Added initial set of script for La Habra volume meshing with topography.

parent 04af6923
Volume Meshes for the La Habra Setting with Mountain Topography
===============================================================
This directory contains the scripts to generate velocity-aware volume meshes with mountain topography.
First, the scripts call Gmsh to generate an initial mesh.
Next, we iterate over the following steps multiple times:
* The mesh is parsed by EDGE-V which generates target edge lengths based on vs.
* Gmsh reads the target lengths and generates a mesh satisfying the specified constraints; no remeshing of the surface mesh is performed.
In a final iteration EDGE-V also increases the mesh-resolution if a jump in vs is detected.
This input is once again parsed by Gmsh (also remeshing the surface mesh) and then handed over to EDGE-V for velocity and LTS annotations as well as partitioning.
EDGE-V used MOAB with the patch ``../moab_int32.patch`` applied.
<?xml version="1.0" encoding="UTF-8"?>
<!--
@file This file is part of EDGE.
@author Alexander Breuer (anbreuer AT ucsd.edu)
@section LICENSE
Copyright (c) 2019-2020, Alexander Breuer
All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
@section DESCRIPTION
EDGE-V configuration for mesh refinement of the La Habra benchmark.
-->
<edge_v>
<mesh>
<periodic>no</periodic>
<files>
<in>la_habra_refined_base.msh</in>
</files>
</mesh>
<velocity_model>
<ucvm>
<source_transformation>
<x_0>1.0</x_0>
<x_1>0.0</x_1>
<x_2>0.0</x_2>
<y_0>0.0</y_0>
<y_1>1.0</y_1>
<y_2>0.0</y_2>
<z_0>0.0</z_0>
<z_1>0.0</z_1>
<z_2>1.0</z_2>
</source_transformation>
<projections>
<source>+proj=tmerc +units=m +axis=enu +no_defs +datum=WGS84 +k=0.9996 +lon_0=-117.916 +lat_0=33.933</source>
<destination>+proj=latlong +datum=WGS84</destination>
</projections>
<models>cvmsi</models>
<model_type>cmb</model_type>
<coordinate_mode>UCVM_COORD_GEO_ELEV</coordinate_mode>
<normalization_rule>
<![CDATA[
// Decription, following https://scec.usc.edu/scecpedia/HighF_2018:
//
// 1. Set Min Vs=500 m/s
// 2. If Vs was lower than 500 m/s and adjusted, then adjust Vp with original Vp/Vs ratio (so that we don’t have the automatic Vs/Vp of 3). We may want to set a minimum value of Vp (Rob to check)
// 3. Then set Max Vp/Vs= 3, if lower Vp to maintain the max of 3 ratio
// limit vs to 500 m/s
if( vs < 500 ) {
// derive vp/vs ratio
var sca := vp / vs;
// adjust velocities
vs := 500;
vp := 500*sca;
};
// limit maximum vp/vs ratio to 3
var sca := vp / vs;
if( sca > 3 ) {
vp := 3*vs;
};
// limit minimum vp/vs ratio to sqrt(2) (lower means negative lambda)
if( sca < 1.415 ) {
vp:= 1.415*vs;
};
]]>
</normalization_rule>
<lower_to_surface>true</lower_to_surface>
</ucvm>
</velocity_model>
<refinement>
<expression>
<![CDATA[
frequency := 1.25;
// use five edges per wavelength in 25km radius
if( sqrt(x*x + y*y) < 25000 ) {
edges_per_wave_length := 5;
}
// decrease linearly from 25km - 40km
else if( sqrt(x*x + y*y) < 40000 ) {
var ratio := (sqrt(x*x + y*y)-25000) / (40000 - 25000);
edges_per_wave_length := 5 - ratio*3.75;
}
// use 1.25 outside
else {
edges_per_wave_length := 1.25;
};
// double resolution in upper 1km
if( z > -1000 ) {
var ratio := (z + 1000) / 1000;
edges_per_wave_length *= 1 + ratio;
};
]]>
</expression>
<out>la_habra_bgm_base.msh</out>
</refinement>
</edge_v>
<?xml version="1.0" encoding="UTF-8"?>
<!--
@file This file is part of EDGE.
@author Alexander Breuer (anbreuer AT ucsd.edu)
@section LICENSE
Copyright (c) 2019-2020, Alexander Breuer
All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
@section DESCRIPTION
EDGE-V configuration for mesh refinement of the La Habra benchmark.
-->
<edge_v>
<mesh>
<periodic>no</periodic>
<files>
<in>la_habra_refined_base.msh</in>
</files>
</mesh>
<velocity_model>
<ucvm>
<source_transformation>
<x_0>1.0</x_0>
<x_1>0.0</x_1>
<x_2>0.0</x_2>
<y_0>0.0</y_0>
<y_1>1.0</y_1>
<y_2>0.0</y_2>
<z_0>0.0</z_0>
<z_1>0.0</z_1>
<z_2>1.0</z_2>
</source_transformation>
<projections>
<source>+proj=tmerc +units=m +axis=enu +no_defs +datum=WGS84 +k=0.9996 +lon_0=-117.916 +lat_0=33.933</source>
<destination>+proj=latlong +datum=WGS84</destination>
</projections>
<models>cvmsi</models>
<model_type>cmb</model_type>
<coordinate_mode>UCVM_COORD_GEO_ELEV</coordinate_mode>
<normalization_rule>
<![CDATA[
// Decription, following https://scec.usc.edu/scecpedia/HighF_2018:
//
// 1. Set Min Vs=500 m/s
// 2. If Vs was lower than 500 m/s and adjusted, then adjust Vp with original Vp/Vs ratio (so that we don’t have the automatic Vs/Vp of 3). We may want to set a minimum value of Vp (Rob to check)
// 3. Then set Max Vp/Vs= 3, if lower Vp to maintain the max of 3 ratio
// limit vs to 500 m/s
if( vs < 500 ) {
// derive vp/vs ratio
var sca := vp / vs;
// adjust velocities
vs := 500;
vp := 500*sca;
};
// limit maximum vp/vs ratio to 3
var sca := vp / vs;
if( sca > 3 ) {
vp := 3*vs;
};
// limit minimum vp/vs ratio to sqrt(2) (lower means negative lambda)
if( sca < 1.415 ) {
vp:= 1.415*vs;
};
]]>
</normalization_rule>
<lower_to_surface>true</lower_to_surface>
</ucvm>
</velocity_model>
<refinement>
<expression>
<![CDATA[
frequency := 1.25;
// use five edges per wavelength in 25km radius
if( sqrt(x*x + y*y) < 25000 ) {
edges_per_wave_length := 5;
}
// decrease linearly from 25km - 40km
else if( sqrt(x*x + y*y) < 40000 ) {
var ratio := (sqrt(x*x + y*y)-25000) / (40000 - 25000);
edges_per_wave_length := 5 - ratio*3.75;
}
// use 1.25 outside
else {
edges_per_wave_length := 1.25;
};
// double resolution in upper 1km
if( z > -1000 ) {
var ratio := (z + 1000) / 1000;
edges_per_wave_length *= 1 + ratio;
};
if( sqrt(x*x + y*y) < 40000 ) {
// decrease target length by up to 1.5x to reach a maximum difference of 25%
// this assumes linear changes in velocity
var diff := maximum_wave_speed_ratio - 1;
if( diff > 0.25 ) {
var scale := min( diff / 0.25, 1.5 );
edges_per_wave_length *= scale;
}
};
]]>
</expression>
<out>la_habra_bgm_grad.msh</out>
</refinement>
</edge_v>
<?xml version="1.0" encoding="UTF-8"?>
<!--
@file This file is part of EDGE.
@author Alexander Breuer (anbreuer AT ucsd.edu)
@section LICENSE
Copyright (c) 2019-2020, Alexander Breuer
All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
@section DESCRIPTION
EDGE-V configuration for mesh refinement of the La Habra benchmark.
-->
<edge_v>
<mesh>
<periodic>no</periodic>
<n_partitions>256</n_partitions>
<files>
<in>la_habra_refined_grad.msh</in>
<out>
<base>part/la_habra_refined_grad</base>
<extension>.h5m</extension>
</out>
</files>
</mesh>
<velocity_model>
<ucvm>
<source_transformation>
<x_0>1.0</x_0>
<x_1>0.0</x_1>
<x_2>0.0</x_2>
<y_0>0.0</y_0>
<y_1>1.0</y_1>
<y_2>0.0</y_2>
<z_0>0.0</z_0>
<z_1>0.0</z_1>
<z_2>1.0</z_2>
</source_transformation>
<projections>
<source>+proj=tmerc +units=m +axis=enu +no_defs +datum=WGS84 +k=0.9996 +lon_0=-117.916 +lat_0=33.933</source>
<destination>+proj=latlong +datum=WGS84</destination>
</projections>
<models>cvmsi</models>
<model_type>cmb</model_type>
<coordinate_mode>UCVM_COORD_GEO_ELEV</coordinate_mode>
<normalization_rule>
<![CDATA[
// Decription, following https://scec.usc.edu/scecpedia/HighF_2018:
//
// 1. Set Min Vs=500 m/s
// 2. If Vs was lower than 500 m/s and adjusted, then adjust Vp with original Vp/Vs ratio (so that we don’t have the automatic Vs/Vp of 3). We may want to set a minimum value of Vp (Rob to check)
// 3. Then set Max Vp/Vs= 3, if lower Vp to maintain the max of 3 ratio
// limit vs to 500 m/s
if( vs < 500 ) {
// derive vp/vs ratio
var sca := vp / vs;
// adjust velocities
vs := 500;
vp := 500*sca;
};
// limit maximum vp/vs ratio to 3
var sca := vp / vs;
if( sca > 3 ) {
vp := 3*vs;
};
// limit minimum vp/vs ratio to sqrt(2) (lower means negative lambda)
if( sca < 1.415 ) {
vp:= 1.415*vs;
};
]]>
</normalization_rule>
<lower_to_surface>true</lower_to_surface>
</ucvm>
</velocity_model>
<time>
<n_groups>5</n_groups>
</time>
</edge_v>
/**
* @file This file is part of EDGE.
*
* @author Alexander Breuer (anbreuer AT ucsd.edu)
*
* @section LICENSE
* Copyright (c) 2020, Alexander Breuer
* Copyright (c) 2018, Regents of the University of California
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
*
* 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
* @section DESCRIPTION
* Tet4 setup for High-F's small La Habra domain with topography.
* The surface mesh is used "as is" without remeshing.
**/
Mesh.Optimize = 1;
// load surface mesh
Merge "../../surface/la_habra_top.stl";
Merge "../../surface/la_habra_left.stl";
Merge "../../surface/la_habra_right.stl";
Merge "../../surface/la_habra_front.stl";
Merge "../../surface/la_habra_back.stl";
Merge "../../surface/la_habra_bottom.stl";
// remove duplicates
Coherence Mesh;
// boundary representation
CreateTopology;
// set free surface boundary
Physical Surface(101) = {1};
// set outflow boundary
Physical Surface(105) = {2,3,4,5,6};
// volume
Surface Loop(1001) = {1,2,3,4,5,6};
Volume(1001) = {1001};
Physical Volume(1) = {1001};
/**
* @file This file is part of EDGE.
*
* @author Alexander Breuer (anbreuer AT ucsd.edu)
*
* @section LICENSE
* Copyright (c) 2020, Alexander Breuer
* Copyright (c) 2018, Regents of the University of California
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
*
* 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
* @section DESCRIPTION
* Tet4 setup for High-F's small La Habra domain with topography.
* The surface mesh is remeshed to satisfy the characteristic length requirements.
**/
Mesh.Optimize = 1;
// load surface mesh
Merge "../../surface/la_habra_top.stl";
Merge "../../surface/la_habra_left.stl";
Merge "../../surface/la_habra_right.stl";
Merge "../../surface/la_habra_front.stl";
Merge "../../surface/la_habra_back.stl";
Merge "../../surface/la_habra_bottom.stl";
// remove duplicates
Coherence Mesh;
// boundary representation
CreateTopology;
// create parametrization for remeshing
CreateGeometry;
// set free surface boundary
Physical Surface(101) = {1};
// set outflow boundary
Physical Surface(105) = {2,3,4,5,6};
// volume
Surface Loop(1001) = {1,2,3,4,5,6};
Volume(1001) = {1001};
Physical Volume(1) = {1001};
#!/bin/bash
##
# @file This file is part of EDGE.
#
# @author Alexander Breuer (breuer AT mytum.de)
#
# @section LICENSE
# Copyright (c) 2020, Alexander Breuer
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
#
# 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# @section DESCRIPTION
# Generates a velocity-adapted background mesh.
##
#SBATCH -J la_habra_mesh_bgm
#SBATCH -o la_habra_mesh_bgm.o%j
#SBATCH -e la_habra_mesh_bgm.e%j
#SBATCH -p nvdimm
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -t 24:00:00
module list
pwd
date
module load intel/18.0.5
module load gcc/9.1.0
module load impi/18.0.5
module load mkl
export PATH=/scratch1/02529/breuera/edge_opt/bench/seismic/wp/la_habra/edge/deps/bin:$PATH
export PATH=/scratch1/02529/breuera/topo_mesh/gmsh/install/bin:$PATH
export OMP_NUM_THREADS=112
gmsh --info
date
edge_v -x la_habra_refined_base.xml
gmsh -3 la_habra_topo_bgm.geo -bgm la_habra_bgm_base.msh -o la_habra_refined_base.msh2
mv la_habra_refined_base.msh2 la_habra_refined_base.msh
date
#!/bin/bash
##
# @file This file is part of EDGE.
#
# @author Alexander Breuer (breuer AT mytum.de)
#
# @section LICENSE
# Copyright (c) 2020, Alexander Breuer
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
#
# 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# @section DESCRIPTION
# Generates the final annotated and partitioned mesh.
##
#SBATCH -J la_habra_mesh_final
#SBATCH -o la_habra_mesh_final.o%j
#SBATCH -e la_habra_mesh_final.e%j
#SBATCH -p nvdimm
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -t 48:00:00
module list
pwd
date
module load intel/18.0.5
module load gcc/9.1.0
module load impi/18.0.5
module load mkl
export PATH=/scratch1/02529/breuera/edge_opt/bench/seismic/wp/la_habra/edge/deps/bin:$PATH
export PATH=/scratch1/02529/breuera/topo_mesh/gmsh/install/bin:$PATH
export OMP_NUM_THREADS=112
gmsh --info
date
echo "refining for velocity gradient"
edge_v -x la_habra_refined_grad.xml
gmsh -3 la_habra_topo_final.geo -bgm la_habra_bgm_grad.msh -o la_habra_refined_grad.msh2
mv la_habra_refined_grad.msh2 la_habra_refined_grad.msh
echo "clustering, annotating and partitioning"
mkdir part
edge_v -x la_habra_refined_part.xml
date
#!/bin/bash
##
# @file This file is part of EDGE.
#
# @author Alexander Breuer (breuer AT mytum.de)
#
# @section LICENSE
# Copyright (c) 2020, Alexander Breuer
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
#
# 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# @section DESCRIPTION
# Generates the intial background mesh.
##
#SBATCH -J la_habra_mesh_initial_bgm
#SBATCH -o la_habra_mesh_initial_bgm.o%j
#SBATCH -e la_habra_mesh_initial_bgm.e%j
#SBATCH -p nvdimm
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -t 06:00:00
module list
pwd
date
module load intel/18.0.5
module load gcc/9.1.0
module load impi/18.0.5
module load mkl
export PATH=/scratch1/02529/breuera/edge_opt/bench/seismic/wp/la_habra/edge/deps/bin:$PATH
export PATH=/scratch1/02529/breuera/topo_mesh/gmsh/install/bin:$PATH
export OMP_NUM_THREADS=112
gmsh --info
date
gmsh -clmax 500 -3 la_habra_topo_bgm.geo -o la_habra_refined_base.msh2
mv la_habra_refined_base.msh2 la_habra_refined_base.msh
date
#!/bin/bash
##
# @file This file is part of EDGE.
#
# @author Alexander Breuer (breuer AT mytum.de)
#
# @section LICENSE
# Copyright (c) 2020, Alexander Breuer
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
#
# 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# @section DESCRIPTION
# Submits the jobs.
##
job_id=$(sbatch run_initial_bgm.slurm)
job_id=$(sbatch --dependency=afterok:${job_id} run_bgm.slurm)
job_id=$(sbatch --dependency=afterok:${job_id} run_bgm.slurm)
job_id=$(sbatch --dependency=afterok:${job_id} run_bgm.slurm)
job_id=$(sbatch --dependency=afterok:${job_id} run_final.slurm)
Markdown is supported
0%
or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment