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PeridigmInstallationGuide.160361722.pdf
Contents
List of Figures
List of Listings
About Peridigm
Description
Adresses
Hardware requirements
Features
Example 1
Example 2
Example 3
License
Peridigm working environment
Dependencies
Linux in a virtual machine
Download Linux Distribution
Install the virtual machine
Download and install virtualization software
Create the virtual machine
Create a shared folder between host and virtual machine
Install the operating system in the virtual machine
User modifications to use shared folders
Save the virtual machine state
Peridigm Linux installation
Tested combinations
CPU-Architecture & operating system
Library and system combinations
Basics
Preliminary remarks
Root .bashrc file
Fortran & C & C[4]++-compiler
CMake
MPI
Python
System libraries
Necessary libraries
Libraries that are not supposed to be installed yet
Libraries
Boost
HDF5
NetCDF-C
Trilinos
Peridigm
Download
Compiling & installation
After building and installing
Install a local version on the cluster
Use of Docker
Running Peridigm
Install ParaView
Linux installation
Windows installation
Install everything for FETranslator
Linux
Java
NetCDF-C
Windows
Java
NetCDF-C
Bibliography
Appendix Build-scripts for Libraries
Boost
Boost 1.55.0
Boost 1.60.0
HDF5
NetCDF-C
Trilinos
Peridigm
CMake script for Peridigm
Script for cloning Peridigm from GitHub and compiling on the STM-Cluster
Make a script executable
Modifications of .bashrc
.bashrc for Peridigm 1.4.1
.bashrc for Peridigm 1.5
Appendix FAQ
Appendix Non-necessary tools & scripts
NEdit
RM-LaTeX
Linux
Windows
Appendix This document
Repository
Typesetting
BSD Documentation License
Peridigm
Peridigm Installation Guide
For Peridigm versions ≥ 1.4.1
Martin Rädel
Deutsches Zentrum
DLR für Luft- und Raumfahrt
German Aerospace Center
Document Identi cation
ii
DLR German Aerospace Center
Composite Structures and Adaptive Systems
Structural Mechanics
Dr. Tobias Wille
38108 Braunschweig
Germany
Tel:
Fax:
Web:
+49 (0)531 295-3701
+49 (0)531 295-3702
http://www.dlr.de/fa/en
Martin Rädel
+49 (0)531 295-2048
Tel:
Fax:
+49 (0)531 295-2232
Mail: martin.raedel@dlr.de
Repository
This document is part of the PeriDoX repository [1].
The complete repository can be found at:
https://github.com/PeriDoX/PeriDoX
Citing
When citing this document, please reference the following:
Martin Rädel, Christian Willberg, Peridigm Users Guide, DLR-IB-FA-BS-2018-23, DLR
Report, 2018, in PeriDoX, DOI: 10.5281/zenodo.1403015
Disclaimer
The contents of this document are provided AS IS. This information could contain tech-
nical inaccuracies, typographical errors and out-of-date information. This document may
be updated or changed without notice at any time. Use of the information is therefore
at your own risk. In no event shall the DLR be liable for special, indirect, incidental or
consequential damages resulting from or related to the use of this document.
Peridigm Installation Guide
DLR
Copyright © 2018 German Aerospace Center (DLR)
Permission is granted to copy, distribute and/or modify this document under the terms
of the BSD Documentation License. A copy of the license is included in the section
entitled BSD Documentation License.
Dieses Dokument darf unter den Bedingungen der BSD Documentation License vervielfältigt,
distribuiert und/oder modi ziert werden. Eine Kopie der Lizenz ist im Kapitel BSD
Documentation License enthalten.
Contents
List of Figures
List of Listings
1. About Peridigm
1.1. Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.2. Adresses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.3. Hardware requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.4. Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.4.1. Example 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.4.2. Example 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.4.3. Example 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.5. License . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.6. Peridigm working environment
. . . . . . . . . . . . . . . . . . . . . . . .
1.7. Dependencies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
vii
viii
1
1
1
1
2
2
2
2
2
3
3
2. Linux in a virtual machine
5
5
2.1. Download Linux Distribution . . . . . . . . . . . . . . . . . . . . . . . . .
5
Install the virtual machine . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.2.
5
2.2.1. Download and install virtualization software . . . . . . . . . . . . .
2.2.2. Create the virtual machine
8
. . . . . . . . . . . . . . . . . . . . . .
2.2.3. Create a shared folder between host and virtual machine . . . . . . 15
Install the operating system in the virtual machine . . . . . . . . . 16
2.2.4.
2.2.5. User modi cations to use shared folders
. . . . . . . . . . . . . . . 21
. . . . . . . . . . . . . . . . . . . . 21
2.2.6. Save the virtual machine state
3. Peridigm Linux installation
23
3.1. Tested combinations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
3.1.1. CPU-Architecture & operating system . . . . . . . . . . . . . . . . 23
3.1.2. Library and system combinations . . . . . . . . . . . . . . . . . . . 24
3.2. Basics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
3.2.1. Preliminary remarks . . . . . . . . . . . . . . . . . . . . . . . . . . 25
3.2.2. Root .bashrc le . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
3.2.3. Fortran & C & C++-compiler . . . . . . . . . . . . . . . . . . . . . 27
3.2.4. CMake . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
3.2.5. MPI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Peridigm Installation Guide
DLR
iv
Contents
v
3.2.6. Python . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
3.3. System libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
3.3.1. Necessary libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
3.3.2. Libraries that are not supposed to be installed yet
. . . . . . . . . 34
3.4. Libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
3.4.1. Boost
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
3.4.2. HDF5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
3.4.3. NetCDF-C . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
3.4.4. Trilinos . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
3.5. Peridigm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
3.5.1. Download . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
3.5.2. Compiling & installation . . . . . . . . . . . . . . . . . . . . . . . . 43
3.5.3. After building and installing . . . . . . . . . . . . . . . . . . . . . . 43
3.5.4.
. . . . . . . . . . . . . . . . . 44
3.5.5. Use of Docker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Install a local version on the cluster
4. Running Peridigm
46
5.
6.
47
Install ParaView
5.1. Linux installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
5.2. Windows installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Install everything for FETranslator
49
6.1. Linux . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
6.1.1. Java . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
6.1.2. NetCDF-C . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
6.2. Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
6.2.1. Java . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
6.2.2. NetCDF-C . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Bibliography
54
Appendix A. Build-scripts for Libraries
A.1. Boost
56
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
A.1.1. Boost 1.55.0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
A.1.2. Boost 1.60.0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
A.2. HDF5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
A.3. NetCDF-C . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
A.4. Trilinos
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
A.5. Peridigm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
A.5.1. CMake script for Peridigm . . . . . . . . . . . . . . . . . . . . . . 60
A.5.2. Script for cloning Peridigm from GitHub and compiling on the
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
A.6. Make a script executable . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
STM-Cluster
Peridigm Installation Guide
DLR
Contents
vi
A.7. Modi cations of .bashrc . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
A.7.1. .bashrc for Peridigm 1.4.1 . . . . . . . . . . . . . . . . . . . . . . 64
A.7.2. .bashrc for Peridigm 1.5 . . . . . . . . . . . . . . . . . . . . . . . 65
Appendix B. FAQ
67
Appendix C. Non-necessary tools & scripts
69
C.1. NEdit
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
C.2. RM-LATEX . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
C.2.1. Linux . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
C.2.2. Windows
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Appendix D. This document
71
D.1. Repository . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
D.2. Typesetting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
BSD Documentation License
72
Peridigm Installation Guide
DLR
List of Figures
Impact failure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.1.
1.2. Tensile test
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.3. Fragmentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.4. Peridigm working environment tree . . . . . . . . . . . . . . . . . . . . . .
1.5. Peridigm package dependencies . . . . . . . . . . . . . . . . . . . . . . . .
2.1. Allow VirtualBox access to devices . . . . . . . . . . . . . . . . . . . . . .
2
2
2
3
4
7
3.1. Peridigm GitHub repository screenshot . . . . . . . . . . . . . . . . . . . . 42
Peridigm Installation Guide
DLR
vii
List of Listings
A.1. Install script for Boost 1.55.0 . . . . . . . . . . . . . . . . . . . . . . . . . 56
A.2. Install script for Boost 1.60.0 . . . . . . . . . . . . . . . . . . . . . . . . . 57
A.3. Install script for HDF5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
A.4. Install script for NetCDF-C . . . . . . . . . . . . . . . . . . . . . . . . . . 58
A.5. CMake script for Trilinos
. . . . . . . . . . . . . . . . . . . . . . . . . . . 58
A.6. CMake script for Peridigm . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
A.7. Script for cloning Peridigm from GitHub and compiling on the STM-Cluster 60
A.8. Modi ed .bashrc- le to set environment variables for Peridigm 1.4.1 . . . 64
A.9. Modi ed .bashrc- le to set environment variables for Peridigm 1.5 . . . . 65
Peridigm Installation Guide
DLR
viii
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