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For workflows that write temp/intermediate files to the current directory, you can create a directory under /n/scratch and cd to it. Run the workflow from your scratch3 scratch directory, specifying full paths to input files in /n/groups or /home and full final output paths to /n/groups or /home. Here is a suggested workflow using example ID "ab123":

• Create a directory under /n/scratch if needed.

• Set up your workflow so that full paths are used to refer to input files in /n/groups or /home.

• Change directories (cd) to your /n/scratch directory, and run the analysis from there:

  • ^{cd /n/scratch3scratch/users/a/ab123}

• Write or copy any needed results back to /n/groups, /home, or your desktop, with copies submitted as an sbatch job or from an interactive session:

  • srun --pty -p interactive -t 0-12:00 /bin/bash

• Delete temporary data, or let it be auto-deleted

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GPU dedicated scratch space (/n/scratch_gpu/users/a/ab123)

Research Computing is no longer providing the /n/scratch_gpu filesystem. Please use /n/scratch instead.

Accessing folders on "research.files.med.harvard.edu" from O2

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