Applications/Voxfe - Revision history

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Pysdlb: Pysdlb moved page Voxfe to Applications/Voxfe without leaving a redirect

2017-04-19T08:57:11Z

Pysdlb moved page Voxfe to Applications/Voxfe without leaving a redirect

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2017-04-19T08:56:41Z

Pysdlb at 08:55, 19 April 2017

2017-04-19T08:55:05Z

Pysdlb: Created page with "TOC ==Application Details== * Description: VOX-FE is voxel-based FE software, developed jointly between the University of Hull's Medical & Biological Engineering Researc..."

2017-04-19T08:48:45Z

Created page with "__TOC__ ==Application Details== * Description: VOX-FE is voxel-based FE software, developed jointly between the University of Hull's Medical & Biological Engineering Researc..."

New page

__TOC__

==Application Details==

* Description: VOX-FE is voxel-based FE software, developed jointly between the University of Hull's Medical & Biological Engineering Research Group and Edinburgh Parallel Computing Centre, with a sophisticated graphical user interface that allows the complex loading regimes that are inevitably present in biomechanical analyses to be readily applied to the model geometry, and the resultant 3D stress and strain patterns to be visualized easily.
* Version: 2.0.1
* Modules: voxfe/2.0.1
* Licence: BSD license.

==Usage==

===Description===

Biological structures, such as bones, have complex geometries and variable material properties, and experience complex and varying applied loads, for example from muscular activity. To understand the true biomechanical performance of these structures is therefore challenging. Experimental measurements can be extremely difficult, are usually not possible in humans, and are ethically undesirable in animals. Computational modelling is an alternative approach with many advantages over experimental methods.

'''VOX-FE''' is voxel-based finite element software specifically developed for the analysis of very large-scale, high-resolution models of complex biological structures. Voxel based modelling allows us to go directly from microCT scan data to finite element models with minimal loss of data and geometry simplifications, thereby capturing all the complex internal and external features. It also allows inclusion of local variation in material properties based on voxel grey scale value. It is these microscopic-level geometry and material property variations that explain much of the complex macroscopic behaviour of bone.

<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">
[username@login] module load voxfe/2.0.1
</pre>

===Parallel processing===

Through '''SLURM''' this would become the script:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

#!/bin/bash

#SBATCH -J voxfe_dragonfly_mandibles
#SBATCH -n 1 # number of cores (nodes) to use
#SBATCH -N 1 # ensure that all cores are on the machine
#SBATCH --ntasks-per-node 28
#SBATCH -D /home/user/Anax_mandible
#SBATCH -o dlb.out
#SBATCH -e dlb.err
#SBATCH -p highmem # puts the job on a compute node
#SBATCH --time=01:00:00 # maximum execution time
#SBATCH --exclusive

module load intel/mpi/64/5.1.3.181
module load petsc/3.7.5
module load parmetis/4.0.3
module load gcc/5.2.0
module load voxfe/2.0.1

mpirun VoxFESolver /home/user/Anax_mandible/mandible_Anax.voxfe_v2.script

</pre>

==Further Information==

* [https://sourceforge.net/projects/vox-fe/ https://sourceforge.net/projects/vox-fe/]

{|
|style="width:5%; border-width: 0" | [[File:icon_home.png]]
|style="width:95%; border-width: 0" |
* [[Main_Page|Home]]
* [[Applications|Application support]]
* [[General|General]]
* [[Training|Training]]
* [[Programming|Programming support]]
|-
|}

← Older revision		Revision as of 11:01, 16 November 2022
Line 120:		Line 120:
	* [https://sourceforge.net/projects/vox-fe/ https://sourceforge.net/projects/vox-fe/]		* [https://sourceforge.net/projects/vox-fe/ https://sourceforge.net/projects/vox-fe/]

−	~~==Navigation==~~	+	{{Modulepagenav}}
−
−	* [[Main_Page\|Home]]
−	~~* [[Applications\|Application support]] *~~
−	* [[General\|General]]
−	* [[Programming\|Programming support]]

← Older revision		Revision as of 08:56, 19 April 2017
Line 105:		Line 105:
	10800683 58 88 149 0.000000000e+00 0.000000000e+00 0.000000000e+00		10800683 58 88 149 0.000000000e+00 0.000000000e+00 0.000000000e+00

		+	</pre>
		+
		+
		+	This is then submitted as follows:
		+	<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
		+	[username@login01 ~]$ sbatch voxfeDEMO.job
		+	Submitted batch job 289332
	</pre>		</pre>

@@ Line 12: / Line 12: @@
 ===Description===
-Biological structures, such as bones, have complex geometries and variable material properties, and experience complex and varying applied loads, for example from muscular activity. To understand the true biomechanical performance of these structures is therefore challenging. Experimental measurements can be extremely difficult, are usually not possible in humans, and are ethically undesirable in animals. Computational modelling is an alternative approach with many advantages over experimental methods.
+Biological structures, such as bones, have complex geometries and variable material properties, and experience complex and varying applied loads, for example from muscular activity. Understanding the true biomechanical performance of these structures is therefore challenging. Experimental measurements can be extremely difficult, are usually not possible in humans, and are ethically undesirable in animals. Computational modelling is an alternative approach with many advantages over experimental methods.
-'''VOX-FE''' is voxel-based finite element software specifically developed for the analysis of very large-scale, high-resolution models of complex biological structures. Voxel based modelling allows us to go directly from microCT scan data to finite element models with minimal loss of data and geometry simplifications, thereby capturing all the complex internal and external features. It also allows inclusion of local variation in material properties based on voxel grey scale value. It is these microscopic-level geometry and material property variations that explain much of the complex macroscopic behaviour of bone.
+'''VOX-FE''' is voxel-based finite element software specifically developed for the analysis of very large-scale, high-resolution models of complex biological structures. Voxel-based modelling allows us to go directly from microCT scan data to finite element models with minimal loss of data and geometry simplifications, thereby capturing all the complex internal and external features. It also allows the inclusion of local variation in material properties based on voxel greyscale value. It is these microscopic-level geometry and material property variations that explain much of the complex macroscopic behaviour of bone.
@@ Line 40: / Line 40: @@
 #SBATCH --time=01:00:00                         # maximum execution time
 #SBATCH --exclusive
 module add intel/mpi/64/5.1.3.181

@@ Line 119: / Line 119: @@
 * [https://sourceforge.net/projects/vox-fe/ https://sourceforge.net/projects/vox-fe/]
-{|
+==Navigation==
-|style="width:5%; border-width: 0" | [[File:icon_home.png]]
 * [[Main_Page|Home]]
-* [[Applications|Application support]]
+* [[Applications|Application support]] *
 * [[General|General]]
 * [[Programming|Programming support]]

@@ Line 18: / Line 18: @@
 <pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">
-[username@login] module load voxfe/2.0.1
+[username@login] module add voxfe/2.0.1
 </pre>

@@ Line 41: / Line 41: @@
 #SBATCH --exclusive
-module load intel/mpi/64/5.1.3.181
+module add intel/mpi/64/5.1.3.181
-module load petsc/3.7.5
+module add petsc/3.7.5
-module load parmetis/4.0.3
+module add parmetis/4.0.3
-module load gcc/5.2.0
+module add gcc/5.2.0
-module load voxfe/2.0.1
+module add voxfe/2.0.1
 mpirun VoxFESolver /home/user/Anax_mandible/mandible_Anax.voxfe_v2.script

← Older revision	Revision as of 08:57, 19 April 2017
(No difference)

@@ Line 23: / Line 23: @@
 ===Parallel processing===
 Through '''SLURM''' this would become the script:
-<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
+<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">
 #!/bin/bash
@@ Line 51: / Line 50: @@
 </pre>
 ==Further Information==