[petsc-users] CMake error in PETSc
Yingjie Wu
yjwu16 at gmail.com
Sun Dec 8 22:38:04 CST 2019
Thank you very much for your help.
My programs are as follows.
Smith, Barry F. <bsmith at mcs.anl.gov> 于2019年12月9日周一 下午12:29写道：
>
> There is something missing in the cmake process that is causing needed
> libraries not to be linked.
>
> Please email your program and your CMake stuff (files you use) so we
> can reproduce the problem and find a fix.
>
> Barry
>
>
> > On Dec 8, 2019, at 10:06 PM, Yingjie Wu <yjwu16 at gmail.com> wrote:
> >
> > Hi,
> > Thank you for your response.
> > This problem has not been solved. I've been reporting errors in the
> process of 'make'. The test example I used comes from: /snes /example
> /tutorials/ex3.c by modifying the suffix of ex3, there will be different
> error messages as following. I checked a lot of DSO problems on the
> Internet and installed a lot of libraries, but the error still haven't been
> solved. I was wondering if I was missing any prefix during the configure of
> PETSc(I use the simplest recommended installation), but there was no
> problem when the program was compiled with the 'makefile' which is
> recommended. Because I need some extra libraries, I have to use cmake.
> > with ex3.c:
> > yjwu at yjwu-XPS-8910:~/tem/build2$ make
> > Scanning dependencies of target Test1
> > [ 50%] Building C object CMakeFiles/Test1.dir/ex3.c.o
> > [100%] Linking C executable Test1
> > /usr/bin/ld: CMakeFiles/Test1.dir/ex3.c.o: undefined reference to symbol
> 'pow@@GLIBC_2.2.5'
> > //lib/x86_64-linux-gnu/libm.so.6: error adding symbols: DSO missing from
> command line
> > collect2: error: ld returned 1 exit status
> > CMakeFiles/Test1.dir/build.make:94: recipe for target 'Test1' failed
> > make[2]: *** [Test1] Error 1
> > CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/Test1.dir/all'
> failed
> > make[1]: *** [CMakeFiles/Test1.dir/all] Error 2
> > Makefile:83: recipe for target 'all' failed
> > make: *** [all] Error 2
> > with ex3.cpp:
> > yjwu at yjwu-XPS-8910:~/tem/build2$ make
> > Scanning dependencies of target Test1
> > [ 50%] Building CXX object CMakeFiles/Test1.dir/ex3.cpp.o
> > [100%] Linking CXX executable Test1
> > /usr/bin/ld: CMakeFiles/Test1.dir/ex3.cpp.o: undefined reference to
> symbol 'MPI_Comm_rank'
> > /home/yjwu/petsc-3.12.2/arch-linux2-c-debug/lib/libmpi.so.12: error
> adding symbols: DSO missing from command line
> > collect2: error: ld returned 1 exit status
> > CMakeFiles/Test1.dir/build.make:94: recipe for target 'Test1' failed
> > make[2]: *** [Test1] Error 1
> > CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/Test1.dir/all'
> failed
> > make[1]: *** [CMakeFiles/Test1.dir/all] Error 2
> > Makefile:83: recipe for target 'all' failed
> > make: *** [all] Error 2
> > Thanks,
> > Yingjie
> >
> > Matthew Knepley <knepley at gmail.com> 于2019年12月6日周五 下午11:46写道：
> > It sounds like your C++ compiler is name mangling the symbol, but the
> library has no mangling.
> > Why are you using C++.
> >
> > Thanks,
> >
> > Matt
> >
> > On Fri, Dec 6, 2019 at 10:44 AM Yingjie Wu <yjwu16 at gmail.com> wrote:
> > Hi,
> > Thank you for your email.
> > The error in the previous program was indeed due to the missing
> "SNESSetFromOptions".
> > I use the /snes/example/tutorial/ex1.cpp as test case. However, I found
> that some of the statements in the program were not compiled and deleted
> the statements containing "MPI_Comm_size", but I don't know how to solve
> this problem.
> > lerui at yu1994-ThinkPad-W520:~/tem2/build2$ cmake ..
> > -- The C compiler identification is GNU 5.4.0
> > -- The CXX compiler identification is GNU 5.4.0
> > -- Check for working C compiler: /usr/bin/cc
> > -- Check for working C compiler: /usr/bin/cc -- works
> > -- Detecting C compiler ABI info
> > -- Detecting C compiler ABI info - done
> > -- Detecting C compile features
> > -- Detecting C compile features - done
> > -- Check for working CXX compiler: /usr/bin/c++
> > -- Check for working CXX compiler: /usr/bin/c++ -- works
> > -- Detecting CXX compiler ABI info
> > -- Detecting CXX compiler ABI info - done
> > -- Detecting CXX compile features
> > -- Detecting CXX compile features - done
> > -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1")
> > -- Checking for one of the modules 'PETSc'
> > pkg include dirs:
> /home/lerui/petsc-3.12.2/arch-linux2-c-debug/include;/home/lerui/petsc-3.12.2/include
> > pkg include libs: petsc
> > pkg ldflags: -L/home/lerui/petsc-3.12.2/arch-linux2-c-debug/lib;-lpetsc
> > -- Configuring done
> > -- Generating done
> > -- Build files have been written to: /home/lerui/tem2/build2
> > lerui at yu1994-ThinkPad-W520:~/tem2/build2$ make
> > Scanning dependencies of target main
> > [ 50%] Building CXX object CMakeFiles/main.dir/ex1.cpp.o
> > [100%] Linking CXX executable main
> > /usr/bin/ld: CMakeFiles/main.dir/ex1.cpp.o: undefined reference to
> symbol 'MPI_Comm_size'
> > /home/lerui/petsc-3.12.2/arch-linux2-c-debug/lib/libmpi.so.12: error
> adding symbols: DSO missing from command line
> > collect2: error: ld returned 1 exit status
> > CMakeFiles/main.dir/build.make:94: recipe for target 'main' failed
> > make[2]: *** [main] Error 1
> > CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/main.dir/all'
> failed
> > make[1]: *** [CMakeFiles/main.dir/all] Error 2
> > Makefile:83: recipe for target 'all' failed
> > make: *** [all] Error 2
> > Thanks,
> > Yingjie
> >
> > Jed Brown <jed at jedbrown.org> 于2019年12月6日周五 上午10:54写道：
> > Yingjie Wu <yjwu16 at gmail.com> writes:
> >
> > > I'm so sorry that I've ignored your previous advices.
> > >
> > > I added a global variable that seems works:
> > >
> > >
> > > export
> > >
> LD_LIBRARY_PATH=/home/lerui/petcs-3.12.2/arch-linux2-c-debug/lib:$LD_LIBRARY_PATH
> > >
> > >
> > > How should I make petsc in a standard position?This eliminates the
> need to
> > > set global variables.
> >
> > You can configure PETSc with --prefix=/your/standard/path, then make
> install.
> >
> > > It seems that some of the options before running fit become
> unavailable:
> > >
> > >
> > > mpiexec -n 1 ./example01cmke -snes_view
> > >
> > >
> > > Options-snes _ view are not used and how should I solve this problem?
> >
> > I don't have your ex1.cpp, but presumably you didn't SNESSetFromOptions?
> >
> >
> > --
> > What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> > -- Norbert Wiener
> >
> > https://www.cse.buffalo.edu/~knepley/
>
>
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#This is a CMake makefile.
cmake_minimum_required(VERSION 2.8.11)
project(Test1)
add_executable(Test1 ex3.cpp)
find_package(PkgConfig REQUIRED)
set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
set(ENV{PKG_CONFIG_PATH} /home/yjwu/petsc-3.12.2/arch-linux2-c-debug/lib/pkgconfig)
pkg_search_module(PETSC REQUIRED PETSc)
message("pkg include dirs: ${PETSC_INCLUDE_DIRS}")
message("pkg include libs: ${PETSC_LIBRARIES}")
message("pkg ldflags: ${PETSC_LDFLAGS}")
include_directories(${PETSC_INCLUDE_DIRS})
target_link_libraries(Test1 ${PETSC_LDFLAGS} pthread)
#set(COOLPROP_STATIC_LIBRARY true CACHE BOOL "Use CoolProp")
#add_subdirectory("${CMAKE_SOURCE_DIR}/externals/CoolProp" "CoolProp")
#target_link_libraries (Test1 CoolProp)
#if (UNIX)
# target_link_libraries (Test1 ${CMAKE_DL_LIBS})
#endif()
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static char help[] = "Newton methods to solve u'' + u^{2} = f in parallel.\n\
This example employs a user-defined monitoring routine and optionally a user-defined\n\
routine to check candidate iterates produced by line search routines.\n\
The command line options include:\n\
-pre_check_iterates : activate checking of iterates\n\
-post_check_iterates : activate checking of iterates\n\
-check_tol <tol>: set tolerance for iterate checking\n\
-user_precond : activate a (trivial) user-defined preconditioner\n\n";
/*T
Concepts: SNES^basic parallel example
Concepts: SNES^setting a user-defined monitoring routine
Processors: n
T*/
/*
Include "petscdm.h" so that we can use data management objects (DMs)
Include "petscdmda.h" so that we can use distributed arrays (DMDAs).
Include "petscsnes.h" so that we can use SNES solvers. Note that this
file automatically includes:
petscsys.h - base PETSc routines
petscvec.h - vectors
petscmat.h - matrices
petscis.h - index sets
petscksp.h - Krylov subspace methods
petscviewer.h - viewers
petscpc.h - preconditioners
petscksp.h - linear solvers
*/
#include <petscdm.h>
#include <petscdmda.h>
#include <petscsnes.h>
/*
User-defined routines.
*/
PetscErrorCode FormJacobian(SNES,Vec,Mat,Mat,void*);
PetscErrorCode FormFunction(SNES,Vec,Vec,void*);
PetscErrorCode FormInitialGuess(Vec);
PetscErrorCode Monitor(SNES,PetscInt,PetscReal,void*);
PetscErrorCode PreCheck(SNESLineSearch,Vec,Vec,PetscBool*,void*);
PetscErrorCode PostCheck(SNESLineSearch,Vec,Vec,Vec,PetscBool*,PetscBool*,void*);
PetscErrorCode PostSetSubKSP(SNESLineSearch,Vec,Vec,Vec,PetscBool*,PetscBool*,void*);
PetscErrorCode MatrixFreePreconditioner(PC,Vec,Vec);
/*
User-defined application context
*/
typedef struct {
DM da; /* distributed array */
Vec F; /* right-hand-side of PDE */
PetscMPIInt rank; /* rank of processor */
PetscMPIInt size; /* size of communicator */
PetscReal h; /* mesh spacing */
PetscBool sjerr; /* if or not to test jacobian domain error */
} ApplicationCtx;
/*
User-defined context for monitoring
*/
typedef struct {
PetscViewer viewer;
} MonitorCtx;
/*
User-defined context for checking candidate iterates that are
determined by line search methods
*/
typedef struct {
Vec last_step; /* previous iterate */
PetscReal tolerance; /* tolerance for changes between successive iterates */
ApplicationCtx *user;
} StepCheckCtx;
typedef struct {
PetscInt its0; /* num of prevous outer KSP iterations */
} SetSubKSPCtx;
int main(int argc,char **argv)
{
SNES snes; /* SNES context */
SNESLineSearch linesearch; /* SNESLineSearch context */
Mat J; /* Jacobian matrix */
ApplicationCtx ctx; /* user-defined context */
Vec x,r,U,F; /* vectors */
MonitorCtx monP; /* monitoring context */
StepCheckCtx checkP; /* step-checking context */
SetSubKSPCtx checkP1;
PetscBool pre_check,post_check,post_setsubksp; /* flag indicating whether we're checking candidate iterates */
PetscScalar xp,*FF,*UU,none = -1.0;
PetscErrorCode ierr;
PetscInt its,N = 5,i,maxit,maxf,xs,xm;
PetscReal abstol,rtol,stol,norm;
PetscBool flg;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&ctx.rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&ctx.size);CHKERRQ(ierr);
ctx.rank=1;
ctx.size=1;
ierr = PetscOptionsGetInt(NULL,NULL,"-n",&N,NULL);CHKERRQ(ierr);
ctx.h = 1.0/(N-1);
ctx.sjerr = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,NULL,"-test_jacobian_domain_error",&ctx.sjerr,NULL);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create nonlinear solver context
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = SNESCreate(PETSC_COMM_WORLD,&snes);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create vector data structures; set function evaluation routine
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Create distributed array (DMDA) to manage parallel grid and vectors
*/
ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,N,1,1,NULL,&ctx.da);CHKERRQ(ierr);
ierr = DMSetFromOptions(ctx.da);CHKERRQ(ierr);
ierr = DMSetUp(ctx.da);CHKERRQ(ierr);
/*
Extract global and local vectors from DMDA; then duplicate for remaining
vectors that are the same types
*/
ierr = DMCreateGlobalVector(ctx.da,&x);CHKERRQ(ierr);
ierr = VecDuplicate(x,&r);CHKERRQ(ierr);
ierr = VecDuplicate(x,&F);CHKERRQ(ierr); ctx.F = F;
ierr = VecDuplicate(x,&U);CHKERRQ(ierr);
/*
Set function evaluation routine and vector. Whenever the nonlinear
solver needs to compute the nonlinear function, it will call this
routine.
- Note that the final routine argument is the user-defined
context that provides application-specific data for the
function evaluation routine.
*/
ierr = SNESSetFunction(snes,r,FormFunction,&ctx);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create matrix data structure; set Jacobian evaluation routine
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = MatCreate(PETSC_COMM_WORLD,&J);CHKERRQ(ierr);
ierr = MatSetSizes(J,PETSC_DECIDE,PETSC_DECIDE,N,N);CHKERRQ(ierr);
ierr = MatSetFromOptions(J);CHKERRQ(ierr);
ierr = MatSeqAIJSetPreallocation(J,3,NULL);CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(J,3,NULL,3,NULL);CHKERRQ(ierr);
/*
Set Jacobian matrix data structure and default Jacobian evaluation
routine. Whenever the nonlinear solver needs to compute the
Jacobian matrix, it will call this routine.
- Note that the final routine argument is the user-defined
context that provides application-specific data for the
Jacobian evaluation routine.
*/
ierr = SNESSetJacobian(snes,J,J,FormJacobian,&ctx);CHKERRQ(ierr);
/*
Optionally allow user-provided preconditioner
*/
ierr = PetscOptionsHasName(NULL,NULL,"-user_precond",&flg);CHKERRQ(ierr);
if (flg) {
KSP ksp;
PC pc;
ierr = SNESGetKSP(snes,&ksp);CHKERRQ(ierr);
ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCSHELL);CHKERRQ(ierr);
ierr = PCShellSetApply(pc,MatrixFreePreconditioner);CHKERRQ(ierr);
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Customize nonlinear solver; set runtime options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Set an optional user-defined monitoring routine
*/
ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,0,0,0,0,400,400,&monP.viewer);CHKERRQ(ierr);
ierr = SNESMonitorSet(snes,Monitor,&monP,0);CHKERRQ(ierr);
/*
Set names for some vectors to facilitate monitoring (optional)
*/
ierr = PetscObjectSetName((PetscObject)x,"Approximate Solution");CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)U,"Exact Solution");CHKERRQ(ierr);
/*
Set SNES/KSP/KSP/PC runtime options, e.g.,
-snes_view -snes_monitor -ksp_type <ksp> -pc_type <pc>
*/
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
/*
Set an optional user-defined routine to check the validity of candidate
iterates that are determined by line search methods
*/
ierr = SNESGetLineSearch(snes, &linesearch);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,NULL,"-post_check_iterates",&post_check);CHKERRQ(ierr);
if (post_check) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Activating post step checking routine\n");CHKERRQ(ierr);
ierr = SNESLineSearchSetPostCheck(linesearch,PostCheck,&checkP);CHKERRQ(ierr);
ierr = VecDuplicate(x,&(checkP.last_step));CHKERRQ(ierr);
checkP.tolerance = 1.0;
checkP.user = &ctx;
ierr = PetscOptionsGetReal(NULL,NULL,"-check_tol",&checkP.tolerance,NULL);CHKERRQ(ierr);
}
ierr = PetscOptionsHasName(NULL,NULL,"-post_setsubksp",&post_setsubksp);CHKERRQ(ierr);
if (post_setsubksp) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Activating post setsubksp\n");CHKERRQ(ierr);
ierr = SNESLineSearchSetPostCheck(linesearch,PostSetSubKSP,&checkP1);CHKERRQ(ierr);
}
ierr = PetscOptionsHasName(NULL,NULL,"-pre_check_iterates",&pre_check);CHKERRQ(ierr);
if (pre_check) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Activating pre step checking routine\n");CHKERRQ(ierr);
ierr = SNESLineSearchSetPreCheck(linesearch,PreCheck,&checkP);CHKERRQ(ierr);
}
/*
Print parameters used for convergence testing (optional) ... just
to demonstrate this routine; this information is also printed with
the option -snes_view
*/
ierr = SNESGetTolerances(snes,&abstol,&rtol,&stol,&maxit,&maxf);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"atol=%g, rtol=%g, stol=%g, maxit=%D, maxf=%D\n",(double)abstol,(double)rtol,(double)stol,maxit,maxf);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Initialize application:
Store right-hand-side of PDE and exact solution
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Get local grid boundaries (for 1-dimensional DMDA):
xs, xm - starting grid index, width of local grid (no ghost points)
*/
ierr = DMDAGetCorners(ctx.da,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
/*
Get pointers to vector data
*/
ierr = DMDAVecGetArray(ctx.da,F,&FF);CHKERRQ(ierr);
ierr = DMDAVecGetArray(ctx.da,U,&UU);CHKERRQ(ierr);
/*
Compute local vector entries
*/
xp = ctx.h*xs;
for (i=xs; i<xs+xm; i++) {
FF[i] = 6.0*xp + PetscPowScalar(xp+1.e-12,6.0); /* +1.e-12 is to prevent 0^6 */
UU[i] = xp*xp*xp;
xp += ctx.h;
}
/*
Restore vectors
*/
ierr = DMDAVecRestoreArray(ctx.da,F,&FF);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(ctx.da,U,&UU);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Evaluate initial guess; then solve nonlinear system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Note: The user should initialize the vector, x, with the initial guess
for the nonlinear solver prior to calling SNESSolve(). In particular,
to employ an initial guess of zero, the user should explicitly set
this vector to zero by calling VecSet().
*/
ierr = FormInitialGuess(x);CHKERRQ(ierr);
ierr = SNESSolve(snes,NULL,x);CHKERRQ(ierr);
ierr = SNESGetIterationNumber(snes,&its);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Number of SNES iterations = %D\n",its);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Check solution and clean up
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Check the error
*/
ierr = VecAXPY(x,none,U);CHKERRQ(ierr);
ierr = VecNorm(x,NORM_2,&norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Norm of error %g Iterations %D\n",(double)norm,its);CHKERRQ(ierr);
if (ctx.sjerr) {
SNESType snestype;
ierr = SNESGetType(snes,&snestype);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"SNES Type %s\n",snestype);CHKERRQ(ierr);
}
/*
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
*/
ierr = PetscViewerDestroy(&monP.viewer);CHKERRQ(ierr);
if (post_check) {ierr = VecDestroy(&checkP.last_step);CHKERRQ(ierr);}
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&r);CHKERRQ(ierr);
ierr = VecDestroy(&U);CHKERRQ(ierr);
ierr = VecDestroy(&F);CHKERRQ(ierr);
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = DMDestroy(&ctx.da);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
/* ------------------------------------------------------------------- */
/*
FormInitialGuess - Computes initial guess.
Input/Output Parameter:
. x - the solution vector
*/
PetscErrorCode FormInitialGuess(Vec x)
{
PetscErrorCode ierr;
PetscScalar pfive = .50;
PetscFunctionBeginUser;
ierr = VecSet(x,pfive);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/* ------------------------------------------------------------------- */
/*
FormFunction - Evaluates nonlinear function, F(x).
Input Parameters:
. snes - the SNES context
. x - input vector
. ctx - optional user-defined context, as set by SNESSetFunction()
Output Parameter:
. f - function vector
Note:
The user-defined context can contain any application-specific
data needed for the function evaluation.
*/
PetscErrorCode FormFunction(SNES snes,Vec x,Vec f,void *ctx)
{
ApplicationCtx *user = (ApplicationCtx*) ctx;
DM da = user->da;
PetscScalar *xx,*ff,*FF,d;
PetscErrorCode ierr;
PetscInt i,M,xs,xm;
Vec xlocal;
PetscFunctionBeginUser;
ierr = DMGetLocalVector(da,&xlocal);CHKERRQ(ierr);
/*
Scatter ghost points to local vector, using the 2-step process
DMGlobalToLocalBegin(), DMGlobalToLocalEnd().
By placing code between these two statements, computations can
be done while messages are in transition.
*/
ierr = DMGlobalToLocalBegin(da,x,INSERT_VALUES,xlocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,x,INSERT_VALUES,xlocal);CHKERRQ(ierr);
/*
Get pointers to vector data.
- The vector xlocal includes ghost point; the vectors x and f do
NOT include ghost points.
- Using DMDAVecGetArray() allows accessing the values using global ordering
*/
ierr = DMDAVecGetArray(da,xlocal,&xx);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,f,&ff);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,user->F,&FF);CHKERRQ(ierr);
/*
Get local grid boundaries (for 1-dimensional DMDA):
xs, xm - starting grid index, width of local grid (no ghost points)
*/
ierr = DMDAGetCorners(da,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,NULL,&M,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);CHKERRQ(ierr);
/*
Set function values for boundary points; define local interior grid point range:
xsi - starting interior grid index
xei - ending interior grid index
*/
if (xs == 0) { /* left boundary */
ff[0] = xx[0];
xs++;xm--;
}
if (xs+xm == M) { /* right boundary */
ff[xs+xm-1] = xx[xs+xm-1] - 1.0;
xm--;
}
/*
Compute function over locally owned part of the grid (interior points only)
*/
d = 1.0/(user->h*user->h);
for (i=xs; i<xs+xm; i++) ff[i] = d*(xx[i-1] - 2.0*xx[i] + xx[i+1]) + xx[i]*xx[i] - FF[i];
/*
Restore vectors
*/
ierr = DMDAVecRestoreArray(da,xlocal,&xx);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,f,&ff);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,user->F,&FF);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&xlocal);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/* ------------------------------------------------------------------- */
/*
FormJacobian - Evaluates Jacobian matrix.
Input Parameters:
. snes - the SNES context
. x - input vector
. dummy - optional user-defined context (not used here)
Output Parameters:
. jac - Jacobian matrix
. B - optionally different preconditioning matrix
. flag - flag indicating matrix structure
*/
PetscErrorCode FormJacobian(SNES snes,Vec x,Mat jac,Mat B,void *ctx)
{
ApplicationCtx *user = (ApplicationCtx*) ctx;
PetscScalar *xx,d,A[3];
PetscErrorCode ierr;
PetscInt i,j[3],M,xs,xm;
DM da = user->da;
PetscFunctionBeginUser;
if (user->sjerr) {
ierr = SNESSetJacobianDomainError(snes);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
Get pointer to vector data
*/
ierr = DMDAVecGetArrayRead(da,x,&xx);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
/*
Get range of locally owned matrix
*/
ierr = DMDAGetInfo(da,NULL,&M,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);CHKERRQ(ierr);
/*
Determine starting and ending local indices for interior grid points.
Set Jacobian entries for boundary points.
*/
if (xs == 0) { /* left boundary */
i = 0; A[0] = 1.0;
ierr = MatSetValues(jac,1,&i,1,&i,A,INSERT_VALUES);CHKERRQ(ierr);
xs++;xm--;
}
if (xs+xm == M) { /* right boundary */
i = M-1;
A[0] = 1.0;
ierr = MatSetValues(jac,1,&i,1,&i,A,INSERT_VALUES);CHKERRQ(ierr);
xm--;
}
/*
Interior grid points
- Note that in this case we set all elements for a particular
row at once.
*/
d = 1.0/(user->h*user->h);
for (i=xs; i<xs+xm; i++) {
j[0] = i - 1; j[1] = i; j[2] = i + 1;
A[0] = A[2] = d; A[1] = -2.0*d + 2.0*xx[i];
ierr = MatSetValues(jac,1,&i,3,j,A,INSERT_VALUES);CHKERRQ(ierr);
}
/*
Assemble matrix, using the 2-step process:
MatAssemblyBegin(), MatAssemblyEnd().
By placing code between these two statements, computations can be
done while messages are in transition.
Also, restore vector.
*/
ierr = MatAssemblyBegin(jac,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayRead(da,x,&xx);CHKERRQ(ierr);
ierr = MatAssemblyEnd(jac,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/* ------------------------------------------------------------------- */
/*
Monitor - Optional user-defined monitoring routine that views the
current iterate with an x-window plot. Set by SNESMonitorSet().
Input Parameters:
snes - the SNES context
its - iteration number
norm - 2-norm function value (may be estimated)
ctx - optional user-defined context for private data for the
monitor routine, as set by SNESMonitorSet()
Note:
See the manpage for PetscViewerDrawOpen() for useful runtime options,
such as -nox to deactivate all x-window output.
*/
PetscErrorCode Monitor(SNES snes,PetscInt its,PetscReal fnorm,void *ctx)
{
PetscErrorCode ierr;
MonitorCtx *monP = (MonitorCtx*) ctx;
Vec x;
PetscFunctionBeginUser;
ierr = PetscPrintf(PETSC_COMM_WORLD,"iter = %D,SNES Function norm %g\n",its,(double)fnorm);CHKERRQ(ierr);
ierr = SNESGetSolution(snes,&x);CHKERRQ(ierr);
ierr = VecView(x,monP->viewer);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/* ------------------------------------------------------------------- */
/*
PreCheck - Optional user-defined routine that checks the validity of
candidate steps of a line search method. Set by SNESLineSearchSetPreCheck().
Input Parameters:
snes - the SNES context
xcurrent - current solution
y - search direction and length
Output Parameters:
y - proposed step (search direction and length) (possibly changed)
changed_y - tells if the step has changed or not
*/
PetscErrorCode PreCheck(SNESLineSearch linesearch,Vec xcurrent,Vec y, PetscBool *changed_y, void * ctx)
{
PetscFunctionBeginUser;
*changed_y = PETSC_FALSE;
PetscFunctionReturn(0);
}
/* ------------------------------------------------------------------- */
/*
PostCheck - Optional user-defined routine that checks the validity of
candidate steps of a line search method. Set by SNESLineSearchSetPostCheck().
Input Parameters:
snes - the SNES context
ctx - optional user-defined context for private data for the
monitor routine, as set by SNESLineSearchSetPostCheck()
xcurrent - current solution
y - search direction and length
x - the new candidate iterate
Output Parameters:
y - proposed step (search direction and length) (possibly changed)
x - current iterate (possibly modified)
*/
PetscErrorCode PostCheck(SNESLineSearch linesearch,Vec xcurrent,Vec y,Vec x,PetscBool *changed_y,PetscBool *changed_x, void * ctx)
{
PetscErrorCode ierr;
PetscInt i,iter,xs,xm;
StepCheckCtx *check;
ApplicationCtx *user;
PetscScalar *xa,*xa_last,tmp;
PetscReal rdiff;
DM da;
SNES snes;
PetscFunctionBeginUser;
*changed_x = PETSC_FALSE;
*changed_y = PETSC_FALSE;
ierr = SNESLineSearchGetSNES(linesearch, &snes);CHKERRQ(ierr);
check = (StepCheckCtx*)ctx;
user = check->user;
ierr = SNESGetIterationNumber(snes,&iter);CHKERRQ(ierr);
/* iteration 1 indicates we are working on the second iteration */
if (iter > 0) {
da = user->da;
ierr = PetscPrintf(PETSC_COMM_WORLD,"Checking candidate step at iteration %D with tolerance %g\n",iter,(double)check->tolerance);CHKERRQ(ierr);
/* Access local array data */
ierr = DMDAVecGetArray(da,check->last_step,&xa_last);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,x,&xa);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
/*
If we fail the user-defined check for validity of the candidate iterate,
then modify the iterate as we like. (Note that the particular modification
below is intended simply to demonstrate how to manipulate this data, not
as a meaningful or appropriate choice.)
*/
for (i=xs; i<xs+xm; i++) {
if (!PetscAbsScalar(xa[i])) rdiff = 2*check->tolerance;
else rdiff = PetscAbsScalar((xa[i] - xa_last[i])/xa[i]);
if (rdiff > check->tolerance) {
tmp = xa[i];
xa[i] = .5*(xa[i] + xa_last[i]);
*changed_x = PETSC_TRUE;
ierr = PetscPrintf(PETSC_COMM_WORLD," Altering entry %D: x=%g, x_last=%g, diff=%g, x_new=%g\n",i,(double)PetscAbsScalar(tmp),(double)PetscAbsScalar(xa_last[i]),(double)rdiff,(double)PetscAbsScalar(xa[i]));CHKERRQ(ierr);
}
}
ierr = DMDAVecRestoreArray(da,check->last_step,&xa_last);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,x,&xa);CHKERRQ(ierr);
}
ierr = VecCopy(x,check->last_step);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/* ------------------------------------------------------------------- */
/*
PostSetSubKSP - Optional user-defined routine that reset SubKSP options when hierarchical bjacobi PC is used
e.g,
mpiexec -n 8 ./ex3 -nox -n 10000 -ksp_type fgmres -pc_type bjacobi -pc_bjacobi_blocks 4 -sub_ksp_type gmres -sub_ksp_max_it 3 -post_setsubksp -sub_ksp_rtol 1.e-16
Set by SNESLineSearchSetPostCheck().
Input Parameters:
linesearch - the LineSearch context
xcurrent - current solution
y - search direction and length
x - the new candidate iterate
Output Parameters:
y - proposed step (search direction and length) (possibly changed)
x - current iterate (possibly modified)
*/
PetscErrorCode PostSetSubKSP(SNESLineSearch linesearch,Vec xcurrent,Vec y,Vec x,PetscBool *changed_y,PetscBool *changed_x, void * ctx)
{
PetscErrorCode ierr;
SetSubKSPCtx *check;
PetscInt iter,its,sub_its,maxit;
KSP ksp,sub_ksp,*sub_ksps;
PC pc;
PetscReal ksp_ratio;
SNES snes;
PetscFunctionBeginUser;
ierr = SNESLineSearchGetSNES(linesearch, &snes);CHKERRQ(ierr);
check = (SetSubKSPCtx*)ctx;
ierr = SNESGetIterationNumber(snes,&iter);CHKERRQ(ierr);
ierr = SNESGetKSP(snes,&ksp);CHKERRQ(ierr);
ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
ierr = PCBJacobiGetSubKSP(pc,NULL,NULL,&sub_ksps);CHKERRQ(ierr);
sub_ksp = sub_ksps[0];
ierr = KSPGetIterationNumber(ksp,&its);CHKERRQ(ierr); /* outer KSP iteration number */
ierr = KSPGetIterationNumber(sub_ksp,&sub_its);CHKERRQ(ierr); /* inner KSP iteration number */
if (iter) {
ierr = PetscPrintf(PETSC_COMM_WORLD," ...PostCheck snes iteration %D, ksp_it %D %D, subksp_it %D\n",iter,check->its0,its,sub_its);CHKERRQ(ierr);
ksp_ratio = ((PetscReal)(its))/check->its0;
maxit = (PetscInt)(ksp_ratio*sub_its + 0.5);
if (maxit < 2) maxit = 2;
ierr = KSPSetTolerances(sub_ksp,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,maxit);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," ...ksp_ratio %g, new maxit %D\n\n",(double)ksp_ratio,maxit);CHKERRQ(ierr);
}
check->its0 = its; /* save current outer KSP iteration number */
PetscFunctionReturn(0);
}
/* ------------------------------------------------------------------- */
/*
MatrixFreePreconditioner - This routine demonstrates the use of a
user-provided preconditioner. This code implements just the null
preconditioner, which of course is not recommended for general use.
Input Parameters:
+ pc - preconditioner
- x - input vector
Output Parameter:
. y - preconditioned vector
*/
PetscErrorCode MatrixFreePreconditioner(PC pc,Vec x,Vec y)
{
PetscErrorCode ierr;
ierr = VecCopy(x,y);CHKERRQ(ierr);
return 0;
}
/*TEST
test:
args: -nox -snes_monitor_cancel -snes_monitor_short -ksp_gmres_cgs_refinement_type refine_always
test:
suffix: 2
nsize: 3
args: -nox -pc_type asm -mat_type mpiaij -snes_monitor_cancel -snes_monitor_short -ksp_gmres_cgs_refinement_type refine_always
test:
suffix: 3
nsize: 2
args: -nox -snes_monitor_cancel -snes_monitor_short -ksp_gmres_cgs_refinement_type refine_always
test:
suffix: 4
args: -nox -pre_check_iterates -post_check_iterates
test:
suffix: 5
requires: double !complex !single
nsize: 2
args: -nox -snes_test_jacobian -snes_test_jacobian_view
test:
suffix: 6
requires: double !complex !single
nsize: 4
args: -test_jacobian_domain_error -snes_converged_reason -snes_check_jacobian_domain_error 1
test:
suffix: 7
requires: double !complex !single
nsize: 4
args: -test_jacobian_domain_error -snes_converged_reason -snes_type newtontr -snes_check_jacobian_domain_error 1
test:
suffix: 8
requires: double !complex !single
nsize: 4
args: -test_jacobian_domain_error -snes_converged_reason -snes_type vinewtonrsls -snes_check_jacobian_domain_error 1
test:
suffix: 9
requires: double !complex !single
nsize: 4
args: -test_jacobian_domain_error -snes_converged_reason -snes_type vinewtonssls -snes_check_jacobian_domain_error 1
test:
suffix: 10
requires: double !complex !single
nsize: 4
args: -test_jacobian_domain_error -snes_converged_reason -snes_type qn -snes_qn_scale_type jacobian -snes_check_jacobian_domain_error 1
test:
suffix: 11
requires: double !complex !single
nsize: 4
args: -test_jacobian_domain_error -snes_converged_reason -snes_type ms -snes_check_jacobian_domain_error 1
TEST*/
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