Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/access-nri/mppnccombine-fast

A fast version of mppnccombine

https://github.com/access-nri/mppnccombine-fast

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.7%) to scientific vocabulary

Keywords

build-ci-enabled component ocean ocean-team tool
Last synced: 6 months ago · JSON representation

Repository

A fast version of mppnccombine

Basic Info
Statistics
  • Stars: 3
  • Watchers: 5
  • Forks: 4
  • Open Issues: 6
  • Releases: 1
Topics
build-ci-enabled component ocean ocean-team tool
Created almost 8 years ago · Last pushed 7 months ago
Metadata Files
Readme License

README.md

mppnccombine-fast

DOI

Build Docs

An accelerated version of the mppnccombine post-processing tool for MOM

Uses HDF5's raw IO functions to speed up collating large datasets - a 0.1 degree model goes from taking 4 hours to collate a compressed variable with mppnccombine, to 6 minutes with mppnccombine-fast running with 16 processes

Documentation at https://mppnccombine-fast.readthedocs.io

Build

mppnccombine-fast requires HDF5 version 1.10.2 or above, as well as NetCDF 4, a C compiler and a MPI library.

Cmake is used for building. A Makefile is also provided for ease of use:

make # Release build

make BUILD_TYPE=Debug # Debug build

make check # Run tests

make PREFIX=/apps/mppncc-fast install # Install mppnccombine-fast to $PREFIX

make doc # Build documentation in doc/_build/html

On Raijin the Makefile loads all required modules

The environment variables $OPENMPI_ROOT, $HDF5_ROOT and $NETCDF_ROOT may be used to help locate libraries at other sites

Use

Use like

mpirun -n 2 mppnccombine-fast --output out.nc input.nc.0000 input.nc.0001 input.nc.0002

Files will be collated along all axes with a domain_distribution attribute

At least 2 MPI ranks need to be used (rank 0 writes the output file, other ranks read). More can be used - input files will be balanced between the MPI ranks.

A full list of options can be found by running

mppnccombine-fast --help

Owner

  • Name: ACCESS-NRI
  • Login: ACCESS-NRI
  • Kind: organization
  • Email: access.nri@anu.edu.au

Australian Earth System Simulator - National Research Infrastructure

GitHub Events

Total
  • Issues event: 6
  • Delete event: 2
  • Issue comment event: 7
  • Member event: 2
  • Push event: 6
  • Pull request review event: 6
  • Pull request review comment event: 4
  • Pull request event: 5
  • Create event: 6
Last Year
  • Issues event: 6
  • Delete event: 2
  • Issue comment event: 7
  • Member event: 2
  • Push event: 6
  • Pull request review event: 6
  • Pull request review comment event: 4
  • Pull request event: 5
  • Create event: 6