Fretransfer is a tool that utilizes part of GFDL's Flexible Modeling System Runtime Environment (FRE) to selectively combine, compress, archive, and transfer raw netCDF files generated by GFDL model simulations as well as other files, all branded as either 'ascii' files, 'history' files, or 'restart' files. It allows for the flexible creation of '.args' files, state files used by the FRE workflow, which are referenced by FRE's output.stager script to set up the above tasks through Slurm batch jobs.
- Python v3.5 or later
- Python modules:
- argparse
- configparser
- datetime
- fnmatch
- glob
- logging
- os
- re
- shutil
- stat
- subprocess
- sys
- supported version of FRE
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Open a terminal on Gaea and clone the repository (ssh)
git clone [email protected]:NOAA-GFDL/fretransfer.git
(https)git clone https://github.com/NOAA-GFDL/fretransfer.git
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Load FRE into your environment
module load fre/bronx-16
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Type
cd fretransfer
, thenpython3 fretransfer.py -h
for a list of options.
*assumes that the binary command for python v3.x is aliased topython3
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Run a model simulation to generate ascii, history, and restart files.
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The following 8 scenarios can be used to execute fretransfer. All examples below utilize history files, but can encompass ascii and restart files as well (note: all file paths must be absolute paths):
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Scenario 1: Combine, tar, and transfer files from Gaea to GFDL Example:
python3 fretransfer.py -expName test_experiment -fileType history -sourceDir /path/to/history/directory -gfdlDir /path/to/GFDL/destination/ -combine -tar -compress -transfer -saveBatchOpts account=gfdl_YOURGROUPLETTER job-name=tar_combine_job mail-type=fail -xferBatchOpts account=gfdl_YOURGROUPLETTER job-name=transfer_job mail-type=fail -submit
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Scenario 2: Combine, no tar, and transfer files Note: Creates 2 separate batch jobs (outputStager and gcp) and saves them outside the sourceDir. Example:
python3 fretransfer.py -expName test_experiment -fileType history -sourceDir /path/to/history/directory -gfdlDir /path/to/GFDL/destination/ -combine -transfer -saveBatchOpts output=/path/for/combine/job/file/stdout account=gfdl_YOURGROUPLETTER job-name=tar_combine_job mail-type=fail -xferBatchOpts output=/path/for/transfer/job/file/stdout account=gfdl_YOURGROUPLETTER job-name=transfer_job mail-type=fail -submit
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Scenario 3: Combine, no tar, no transfer Example:
python3 fretransfer.py -expName test_experiment -fileType history -sourceDir /path/to/history/directory -gfdlDir /path/to/GFDL/destination/ -combine -saveBatchOpts output=/path/for/combine/job/file/stdout account=gfdl_YOURGROUPLETTER job-name=tar_combine_job mail-type=fail -submit
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Scenario 4: No combine, tar, transfer Example:
python3 fretransfer.py -expName test_experiment -fileType history -sourceDir /path/to/history/directory -gfdlDir /path/to/GFDL/destination/ -tar -compress -transfer -saveBatchOpts output=/path/for/tar/job/file/stdout account=gfdl_YOURGROUPLETTER job-name=tar_combine_job mail-type=fail -xferBatchOpts output=/path/for/transfer/job/file/stdout account=gfdl_YOURGROUPLETTER job-name=transfer_job mail-type=fail -submit
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Scenario 5: No combine, no tar, transfer Note: If a .tar file exists outside the sourceDir, fretransfer will natively call output.stager. If not (i.e. only combined files present, mixture of uncombined/combined, and desiring to transfer a directory of all uncombined files), fretransfer will create a gcp batch job and submit it. Example:
python3 fretransfer.py -expName test_experiment -fileType history -sourceDir /path/to/history/directory -gfdlDir /path/to/GFDL/destination/ -transfer -xferBatchOpts output=/path/for/transfer/job/file/stdout account=gfdl_YOURGROUPLETTER job-name=transfer_job mail-type=fail -submit
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Scenario 6: No combine, no tar, no transfer (dry run) Example:
python3 fretransfer.py -expName test_experiment -fileType history -sourceDir /path/to/history/directory -gfdlDir /path/to/GFDL/destination/
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Scenario 7: Combine, tar, no transfer Example:
python3 fretransfer.py -expName test_experiment -fileType history -sourceDir /path/to/history/directory -gfdlDir /path/to/GFDL/destination/ -combine -tar -compress -saveBatchOpts account=gfdl_YOURGROUPLETTER job-name=tar_combine_job mail-type=fail -submit
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Scenario 8: No combine, tar, no transfer Example:
python3 fretransfer.py -expName test_experiment -fileType history -sourceDir /path/to/history/directory -gfdlDir /path/to/GFDL/destination/ -tar -saveBatchOpts account=gfdl_YOURGROUPLETTER job-name=tar_combine_job mail-type=fail -submit
Note: Only using '-tar' will create an uncompressed archive file. Use '-compress' for the vice versa.
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It you are having problems using the code, open an issue in the fretransfer repository:
https://github.com/NOAA-GFDL/fretransfer/issues
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