Compiling in Linux

This page explains several command-line methods to compile the code engines in Linux or Unix systems.

Introduction

The nairn-mpm-fea code engines can easily be compiled on any Linux system with a C++ compiler and with xerces already installed. Below are details on specific systems that are already set up for compilation, already have xerces, and are currently in use for OSParticulas, NairnMPM, and NairnFEA. See the section on other systems for compilation on other Linux/Unix systems.

In brief, each system simply requires a custom argument to the make command. After compilation is over see below for generic details that apply to all system.

HPC Cluster (Oregon State University)

If you are using the HPC cluster in the Oregon State University, Wood Science & Engineering Department, use a simple make command. This system is the default system for compiling the code. The commands for OSParticulas and NairnMPM are:

cd nairn-mpm-fea/NairnMPM/build
make -j N

and for NairnFEA are:

cd nairn-mpm-fea/NairnFEA/build
make -j N

where the -j N tells the make to compile in parallel using N cores.

MPM Workstation (Oregon State University)

If you are using mpm in the Oregon State University, Wood Science & Engineering Department, the commands for OSParticulas and NairnMPM are:

cd nairn-mpm-fea/NairnMPM/build
make -j 12 SYSTEM=mpm

and for NairnFEA are:

 cd nairn-mpm-fea/NairnFEA/build
 make -j 12 SYSTEM=mpm

where the -j 12 tells the make to compile in parallel using the 12 cores on this workstation.

Zia Workstation (CISRO)

If you are using Zia Linux system, the commands for OSParticulas and NairnMPM are:

cd nairn-mpm-fea/NairnMPM/build
make -j N SYSTEM=zia

and for NairnFEA are:

 cd nairn-mpm-fea/NairnFEA/build
 make -j N SYSTEM=zia

where the -j N tells the make to compile in parallel using N cores.

Compilation on Supported Linux Systems

The commands for the above system will compile all source code and install the executables in nairn-mpm-fea/NairnMPM/input or nairn-mpm-fea/NairnFEA/input, respectively. If you follow successful compilation with

 make install

the relevant executable and DTD file will be copied to a bin folder in your home directory (which should exist). It is convenient to have that directory in your default $PATH variable such that launching calculations only needs the binary name.

Besides the SYSTEM parameter to specify a supported system, you can pass additional parameters to the make command to alter the compilation process. See comments in the makefile for all the latest options.

Other Linux Systems

Compiling on any Linux/Unix system should be straightforward, with the most difficult step usually being installing and link to the xerces library. The key steps needed for successful compilation:

1. Use a compatible C++ compiler. To compile parallel version of the code, you need a compiler that supports OpenMP. For gcc, the version should be 4.8 or newer. Non-gcc compilers such as clang-mp work as well.
2. Validation and parsing of the XML files are handled using free third party software from the Apache Software Foundation called the xerces validating XML parser. You will need to download xerces and install it on your system. It is available in binary installs for many systems. For others systems you will need to download the source code and build it. Since revision 274 of the nairn-mpm-fea project, the codes require xerces 3.0 or newer. Prior to this revision, the codes requied xerces 2.8 or older. Unfortunately, the new versions of xerces are not compatible with the older ones.
3. Compiling of OSParticulas, NairnMPM, and NairnFEA needs access to all the xerces header files. These are provided in the xerces source code downloads. Even if your system has the xerces binary installed, it may not have the header files. You can get them by downloading the xerces source code, even though you will not need to build it.

Once a suitable compiler, the xerces binary, and xerces header files are installed, compilation may require editing the makefiles in the nairn-mpm-fea folders. Specifically, you will need to edit the makefiles in the NairnMPM/buildand NairnFEA/build directories and set at least the following variables if the default settings are not correct for your system:

1. The variable CC: set it to the desired C++ compiler.
2. The variable xercesSo: set it to the path name to the xerces library binary file.
3. The variable headersPath: set it to the path name to the folder containing the xercesc folder of header files.

After setting the variables, use a standard make command to compile the code. If it compiles, but will not load the xerces library at runtime, you will have to find the system-dependent method to provide the path to the xerces library and make sure the system can find the xerces library.

If you successfully get the code compiled and running on a system that is not listed above, please edit this wiki page to document it, or send email to John.Nairn@oregonstate.edu with the system name and step-by-step instructions for compiling and running the code.