slmr 0.3.5

A scripting system for the Last Millennium Reanalysis (LMR) project.

sLMR

This is a scripting system for the Last Millennium Reanalysis project, or LMR.

Package dependencies

• p2k: A collection of functions used for PAGES2k dataset analysis (pip install p2k)
• tqdm: A fast, extensible progress bar for Python and CLI (pip install tqdm)
• prysm-api: The API for PRoxY System Modeling (PRYSM) (pip install prysm-api)
• dotmap: Dot access dictionary with dynamic hierarchy creation and ordered iteration (pip install dotmap)
• xarray: N-D labeled arrays and datasets in Python (pip install xarray)
• netCDF4: the python interface for netCDF4 format (conda install netCDF4)
• pyspharm: an object-oriented python interface to the NCAR SPHEREPACK library (conda install -c conda-forge pyspharm)

Features

• [v0.1] Running LMR with Slurm on a cluster with just one command line
• [v0.2] Post-processing: pick files with the same filename from different directories
• [v0.3] LMR Turbo (LMRt): the packaged version of the LMR framework with multiprocessing support
  • a quickstart notebook
  • a notebook on building Ye files

How to install

Simply

pip install slmr

and there will be an executable command slmr in your PATH.

Usage examples

Below are some usage examples of slmr. For more details, please check

slmr -h

Running LMR with Slurm

We need to prepare all the data and configurations required for LMR first, then we are able to run LMR with Slurm on a cluster with just one command line:

slmr job -c config.yml -n 4 -nn hungus -rp 0 2000 -em [e-mail] -x test_ccsm4

# slmr job: use the mode of submitting a slurm job
# -c config.yml: use "config.yml" as a configuration template
# -n 4 -nn hungus: run LRM with 4 threads on the node "hungus"
# -rp 0 2000: reconstruction period to be from 0 to 2000 C.E.
# -em [e-mail]: notification will be sent to "[e-mail]"
# -x test_ccsm4: the experiment is named as "test_ccsm4"

Post-processing: pick files

slmr pp pick_files -f gmt.npz -d dir1 dir2 -s ./gmt_files

# slmr pp: use the mode of post-processing
# pick_files: the post-processing task to be pick_files
# -f gmt.npz: pick files named as "gmt.npz"
# -d dir1 dir2: pick files from the specified directories dir1 and dir2; more dirs can be followed
# -s ./gmt_files: save the found files to the directory "./gmt_files"

License

MIT License

Copyright (c) 2018 Feng Zhu