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. It is owned by Chris 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. 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 is only working in the serial mode. 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 Fast Fourier Transform (FFT) 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 in the head of makefile.sys file.

In makefile.setup file, you can select various 'make' settings and switches, 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 important macro DEFS. The cylinder codes behave differently depending on how DEFS is defined.

DEFS += -D_CYL

Needs to be included for cylinder codes.

DEFS += -D_NOBEMSTRESS

No boundary image stress will be considered.

DEFS += -D_NOYOFFESTRESS

No Yoffe stress will be considered.

DEFS += -D_NULLCYLSTRESS

Ignore all image stress. (BEM, Yoffe, Virtual seg.(??))

DEFS += -D_NOVIRTUALSEG

No force contribution from virtual segments.(??)

DEFS += -D_CYLMETHOD1

If defined, grid stress is used for image stress calculation. If not, Green stress is used.

DEFS += -D_WRITENODEFORCE

Will write nodal force data in force.out file. Each line of the file contains nodal position x, y, z and nodal force f_x, f_y and f_z.

DEFS += -D_PRINTCYLSTRESS

Will write nodal force in force.out and stress in stress.out files. Each line of stress.out contains grid position r, θ, z and stress components σ₁₁, σ₂₂, σ₃₃, σ₂₃, σ₃₁, σ₁₂. (??)

Depending on your need, you can selectively define DEFS macro.

You can make the executible file, paradiscyl by simply typing

$ make

and you will see paradiscyl in the directory ../bin/.

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Notes