Petsc - Revision history

Admin: /* Petsc Makefiles */

2017-10-10T01:04:26Z

Petsc Makefiles

← Older revision		Revision as of 01:04, 10 October 2017
Line 111:		Line 111:
	''Note: this section will presume you are building a C++ program. If you're building a C program, there are many examples provided by Petsc. These can be found using:''		''Note: this section will presume you are building a C++ program. If you're building a C program, there are many examples provided by Petsc. These can be found using:''

	<~~syntaxhighlight~~>		<pre>
	$ cd /path/to/src/of/petsc-3.0.0/src		$ cd /path/to/src/of/petsc-3.0.0/src

Line 137:		Line 137:
	./vec/vec/examples		./vec/vec/examples

	</~~syntaxhighlight~~>		</pre>

	''For more on building Makefiles, see [[Make]].		''For more on building Makefiles, see [[Make]].
Line 145:		Line 145:
	To begin, information contained in variables that make can understand must be included using make's <code>include</code> command:		To begin, information contained in variables that make can understand must be included using make's <code>include</code> command:

	<~~syntaxhighlight lang="make"~~>		<pre>
	include ${PETSC_DIR}/conf/base		include ${PETSC_DIR}/conf/base
	</~~syntaxhighlight~~>		</pre>

	in turn, <code>${PETSC_DIR}/conf/base</code> includes several other files. The information contained in these files includes linker and compiler commands, <code>-L</code> and <code>-l</code> library flags for compilers, include directories, etc.		in turn, <code>${PETSC_DIR}/conf/base</code> includes several other files. The information contained in these files includes linker and compiler commands, <code>-L</code> and <code>-l</code> library flags for compilers, include directories, etc.
Line 157:		Line 157:
	As shown above, several variables must be declared. The path to the Petsc directory is useful, so it is put into the <code>$(PETSC_DIR)</code> make macro. Additionally, other variables are defined by including files provided by Petsc.		As shown above, several variables must be declared. The path to the Petsc directory is useful, so it is put into the <code>$(PETSC_DIR)</code> make macro. Additionally, other variables are defined by including files provided by Petsc.

	<~~syntaxhighlight lang="make"~~>		<pre>
	PETSC_DIR=/path/to/petsc-3.0.0		PETSC_DIR=/path/to/petsc-3.0.0

	include ${PETSC_DIR}/conf/base		include ${PETSC_DIR}/conf/base
	</~~syntaxhighlight~~>		</pre>

	=== Section 2: Files ===		=== Section 2: Files ===
Line 167:		Line 167:
	There are lots of ways to keep your Makefiles short and to the point. First, a list of files containing source code can be defined:		There are lots of ways to keep your Makefiles short and to the point. First, a list of files containing source code can be defined:

	<~~syntaxhighlight lang="make"~~>		<pre>
	SRC_FILES = \		SRC_FILES = \
	BoundaryConditionFactory.cc \		BoundaryConditionFactory.cc \
Line 177:		Line 177:
	TimerFactory.cc \		TimerFactory.cc \
	GmresSolver.cc \		GmresSolver.cc \
	</~~syntaxhighlight~~>		</pre>

	and a make macro can be used to create an analogous list, but replacing all ".cc" suffixes with ".o":		and a make macro can be used to create an analogous list, but replacing all ".cc" suffixes with ".o":

	<~~syntaxhighlight lang="make"~~>		<pre>
	OBJ_FILES = $(SRC_FILES:%.cc=%.o)		OBJ_FILES = $(SRC_FILES:%.cc=%.o)
	</~~syntaxhighlight~~>		</pre>

	=== Section 3: Make targets ===		=== Section 3: Make targets ===
Line 191:		Line 191:
	The first target should define how to build non-Petsc object files:		The first target should define how to build non-Petsc object files:

	<~~syntaxhighlight lang="make"~~>		<pre>
	%.o: %.cc		%.o: %.cc
	g++ -c -Wall -I. $< -o $@		g++ -c -Wall -I. $< -o $@
	</~~syntaxhighlight~~>		</pre>

	The second target should define how to build Petsc object files. This example encapsulates all Petsc-related calls in the driver and in a GMRES solver class, so the target is only defined for those file. If there were more files using Petsc, a list could be constructed, and a make target generated from that rule.		The second target should define how to build Petsc object files. This example encapsulates all Petsc-related calls in the driver and in a GMRES solver class, so the target is only defined for those file. If there were more files using Petsc, a list could be constructed, and a make target generated from that rule.

	<~~syntaxhighlight lang="make"~~>		<pre>
	GmresSolver.o: GmresSolver.cc		GmresSolver.o: GmresSolver.cc
	${PETSC_COMPILE} -c -Wall -I. -I$(PETSC_DIR)/inc		${PETSC_COMPILE} -c -Wall -I. -I$(PETSC_DIR)/inc
	</~~syntaxhighlight~~>		</pre>

	This rule uses some include directives to point the compiler to the Petsc header files and objects used in the source code file GmresSolver.cc.		This rule uses some include directives to point the compiler to the Petsc header files and objects used in the source code file GmresSolver.cc.
Line 207:		Line 207:
	Finally, the driver make target, which compiles the driver and links all compiled objects to the driver, requires Petsc libraries to be linked in as well (see the [[Presentations]] page, Scientific Computing Summer Workshop 2, for details).		Finally, the driver make target, which compiles the driver and links all compiled objects to the driver, requires Petsc libraries to be linked in as well (see the [[Presentations]] page, Scientific Computing Summer Workshop 2, for details).

	<~~syntaxhighlight lang="make"~~>		<pre>
	Laplace: Laplace.cc $(OBJ_FILES)		Laplace: Laplace.cc $(OBJ_FILES)
	-${CLINKER} Laplace.cc -o bin.x $(OBJ_FILES) ${PETSC_LIB} -I$(PETSC_DIR)/include		-${CLINKER} Laplace.cc -o bin.x $(OBJ_FILES) ${PETSC_LIB} -I$(PETSC_DIR)/include
	</~~syntaxhighlight~~>		</pre>

	A couple of things to note here. First, when linking my driver source code, I'm adding <code>${PETSC_LIB}</code> (which adds all of the library links that I will need) because I've got an <code>#include "petsc.h"</code> and <code>#include "petscksp.h"</code> in my driver source code (the <code>${PETSC_LIB}</code> variable includes all Petsc libraries during linking, so it's good to use it instead of, say, <code>${PETSC_KSP_LIB}</code>, just to be safe). Second, I have to link everything using <code>-${CLINKER}</code> (minus sign and all). If I were to compile Petsc to use C, then <code>$CLINKER</code> would point to <code>mpicc</code>, or whatever MPI C-compiler my MPI distribution happened to provide. However, using the configure flag <code>--with-clanguage=c++</code> makes the variable <code>${CLINKER}</code> point to <code>mpic++</code>, or whatever C++-compiler my MPI distribution happens to provide.		A couple of things to note here. First, when linking my driver source code, I'm adding <code>${PETSC_LIB}</code> (which adds all of the library links that I will need) because I've got an <code>#include "petsc.h"</code> and <code>#include "petscksp.h"</code> in my driver source code (the <code>${PETSC_LIB}</code> variable includes all Petsc libraries during linking, so it's good to use it instead of, say, <code>${PETSC_KSP_LIB}</code>, just to be safe). Second, I have to link everything using <code>-${CLINKER}</code> (minus sign and all). If I were to compile Petsc to use C, then <code>$CLINKER</code> would point to <code>mpicc</code>, or whatever MPI C-compiler my MPI distribution happened to provide. However, using the configure flag <code>--with-clanguage=c++</code> makes the variable <code>${CLINKER}</code> point to <code>mpic++</code>, or whatever C++-compiler my MPI distribution happens to provide.

Admin: /* Source code */

2017-10-10T01:03:24Z

Source code

← Older revision		Revision as of 01:03, 10 October 2017
Line 97:		Line 97:
	A compiler directive can be used in C or C++ code to check if Petsc is being used:		A compiler directive can be used in C or C++ code to check if Petsc is being used:

	<~~syntaxhighlight lang="cpp"~~>		<pre>
	#ifdef HAVE_PETSC		#ifdef HAVE_PETSC
	#include "petsc.h"		#include "petsc.h"
	#endif		#endif
	</~~syntaxhighlight~~>		</pre>

	This is useful if, for example, you want to build a program that will run with or without Petsc.		This is useful if, for example, you want to build a program that will run with or without Petsc.

Admin: /* Petsc 3.0.0 */

2017-10-10T01:03:03Z

Petsc 3.0.0

← Older revision		Revision as of 01:03, 10 October 2017
Line 31:		Line 31:
	Petsc 3.0.0 can be installed using the configure line:		Petsc 3.0.0 can be installed using the configure line:

	<~~syntaxhighlight~~>		<pre>
	/path/to/source/of/petsc-3.0.0/config/configure.py \		/path/to/source/of/petsc-3.0.0/config/configure.py \
	--prefix=/path/to/petsc-3.0.0 \		--prefix=/path/to/petsc-3.0.0 \
Line 41:		Line 41:
	--with-fc=0 \		--with-fc=0 \
	PETSC_DIR=/path/to/source/of/petsc-3.0.0		PETSC_DIR=/path/to/source/of/petsc-3.0.0
	</~~syntaxhighlight~~>		</pre>

	The build process is similar to the above:		The build process is similar to the above:

Admin: /* Petsc 2.3.3 */

2017-10-10T01:01:22Z

Petsc 2.3.3

← Older revision		Revision as of 01:01, 10 October 2017
Line 7:		Line 7:
	Petsc 2.3. can be installed using the following configure line. This will require installation of MPI (I suggest [[OpenMPI]]).		Petsc 2.3. can be installed using the following configure line. This will require installation of MPI (I suggest [[OpenMPI]]).

	<~~syntaxhighlight~~>		<pre>
	/path/to/source/of/petsc-2.3.3/config/configure.py \		/path/to/source/of/petsc-2.3.3/config/configure.py \
	--prefix=/path/to/petsc-2.3.3 \		--prefix=/path/to/petsc-2.3.3 \
Line 15:		Line 15:
	--with-mpi-dir=/path/to/mpi \		--with-mpi-dir=/path/to/mpi \
	PETSC_DIR=/path/to/source/of/petsc-2.3.3		PETSC_DIR=/path/to/source/of/petsc-2.3.3
	</~~syntaxhighlight~~>		</pre>

	To make this a debug build, add <code>--with-debugging=1</code> to the configure line.		To make this a debug build, add <code>--with-debugging=1</code> to the configure line.

Admin at 16:32, 28 May 2011

2011-05-28T16:32:59Z

← Older revision		Revision as of 16:32, 28 May 2011
Line 233:		Line 233:


			{{Programs}}
	~~[[Category:~~Programs]]		{{Math Programs}}
	~~[[Category:Computers]]~~
	~~[[Category:~~Math Programs]]

Admin at 01:49, 19 May 2011

2011-05-19T01:49:28Z

← Older revision		Revision as of 01:49, 19 May 2011
Line 236:		Line 236:
	[[Category:Programs]]		[[Category:Programs]]
	[[Category:Computers]]		[[Category:Computers]]
			[[Category:Math Programs]]

Admin: /* Petsc 2.3.3 */

2011-05-19T01:36:54Z

Petsc 2.3.3

← Older revision		Revision as of 01:36, 19 May 2011
Line 5:		Line 5:
	== Petsc 2.3.3 ==		== Petsc 2.3.3 ==

	Petsc 2.3. can be installed using the following configure line. This will require installation of MPI (I suggest [[~~LAM MPI~~]]).		Petsc 2.3. can be installed using the following configure line. This will require installation of MPI (I suggest [[OpenMPI]]).

	<syntaxhighlight>		<syntaxhighlight>

Admin at 01:31, 3 December 2010

2010-12-03T01:31:07Z

← Older revision		Revision as of 01:31, 3 December 2010
Line 224:		Line 224:
	* [[Example Petsc Makefile]]		* [[Example Petsc Makefile]]
	* [[Hypre]]		* [[Hypre]]
	* [[CFD]]		* [[Make]]



			* [[CFD Lectures\|Computational fluid dynamics]] (lecture notes)
			* [[PDE Lectures\|Partial differential equations]] (lecture notes)

Admin at 01:26, 3 December 2010

2010-12-03T01:26:58Z

← Older revision	Revision as of 01:26, 3 December 2010
Line 218:	Line 218:



		= See Also =

		* [[C++]]
		* [[Example Petsc Makefile]]
		* [[Hypre]]
		* [[CFD]]

Admin at 01:26, 3 December 2010

2010-12-03T01:26:12Z

← Older revision		Revision as of 01:26, 3 December 2010
Line 222:		Line 222:


	[[Category:~~Software~~]]		[[Category:Programs]]
	[[Category:Computers]]		[[Category:Computers]]