PARADISCYL:How-To-Install

Manual 01 for ParaDiS Cylinder Codes

How to install

This document describes the extension of the ParaDiS program that implements the cylindrical free surface boundary condition. This extension is based on Weinberger and Cai, J. Mech. Phys. Solids, 55, 2027 (2007)(PDF). The code is written by Chris Weinberger and Wei Cai and is not included in the standard distribution of ParaDiS. Keonwook Kang wrote the first draft of this document, which was later revised by Chris Weinberger and Wei Cai. Questions on this document should be addressed to Chris Weinberger. Please read the manual of ParaDiS before reading this document.

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Library Requirements

Even though the standard ParaDiS distribution can be compiled and run on parallel computers, the cylinder extension currently can run only in serial. To compile the code, you need GNU scientific libraries (libgsl and libgslcblas) and DFT library (libfftw3). The code should compile on Linux workstations. Preferably we should use the intel compiler icc but you may also try to compile it with gcc. Free evaluation verion of intel compilers can be downloaded from the Intel Software Network Site.

libgsl and libgslcblas

The GNU Scientific library can be downloaded at http://www.gnu.org/software/gsl/. It can be installed by the following commands.

# mv ./gsl-1.9.tar.gz /usr/local/src/
# cd /usr/local/src
# tar -zxvf gsl-1.9.tar.gz
# cd gsl-1.9
# ./configure
# make
# make install

This will intall the gsl libraries will be installed at /usr/local/lib/.

libfftw3

The image stress calculation requires the use of discrete Fourier transform (DFT). In particular, we will use the Fastest Fourier Transform in the West (FFTW), the standard in DFT programs, provided by the FFTW library, which can be installed by the following commands.

# mv ./fftw-3.1.2.tar.gz /usr/local/src/
# cd /usr/local/src
# tar -zxvf fftw-3.1.2.tar.gz
# cd fftw-3.1.2
# ./configure
# make 
# make install

This will install library files libfftw3.a and libfftw3.la in /usr/local/lib/.

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Compile

First, you need to download the standard ParaDiS distribution from http://paradis.stanford.edu . The cylinder code, however, is in the cylinder/ subdirectory that is not included in the standard ParaDiS distribution. If you have the cylinder code, go to the cylinder/ subdirectory.

$ cd ParaDiS/cylinder

This directory contains a makefile, which also make references to the standard makefiles ../makefile.sys and ../makefile.setup in the parent directory.

makefile.sys defines system-dependent compilers and compiling options for different systems such as linux, aix, etc. The pre-defined system types and their descriptions are listed at the beginning of the makefile.sys file.

In makefile.setup, you can select various 'make' settings, some of which are explained below.

SYS

select system type. you can use SYS = linux

MODE

set serial or parallel mode. you need to use MODE = SERIAL

XLIB_MODE

enable or disable xwindow plotting capability. you can use XLIB_MODE = ON

OPT

define optimization level. you can use OPT = -O3

In makefile, there is an important macro DEFS. The cylinder codes behave differently depending on how DEFS is defined.

DEFS += -D_CYL

Needs to be included to activate cylinder specific functions.

DEFS += -D_NOBEMSTRESS

Disables the calculation of the general image stress by our spectral methods. This is a misnomer, there is no boundary element method (BEM) involved

DEFS += -D_NOYOFFESTRESS

Disables the Yoffe Image Stress. See Modelling Simul. Mater. Sci. Eng. 14, 1139 (2006) (PDF)

DEFS += -D_NULLCYLSTRESS

Ignore all image stress calculations (including BEM, Yoffe, Virtual segment contributions).

DEFS += -D_NOVIRTUALSEG

No force contribution from virtual segments. Do not use this flag unless you are absolutely sure you know what you are doing!

DEFS += -D_CYLMETHOD1

If defined, analytic expressions using Bessel functions are used for image stress calculation. If not, the Greens function method is used to compute image stress. .

DEFS += -D_WRITENODEFORCE

If defined, code will write nodal force data in force.out file after the first nodal force evaluation and immediately exit. Each line of the file contains nodal position x, y, z and nodal force f_x, f_y and f_z.

DEFS += -D_PRINTCYLSTRESS

If defined, code will write nodal force data in force.out and stress field in stress.out files. Each line of stress.out contains grid position r, θ, z and stress components σ₁₁, σ₂₂, σ₃₃, σ₂₃, σ₃₁, σ₁₂.

To compile, type

$ make

and executable file paradiscyl should appear in the directory ../bin/.

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Notes