PARADISCYL:How-To-Install - Revision history

Cweinber: Chris Edited a few things including removing all references to "BEM"

2008-10-25T18:02:52Z

Chris Edited a few things including removing all references to "BEM"

← Older revision		Revision as of 18:02, 25 October 2008
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	<DIV>		<DIV>

	This document describes the extension of the [http://paradis.stanford.edu 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)([http://micro.stanford.edu/~caiwei/papers/Weinberger07jmps-image.pdf 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. Questions on this document should be addressed to [[Chris Weinberger]]. Please read the [[Overview of ParaDiS 2.2 \| manual of ParaDiS]] before reading this document.		This document describes the extension of the [http://paradis.stanford.edu 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)([http://micro.stanford.edu/~caiwei/papers/Weinberger07jmps-image.pdf 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 [[Overview of ParaDiS 2.2 \| manual of ParaDiS]] before reading this document.

	----		----
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	== Library Requirements ==		== 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 [http://www.intel.com/cd/software/products/asmo-na/eng/compilers/284132.htm Intel Software Network Site].		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 [http://www.intel.com/cd/software/products/asmo-na/eng/compilers/284132.htm Intel Software Network Site].

	'''libgsl and libgslcblas'''		'''libgsl and libgslcblas'''
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	'''libfftw3'''		'''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 [http://www.fftw.org/ FFTW] library, which can be installed by the following commands.		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 [http://www.fftw.org/ FFTW] library, which can be installed by the following commands.

	# mv ./fftw-3.1.2.tar.gz /usr/local/src/		# mv ./fftw-3.1.2.tar.gz /usr/local/src/
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	::;DEFS += -D_CYL : Needs to be included to activate cylinder specific functions.		::;DEFS += -D_CYL : Needs to be included to activate cylinder specific functions.
	::;DEFS += -D_NOBEMSTRESS : No ~~boundary element~~ calculation of the image stress ~~contribution~~.		::;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 : No Yoffe ~~image stress will be~~ ~~applied~~. See Modelling Simul. Mater. Sci. Eng. 14, 1139 (2006) ([http://micro.stanford.edu/~caiwei/papers/Tang06msmse-hybrid.pdf PDF])		::;DEFS += -D_NOYOFFESTRESS : Disables the Yoffe Image Stress. See Modelling Simul. Mater. Sci. Eng. 14, 1139 (2006) ([http://micro.stanford.edu/~caiwei/papers/Tang06msmse-hybrid.pdf PDF])
	::;DEFS += -D_NULLCYLSTRESS : Ignore all image stress calculations (including BEM, Yoffe, Virtual segment contributions).		::;DEFS += -D_NULLCYLSTRESS : Ignore all image stress calculations (including BEM, Yoffe, Virtual segment contributions).
	::;DEFS += -D_NOVIRTUALSEG : No force contribution from virtual segments.		::;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 ~~(BEM contribution)~~. If not, ~~Green~~ function ~~of body forces~~ is used to compute image stress. ~~stress is used~~. <ref>For details of each method, refer C. R. Weinberger and Wei Cai, '''Computing Image Stress in an Elastic Cylinder''', ''Journal of the Mechanics and Physics of Solids'','''55''' (2007) 2027--2054 ([http://micro.stanford.edu/~caiwei/papers/Weinberger07jmps-image.pdf PDF]) </ref>		::;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. . <ref>For details of each method, refer C. R. Weinberger and Wei Cai, '''Computing Image Stress in an Elastic Cylinder''', ''Journal of the Mechanics and Physics of Solids'','''55''' (2007) 2027--2054 ([http://micro.stanford.edu/~caiwei/papers/Weinberger07jmps-image.pdf PDF]) </ref>
	::;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''<sub>x</sub>, ''f''<sub>y</sub> and ''f''<sub>z</sub>.		::;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''<sub>x</sub>, ''f''<sub>y</sub> and ''f''<sub>z</sub>.
	::;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 ''σ''<sub>11</sub>, ''σ''<sub>22</sub>, ''σ''<sub>33</sub>, ''σ''<sub>23</sub>, ''σ''<sub>31</sub>, ''σ''<sub>12</sub>.		::;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 ''σ''<sub>11</sub>, ''σ''<sub>22</sub>, ''σ''<sub>33</sub>, ''σ''<sub>23</sub>, ''σ''<sub>31</sub>, ''σ''<sub>12</sub>.
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	THIS ISSUE IS RESOLVED!!!		THIS ISSUE IS RESOLVED!!!

	Note that currently defining '''DEFS += -D_CYLMETHOD1''' will generate the following error. The issue will be figured out soon. Until that moment, ~~commnet~~ out the corresponding line in makefile.		Note that currently defining '''DEFS += -D_CYLMETHOD1''' will generate the following error. The issue will be figured out soon. Until that moment, comment out the corresponding line in makefile.

	gsl: bessel_In.c:202: ERROR: overflow		gsl: bessel_In.c:202: ERROR: overflow

Caiwei at 08:49, 25 October 2008

2008-10-25T08:49:22Z

← Older revision		Revision as of 08:49, 25 October 2008
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	<DIV>		<DIV>

	This document describes the extension of the [http://paradis.stanford.edu 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)([http://micro.stanford.edu/~caiwei/papers/Weinberger07jmps-image.pdf 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 [[Overview of ParaDiS 2.2 \| manual of ParaDiS]] before reading this document.		This document describes the extension of the [http://paradis.stanford.edu 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)([http://micro.stanford.edu/~caiwei/papers/Weinberger07jmps-image.pdf 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. Questions on this document should be addressed to [[Chris Weinberger]]. Please read the [[Overview of ParaDiS 2.2 \| manual of ParaDiS]] before reading this document.

	----		----

Caiwei: How-To-Install moved to PARADISCYL:How-To-Install

2008-10-25T07:07:56Z

How-To-Install moved to PARADISCYL:How-To-Install

← Older revision	Revision as of 07:07, 25 October 2008
(No difference)

Caiwei: /* Compile */

2008-10-25T06:51:52Z

Compile

← Older revision		Revision as of 06:51, 25 October 2008
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	::;DEFS += -D_NULLCYLSTRESS : Ignore all image stress calculations (including BEM, Yoffe, Virtual segment contributions).		::;DEFS += -D_NULLCYLSTRESS : Ignore all image stress calculations (including BEM, Yoffe, Virtual segment contributions).
	::;DEFS += -D_NOVIRTUALSEG : No force contribution from virtual segments.		::;DEFS += -D_NOVIRTUALSEG : No force contribution from virtual segments.
	::;DEFS += -D_CYLMETHOD1 : If defined, analytic expressions using Bessel functions are used for image stress calculation (BEM contribution). If not, Green function of body forces is used to compute image stress. stress is used. <ref>For details of each method, refer C. R. Weinberger and Wei Cai, '''Computing Image Stress in an Elastic Cylinder''', ''Journal of the Mechanics and Physics of Solids'','''55''' (2007) 2027--2054</ref>		::;DEFS += -D_CYLMETHOD1 : If defined, analytic expressions using Bessel functions are used for image stress calculation (BEM contribution). If not, Green function of body forces is used to compute image stress. stress is used. <ref>For details of each method, refer C. R. Weinberger and Wei Cai, '''Computing Image Stress in an Elastic Cylinder''', ''Journal of the Mechanics and Physics of Solids'','''55''' (2007) 2027--2054 ([http://micro.stanford.edu/~caiwei/papers/Weinberger07jmps-image.pdf PDF]) </ref>
	::;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''<sub>x</sub>, ''f''<sub>y</sub> and ''f''<sub>z</sub>.		::;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''<sub>x</sub>, ''f''<sub>y</sub> and ''f''<sub>z</sub>.
	::;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 ''σ''<sub>11</sub>, ''σ''<sub>22</sub>, ''σ''<sub>33</sub>, ''σ''<sub>23</sub>, ''σ''<sub>31</sub>, ''σ''<sub>12</sub>.		::;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 ''σ''<sub>11</sub>, ''σ''<sub>22</sub>, ''σ''<sub>33</sub>, ''σ''<sub>23</sub>, ''σ''<sub>31</sub>, ''σ''<sub>12</sub>.

Caiwei: /* Compile */

2008-10-25T06:50:31Z

Compile

← Older revision		Revision as of 06:50, 25 October 2008
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	::;DEFS += -D_CYLMETHOD1 : If defined, analytic expressions using Bessel functions are used for image stress calculation (BEM contribution). If not, Green function of body forces is used to compute image stress. stress is used. <ref>For details of each method, refer C. R. Weinberger and Wei Cai, '''Computing Image Stress in an Elastic Cylinder''', ''Journal of the Mechanics and Physics of Solids'','''55''' (2007) 2027--2054</ref>		::;DEFS += -D_CYLMETHOD1 : If defined, analytic expressions using Bessel functions are used for image stress calculation (BEM contribution). If not, Green function of body forces is used to compute image stress. stress is used. <ref>For details of each method, refer C. R. Weinberger and Wei Cai, '''Computing Image Stress in an Elastic Cylinder''', ''Journal of the Mechanics and Physics of Solids'','''55''' (2007) 2027--2054</ref>
	::;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''<sub>x</sub>, ''f''<sub>y</sub> and ''f''<sub>z</sub>.		::;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''<sub>x</sub>, ''f''<sub>y</sub> and ''f''<sub>z</sub>.
	::;DEFS += -D_PRINTCYLSTRESS : If defined, code will write stress field in '''stress.out''' files. Each line of '''stress.out''' contains grid position ''r'', ''θ'', ''z'' and stress components ''σ''<sub>11</sub>, ''σ''<sub>22</sub>, ''σ''<sub>33</sub>, ''σ''<sub>23</sub>, ''σ''<sub>31</sub>, ''σ''<sub>12</sub>.		::;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 ''σ''<sub>11</sub>, ''σ''<sub>22</sub>, ''σ''<sub>33</sub>, ''σ''<sub>23</sub>, ''σ''<sub>31</sub>, ''σ''<sub>12</sub>.

	<!--		<!--

Caiwei: /* Compile */

2008-10-25T06:48:07Z

Compile

← Older revision		Revision as of 06:48, 25 October 2008
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	== Compile ==		== 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.		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		$ cd ParaDiS/cylinder
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	This directory contains a '''makefile''', which also make references to the standard makefiles '''../makefile.sys''' and '''../makefile.setup''' in the parent directory.		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.		'''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''' ~~file~~, you can select various 'make' settings ~~and switches~~, some of which are explained below.		In '''makefile.setup''', you can select various 'make' settings, some of which are explained below.

	::;SYS : select system type. you can use '''SYS = linux'''		::;SYS : select system type. you can use '''SYS = linux'''
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	::;OPT : define optimization level. you can use '''OPT = -O3'''		::;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.		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 ~~for~~ cylinder ~~codes~~.		::;DEFS += -D_CYL : Needs to be included to activate cylinder specific functions.
	::;DEFS += -D_NOBEMSTRESS : No boundary ~~image~~ ~~stress~~ ~~will~~ be ~~considered~~.		::;DEFS += -D_NOBEMSTRESS : No boundary element calculation of the image stress contribution.
	::;DEFS += -D_NOYOFFESTRESS : No Yoffe stress will be ~~considered~~.		::;DEFS += -D_NOYOFFESTRESS : No Yoffe image stress will be applied. See Modelling Simul. Mater. Sci. Eng. 14, 1139 (2006) ([http://micro.stanford.edu/~caiwei/papers/Tang06msmse-hybrid.pdf PDF])
	::;DEFS += -D_NULLCYLSTRESS : Ignore all image stress. (BEM, Yoffe, Virtual ~~seg.(??)~~)		::;DEFS += -D_NULLCYLSTRESS : Ignore all image stress calculations (including BEM, Yoffe, Virtual segment contributions).
	::;DEFS += -D_NOVIRTUALSEG : No force contribution from virtual segments.~~(??)~~		::;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.<ref>For details of each method, refer C. R. Weinberger and Wei Cai, '''Computing Image Stress in an Elastic Cylinder''', ''Journal of the Mechanics and Physics of Solids'','''55''' (2007) 2027--2054</ref>		::;DEFS += -D_CYLMETHOD1 : If defined, analytic expressions using Bessel functions are used for image stress calculation (BEM contribution). If not, Green function of body forces is used to compute image stress. stress is used. <ref>For details of each method, refer C. R. Weinberger and Wei Cai, '''Computing Image Stress in an Elastic Cylinder''', ''Journal of the Mechanics and Physics of Solids'','''55''' (2007) 2027--2054</ref>
	::;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''<sub>x</sub>, ''f''<sub>y</sub> and ''f''<sub>z</sub>.		::;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''<sub>x</sub>, ''f''<sub>y</sub> and ''f''<sub>z</sub>.
	::;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 ''σ''<sub>11</sub>, ''σ''<sub>22</sub>, ''σ''<sub>33</sub>, ''σ''<sub>23</sub>, ''σ''<sub>31</sub>, ''σ''<sub>12</sub>. ~~(??)~~		::;DEFS += -D_PRINTCYLSTRESS : If defined, code will write stress field in '''stress.out''' files. Each line of '''stress.out''' contains grid position ''r'', ''θ'', ''z'' and stress components ''σ''<sub>11</sub>, ''σ''<sub>22</sub>, ''σ''<sub>33</sub>, ''σ''<sub>23</sub>, ''σ''<sub>31</sub>, ''σ''<sub>12</sub>.

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

	<!--		<!--
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	-->		-->

			To compile, type
	You can make the executible file, '''paradiscyl''' by simply typing

	$ make		$ make

	and ~~you~~ ~~will see~~ '''paradiscyl''' in the directory ../bin/.		and executable file '''paradiscyl''' should appear in the directory ../bin/.

	----		----

Caiwei: /* Library Requirements */

2008-10-25T06:36:00Z

Library Requirements

← Older revision		Revision as of 06:36, 25 October 2008
Line 25:		Line 25:

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


	'''libfftw3'''		'''libfftw3'''

Caiwei at 22:49, 24 October 2008

2008-10-24T22:49:09Z

← Older revision		Revision as of 22:49, 24 October 2008
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	----		----

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

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

	Note that this version of ParaDiS has branched out from the public ParaDiS codes v.2.2 downloadable from the
	[http://paradis.stanford.edu 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.

	----

	== MAKE ==
	Move into '''cylinder''' subdirectory.

	$ cd ParaDiS/cylinder		$ 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.
	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.		'''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.
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	In '''makefile.setup''' file, you can select various 'make' settings and switches, some of which are explained below.		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'''		::;SYS : select system type. you can use '''SYS = linux'''
	::;MODE : set serial or parallel mode. ~~''ex''.~~ '''MODE = SERIAL'''		::;MODE : set serial or parallel mode. you need to use '''MODE = SERIAL'''
	::;XLIB_MODE : enable or disable xwindow plotting capability. ~~''ex''.~~ '''XLIB_MODE = ON'''		::;XLIB_MODE : enable or disable xwindow plotting capability. you can use '''XLIB_MODE = ON'''
	::;OPT : define optimization level. ~~''ex''.~~ '''OPT = -O3'''		::;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.		In '''makefile''', there is important macro '''DEFS'''. The cylinder codes behave differently depending on how '''DEFS''' is defined.

Caiwei: /* Library Requirements */

2008-10-24T22:39:22Z

Library Requirements

← Older revision		Revision as of 22:39, 24 October 2008
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	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 [http://www.intel.com/cd/software/products/asmo-na/eng/compilers/284132.htm Intel Software Network Site].		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 [http://www.intel.com/cd/software/products/asmo-na/eng/compilers/284132.htm Intel Software Network Site].

	~~====~~ libgsl and libgslcblas ~~====~~		'''libgsl and libgslcblas'''

	GNU Scientific library can be downloaded at http://www.gnu.org/software/gsl/.
	~~Install~~ ~~gsl~~ library by the following ~~procedures~~.		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/		# mv ./gsl-1.9.tar.gz /usr/local/src/
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	# make install		# make install

	~~The~~ libraries will be installed at /usr/local/lib/.		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 [http://www.fftw.org/ FFTW] library, which can be installed by the following commands.
⚫	~~====~~ libfftw3 ~~====~~
	C subroutine library for computing the discrete Fourier transform (DFT). Download from [http://www.fftw.org/ FFTW home page]. To install the library, run the following commands.

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

	libfftw3.a and libfftw3.la ~~will be installed at~~ /usr/local/lib/.		This will install library files libfftw3.a and libfftw3.la in /usr/local/lib/.
	----		----

Caiwei: /* Library Requirements */

2008-10-24T22:35:57Z

Library Requirements

← Older revision		Revision as of 22:35, 24 October 2008
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	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 [http://www.intel.com/cd/software/products/asmo-na/eng/compilers/284132.htm Intel Software Network Site].		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 [http://www.intel.com/cd/software/products/asmo-na/eng/compilers/284132.htm Intel Software Network Site].

	=== libgsl and libgslcblas ===		==== libgsl and libgslcblas ====
	GNU Scientific library can be downloaded at http://www.gnu.org/software/gsl/.		GNU Scientific library can be downloaded at http://www.gnu.org/software/gsl/.
	Install gsl library by the following procedures.		Install gsl library by the following procedures.
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	The libraries will be installed at /usr/local/lib/.		The libraries will be installed at /usr/local/lib/.

	=== libfftw3 ===		==== libfftw3 ====
	C subroutine library for computing the discrete Fourier transform (DFT). Download from [http://www.fftw.org/ FFTW home page]. To install the library, run the following commands.		C subroutine library for computing the discrete Fourier transform (DFT). Download from [http://www.fftw.org/ FFTW home page]. To install the library, run the following commands.