The purpose of this page is to document E3SM project’s policy for managing the E3SM simulations that need to be archived, including official simulations and important internal working simulations. The following steps are required to be done immediately after simulation completion to avoid data loss/corruption and time consuming re-runs.
Note E3SM’s policy change: All 3 steps are now required steps.
1. Short term archiving
Please note that this is a required step per latest E3SM policy.
Use CIME short-term archiving utility to reorganize model output to avoid having tens of thousands of output files in the single run/ sub-directory. Typical usage:
cd case_scripts ./case.st_archive --force-move
The ‘force-move’ option will greatly speed-up short term archiving by moving rather than copying files. You can also invoke short term archiving periodically while the simulation is progressing. To do so safely, use additional options:
cd case_scripts ./case.st_archive --force-move --last-date 2005-01-01 --no-incomplete-logs
2. Archive to NERSC HPSS using zstash
Note that using zstash is required when archiving E3SM data. For the systems that do not provide HPSS, use zstash with “--hpss=none” to create a tar files to be then copied to LLNL for permanent storage.
The original model output should be archived on NERSC HPSS using zstash:
If a simulation was run on systems with HPSS: run zstash to archive the data to the local HPSS tape. If the HPSS is not on NERSC, use Globus to transfer the zstash *.tar and index.db files to NERSC HPSS:
If data were archived on Theta HPSS, to transfer to NERSC HPSS, use the Globus endpoint alcf#dtn_hpss and NERSC HPSS. (Make sure to opt for “verify file integrity after transfer“ as a transfer and Sync option, which checks if source and destination file checksums match)
If a simulation was run on a system without HPSS (i.e., anvil and compy): run zstash to generate index.db and tar files locally [Note: this zstash feature is available after version 0.4.1] and transfer these files to NERSC HPSS using Globus].
Make sure permissions are correct for files on HPSS (Please make the directory group/project readable, once publication is authorized that will be changed to world-readable).
If you keep seeing issues with a specific transfer between endpoints, you can email
support@globus.orgwith the transfer ID. They can look at the transfer logs and facilitate the conversation between the endpoint admins.
Notes on using zstash:
To archive output from an E3SM simulation located under $CSCRATCH/E3SM_simulations/20170731.F20TR.ne30_ne30.edison:
$ cd $CSCRATCH/E3SM_simulations/20170731.F20TR.ne30_ne30.edison $ zstash create --hpss=test/E3SM_simulations/20170731.F20TR.ne30_ne30.edison .
The above command should generate optimized tar file(s) and the corresponding index database (index.db), saving checksums and additional metadata of the tar file(s).
It is highly recommended that you verify the integrity of the tar files after archiving with zstash on both the local machine and NERSC. The safest way to do so is to go to a new, empty directory and run:
$ zstash check --hpss=test/E3SM_simulations/20170731.F20TR.ne30_ne30.edison
If you encounter an error, save your original data. You may need to re-upload it via zstash create
The zstash documentation and best practices for E3SM can be found at: https://e3sm-project.github.io/zstash/_build/html/master/index.html
3. Document HPSS locations
Documenting the HPSS locations on a central confluence page is a required step and it is helpful for everyone in the project who might have a need to locate the files. Members from infrastructure group will be closely monitoring these pages. Once a new simulation is entered, the data will be copied to a centralized space at LLNL (E3SM Archive - Data Source and Transfer Status ) for further post-processing (i.e. ESGF publication). A default set of simulation data will be published to ESGF for official simulations. Please drop an email to Jill Chengzhu Zhang (zhang40@llnl.gov) and e3sm-data-support@llnl.gov for special publication requirements (i.e., specify years, cmip publication, etc.). Each simulation and NGD group has its own confluence pages documenting the simulation output archive locations:
Water Cycle: DECK v1, High-res Coupled v1
BGC: /wiki/spaces/EBGC/pages/1056145509
Cryosphere: /wiki/spaces/ECG/pages/1736933506
NGD-Atmosphere Physics
NGD-Land
NGD-SCREAM
Note: For non-official simulations (one-off tuning runs, sensitivity study for research papers, etc.), please have a separate table with a note column, indicating how long the archive is desired to be kept or “don’t delete until data being published to ESGF“. These files may be given lower priority to be kept once our NERSC HPSS quota is reached.