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nemo_copydir

Purpose

When running codes on a single data set repeatedly, the Nemo cluster can overload some of its fileservers. To remedy this, we developed nemo_copydir to distribute a directory sturcture to the local hard disks on each of Nemo's execute nodes. This is accomplished via a "tree copy": The data is copied from the file server to one cluster node, A. The data is then copied from A to two more cluster nodes, B and C. B will then copy to D and E, and C will copy to F and G. This process continues until the data is copied across all online cluster nodes. Our tests have shown that copying 10 GB of data takes approximately two hours.

Usage

nemo_copydir will generate a Condor DAG, and will copy the data from, i.e. /path/to/data to the local hard disks on the Nemo nodes under /data/localscratch, i.e. /data/localscratch/rosso

    Copying Data

  1. Make a directory under your home directory where Condor can write files. In this example, I'll use /home/rosso/copydir_test
  2. In that directory, run
    nemo_copydir --source /path/to/data --target rosso --logfile /people/rosso/copydir.log --copy
    This will generate a DAG, called mover.dag, to perform the copy. Remember, it's best to use /people for condor log files. Condor standard error and standard output redirection files will be stored in my copydir_test directory.
  3. Submit the dag:
    condor_submit_dag mover.dag
    This will start the copy. To track progress, you may run
    tail -f mover.dag.dagman.out

    Removing Data

Simply replace

--copy
with
--remove
when running nemo_copydir and submit the new dag.

Further Information

For additional information about nemo_copydir, run

nemo_copydir --help
. If you have additional questions or are having difficulty with the script, send a detailed email to
uwm-help@gravity.phys.uwm.edu
.

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Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.