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Merged
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Jul 25, 2018
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[test] Adapt the petsc test for PE 18.07 #404

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9b2c7b9
Adapt the petsc test for PE 18.07
Jul 24, 2018
3e6098e
Merge branch 'master' into bugfix/petsc_adapt_pe18.07
Jul 25, 2018
098e47e
Address PR comments
Jul 25, 2018
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49 changes: 16 additions & 33 deletions cscs-checks/libraries/petsc/petsc_helloworld.py
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Original file line number Diff line number Diff line change
@@ -1,24 +1,13 @@
import filecmp
import os
import reframe as rfm
import reframe.utility.sanity as sn

from reframe.core.pipeline import RegressionTest


@sn.sanity_function
def sanity_filecmp(output, reference):
return sn.assert_true(
filecmp.cmp(output, reference, shallow=False),
msg="files are not the same: `%s', `%s'" % (output, reference)
)


class PetscPoisson2DCheck(RegressionTest):
def __init__(self, variant, **kwargs):
super().__init__('petsc_2dpoisson_%s' % variant,
os.path.dirname(__file__), **kwargs)
@rfm.parameterized_test(['dynamic'], ['static'])
class PetscPoisson2DCheck(rfm.RegressionTest):
def __init__(self, variant):
super().__init__()
self.descr = ('Compile/run PETSc 2D Poisson example with cray-petsc '
'(%s linking case)') % variant
'(%s linking)') % variant
self.valid_systems = ['daint:gpu', 'daint:mc',
'dom:gpu', 'dom:mc']
self.valid_prog_environs = ['PrgEnv-cray', 'PrgEnv-gnu',
Expand All @@ -27,22 +16,16 @@ def __init__(self, variant, **kwargs):
self.modules = ['cray-petsc']
self.num_tasks = 16
self.num_tasks_per_node = 8
self.dynamic = True if variant == 'dynamic' else False
self.executable_opts = ['-da_grid_x 4', '-da_grid_y 4', '-mat_view',
'> petsc_poisson2d.out']
self.build_system = 'SingleSource'
if variant == 'dynamic':
self.build_system.cflags = ['-dynamic']

self.maintainers = ['WS', 'AJ']
self.tags = {'production'}
self.executable_opts = ['-da_grid_x 4', '-da_grid_y 4', '-ksp_monitor']

self.sanity_patterns = sanity_filecmp(
'petsc_poisson2d.out', 'petsc_poisson2d.ref')
# Check the final residual norm for convergence
norm = sn.extractsingle(r'\s+\d+\s+KSP Residual norm\s+(?P<norm>\S+)',
self.stdout, 'norm', float, -1)
self.sanity_patterns = sn.assert_lt(norm, 1.0e-5)

def compile(self):
if self.dynamic:
self.current_environ.cxxflags = '-dynamic'
super().compile()


def _get_checks(**kwargs):
return [PetscPoisson2DCheck('dynamic', **kwargs),
PetscPoisson2DCheck('static', **kwargs)]
self.tags = {'production'}
self.maintainers = ['WS', 'AJ', 'TM']
36 changes: 0 additions & 36 deletions cscs-checks/libraries/petsc/src/petsc_poisson2d.ref
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116 changes: 58 additions & 58 deletions cscs-checks/libraries/petsc/src/poisson2d.c
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Original file line number Diff line number Diff line change
Expand Up @@ -11,11 +11,13 @@
Contributed by Michael Boghosian <boghmic@iit.edu>, 2008,
based on petsc/src/ksp/ksp/examples/tutorials/ex29.c and ex32.c

Compare to ex66.c

Example of Usage:
./ex50 -da_grid_x 3 -da_grid_y 3 -pc_type mg -da_refine 3 -ksp_monitor -ksp_view -dm_view draw -draw_pause -1
./ex50 -da_grid_x 100 -da_grid_y 100 -pc_type mg -pc_mg_levels 1 -mg_levels_0_pc_type ilu -mg_levels_0_pc_factor_levels 1 -ksp_monitor -ksp_view
./ex50 -da_grid_x 100 -da_grid_y 100 -pc_type mg -pc_mg_levels 1 -mg_levels_0_pc_type lu -mg_levels_0_pc_factor_shift_type NONZERO -ksp_monitor
mpiexec -n 4 ./ex50 -da_grid_x 3 -da_grid_y 3 -pc_type mg -da_refine 10 -ksp_monitor -ksp_view -log_summary
mpiexec -n 4 ./ex50 -da_grid_x 3 -da_grid_y 3 -pc_type mg -da_refine 10 -ksp_monitor -ksp_view -log_view
*/

static char help[] = "Solves 2D Poisson equation using multigrid.\n\n";
Expand All @@ -28,37 +30,28 @@ static char help[] = "Solves 2D Poisson equation using multigrid.\n\n";

extern PetscErrorCode ComputeJacobian(KSP,Mat,Mat,void*);
extern PetscErrorCode ComputeRHS(KSP,Vec,void*);
extern PetscErrorCode ComputeTrueSolution(DM, Vec);
extern PetscErrorCode VecView_VTK(Vec, const char [], const char []);

typedef enum {DIRICHLET, NEUMANN} BCType;

typedef struct {
PetscScalar uu, tt;
BCType bcType;
} UserContext;

#undef __FUNCT__
#define __FUNCT__ "main"
int main(int argc,char **argv)
{
KSP ksp;
DM da;
UserContext user;
PetscInt bc;
PetscErrorCode ierr;

PetscInitialize(&argc,&argv,(char*)0,help);
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,-11,-11,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,&da);CHKERRQ(ierr);
ierr = KSPSetDM(ksp,(DM)da);
ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,11,11,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,&da);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = KSPSetDM(ksp,(DM)da);CHKERRQ(ierr);
ierr = DMSetApplicationContext(da,&user);CHKERRQ(ierr);

user.uu = 1.0;
user.tt = 1.0;
bc = (PetscInt)NEUMANN; /* Use Neumann Boundary Conditions */
user.bcType = (BCType)bc;


ierr = KSPSetComputeRHS(ksp,ComputeRHS,&user);CHKERRQ(ierr);
ierr = KSPSetComputeOperators(ksp,ComputeJacobian,&user);CHKERRQ(ierr);
Expand All @@ -67,12 +60,10 @@ int main(int argc,char **argv)

ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
ierr = PetscFinalize();
return ierr;
}

#undef __FUNCT__
#define __FUNCT__ "ComputeRHS"
PetscErrorCode ComputeRHS(KSP ksp,Vec b,void *ctx)
{
UserContext *user = (UserContext*)ctx;
Expand All @@ -81,6 +72,7 @@ PetscErrorCode ComputeRHS(KSP ksp,Vec b,void *ctx)
PetscScalar Hx,Hy,pi,uu,tt;
PetscScalar **array;
DM da;
MatNullSpace nullspace;

PetscFunctionBeginUser;
ierr = KSPGetDM(ksp,&da);CHKERRQ(ierr);
Expand All @@ -91,7 +83,6 @@ PetscErrorCode ComputeRHS(KSP ksp,Vec b,void *ctx)
Hy = 1.0/(PetscReal)(N);

ierr = DMDAGetCorners(da,&xs,&ys,0,&xm,&ym,0);CHKERRQ(ierr); /* Fine grid */
/* printf(" M N: %d %d; xm ym: %d %d; xs ys: %d %d\n",M,N,xm,ym,xs,ys); */
ierr = DMDAVecGetArray(da, b, &array);CHKERRQ(ierr);
for (j=ys; j<ys+ym; j++) {
for (i=xs; i<xs+xm; i++) {
Expand All @@ -104,26 +95,20 @@ PetscErrorCode ComputeRHS(KSP ksp,Vec b,void *ctx)

/* force right hand side to be consistent for singular matrix */
/* note this is really a hack, normally the model would provide you with a consistent right handside */
if (user->bcType == NEUMANN) {
MatNullSpace nullspace;

ierr = MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,0,0,&nullspace);CHKERRQ(ierr);
ierr = MatNullSpaceRemove(nullspace,b);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nullspace);CHKERRQ(ierr);
}
ierr = MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,0,0,&nullspace);CHKERRQ(ierr);
ierr = MatNullSpaceRemove(nullspace,b);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nullspace);CHKERRQ(ierr);
PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "ComputeJacobian"
PetscErrorCode ComputeJacobian(KSP ksp,Mat J, Mat jac,void *ctx)
{
UserContext *user = (UserContext*)ctx;
PetscErrorCode ierr;
PetscInt i, j, M, N, xm, ym, xs, ys, num, numi, numj;
PetscScalar v[5], Hx, Hy, HydHx, HxdHy;
MatStencil row, col[5];
DM da;
MatNullSpace nullspace;

PetscFunctionBeginUser;
ierr = KSPGetDM(ksp,&da);CHKERRQ(ierr);
Expand All @@ -138,29 +123,26 @@ PetscErrorCode ComputeJacobian(KSP ksp,Mat J, Mat jac,void *ctx)
row.i = i; row.j = j;

if (i==0 || j==0 || i==M-1 || j==N-1) {
if (user->bcType == DIRICHLET) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Dirichlet boundary conditions not supported !\n");
else if (user->bcType == NEUMANN) {
num=0; numi=0; numj=0;
if (j!=0) {
v[num] = -HxdHy; col[num].i = i; col[num].j = j-1;
num++; numj++;
}
if (i!=0) {
v[num] = -HydHx; col[num].i = i-1; col[num].j = j;
num++; numi++;
}
if (i!=M-1) {
v[num] = -HydHx; col[num].i = i+1; col[num].j = j;
num++; numi++;
}
if (j!=N-1) {
v[num] = -HxdHy; col[num].i = i; col[num].j = j+1;
num++; numj++;
}
v[num] = ((PetscReal)(numj)*HxdHy + (PetscReal)(numi)*HydHx); col[num].i = i; col[num].j = j;
num++;
ierr = MatSetValuesStencil(jac,1,&row,num,col,v,INSERT_VALUES);CHKERRQ(ierr);
num=0; numi=0; numj=0;
if (j!=0) {
v[num] = -HxdHy; col[num].i = i; col[num].j = j-1;
num++; numj++;
}
if (i!=0) {
v[num] = -HydHx; col[num].i = i-1; col[num].j = j;
num++; numi++;
}
if (i!=M-1) {
v[num] = -HydHx; col[num].i = i+1; col[num].j = j;
num++; numi++;
}
if (j!=N-1) {
v[num] = -HxdHy; col[num].i = i; col[num].j = j+1;
num++; numj++;
}
v[num] = ((PetscReal)(numj)*HxdHy + (PetscReal)(numi)*HydHx); col[num].i = i; col[num].j = j;
num++;
ierr = MatSetValuesStencil(jac,1,&row,num,col,v,INSERT_VALUES);CHKERRQ(ierr);
} else {
v[0] = -HxdHy; col[0].i = i; col[0].j = j-1;
v[1] = -HydHx; col[1].i = i-1; col[1].j = j;
Expand All @@ -173,13 +155,31 @@ PetscErrorCode ComputeJacobian(KSP ksp,Mat J, Mat jac,void *ctx)
}
ierr = MatAssemblyBegin(jac,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(jac,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
if (user->bcType == NEUMANN) {
MatNullSpace nullspace;

ierr = MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,0,0,&nullspace);CHKERRQ(ierr);
ierr = MatSetNullSpace(jac,nullspace);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nullspace);CHKERRQ(ierr);
}
ierr = MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,0,0,&nullspace);CHKERRQ(ierr);
ierr = MatSetNullSpace(J,nullspace);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nullspace);CHKERRQ(ierr);
PetscFunctionReturn(0);
}



/*TEST

build:
requires: !complex !single

test:
args: -pc_type mg -pc_mg_type full -ksp_type cg -ksp_monitor_short -da_refine 3 -mg_coarse_pc_type svd -ksp_view

test:
suffix: 2
nsize: 4
args: -pc_type mg -pc_mg_type full -ksp_type cg -ksp_monitor_short -da_refine 3 -mg_coarse_pc_type redundant -mg_coarse_redundant_pc_type svd -ksp_view

test:
suffix: 3
nsize: 2
args: -pc_type mg -pc_mg_type full -ksp_monitor_short -da_refine 5 -mg_coarse_ksp_type cg -mg_coarse_ksp_converged_reason -mg_coarse_ksp_rtol 1e-2 -mg_coarse_ksp_max_it 5 -mg_coarse_pc_type none -pc_mg_levels 2 -ksp_type pipefgmres -ksp_pipefgmres_shift 1.5

TEST*/