PARADISCYL:Test-Run

Manual 02 for ParaDiS Cylinder Codes
How to run test simulations

Keonwook Kang and Wei Cai

Original date : Oct 2 , 2008

Latest update on Oct 2 , 2008

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Run command

The ParaDis Cylinder command line format is exactly same with that of the original ParaDiS codes. The line format is:

paradiscyl [-r <numCycles>] [-d dataFile] <controlFile>

where:

	<ctrlFile>		Specifies the name of the ParaDiS control parameter file
	-d <dataFile>		Specifies the base name of the file(s) containing the nodal data for the run. If this file name is not supplied, the code looks for a data file named the same as the control file with the file name suffix (if any) replaced with ".data"
	-r  <numCycles>		Causes the code to execute a series of <numCycles> cycles during which no force calculations or dislocation movement will occur. These cycles will be used strictly for load-balancing purposes and will be done before the normal cycles. This can be useful when a simulation is started with a uniform domain decomposition and needs time to converge on an optimal decomposition as would occur when restarting a simulation on a different number of cpus

Examples

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Download

Download the latest ParaDiS codes from micro repository site using subversion checkout command.

 $ mkdir ParaDiS
 $ svn co https://micro.stanford.edu/svn/ParaDiS ./ParaDiS

Note that this version of ParaDiS has branched out from the public ParaDiS codes v.2.2 downloadable from the official site. You see there are extra subdirectories such as aniso, cylinder, halfspace, matlab, thinfilm and fem in this version of ParaDiS codes. Each subdirectory contains additional source codes for its own purpose. For example, source codes in cylinder directory enable to run ParaDiS simulation of dislocations inside cylindrical geometry taking account of the image stress and Yoffe stress.

YWindow: yview:
Mouse drag to rotate
Hot Keys:
F1        : display this message
Up        : rotate up
Down      : rotate down
Left      : rotate left
Right     : rotate right
PgUp      : rotate counterclockwise
PgDn      : rotate clockwise
Home      : back to initial viewpoint
Space     : stop rotate
p         : toggle pause
t         : translation
s         : scaling
d         : move projection infinity point
r         : rotation
f         : toggle pbc enableness
m         : toggle drawframe
g         : pbc glide
x         : pbc shift in x
y         : pbc shift in y
z         : pbc shift in z
w         : print window specification
F9        : output gif
F10       : output postscript

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MAKE

Move into cylinder subdirectory.

$ cd ParaDiS/cylinder

There is a make description file, makefile, at the top of which, it includes ../makefile.sys and ../makefile.setup from the upper 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. ex. SYS = linux

MODE

set serial or parallel mode. ex. MODE = SERIAL

XLIB_MODE

enable or disable xwindow plotting capability. ex. XLIB_MODE = ON

OPT

define optimization level. ex. 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, σ₁₂, σ₂₃, σ₃₁. (??)

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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Problems and solutions

./bin/paradiscyl: error while loading shared libraries: libgsl.so.0: cannot open
shared object file: No such file or directory

Fatal: ReadControlFile: Error 2 opening file XXXX

gsl: bessel_In.c:202: ERROR: overflow
Default GSL error handler invoked.
Aborted