.


/jobfs

  • Intended for I/O intensive jobs providing scratch space only for the lifetime of the job. 
  • Only accessible on the execution node (ie. not on a login node).
  • Allocated by using the -ljobfs=?? option to qsub, eg. -ljobfs=5GB requests 5 GB. Use integers and units of MB or GB (not case-sensitive). The maximum request must be less than or equal to the local disc storage of the node/s
  • NOT backed up
  • /jobfs directories are associated with a currently running job and are automatically deleted at the jobs completion.
  • Your batch job can access its jobfs via the environment variable PBS_JOBFS. Jobs spanning multiple nodes with local JOBFS space on each node should use the /opt/pbs/bin/pbsdsh -N ... command in the batch script to act on all JOBFS directories, e.g.           

    Code Block
    languagebash
    /opt/pbs/bin/pbsdsh -N ls $PBS_JOBFS



  • For example, if you want local copies of files generated before the current batch run you can do the following to make them available on each nodes' jobfs area.
      

    Code Block
    languagebash
    /opt/pbs/bin/pbsdsh -N cp original_file $PBS_JOBFS


    Note

    Don’t put any quotes around the command issued under pbsdsh.


    Note

    It is not possible to use the netmv command to save data which exists on a /jobfs filesystem – files must be copied to /short first.


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