MPAS | Mesh Connectivity (graph.info) file for the mesh

1. https://mpas-dev.github.io/
2. /MPAS-Model/releases
3. MPAS-Atmosphere Users' Guide V4.0
4. MPAS-Atmosphere Users' Guide V5.3
5. MPAS-Atmosphere Users' Guide V6.3
6. MPAS-Atmosphere Users' Guide V7.0
7. MPAS-Atmosphere Users' Guide V8.2.0
8. Joint WRF/MPAS Users Workshop 2024

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MPAS-Atmosphere Meshes

• https://www2.mmm.ucar.edu/projects/mpas/site/access_code/meshes.html

Several resolutions of quasi-uniform and refined meshes are available for download. Each mesh download provides the following:

• an SCVT mesh on the unit sphere
• the mesh connectivity (graph.info) file for the mesh
• partitionings of the mesh (e.g., graph.info.part.32) for various MPI task counts

Additionally, for quasi-uniform meshes, “static” files using the default datasets are available. The static file downloads provide single-precision static files in CDF-5/64-bit data format and mesh connectivity files.

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Script for graph.info

▶

grid2graph.sh

#!/bin/bash

#------------------------------------------------#
# Author:         wpsze
# Email:          wpsze@gmail.com
# File:           grid2graph.sh
# Date:           2025-07-29 17:05:24
# Version:        0.0 
# Description:    The purpose of the script
# Copyright (C):  2025 All rights reserved
#------------------------------------------------#

#set -e # stop the shell on first error
#set -u # fail when using an undefined variable
#set -x # echo script lines as they are executed
set -o pipefail


source /home/wpsze/micromamba/etc/profile.d/micromamba.sh
micromamba activate venv
export SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"

file=$1
ncells=`ncdump -h $file | grep "nCells = " | cut -d ' ' -f3`
nedges=`ncdump -h $file | grep "nEdges = " | cut -d ' ' -f3`
maxedges=`ncdump -h $file | grep "maxEdges = " | cut -d ' ' -f3`
echo $ncells $nedges
ncdump -v cellsOnCell $file | sed -e "s/[\,,;]//g" | grep -E "^  [0-9][0-9]*" | awk '{ while(++i<=NF) printf (!a[$i]++) ? $i FS : ""; i=split("",a); print ""}'

Take MPAS-120km as example,

▶

graph.info

40962 122880
10247 10243 10244 10245 10246 0 
10248 10249 10250 10251 10252 0 
10254 10255 10256 10257 10253 0 
10262 10258 10259 10260 10261 0 
10266 10267 10263 10264 10265 0 
10272 10268 10269 10270 10271 0 
10273 10274 10275 10276 10277 0 
10280 10281 10282 10278 10279 0 
10284 10285 10286 10287 10283 0
......

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Metis

METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes developed in our lab.

Download: - http://glaros.dtc.umn.edu/gkhome/metis/metis/download

MPAS | install Metis

gpmetis

gpmetis -minconn -contig -niter=200 graph.info <num_core>

which num_core = 12 or ...

If generating graph.info for new mesh

def create_graph_file(self, graphFname):
    """ Create a graph.info file for the current mesh """

    # In the limited_area program, this function will always create
    # a graph.info file for a regional mesh. Thus, the variables here
    # are not preloaded and are being read from disk

def create_partiton_fname(self, name, mesh, **kwargs):
    """ Generate the filename for the regional graph.info file"""
    return name+'.graph.info'

References

1. gpmetis error | Nov 12, 2024
   1. should probably look like 512 513 514 509 510 511
   2. Here's the part of the MPAS-Limited-Area tool that should be writing this connectivity info: MPAS-Limited-Area/limited_area/mesh.py at v2.1 · MPAS-Dev/MPAS-Limited-Area.
   3. We've merge changes to support NumPy 2.x into the MPAS-Limited-Area main branch through MPAS-Dev/MPAS-Limited-Area PR #47. Thanks again for finding this issue!