[cig-commits] [commit] rajesh-petsc, rajesh-petsc-schur: configure.ac now checks for the existence of PETSc libraries if --with-petsc=yes is specified. All PETSc related code is enclosed by USE_PETSC conditional compilation guards (0c79a2e)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Wed Nov 5 19:03:09 PST 2014
Repository : https://github.com/geodynamics/citcoms
On branches: rajesh-petsc,rajesh-petsc-schur
Link : https://github.com/geodynamics/citcoms/compare/464e1b32299b15819f93efd98d969cddb84dfe51...f97ae655a50bdbd6dac1923a3471ee4dae178fbd
>---------------------------------------------------------------
commit 0c79a2e64a9bb09c1747a39dfb64223769f738f7
Author: Rajesh Kommu <rajesh.kommu at gmail.com>
Date: Thu Aug 21 13:30:40 2014 -0700
configure.ac now checks for the existence of PETSc libraries if
--with-petsc=yes is specified. All PETSc related code is enclosed by
USE_PETSC conditional compilation guards
>---------------------------------------------------------------
0c79a2e64a9bb09c1747a39dfb64223769f738f7
bin/Citcom.c | 9 ++++++++-
configure.ac | 11 +++++++++++
lib/Drive_solvers.c | 5 +++++
lib/Instructions.c | 4 ++--
lib/Petsc_citcoms.c | 4 ++++
lib/Stokes_flow_Incomp.c | 18 ++++++++++++++++--
lib/global_defs.h | 9 +++++++--
lib/petsc_citcoms.h | 4 ++++
lib/prototypes.h | 4 ----
9 files changed, 57 insertions(+), 11 deletions(-)
diff --git a/bin/Citcom.c b/bin/Citcom.c
index 4dd3e90..84fe2da 100644
--- a/bin/Citcom.c
+++ b/bin/Citcom.c
@@ -70,10 +70,13 @@ int main(argc,argv)
struct All_variables *E;
MPI_Comm world;
+#ifdef USE_PETSC
PetscErrorCode ierr;
-
ierr = PetscInitialize(&argc, &argv, NULL, NULL);
CHKERRQ(ierr);
+#else
+ MPI_Init(&argc, &argv); /* added here to allow command-line input */
+#endif
if (argc < 2) {
fprintf(stderr,"Usage: %s PARAMETERFILE\n", argv[0]);
@@ -85,7 +88,11 @@ int main(argc,argv)
/* this section reads input, allocates memory, and set some initial values;
* replaced by CitcomS.Controller.initialize() and
* CitcomS.Solver.initialize() in Pyre. */
+#ifdef USE_PETSC
world = PETSC_COMM_WORLD;
+#else
+ world = MPI_COMM_WORLD;
+#endif
E = citcom_init(&world); /* allocate global E and do initializaion here */
/* define common aliases for full/regional functions */
diff --git a/configure.ac b/configure.ac
index 4193fb5..6b3e9c7 100644
--- a/configure.ac
+++ b/configure.ac
@@ -35,6 +35,12 @@ AM_INIT_AUTOMAKE([foreign])
# 'configure' options
AC_ARG_VAR(PYTHON, [Python interpreter])
AC_ARG_VAR(PYTHONPATH, [Python module search path])
+AC_ARG_WITH([petsc],
+ [AC_HELP_STRING([--with-petsc],
+ [use PETSc library @<:@default=no@:>@])],
+ [want_petsc="$withval"],
+ [want_petsc=no])
+AM_CONDITIONAL([COND_PETSC], [test "$want_petsc" = yes])
AC_ARG_WITH([pyre],
[AC_HELP_STRING([--with-pyre],
[build Pyre modules @<:@default=no@:>@])],
@@ -74,6 +80,10 @@ AC_PROG_CXX([mpicxx mpic++ mpiCC hcp mpCC mpxlC mpxlC_r cmpic++ g++ c++ gpp aCC
# Checking a system header here so that CPP is always defined
AC_CHECK_HEADERS([malloc.h])
+if test "$want_petsc" = yes; then
+ CIT_PATH_PETSC(3.5.1,[CPPFLAGS="-DUSE_PETSC $CPPFLAGS"],[AC_MSG_ERROR([PETSc Library not found])])
+fi
+
if test "$want_pyre" = yes; then
# Check for Python.
AM_PATH_PYTHON([2.3])
@@ -270,6 +280,7 @@ echo -e "\t with-pyre: " $want_pyre
echo -e "\t with-exchanger: " $want_exchanger
echo -e "\t with-hdf5: " $want_hdf5
echo -e "\t with-ggrd: " $want_ggrd
+echo -e "\t with-petsc: " $want_petsc
echo
dnl end of configure.ac
diff --git a/lib/Drive_solvers.c b/lib/Drive_solvers.c
index 89fcc32..d85b1e5 100644
--- a/lib/Drive_solvers.c
+++ b/lib/Drive_solvers.c
@@ -30,7 +30,10 @@
#include "element_definitions.h"
#include "global_defs.h"
#include "drive_solvers.h"
+
+#ifdef USE_PETSC
#include "petsc_citcoms.h"
+#endif
double global_vdot();
double vnorm_nonnewt();
@@ -52,6 +55,7 @@ void general_stokes_solver_setup(struct All_variables *E)
for (m=1;m<=E->sphere.caps_per_proc;m++)
E->elt_k[i][m]=(struct EK *)malloc((E->lmesh.NEL[i]+1)*sizeof(struct EK));
+#ifdef USE_PETSC
/*
* PETSc related initialization
*/
@@ -149,6 +153,7 @@ void general_stokes_solver_setup(struct All_variables *E)
/************************************************************
* End PETSc Initialization
************************************************************/
+#endif
}
void general_stokes_solver(struct All_variables *E)
diff --git a/lib/Instructions.c b/lib/Instructions.c
index a9b2f53..1c0c811 100644
--- a/lib/Instructions.c
+++ b/lib/Instructions.c
@@ -777,14 +777,14 @@ void read_initial_settings(struct All_variables *E)
the tracer input */
(E->problem_settings)(E);
-
+#ifdef USE_PETSC
/* PETSc related flags */
input_boolean("use_petsc",&E->control.use_petsc,"on",m);
input_boolean("petsc_linear",&E->control.petsc_linear,"on",m);
input_boolean("petsc_nonlinear",&E->control.petsc_nonlinear,"off",m);
input_boolean("petsc_schur",&E->control.petsc_schur,"off",m);
input_float("petsc_uzawa_tol", &E->control.petsc_uzawa_tol, "1e-6", m);
-
+#endif
check_settings_consistency(E);
return;
}
diff --git a/lib/Petsc_citcoms.c b/lib/Petsc_citcoms.c
index 5bc8746..871400d 100644
--- a/lib/Petsc_citcoms.c
+++ b/lib/Petsc_citcoms.c
@@ -1,3 +1,5 @@
+#ifdef USE_PETSC
+
#include "global_defs.h"
#include "element_definitions.h"
#include "petsc_citcoms.h"
@@ -308,3 +310,5 @@ PetscErrorCode MatShellMult_div_rho_u( Mat DC, Vec U, Vec DU )
ierr = VecRestoreArray(DU, &DUData); CHKERRQ(ierr);
PetscFunctionReturn(0);
}
+
+#endif /* USE_PETSC */
diff --git a/lib/Stokes_flow_Incomp.c b/lib/Stokes_flow_Incomp.c
index ec2225e..3acae42 100644
--- a/lib/Stokes_flow_Incomp.c
+++ b/lib/Stokes_flow_Incomp.c
@@ -34,9 +34,12 @@
#include <sys/types.h>
#include "element_definitions.h"
#include "global_defs.h"
-#include "petsc_citcoms.h"
#include <stdlib.h>
+#ifdef USE_PETSC
+#include "petsc_citcoms.h"
+#endif
+
void myerror(struct All_variables *,char *);
static void solve_Ahat_p_fhat(struct All_variables *E,
@@ -52,6 +55,7 @@ static void solve_Ahat_p_fhat_iterCG(struct All_variables *E,
double **V, double **P, double **F,
double imp, int *steps_max);
+#ifdef USE_PETSC
static PetscErrorCode solve_Ahat_p_fhat_PETSc_Schur(struct All_variables *E,
double **V, double **P, double **F, double imp, int *steps_max);
@@ -60,6 +64,7 @@ static PetscErrorCode solve_Ahat_p_fhat_CG_PETSc(struct All_variables *E,
static PetscErrorCode solve_Ahat_p_fhat_BiCG_PETSc(struct All_variables *E,
double **V, double **P, double **F, double imp, int *steps_max);
+#endif
static void initial_vel_residual(struct All_variables *E,
double **V, double **P, double **F,
@@ -174,6 +179,7 @@ static void solve_Ahat_p_fhat(struct All_variables *E,
double **V, double **P, double **F,
double imp, int *steps_max)
{
+#ifdef USE_PETSC
if(E->control.use_petsc)
{
if(E->control.petsc_schur) // use Schur complement reduction
@@ -197,6 +203,7 @@ static void solve_Ahat_p_fhat(struct All_variables *E,
}
else // the original non-PETSc CitcomS code
{
+#endif
if(E->control.inv_gruneisen == 0)
solve_Ahat_p_fhat_CG(E, V, P, F, imp, steps_max);
else {
@@ -207,9 +214,12 @@ static void solve_Ahat_p_fhat(struct All_variables *E,
else
myerror(E, "Error: unknown Uzawa iteration\n");
}
+#ifdef USE_PETSC
}
+#endif
}
+#ifdef USE_PETSC
static PetscErrorCode solve_Ahat_p_fhat_PETSc_Schur(struct All_variables *E,
double **V, double **P, double **F, double imp, int *steps_max)
{
@@ -327,6 +337,7 @@ static PetscErrorCode solve_Ahat_p_fhat_PETSc_Schur(struct All_variables *E,
PetscFunctionReturn(0);
}
+#endif
/* Solve incompressible Stokes flow using
* conjugate gradient (CG) iterations
@@ -597,6 +608,7 @@ static void solve_Ahat_p_fhat_CG(struct All_variables *E,
return;
}
+#ifdef USE_PETSC
/*
* Implementation of the Conjugate Gradient Uzawa algorithm using PETSc
* Vec, Mat and KSPSolve
@@ -1093,6 +1105,7 @@ static PetscErrorCode solve_Ahat_p_fhat_BiCG_PETSc( struct All_variables *E,
PetscFunctionReturn(0);
}
+#endif /* USE_PETSC */
/* Solve compressible Stokes flow using
* bi-conjugate gradient stablized (BiCG-stab) iterations
@@ -1436,10 +1449,11 @@ static void solve_Ahat_p_fhat_iterCG(struct All_variables *E,
for(i=0;i<neq;i++) old_v[m][i] = V[m][i];
for(i=1;i<=npno;i++) old_p[m][i] = P[m][i];
}
-
+#ifdef USE_PETSC
if(E->control.use_petsc)
solve_Ahat_p_fhat_CG_PETSc(E, V, P, F, imp, &cycles);
else
+#endif
solve_Ahat_p_fhat_CG(E, V, P, F, imp, &cycles);
diff --git a/lib/global_defs.h b/lib/global_defs.h
index 6087f60..1b2abae 100644
--- a/lib/global_defs.h
+++ b/lib/global_defs.h
@@ -44,9 +44,11 @@ to functions across the whole filespace of CITCOM.
#include <stdio.h>
#include <stdlib.h>
#include <mpi.h>
+
+#ifdef USE_PETSC
#include <petscksp.h>
#include <petscsnes.h>
-
+#endif
#ifdef USE_HDF5
@@ -558,13 +560,14 @@ struct CONTROL {
int print_convergence;
int sdepv_print_convergence;
-
+#ifdef USE_PETSC
/* PETSc flags */
int use_petsc;
int petsc_linear;
int petsc_nonlinear;
int petsc_schur;
float petsc_uzawa_tol;
+#endif
};
@@ -752,6 +755,7 @@ struct All_variables {
#include "viscosity_descriptions.h"
#include "advection.h"
+#ifdef USE_PETSC
/* PETSc related data structures */
Mat K, G, D, DC;
KSP ksp;
@@ -760,6 +764,7 @@ struct All_variables {
Vec PVec, NPVec, UVec, FVec;
struct MatMultShell mtx_del2_u, mtx_grad_p, mtx_div_u, mtx_div_rho_u;
struct MultiGrid_PC pcshell_ctx;
+#endif
FILE *fp;
FILE *fptime;
diff --git a/lib/petsc_citcoms.h b/lib/petsc_citcoms.h
index a90233b..73ff3ed 100644
--- a/lib/petsc_citcoms.h
+++ b/lib/petsc_citcoms.h
@@ -2,6 +2,8 @@
#ifndef __CitcomS__PETSc__h__
#define __CitcomS__PETSc__h__
+#ifdef USE_PETSC
+
#include <petscksp.h>
#ifdef __cplusplus
@@ -29,4 +31,6 @@ PetscErrorCode MatShellMult_div_rho_u( Mat D, Vec U, Vec DU );
}
#endif
+#endif /* USE_PETSC */
+
#endif // __CitcomS__PETSc__h__
diff --git a/lib/prototypes.h b/lib/prototypes.h
index c7aeaec..a2006ea 100644
--- a/lib/prototypes.h
+++ b/lib/prototypes.h
@@ -263,15 +263,12 @@ void get_prem(double, double *, double *, double *);
void compute_seismic_model(struct All_variables *, double *, double *, double *);
/* Nodal_mesh.c */
void v_from_vector(struct All_variables *);
-//PetscErrorCode v_from_vector_petsc(struct All_variables *);
void assign_v_to_vector(struct All_variables *);
void v_from_vector_pseudo_surf(struct All_variables *);
-//PetscErrorCode v_from_vector_pseudo_surf_petsc(struct All_variables *);
void velo_from_element(struct All_variables *, float [4][9], int, int, int);
void velo_from_element_d(struct All_variables *, double [4][9], int, int, int);
void p_to_nodes(struct All_variables *, double **, float **, int);
-//PetscErrorCode p_to_nodes_petsc(struct All_variables *, Vec, Vec, int);
void visc_from_gint_to_nodes(struct All_variables *, float **, float **, int);
void visc_from_nodes_to_gint(struct All_variables *, float **, float **, int);
@@ -492,7 +489,6 @@ void get_angle_sphere_cap(double [4][5], double [6]);
double get_angle(double [4], double [4]);
/* Stokes_flow_Incomp.c */
void solve_constrained_flow_iterative(struct All_variables *);
-//PetscErrorCode solve_constrained_flow_iterative_petsc(struct All_variables *);
/* Topo_gravity.c */
void get_STD_topo(struct All_variables *, float **, float **, float **, float **, int);
void get_STD_freesurf(struct All_variables *, float **);
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