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Corrections for PETSc 3.7 and detection of PETSC version to enable TAO

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This commit is contained in:
Nicolas Richart 2016-06-27 20:52:05 +02:00
parent 3ea9d1e665
commit 9026fb8e8a
3 changed files with 436 additions and 0 deletions
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3
var/spack/repos/builtin/packages/fenics/package.py
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@ -57,6 +57,9 @@ class Fenics(Package):
# variant('slepc4py', default=True, description='Uses SLEPc4py')
# variant('pastix', default=True, description='Compile with Pastix')
patch('petsc-3.7.patch', when='^petsc@3.7:')
patch('petsc-version-detection.patch', when='@:1.6.1')
extends('python')
depends_on('py-numpy')

394
var/spack/repos/builtin/packages/fenics/petsc-3.7.patch Normal file
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@ -0,0 +1,394 @@
diff -Naur dolfin-1.6.0/dolfin/common/SubSystemsManager.cpp dolfin-1.6.0.new/dolfin/common/SubSystemsManager.cpp
--- dolfin-1.6.0/dolfin/common/SubSystemsManager.cpp 2015-07-28 17:05:55.000000000 +0200
+++ dolfin-1.6.0.new/dolfin/common/SubSystemsManager.cpp 2016-06-26 23:42:56.391929550 +0200
@@ -179,7 +179,7 @@
PetscInitialized(&is_initialized);
if (is_initialized)
{
- PetscOptionsInsert(&argc, &argv, PETSC_NULL);
+ PetscOptionsInsert(NULL, &argc, &argv, PETSC_NULL);
}
else
{
@@ -187,12 +187,12 @@
PetscInitializeNoArguments();
// Set options to avoid common failures with some 3rd party solvers
- PetscOptionsSetValue("-mat_mumps_icntl_7", "0");
- PetscOptionsSetValue("-mat_superlu_dist_colperm", "MMD_AT_PLUS_A");
+ PetscOptionsSetValue(NULL, "-mat_mumps_icntl_7", "0");
+ PetscOptionsSetValue(NULL, "-mat_superlu_dist_colperm", "MMD_AT_PLUS_A");
// Pass command line arguments to PETSc (will overwrite any
// default above)
- PetscOptionsInsert(&argc, &argv, PETSC_NULL);
+ PetscOptionsInsert(NULL, &argc, &argv, PETSC_NULL);
}
// Set PETSc
diff -Naur dolfin-1.6.0/dolfin/la/PETScKrylovSolver.cpp dolfin-1.6.0.new/dolfin/la/PETScKrylovSolver.cpp
--- dolfin-1.6.0/dolfin/la/PETScKrylovSolver.cpp 2015-07-28 17:05:55.000000000 +0200
+++ dolfin-1.6.0.new/dolfin/la/PETScKrylovSolver.cpp 2016-06-26 23:33:02.418351380 +0200
@@ -564,6 +564,11 @@
return solve(x, b);
}
//-----------------------------------------------------------------------------
+PetscErrorCode PETScKrylovSolver::ksp_monitor_norm(KSP ksp, PetscInt n, PetscReal rnorm, void *vf)
+{
+ KSPMonitorTrueResidualNorm(ksp, n, rnorm, static_cast<PetscViewerAndFormat *>(vf));
+}
+//-----------------------------------------------------------------------------
void PETScKrylovSolver::set_petsc_ksp_options()
{
PetscErrorCode ierr;
@@ -585,7 +590,8 @@
const bool monitor_convergence = parameters["monitor_convergence"];
if (monitor_convergence)
{
- ierr = KSPMonitorSet(_ksp, KSPMonitorTrueResidualNorm, 0, 0);
+ PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_DEFAULT, &_vf);
+ ierr = KSPMonitorSet(_ksp, ksp_monitor_norm, _vf, 0);
if (ierr != 0) petsc_error(ierr, __FILE__, "KSPMonitorSet");
}
diff -Naur dolfin-1.6.0/dolfin/la/PETScKrylovSolver.h dolfin-1.6.0.new/dolfin/la/PETScKrylovSolver.h
--- dolfin-1.6.0/dolfin/la/PETScKrylovSolver.h 2015-07-28 17:05:55.000000000 +0200
+++ dolfin-1.6.0.new/dolfin/la/PETScKrylovSolver.h 2016-06-26 23:19:40.767042975 +0200
@@ -179,6 +179,12 @@
// PETSc solver pointer
KSP _ksp;
+ // viewer for monitoring
+ PetscViewerAndFormat* _vf;
+
+ // monitoring function
+ static PetscErrorCode ksp_monitor_norm(KSP ksp, PetscInt n, PetscReal rnorm, void *ctx);
+
// DOLFIN-defined PETScUserPreconditioner
PETScUserPreconditioner* pc_dolfin;
diff -Naur dolfin-1.6.0/dolfin/la/PETScLUSolver.cpp dolfin-1.6.0.new/dolfin/la/PETScLUSolver.cpp
--- dolfin-1.6.0/dolfin/la/PETScLUSolver.cpp 2015-07-28 17:05:55.000000000 +0200
+++ dolfin-1.6.0.new/dolfin/la/PETScLUSolver.cpp 2016-06-26 23:13:36.903732301 +0200
@@ -246,14 +246,14 @@
if (parameters["num_threads"].is_set())
{
// Use number of threads specified for LU solver
- ierr = PetscOptionsSetValue("-mat_pastix_threadnbr",
+ ierr = PetscOptionsSetValue(NULL, "-mat_pastix_threadnbr",
parameters["num_threads"].value_str().c_str());
if (ierr != 0) petsc_error(ierr, __FILE__, "PetscOptionsSetValue");
}
else
{
// Use global number of threads
- ierr = PetscOptionsSetValue("-mat_pastix_threadnbr",
+ ierr = PetscOptionsSetValue(NULL, "-mat_pastix_threadnbr",
dolfin::parameters["num_threads"].value_str().c_str());
if (ierr != 0) petsc_error(ierr, __FILE__, "PetscOptionsSetValue");
}
diff -Naur dolfin-1.6.0/dolfin/la/PETScOptions.cpp dolfin-1.6.0.new/dolfin/la/PETScOptions.cpp
--- dolfin-1.6.0/dolfin/la/PETScOptions.cpp 2015-07-28 17:05:55.000000000 +0200
+++ dolfin-1.6.0.new/dolfin/la/PETScOptions.cpp 2016-06-26 23:37:58.613121118 +0200
@@ -54,7 +54,7 @@
{
SubSystemsManager::init_petsc();
PetscErrorCode ierr;
- ierr = PetscOptionsClearValue(option.c_str());
+ ierr = PetscOptionsClearValue(NULL, option.c_str());
if (ierr != 0)
{
dolfin_error("PETScOptions.cpp",
diff -Naur dolfin-1.6.0/dolfin/la/PETScOptions.h dolfin-1.6.0.new/dolfin/la/PETScOptions.h
--- dolfin-1.6.0/dolfin/la/PETScOptions.h 2015-07-28 17:05:55.000000000 +0200
+++ dolfin-1.6.0.new/dolfin/la/PETScOptions.h 2016-06-26 23:37:54.352023709 +0200
@@ -65,7 +65,7 @@
PetscErrorCode ierr;
std::string _option = "-" + option;
- ierr = PetscOptionsSetValue(_option.c_str(),
+ ierr = PetscOptionsSetValue(NULL, _option.c_str(),
boost::lexical_cast<std::string>(value).c_str());
if (ierr != 0)
{
diff -Naur dolfin-1.6.0/dolfin/la/SLEPcEigenSolver.cpp dolfin-1.6.0.new/dolfin/la/SLEPcEigenSolver.cpp
--- dolfin-1.6.0/dolfin/la/SLEPcEigenSolver.cpp 2015-07-28 17:05:55.000000000 +0200
+++ dolfin-1.6.0.new/dolfin/la/SLEPcEigenSolver.cpp 2016-06-26 23:35:25.930631132 +0200
@@ -99,6 +99,19 @@
solve(_matA->size(0));
}
//-----------------------------------------------------------------------------
+PetscErrorCode SLEPcEigenSolver::eps_monitor(EPS eps, PetscInt its, PetscInt nconv, PetscScalar* eigr,
+ PetscScalar* eigi, PetscReal* errest,
+ PetscInt nest, void *vf)
+{
+ EPSMonitorAll(eps, its, nconv, eigr, eigi, errest, nest,
+ static_cast<PetscViewerAndFormat *>(vf));
+}
+//-----------------------------------------------------------------------------
+PetscErrorCode SLEPcEigenSolver::ksp_monitor(KSP ksp, PetscInt n, PetscReal rnorm, void *vf)
+{
+ KSPMonitorDefault(ksp, n, rnorm, static_cast<PetscViewerAndFormat *>(vf));
+}
+//-----------------------------------------------------------------------------
void SLEPcEigenSolver::solve(std::size_t n)
{
dolfin_assert(_matA);
@@ -139,10 +152,11 @@
{
KSP ksp;
ST st;
- EPSMonitorSet(_eps, EPSMonitorAll, NULL, NULL);
+ PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_DEFAULT, &_vf);
+ EPSMonitorSet(_eps, eps_monitor, _vf, NULL);
EPSGetST(_eps, &st);
STGetKSP(st, &ksp);
- KSPMonitorSet(ksp, KSPMonitorDefault, NULL, NULL);
+ KSPMonitorSet(ksp, ksp_monitor, _vf, NULL);
EPSView(_eps, PETSC_VIEWER_STDOUT_SELF);
}
diff -Naur dolfin-1.6.0/dolfin/la/SLEPcEigenSolver.h dolfin-1.6.0.new/dolfin/la/SLEPcEigenSolver.h
--- dolfin-1.6.0/dolfin/la/SLEPcEigenSolver.h 2015-07-28 17:05:55.000000000 +0200
+++ dolfin-1.6.0.new/dolfin/la/SLEPcEigenSolver.h 2016-06-26 23:36:08.784610612 +0200
@@ -231,6 +231,11 @@
// SLEPc solver pointer
EPS _eps;
+ PetscViewerAndFormat* _vf;
+ static PetscErrorCode eps_monitor(EPS eps, int its, int nconv, PetscScalar *eigr,
+ PetscScalar *eigi, PetscReal* errest,
+ int nest, void *mctx);
+ static PetscErrorCode ksp_monitor(KSP ksp, PetscInt n, PetscReal rnorm, void *vf);
};
}
diff -Naur dolfin-1.6.0/dolfin/nls/PETScSNESSolver.cpp dolfin-1.6.0.new/dolfin/nls/PETScSNESSolver.cpp
--- dolfin-1.6.0/dolfin/nls/PETScSNESSolver.cpp 2015-07-28 17:05:55.000000000 +0200
+++ dolfin-1.6.0.new/dolfin/nls/PETScSNESSolver.cpp 2016-06-26 23:19:40.166029256 +0200
@@ -195,6 +195,15 @@
return this->solve(nonlinear_problem, x);
}
//-----------------------------------------------------------------------------
+PetscErrorCode
+PETScSNESSolver::snes_monitor(SNES snes, PetscInt its,
+ PetscReal fgnorm, void *vf)
+{
+ PetscViewerAndFormat * _vf = static_cast<PetscViewerAndFormat *>(vf);
+ SNESMonitorDefault(snes, its, fgnorm, _vf);
+ return(0);
+}
+//-----------------------------------------------------------------------------
void
PETScSNESSolver::init(NonlinearProblem& nonlinear_problem,
GenericVector& x)
@@ -237,9 +246,11 @@
}
// Set some options from the parameters
- if (report)
- SNESMonitorSet(_snes, SNESMonitorDefault, PETSC_NULL, PETSC_NULL);
-
+ if (report) {
+ PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_DEFAULT, &_snes_ctx.vf);
+ SNESMonitorSet(_snes, PETScSNESSolver::snes_monitor, _snes_ctx.vf, PETSC_NULL);
+ }
+
// Set the bounds, if any
set_bounds(x);
@@ -293,8 +304,8 @@
SNESGetLineSearch(_snes, &linesearch);
#endif
- if (report)
- SNESLineSearchSetMonitor(linesearch, PETSC_TRUE);
+ // if (report)
+ // SNESLineSearchSetMonitor(linesearch, PETSC_TRUE);
const std::string line_search_type = std::string(parameters["line_search"]);
SNESLineSearchSetType(linesearch, line_search_type.c_str());
@@ -466,6 +477,24 @@
}
#endif
//-----------------------------------------------------------------------------
+PetscErrorCode
+PETScSNESSolver::ksp_monitor(KSP ksp, PetscInt n,
+ PetscReal rnorm, void *vf)
+{
+ PetscViewerAndFormat * _vf = static_cast<PetscViewerAndFormat *>(vf);
+ KSPMonitorDefault(ksp, n, rnorm, _vf);
+ return(0);
+}
+//-----------------------------------------------------------------------------
+PetscErrorCode
+PETScSNESSolver::ksp_monitor_norm(KSP ksp, PetscInt n,
+ PetscReal rnorm, void *vf)
+{
+ PetscViewerAndFormat * _vf = static_cast<PetscViewerAndFormat *>(vf);
+ KSPMonitorTrueResidualNorm(ksp, n, rnorm, _vf);
+ return(0);
+}
+//-----------------------------------------------------------------------------
void PETScSNESSolver::set_linear_solver_parameters()
{
KSP ksp;
@@ -482,7 +511,7 @@
PetscObjectGetComm((PetscObject)_snes, &comm);
if (parameters["report"])
- KSPMonitorSet(ksp, KSPMonitorDefault, PETSC_NULL, PETSC_NULL);
+ KSPMonitorSet(ksp, PETScSNESSolver::ksp_monitor, _snes_ctx.vf, PETSC_NULL);
const std::string linear_solver = parameters["linear_solver"];
const std::string preconditioner = parameters["preconditioner"];
@@ -518,7 +547,7 @@
KSPSetInitialGuessNonzero(ksp, PETSC_FALSE);
if (krylov_parameters["monitor_convergence"])
- KSPMonitorSet(ksp, KSPMonitorTrueResidualNorm, 0, 0);
+ KSPMonitorSet(ksp, PETScSNESSolver::ksp_monitor_norm, _snes_ctx.vf, 0);
// Set tolerances
const int max_iters = krylov_parameters["maximum_iterations"];
diff -Naur dolfin-1.6.0/dolfin/nls/PETScSNESSolver.h dolfin-1.6.0.new/dolfin/nls/PETScSNESSolver.h
--- dolfin-1.6.0/dolfin/nls/PETScSNESSolver.h 2015-07-28 17:05:55.000000000 +0200
+++ dolfin-1.6.0.new/dolfin/nls/PETScSNESSolver.h 2016-06-26 22:31:21.554129282 +0200
@@ -24,6 +24,7 @@
#include <map>
#include <petscsnes.h>
+#include <petscviewer.h>
#include <memory>
#include <dolfin/nls/NewtonSolver.h>
#include <dolfin/parameter/Parameters.h>
@@ -124,8 +125,15 @@
Vec f_tmp;
const PETScVector* xl;
const PETScVector* xu;
+ PetscViewerAndFormat* vf;
};
+
+ // monitoring functions
+ static PetscErrorCode snes_monitor(SNES snes, PetscInt its, PetscReal fgnorm, void* ctx);
+ static PetscErrorCode ksp_monitor(KSP ksp, PetscInt n, PetscReal rnorm, void *ctx);
+ static PetscErrorCode ksp_monitor_norm(KSP ksp, PetscInt n, PetscReal rnorm, void *ctx);
+
// PETSc solver pointer
SNES _snes;
diff -Naur dolfin-1.6.0/dolfin/nls/PETScTAOSolver.cpp dolfin-1.6.0.new/dolfin/nls/PETScTAOSolver.cpp
--- dolfin-1.6.0/dolfin/nls/PETScTAOSolver.cpp 2015-07-28 17:05:55.000000000 +0200
+++ dolfin-1.6.0.new/dolfin/nls/PETScTAOSolver.cpp 2016-06-27 19:14:47.367885081 +0200
@@ -186,6 +186,15 @@
init(optimisation_problem, x.down_cast<PETScVector>(), lb, ub);
}
//-----------------------------------------------------------------------------
+PetscErrorCode
+PETScTAOSolver::ksp_monitor_norm(KSP ksp, PetscInt n,
+ PetscReal rnorm, void * vf)
+{
+ PetscViewerAndFormat * _vf = static_cast<PetscViewerAndFormat *>(vf);
+ KSPMonitorTrueResidualNorm(ksp, n, rnorm, _vf);
+ return(0);
+}
+//-----------------------------------------------------------------------------
void PETScTAOSolver::init(OptimisationProblem& optimisation_problem,
PETScVector& x,
const PETScVector& lb,
@@ -365,9 +374,7 @@
set_tao(parameters["method"]);
// Set tolerances
- TaoSetTolerances(_tao, parameters["function_absolute_tol"],
- parameters["function_relative_tol"],
- parameters["gradient_absolute_tol"],
+ TaoSetTolerances(_tao, parameters["gradient_absolute_tol"],
parameters["gradient_relative_tol"],
parameters["gradient_t_tol"]);
@@ -490,8 +497,10 @@
KSPSetInitialGuessNonzero(ksp, PETSC_FALSE);
// KSP monitor
- if (krylov_parameters["monitor_convergence"])
- KSPMonitorSet(ksp, KSPMonitorTrueResidualNorm, 0, 0);
+ if (krylov_parameters["monitor_convergence"]) {
+ PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_DEFAULT, &vf);
+ KSPMonitorSet(ksp, ksp_monitor_norm, vf, 0);
+ }
// Get integer tolerances (to take care of casting to PetscInt)
const int max_iter = krylov_parameters["maximum_iterations"];
diff -Naur dolfin-1.6.0/dolfin/nls/PETScTAOSolver.h dolfin-1.6.0.new/dolfin/nls/PETScTAOSolver.h
--- dolfin-1.6.0/dolfin/nls/PETScTAOSolver.h 2015-07-28 17:05:55.000000000 +0200
+++ dolfin-1.6.0.new/dolfin/nls/PETScTAOSolver.h 2016-06-27 19:08:00.634361160 +0200
@@ -146,6 +146,10 @@
// TAO pointer
Tao _tao;
+ // monitoring functions
+ PetscViewerAndFormat* vf;
+ static PetscErrorCode ksp_monitor_norm(KSP ksp, PetscInt n, PetscReal rnorm, void *ctx);
+
// Update parameters when tao/ksp/pc_types are explictly given
void update_parameters(const std::string tao_type,
const std::string ksp_type,
diff -Naur dolfin-1.6.0/dolfin/nls/TAOLinearBoundSolver.cpp dolfin-1.6.0.new/dolfin/nls/TAOLinearBoundSolver.cpp
--- dolfin-1.6.0/dolfin/nls/TAOLinearBoundSolver.cpp 2015-07-28 17:05:55.000000000 +0200
+++ dolfin-1.6.0.new/dolfin/nls/TAOLinearBoundSolver.cpp 2016-06-27 19:17:10.390216576 +0200
@@ -313,9 +313,7 @@
dolfin_assert(_tao);
// Set tolerances
- TaoSetTolerances(_tao, parameters["function_absolute_tol"],
- parameters["function_relative_tol"],
- parameters["gradient_absolute_tol"],
+ TaoSetTolerances(_tao, parameters["gradient_absolute_tol"],
parameters["gradient_relative_tol"],
parameters["gradient_t_tol"]);
@@ -340,6 +338,15 @@
set_solver(method);
}
//-----------------------------------------------------------------------------
+PetscErrorCode
+TAOLinearBoundSolver::ksp_monitor_norm(KSP ksp, PetscInt n,
+ PetscReal rnorm, void * vf)
+{
+ PetscViewerAndFormat * _vf = static_cast<PetscViewerAndFormat *>(vf);
+ KSPMonitorTrueResidualNorm(ksp, n, rnorm, _vf);
+ return(0);
+}
+//-----------------------------------------------------------------------------
void TAOLinearBoundSolver::set_ksp_options()
{
dolfin_assert(_tao);
@@ -360,8 +367,10 @@
else
KSPSetInitialGuessNonzero(ksp, PETSC_FALSE);
- if (krylov_parameters["monitor_convergence"])
- KSPMonitorSet(ksp, KSPMonitorTrueResidualNorm, 0, 0);
+ if (krylov_parameters["monitor_convergence"]) {
+ PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_DEFAULT, &vf);
+ KSPMonitorSet(ksp, ksp_monitor_norm, vf, 0);
+ }
// Set tolerances
const int max_ksp_it = krylov_parameters["maximum_iterations"];
diff -Naur dolfin-1.6.0/dolfin/nls/TAOLinearBoundSolver.h dolfin-1.6.0.new/dolfin/nls/TAOLinearBoundSolver.h
--- dolfin-1.6.0/dolfin/nls/TAOLinearBoundSolver.h 2015-07-28 17:05:55.000000000 +0200
+++ dolfin-1.6.0.new/dolfin/nls/TAOLinearBoundSolver.h 2016-06-27 19:08:09.157561005 +0200
@@ -174,6 +174,10 @@
// Tao solver pointer
Tao _tao;
+ // monitoring functions
+ PetscViewerAndFormat* vf;
+ static PetscErrorCode ksp_monitor_norm(KSP ksp, PetscInt n, PetscReal rnorm, void *ctx);
+
// Petsc preconditioner
std::shared_ptr<PETScPreconditioner> preconditioner;

39
var/spack/repos/builtin/packages/fenics/petsc-version-detection.patch Normal file
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@ -0,0 +1,39 @@
--- dolfin-1.6.0.orig/cmake/modules/FindPETSc.cmake 2015-07-28 17:05:55.000000000 +0200
+++ dolfin-1.6.0/cmake/modules/FindPETSc.cmake 2016-06-27 17:16:02.484402705 +0200
@@ -207,13 +207,7 @@
endif()
-# Build PETSc test program
-if (DOLFIN_SKIP_BUILD_TESTS)
- set(PETSC_TEST_RUNS TRUE)
- set(PETSC_VERSION "UNKNOWN")
- set(PETSC_VERSION_OK TRUE)
-elseif (FOUND_PETSC_CONF)
-
+if (FOUND_PETSC_CONF)
# Set flags for building test program
set(CMAKE_REQUIRED_INCLUDES ${PETSC_INCLUDE_DIRS})
set(CMAKE_REQUIRED_LIBRARIES ${PETSC_LIBRARIES})
@@ -271,7 +265,10 @@
set(PETSC_VERSION_OK TRUE)
endif()
mark_as_advanced(PETSC_VERSION_OK)
+endif()
+ # Build PETSc test program
+if (NOT DOLFIN_SKIP_BUILD_TESTS AND FOUND_PETSC_CONF)
# Run PETSc test program
set(PETSC_TEST_LIB_CPP
"${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/petsc_test_lib.cpp")
@@ -359,7 +356,9 @@
else()
message(STATUS "PETSc configured without Cusp support")
endif()
-
+else()
+ set(PETSC_TEST_RUNS TRUE)
+
endif()
# Check sizeof(PetscInt)