Introduction

topIIvol meshing tool provides sequential/parallel tools for creating volumetric tetrahedral meshes from a given topology (point-cloud *.xyz). The volumetric meshes can be extracted in Gmsh's *.msh format or medit's *.mesh format. The framework is written in C++, and uses MPI I/O and MPI for parallelization. One could produce distributed meshes suitable for domain-decomposition based solvers or simply non distributed meshes (single mesh) suitable for a sequential/parallel solver.

topIIvol consists a total of four tools:

1. topIIvol_PreProc

This tool is a point-cloud preprocessor. Often point-cloud data is huge and requires some alterations. This tool takes in a point-cloud as an input (.xyz). It can be used to coarsen a structured point cloud, by skipping a specified n number of points.

2. topIIvol_Mesher

This is a sequential computing tool. This tool takes in a point-cloud as an input (.xyz) and generates volumetric meshes that can be extracted in Gmsh's *.msh format or medit's *.mesh and *.meshb format.

3. topIIvol_ParMesher

This is a parallel computing tool. This tool takes in a point-cloud as an input (.xyz) and generates volumetric meshes that can be extracted in medit's *.mesh format.

4. topIIvol_DistMesher

This is a tool to create embarrassingly parallel distributed meshes. The mesher takes in a point-cloud as an input (.xyz) and outputs distributed mesh.

Installation process

Before you begin installing topIIvol please check if your system meets the dependencies.

Dependencies

• automake
• C++
• MPI

Now that I have all the dependencies what next

Goto top-ii-vol-Source folder and

• step 1

autoreconf -i

• step 2

./configure 

Note: ./configure will install topIIvol in /usr/local/bin or /usr/bin, you generally need to be a superuser (sudoer) to have access to these directories. If you prefer to install at any other directory of choice --prefix=Your/Own/Path with ./configure:

./configure --prefix=Your/Own/Path 

• step 3

make

• step 4

make check

• step 5

sudo make install

Note: if you used --prefix during the configure phase, you can avoid using sudo for this step and simply make install.

• Step 6 (optional)

make tutorials

this will install some basic tutorial at $HOME/topIIvol-tutorials.

Running topIIvol

If the compilation went successful you should have three tools at your disposal topIIvol_ParMesher, topIIvol_Mesher, topIIvol_PreProc, and topIIvol_DistMesher. These tools can be worked with command line inputs. Normally, these tools should be present in /usr/local/bin or /usr/bin folder, or else if you used --prefix=your/directory at the time of configure then these tools should be present in your/directory/bin.

How to use topIIvol_PreProc ?

• If you wish to coarsen your mesh by skipping 10 points in x and y direction

topIIvol_PreProc --xpoints 500 --ypoints 451 --xskip 10 --yskip 10 \
--in ./../etc/DEM_10m.xyz --out out-coarse.xyz

Command-line option definitions

Option	Type	Comment
--xpoints	[int]	These are # of x points present in your point cloud.
--ypoints	[int]	These are # of y points present in your point cloud.
--xskip	[int]	These are # of periodic x points you would like to skip.
--yskip	[int]	These are # of periodic y points you would like to skip.
--in	[string]	Sting to provide the input point cloud file .xyz
--out	[string]	Sting to provide the output coarsened/stripped point cloud file .xyz

Note that after successfully running ./topIIvol_PreProcthere will be a info file info-<out-coarse.xyz>.txt that give the number of x an y points in the coarsened mesh cloud.

How to use topIIvol_Mesher ?

This is the sequential mesher

• For sequential mesher producing *.mesh mesh.

topIIvol_Mesher --xpoints 32 --ypoints 29 --zpoints 15 --depth -1000 \
--in ./../etc/DEM_160m.xyz --out out-mesh.mesh --mesh mesh

• For sequential mesher producing *.msh mesh.

topIIvol_Mesher ---xpoints 32 --ypoints 29 --zpoints 15 --depth -1000 \
--in ./../etc/DEM_160m.xyz --out out-mesh.msh  --mesh msh

Command-line option definitions

Option	Type	Comment
--xpoints	[int]	These are # of x points present in your point cloud.
--ypoints	[int]	These are # of y points present in your point cloud.
--zpoints	[int]	These are # of z points intended in the z direction.
--in	[string]	Sting to provide the input point cloud file .xyz
--out	[string]	Sting to provide the output mesh file .mesh
--depth	[int]	This is the depth of the mesh needed.
--mesh	[string]	To specify the kind of mesh needed

How to use topIIvol_ParMesher ?

This is the parallel mesher (still under heavy development)

• For parallel mesher producing *.mesh mesh with 2 MPI ranks.

mpirun -n 2 topIIvol_ParMesher --xpoints 32 --ypoints 29 --zpoints 15 \
--depth -2000 --in ./../etc/DEM_160m.xyz  --out Parallel-out-mesh.mesh

Command-line option definitions

Option	Type	Comment
--xpoints	[int]	These are # of x points present in your point cloud.
--ypoints	[int]	These are # of y points present in your point cloud.
--zpoints	[int]	These are # of z points intended in the z direction.
--in	[string]	Sting to provide the input point cloud file .xyz
--out	[string]	Sting to provide the output mesh file .mesh
-n	[int]	Provide the # of MPI ranks.

How to use topIIvol_DistMesher ?

This is tool to created distributed mesh from partitioned point cloud

• Examples 3D partitioning of distributed mesher producing *.mesh mesh with 24 MPI ranks (with 24 subdomains divided between x, y and z directions):

mpirun -n 24 topIIvol_DistMesher --zpoints 50 --xpoints 32 --ypoints 29 \
--depth -1000 --partition_x 2 --partition_y 3 --partition_z 4 \
--out top-ii-vol-mesh  --in ./../etc/DEM_160m.xyz

or

mpirun -n 24 topIIvol_DistMesher  --zpoints 50 --xpoints 32 --ypoints 29 \
--depth -1000 --partition_x 3 --partition_y 2 --partition_z 4 \
--out top-ii-vol-mesh  --in ./../etc/DEM_160m.xyz

or

mpirun -n 24 topIIvol_DistMesher  --zpoints 50 --xpoints 32 --ypoints 29 \
--depth -1000 --partition_x 2 --partition_y 2 --partition_z 6 \
--out top-ii-vol-mesh  --in ./../etc/DEM_160m.xyz

• Examples 2D partitioning of distributed mesher producing *.mesh mesh with 8 MPI ranks (with the 8 subdomains divided between x and y directions):

mpirun -n 8 topIIvol_DistMesher --zpoints 50 --xpoints 32 --ypoints 29 \
--depth -1000 --partition_x 2 --partition_y 4 --partition_z 1 \
--out top-ii-vol-mesh  --in ./../etc/DEM_160m.xyz

or

mpirun -n 8 topIIvol_DistMesher --zpoints 50 --xpoints 32 --ypoints 29 \
--depth -1000 --partition_x 4 --partition_y 2 --partition_z 1 \
--out top-ii-vol-mesh  --in ./../etc/DEM_160m.xyz

• Examples 2D partitioning of distributed mesher producing *.mesh mesh with 6 MPI ranks (with the 6 subdomains divided between x and z directions):

mpirun -n 6 topIIvol_DistMesher --zpoints 50 --xpoints 32 --ypoints 29 \
--depth -1000 --partition_x 2 --partition_y 1 --partition_z 3 \
--out top-ii-vol-mesh  --in ./../etc/DEM_160m.xyz

or

mpirun -n 6 topIIvol_DistMesher --zpoints 50 --xpoints 32 --ypoints 29 \
--depth -1000 --partition_x 3 --partition_y 1 --partition_z 2 \
--out top-ii-vol-mesh  --in ./../etc/DEM_160m.xyz

• Examples 2D partitioning of distributed mesher producing *.mesh mesh with 16 MPI ranks (with the 16 subdomains divided between y and z directions):

mpirun -n 16 topIIvol_DistMesher --zpoints 50 --xpoints 32 --ypoints 29 \
--depth -1000 --partition_x 1 --partition_y 8 --partition_z 2 \
--out top-ii-vol-mesh  --in ./../etc/DEM_160m.xyz

or

mpirun -n 16 topIIvol_DistMesher --zpoints 50 --xpoints 32 --ypoints 29 \
--depth -1000 --partition_x 1 --partition_y 2 --partition_z 8 \
--out top-ii-vol-mesh  --in ./../etc/DEM_160m.xyz

or

mpirun -n 16 topIIvol_DistMesher --zpoints 50 --xpoints 32 --ypoints 29 \
--depth -1000 --partition_x 1 --partition_y 4 --partition_z 4 \
--out top-ii-vol-mesh  --in ./../etc/DEM_160m.xyz

• Examples 1D partitioning of distributed mesher producing *.mesh mesh with 4 MPI ranks (letting the algorithm decide the partition direction):

mpirun -n 4 topIIvol_DistMesher --zpoints 50 --xpoints 32 --ypoints 29 \
--depth -1000 --out top-ii-vol-mesh  --in ./../etc/DEM_160m.xyz

• Examples 1D partitioning of distributed mesher producing *.mesh mesh with 4 MPI ranks (enforced partitioning in x direction):

mpirun -n 4 topIIvol_DistMesher  --zpoints 50 --xpoints 32 --ypoints 29 \
--depth -1000 --partition_x 4 --partition_y 1 --partition_z 1 \
--out top-ii-vol-mesh  --in ./../etc/DEM_160m.xyz

• Examples 1D partitioning of distributed mesher producing *.mesh mesh with 8 MPI ranks (enforced partitioning in y direction):

mpirun -n 8 topIIvol_DistMesher  --zpoints 50 --xpoints 32 --ypoints 29 \
--depth -1000 --partition_x 1 --partition_y 8 --partition_z 1 \
--out top-ii-vol-mesh  --in ./../etc/DEM_160m.xyz

• Examples 1D partitioning of distributed mesher producing *.mesh mesh with 3 MPI ranks (enforced partitioning in z direction):

mpirun -n 3 topIIvol_DistMesher  --zpoints 50 --xpoints 32 --ypoints 29 \
--depth -1000 --partition_x 1 --partition_y 1 --partition_z 3 \
--out top-ii-vol-mesh  --in ./../etc/DEM_160m.xyz

Command-line option definitions

Option	Type	Comment
--xpoints	[int]	These are # of x points present in your point cloud.
--ypoints	[int]	These are # of y points present in your point cloud.
--zpoints	[int]	These are # of z points intended in the z direction.
--partition_x	[int]	These are # of x partitions in x direction.
--partition_y	[int]	These are # of y partitions in y direction.
--partition_z	[int]	These are # of z partitions in z direction.
--in	[string]	Sting to provide the input point cloud file .xyz
--out	[string]	Sting to provide the output mesh file .mesh
-np	[int]	Provide the # of MPI ranks.

To report bugs, issues, feature-requests contact:*

• mohd-afeef.badri@cea.fr
• mohd-afeef.badri@hotmail.com

Point cloud

Surface triangulation of point cloud

Finite element solution field