/usr/include/deal.II/lac/parallel_vector.templates.h is in libdeal.ii-dev 8.4.2-2+b1.
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//
// Copyright (C) 2011 - 2015 by the deal.II authors
//
// This file is part of the deal.II library.
//
// The deal.II library is free software; you can use it, redistribute
// it, and/or modify it under the terms of the GNU Lesser General
// Public License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
// The full text of the license can be found in the file LICENSE at
// the top level of the deal.II distribution.
//
// ---------------------------------------------------------------------
#ifndef dealii__parallel_vector_templates_h
#define dealii__parallel_vector_templates_h
#include <deal.II/base/config.h>
#include <deal.II/lac/parallel_vector.h>
#include <deal.II/lac/vector_view.h>
#include <deal.II/lac/petsc_parallel_vector.h>
#include <deal.II/lac/trilinos_vector.h>
DEAL_II_NAMESPACE_OPEN
namespace parallel
{
namespace distributed
{
template <typename Number>
void
Vector<Number>::clear_mpi_requests ()
{
#ifdef DEAL_II_WITH_MPI
for (size_type j=0; j<compress_requests.size(); j++)
MPI_Request_free(&compress_requests[j]);
compress_requests.clear();
for (size_type j=0; j<update_ghost_values_requests.size(); j++)
MPI_Request_free(&update_ghost_values_requests[j]);
update_ghost_values_requests.clear();
#endif
}
template <typename Number>
void
Vector<Number>::resize_val (const size_type new_alloc_size)
{
if (new_alloc_size > allocated_size)
{
Assert (((allocated_size > 0 && val != 0) ||
val == 0), ExcInternalError());
if (val != 0)
free(val);
Utilities::System::posix_memalign ((void **)&val, 64, sizeof(Number)*new_alloc_size);
allocated_size = new_alloc_size;
}
else if (new_alloc_size == 0)
{
if (val != 0)
free(val);
val = 0;
allocated_size = 0;
}
}
template <typename Number>
void
Vector<Number>::reinit (const size_type size,
const bool omit_zeroing_entries)
{
clear_mpi_requests();
// check whether we need to reallocate
resize_val (size);
// reset vector view
vector_view.reinit (size, val);
// delete previous content in import data
if (import_data != 0)
delete[] import_data;
import_data = 0;
// set partitioner to serial version
partitioner.reset (new Utilities::MPI::Partitioner (size));
// set entries to zero if so requested
if (omit_zeroing_entries == false)
this->operator = (Number());
vector_is_ghosted = false;
}
template <typename Number>
template <typename Number2>
void
Vector<Number>::reinit (const Vector<Number2> &v,
const bool omit_zeroing_entries)
{
clear_mpi_requests();
Assert (v.partitioner.get() != 0, ExcNotInitialized());
// check whether the partitioners are
// different (check only if the are allocated
// differently, not if the actual data is
// different)
if (partitioner.get() != v.partitioner.get())
{
partitioner = v.partitioner;
const size_type new_allocated_size = partitioner->local_size() +
partitioner->n_ghost_indices();
resize_val (new_allocated_size);
vector_view.reinit (partitioner->local_size(), val);
}
else
Assert (vector_view.size() == partitioner->local_size(),
ExcInternalError());
if (omit_zeroing_entries == false)
this->operator= (Number());
if (import_data != 0)
{
delete [] import_data;
// do not reallocate import_data directly, but only upon request. It
// is only used as temporary storage for compress() and
// update_ghost_values, and we might have vectors where we never
// call these methods and hence do not need to have the storage.
import_data = 0;
}
vector_is_ghosted = false;
}
template <typename Number>
void
Vector<Number>::reinit (const IndexSet &locally_owned_indices,
const IndexSet &ghost_indices,
const MPI_Comm communicator)
{
// set up parallel partitioner with index sets and communicator
std_cxx11::shared_ptr<const Utilities::MPI::Partitioner> new_partitioner
(new Utilities::MPI::Partitioner (locally_owned_indices,
ghost_indices, communicator));
reinit (new_partitioner);
}
template <typename Number>
void
Vector<Number>::reinit (const IndexSet &locally_owned_indices,
const MPI_Comm communicator)
{
// set up parallel partitioner with index sets and communicator
std_cxx11::shared_ptr<const Utilities::MPI::Partitioner> new_partitioner
(new Utilities::MPI::Partitioner (locally_owned_indices,
communicator));
reinit (new_partitioner);
}
template <typename Number>
void
Vector<Number>::reinit (const std_cxx11::shared_ptr<const Utilities::MPI::Partitioner> &partitioner_in)
{
clear_mpi_requests();
partitioner = partitioner_in;
// set vector size and allocate memory
const size_type new_allocated_size = partitioner->local_size() +
partitioner->n_ghost_indices();
resize_val (new_allocated_size);
vector_view.reinit (partitioner->local_size(), val);
// initialize to zero
this->operator= (Number());
if (import_data != 0)
{
delete [] import_data;
// do not reallocate import_data directly, but only upon request. It
// is only used as temporary storage for compress() and
// update_ghost_values, and we might have vectors where we never
// call these methods and hence do not need to have the storage.
import_data = 0;
}
vector_is_ghosted = false;
}
#ifdef DEAL_II_WITH_PETSC
namespace internal
{
template <typename PETSC_Number, typename Number>
void copy_petsc_vector (const PETSC_Number *petsc_start_ptr,
const PETSC_Number *petsc_end_ptr,
Number *ptr)
{
std::copy(petsc_start_ptr, petsc_end_ptr, ptr);
}
template <typename PETSC_Number, typename Number>
void copy_petsc_vector (const std::complex<PETSC_Number> *petsc_start_ptr,
const std::complex<PETSC_Number> *petsc_end_ptr,
std::complex<Number> *ptr)
{
std::copy(petsc_start_ptr, petsc_end_ptr, ptr);
}
template <typename PETSC_Number, typename Number>
void copy_petsc_vector (const std::complex<PETSC_Number> *petsc_start_ptr,
const std::complex<PETSC_Number> *petsc_end_ptr,
Number *ptr)
{
AssertThrow(false, ExcMessage("Tried to copy complex -> real"));
}
}
template <typename Number>
Vector<Number> &
Vector<Number>::operator = (const PETScWrappers::MPI::Vector &petsc_vec)
{
Assert(petsc_vec.locally_owned_elements() == locally_owned_elements(),
StandardExceptions::ExcInvalidState());
// get a representation of the vector and copy it
PetscScalar *start_ptr;
int ierr = VecGetArray (static_cast<const Vec &>(petsc_vec), &start_ptr);
AssertThrow (ierr == 0, ExcPETScError(ierr));
const size_type vec_size = local_size();
internal::copy_petsc_vector (start_ptr, start_ptr + vec_size, begin());
// restore the representation of the vector
ierr = VecRestoreArray (static_cast<const Vec &>(petsc_vec), &start_ptr);
AssertThrow (ierr == 0, ExcPETScError(ierr));
// spread ghost values between processes?
if (vector_is_ghosted || petsc_vec.has_ghost_elements())
update_ghost_values();
// return a pointer to this object per normal c++ operator overloading
// semantics
return *this;
}
#endif
#ifdef DEAL_II_WITH_TRILINOS
template <typename Number>
Vector<Number> &
Vector<Number>::operator = (const TrilinosWrappers::MPI::Vector &trilinos_vec)
{
if (trilinos_vec.has_ghost_elements() == false)
{
Assert(trilinos_vec.locally_owned_elements() == locally_owned_elements(),
StandardExceptions::ExcInvalidState());
}
else
// ghosted trilinos vector must contain the local range of this vector
// which is contiguous
{
Assert((trilinos_vec.locally_owned_elements() & locally_owned_elements())
== locally_owned_elements(),
StandardExceptions::ExcInvalidState());
}
// create on trilinos data
const std::size_t start_index =
trilinos_vec.vector_partitioner().NumMyElements() > 0 ?
trilinos_vec.vector_partitioner().
LID(static_cast<TrilinosWrappers::types::int_type>(this->local_range().first)) : 0;
const VectorView<double> in_view (local_size(), trilinos_vec.begin()+start_index);
static_cast<dealii::Vector<Number>&>(vector_view) =
static_cast<const dealii::Vector<double>&>(in_view);
// spread ghost values between processes?
if (vector_is_ghosted || trilinos_vec.has_ghost_elements())
update_ghost_values();
// return a pointer to this object per normal c++ operator overloading
// semantics
return *this;
}
#endif
template <typename Number>
void
Vector<Number>::copy_from (const Vector<Number> &c,
const bool call_update_ghost_values)
{
AssertDimension (local_range().first, c.local_range().first);
AssertDimension (local_range().second, c.local_range().second);
AssertDimension (vector_view.size(), c.vector_view.size());
vector_view = c.vector_view;
if (call_update_ghost_values == true)
update_ghost_values();
else
vector_is_ghosted = false;
}
template <typename Number>
void
Vector<Number>::compress_start (const unsigned int counter,
::dealii::VectorOperation::values operation)
{
(void)counter;
(void)operation;
Assert (vector_is_ghosted == false,
ExcMessage ("Cannot call compress() on a ghosted vector"));
#ifdef DEAL_II_WITH_MPI
// nothing to do for insert (only need to zero ghost entries in
// compress_finish()). in debug mode we want to check consistency
// of the inserted data, therefore the communication is still
// initialized. Having different code in debug and optimized mode is
// somewhat dangerous, but it really saves communication so it seems
// still worthwhile.
#ifndef DEBUG
if (operation == VectorOperation::insert)
return;
#endif
const Utilities::MPI::Partitioner &part = *partitioner;
// nothing to do when we neither have import
// nor ghost indices.
if (part.n_ghost_indices()==0 && part.n_import_indices()==0)
return;
// make this function thread safe
Threads::Mutex::ScopedLock lock (mutex);
const unsigned int n_import_targets = part.import_targets().size();
const unsigned int n_ghost_targets = part.ghost_targets().size();
// Need to send and receive the data. Use non-blocking communication,
// where it is generally less overhead to first initiate the receive and
// then actually send the data
if (compress_requests.size() == 0)
{
// set channels in different range from update_ghost_values channels
const unsigned int channel = counter + 400;
unsigned int current_index_start = 0;
compress_requests.resize (n_import_targets + n_ghost_targets);
// allocate import_data in case it is not set up yet
if (import_data == 0)
import_data = new Number[part.n_import_indices()];
for (unsigned int i=0; i<n_import_targets; i++)
{
AssertThrow (static_cast<size_type>(part.import_targets()[i].second)*
sizeof(Number) <
static_cast<size_type>(std::numeric_limits<int>::max()),
ExcMessage("Index overflow: Maximum message size in MPI is 2GB. "
"The number of ghost entries times the size of 'Number' "
"exceeds this value. This is not supported."));
MPI_Recv_init (&import_data[current_index_start],
part.import_targets()[i].second*sizeof(Number),
MPI_BYTE,
part.import_targets()[i].first,
part.import_targets()[i].first +
part.n_mpi_processes()*channel,
part.get_communicator(),
&compress_requests[i]);
current_index_start += part.import_targets()[i].second;
}
AssertDimension(current_index_start, part.n_import_indices());
Assert (part.local_size() == vector_view.size(), ExcInternalError());
current_index_start = part.local_size();
for (unsigned int i=0; i<n_ghost_targets; i++)
{
AssertThrow (static_cast<size_type>(part.ghost_targets()[i].second)*
sizeof(Number) <
static_cast<size_type>(std::numeric_limits<int>::max()),
ExcMessage("Index overflow: Maximum message size in MPI is 2GB. "
"The number of ghost entries times the size of 'Number' "
"exceeds this value. This is not supported."));
MPI_Send_init (&this->val[current_index_start],
part.ghost_targets()[i].second*sizeof(Number),
MPI_BYTE,
part.ghost_targets()[i].first,
part.this_mpi_process() +
part.n_mpi_processes()*channel,
part.get_communicator(),
&compress_requests[n_import_targets+i]);
current_index_start += part.ghost_targets()[i].second;
}
AssertDimension (current_index_start,
part.local_size()+part.n_ghost_indices());
}
AssertDimension(n_import_targets + n_ghost_targets,
compress_requests.size());
if (compress_requests.size() > 0)
{
int ierr = MPI_Startall(compress_requests.size(),&compress_requests[0]);
(void)ierr;
Assert (ierr == MPI_SUCCESS, ExcInternalError());
}
#endif
}
template <typename Number>
void
Vector<Number>::compress_finish (::dealii::VectorOperation::values operation)
{
#ifdef DEAL_II_WITH_MPI
// in optimized mode, no communication was started, so leave the
// function directly (and only clear ghosts)
#ifndef DEBUG
if (operation == VectorOperation::insert)
{
zero_out_ghosts();
return;
}
#endif
const Utilities::MPI::Partitioner &part = *partitioner;
// nothing to do when we neither have import nor ghost indices.
if (part.n_ghost_indices()==0 && part.n_import_indices()==0)
return;
// make this function thread safe
Threads::Mutex::ScopedLock lock (mutex);
const unsigned int n_import_targets = part.import_targets().size();
const unsigned int n_ghost_targets = part.ghost_targets().size();
if (operation != dealii::VectorOperation::insert)
AssertDimension (n_ghost_targets+n_import_targets,
compress_requests.size());
// first wait for the receive to complete
if (compress_requests.size() > 0 && n_import_targets > 0)
{
int ierr = MPI_Waitall (n_import_targets, &compress_requests[0],
MPI_STATUSES_IGNORE);
(void)ierr;
Assert (ierr == MPI_SUCCESS, ExcInternalError());
Number *read_position = import_data;
std::vector<std::pair<unsigned int, unsigned int> >::const_iterator
my_imports = part.import_indices().begin();
// If the operation is no insertion, add the imported data to the
// local values. For insert, nothing is done here (but in debug mode
// we assert that the specified value is either zero or matches with
// the ones already present
if (operation != dealii::VectorOperation::insert)
for ( ; my_imports!=part.import_indices().end(); ++my_imports)
for (unsigned int j=my_imports->first; j<my_imports->second; j++)
local_element(j) += *read_position++;
else
for ( ; my_imports!=part.import_indices().end(); ++my_imports)
for (unsigned int j=my_imports->first; j<my_imports->second;
j++, read_position++)
Assert(*read_position == 0. ||
std::abs(local_element(j) - *read_position) <=
std::abs(local_element(j)) * 1000. *
std::numeric_limits<Number>::epsilon(),
ExcNonMatchingElements(*read_position, local_element(j),
part.this_mpi_process()));
AssertDimension(read_position-import_data,part.n_import_indices());
}
if (compress_requests.size() > 0 && n_ghost_targets > 0)
{
int ierr = MPI_Waitall (n_ghost_targets,
&compress_requests[n_import_targets],
MPI_STATUSES_IGNORE);
(void)ierr;
Assert (ierr == MPI_SUCCESS, ExcInternalError());
}
else
AssertDimension (part.n_ghost_indices(), 0);
zero_out_ghosts ();
#else
(void)operation;
#endif
}
template <typename Number>
void
Vector<Number>::update_ghost_values_start (const unsigned int counter) const
{
#ifdef DEAL_II_WITH_MPI
const Utilities::MPI::Partitioner &part = *partitioner;
// nothing to do when we neither have import nor ghost indices.
if (part.n_ghost_indices()==0 && part.n_import_indices()==0)
return;
// make this function thread safe
Threads::Mutex::ScopedLock lock (mutex);
const unsigned int n_import_targets = part.import_targets().size();
const unsigned int n_ghost_targets = part.ghost_targets().size();
// Need to send and receive the data. Use non-blocking communication,
// where it is generally less overhead to first initiate the receive and
// then actually send the data
if (update_ghost_values_requests.size() == 0)
{
Assert (part.local_size() == vector_view.size(),
ExcInternalError());
size_type current_index_start = part.local_size();
update_ghost_values_requests.resize (n_import_targets+n_ghost_targets);
for (unsigned int i=0; i<n_ghost_targets; i++)
{
// allow writing into ghost indices even though we are in a
// const function
MPI_Recv_init (const_cast<Number *>(&val[current_index_start]),
part.ghost_targets()[i].second*sizeof(Number),
MPI_BYTE,
part.ghost_targets()[i].first,
part.ghost_targets()[i].first +
counter*part.n_mpi_processes(),
part.get_communicator(),
&update_ghost_values_requests[i]);
current_index_start += part.ghost_targets()[i].second;
}
AssertDimension (current_index_start,
part.local_size()+part.n_ghost_indices());
// allocate import_data in case it is not set up yet
if (import_data == 0 && part.n_import_indices() > 0)
import_data = new Number[part.n_import_indices()];
current_index_start = 0;
for (unsigned int i=0; i<n_import_targets; i++)
{
MPI_Send_init (&import_data[current_index_start],
part.import_targets()[i].second*sizeof(Number),
MPI_BYTE, part.import_targets()[i].first,
part.this_mpi_process() +
part.n_mpi_processes()*counter,
part.get_communicator(),
&update_ghost_values_requests[n_ghost_targets+i]);
current_index_start += part.import_targets()[i].second;
}
AssertDimension (current_index_start, part.n_import_indices());
}
// copy the data that is actually to be send to the import_data field
if (part.n_import_indices() > 0)
{
Assert (import_data != 0, ExcInternalError());
Number *write_position = import_data;
std::vector<std::pair<unsigned int, unsigned int> >::const_iterator
my_imports = part.import_indices().begin();
for ( ; my_imports!=part.import_indices().end(); ++my_imports)
for (unsigned int j=my_imports->first; j<my_imports->second; j++)
*write_position++ = local_element(j);
}
AssertDimension (n_import_targets+n_ghost_targets,
update_ghost_values_requests.size());
if (update_ghost_values_requests.size() > 0)
{
int ierr = MPI_Startall(update_ghost_values_requests.size(),
&update_ghost_values_requests[0]);
(void)ierr;
Assert (ierr == MPI_SUCCESS, ExcInternalError());
}
#else
(void)counter;
#endif
}
template <typename Number>
void
Vector<Number>::update_ghost_values_finish () const
{
#ifdef DEAL_II_WITH_MPI
// wait for both sends and receives to complete, even though only
// receives are really necessary. this gives (much) better performance
AssertDimension (partitioner->ghost_targets().size() +
partitioner->import_targets().size(),
update_ghost_values_requests.size());
if (update_ghost_values_requests.size() > 0)
{
// make this function thread safe
Threads::Mutex::ScopedLock lock (mutex);
int ierr = MPI_Waitall (update_ghost_values_requests.size(),
&update_ghost_values_requests[0],
MPI_STATUSES_IGNORE);
(void)ierr;
Assert (ierr == MPI_SUCCESS, ExcInternalError());
}
#endif
vector_is_ghosted = true;
}
template <typename Number>
void
Vector<Number>::swap (Vector<Number> &v)
{
#ifdef DEAL_II_WITH_MPI
#ifdef DEBUG
if (Utilities::MPI::job_supports_mpi())
{
// make sure that there are not outstanding requests from updating
// ghost values or compress
int flag = 1;
if (update_ghost_values_requests.size()>0)
{
int ierr = MPI_Testall (update_ghost_values_requests.size(),
&update_ghost_values_requests[0],
&flag, MPI_STATUSES_IGNORE);
Assert (ierr == MPI_SUCCESS, ExcInternalError());
Assert (flag == 1,
ExcMessage("MPI found unfinished update_ghost_values() requests"
"when calling swap, which is not allowed"));
}
if (compress_requests.size()>0)
{
int ierr = MPI_Testall (compress_requests.size(), &compress_requests[0],
&flag, MPI_STATUSES_IGNORE);
Assert (ierr == MPI_SUCCESS, ExcInternalError());
Assert (flag == 1,
ExcMessage("MPI found unfinished compress() requests "
"when calling swap, which is not allowed"));
}
}
#endif
std::swap (compress_requests, v.compress_requests);
std::swap (update_ghost_values_requests, v.update_ghost_values_requests);
#endif
std::swap (partitioner, v.partitioner);
std::swap (allocated_size, v.allocated_size);
std::swap (val, v.val);
std::swap (import_data, v.import_data);
std::swap (vector_is_ghosted, v.vector_is_ghosted);
// vector view cannot be swapped so reset it manually (without touching
// the vector elements)
vector_view.reinit (partitioner->local_size(), val);
v.vector_view.reinit (v.partitioner->local_size(), v.val);
}
template <typename Number>
inline
bool
Vector<Number>::partitioners_are_compatible
(const Utilities::MPI::Partitioner &part) const
{
return partitioner->is_compatible (part);
}
template <typename Number>
inline
bool
Vector<Number>::partitioners_are_globally_compatible
(const Utilities::MPI::Partitioner &part) const
{
return partitioner->is_globally_compatible (part);
}
template <typename Number>
std::size_t
Vector<Number>::memory_consumption () const
{
std::size_t memory = sizeof(*this);
memory += sizeof (Number) * static_cast<std::size_t>(allocated_size);
// if the partitioner is shared between more processors, just count a
// fraction of that memory, since we're not actually using more memory
// for it.
if (partitioner.use_count() > 0)
memory += partitioner->memory_consumption()/partitioner.use_count()+1;
if (import_data != 0)
memory += (static_cast<std::size_t>(partitioner->n_import_indices())*
sizeof(Number));
return memory;
}
template <typename Number>
void
Vector<Number>::print (std::ostream &out,
const unsigned int precision,
const bool scientific,
const bool across) const
{
Assert (partitioner.get() !=0, ExcInternalError());
AssertThrow (out, ExcIO());
std::ios::fmtflags old_flags = out.flags();
unsigned int old_precision = out.precision (precision);
out.precision (precision);
if (scientific)
out.setf (std::ios::scientific, std::ios::floatfield);
else
out.setf (std::ios::fixed, std::ios::floatfield);
// to make the vector write out all the information in order, use as
// many barriers as there are processors and start writing when it's our
// turn
#ifdef DEAL_II_WITH_MPI
if (partitioner->n_mpi_processes() > 1)
for (unsigned int i=0; i<partitioner->this_mpi_process(); i++)
MPI_Barrier (partitioner->get_communicator());
#endif
out << "Process #" << partitioner->this_mpi_process() << std::endl
<< "Local range: [" << partitioner->local_range().first << ", "
<< partitioner->local_range().second << "), global size: "
<< partitioner->size() << std::endl
<< "Vector data:" << std::endl;
if (across)
for (size_type i=0; i<partitioner->local_size(); ++i)
out << local_element(i) << ' ';
else
for (size_type i=0; i<partitioner->local_size(); ++i)
out << local_element(i) << std::endl;
out << std::endl;
if (vector_is_ghosted)
{
out << "Ghost entries (global index / value):" << std::endl;
if (across)
for (size_type i=0; i<partitioner->n_ghost_indices(); ++i)
out << '(' << partitioner->ghost_indices().nth_index_in_set(i)
<< '/' << local_element(partitioner->local_size()+i) << ") ";
else
for (size_type i=0; i<partitioner->n_ghost_indices(); ++i)
out << '(' << partitioner->ghost_indices().nth_index_in_set(i)
<< '/' << local_element(partitioner->local_size()+i) << ")"
<< std::endl;
out << std::endl;
}
out << std::flush;
#ifdef DEAL_II_WITH_MPI
if (partitioner->n_mpi_processes() > 1)
{
MPI_Barrier (partitioner->get_communicator());
for (unsigned int i=partitioner->this_mpi_process()+1;
i<partitioner->n_mpi_processes(); i++)
MPI_Barrier (partitioner->get_communicator());
}
#endif
AssertThrow (out, ExcIO());
// reset output format
out.flags (old_flags);
out.precision(old_precision);
}
} // end of namespace distributed
} // end of namespace parallel
DEAL_II_NAMESPACE_CLOSE
#endif
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