Merge branch 'feature/mpi_wrapper_library' into 'master'

added code from the mpi14 library for parallel mpi communication with a nice wrapper interface

See merge request !83

src/amdis/common/CMakeLists.txt

@@ -34,3 +34,5 @@ install(FILES
     TypeTraits.hpp
     ValueCategory.hpp
 DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/amdis/common)
+
+add_subdirectory(parallel)
\ No newline at end of file

src/amdis/common/parallel/CMakeLists.txt

+install(FILES
+    Collective.hpp
+    Communicator.hpp
+    Communicator.inc.hpp
+    MpiTraits.hpp
+    RecvDynamicSize.hpp
+    Request.hpp
+    RequestChain.hpp
+    RequestOperations.hpp
+DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/amdis/common/parallel)

src/amdis/common/parallel/Collective.hpp

+#pragma once
+
+#if HAVE_MPI
+#include <array>
+#include <vector>
+
+#include <mpi.h>
+
+#include <amdis/common/parallel/Request.hpp>
+#include <amdis/common/parallel/MpiTraits.hpp>
+
+namespace AMDiS { namespace Mpi
+{
+  template <class T, class Operation>
+  void all_reduce(MPI_Comm comm, T const& in, T& out, Operation)
+  {
+    MPI_Allreduce(&in, &out, 1, type_to_mpi<T>(), op_to_mpi<Operation>(), comm);
+  }
+
+  template <class T, class Operation>
+  void all_reduce(MPI_Comm comm, T& inout, Operation)
+  {
+    MPI_Allreduce(MPI_IN_PLACE, &inout, 1, type_to_mpi<T>(), op_to_mpi<Operation>(), comm);
+  }
+
+
+  template <class T>
+  void all_gather(MPI_Comm comm, T const& in, std::vector<T>& out)
+  {
+    int size = 1;
+    MPI_Comm_size(comm, &size);
+    out.resize(size);
+    MPI_Allgather(to_void_ptr(&in), 1, type_to_mpi<T>(), to_void_ptr(out.data()), 1, type_to_mpi<T>(), comm);
+  }
+
+  template <class T, std::size_t N>
+  void all_gather(MPI_Comm comm, std::array<T,N> const& in, std::vector<T>& out)
+  {
+    int size = 1;
+    MPI_Comm_size(comm, &size);
+    out.resize(size * N);
+    MPI_Allgather(to_void_ptr(in.data()), N, type_to_mpi<T>(), to_void_ptr(out.data()), N, type_to_mpi<T>(), comm);
+  }
+
+
+  template <class T>
+  std::vector<T> all_gather(MPI_Comm comm, T const& in)
+  {
+    int size = 1;
+    MPI_Comm_size(comm, &size);
+    std::vector<T> out(size);
+    MPI_Allgather(to_void_ptr(&in), 1, type_to_mpi<T>(), to_void_ptr(out.data()), 1, type_to_mpi<T>(), comm);
+    return out;
+  }
+
+  template <class T, std::size_t N>
+  std::vector<T> all_gather(MPI_Comm comm, std::array<T,N> const& in)
+  {
+    int size = 1;
+    MPI_Comm_size(comm, &size);
+    std::vector<T> out(size * N);
+    MPI_Allgather(to_void_ptr(in.data()), N, type_to_mpi<T>(), to_void_ptr(out.data()), N, type_to_mpi<T>(), comm);
+    return out;
+  }
+
+
+  template <class T>
+  Request iall_gather(MPI_Comm comm, T const& in, std::vector<T>& out)
+  {
+    int size = 1;
+    MPI_Comm_size(comm, &size);
+    out.resize(size);
+    MPI_Request request;
+    MPI_Iallgather(to_void_ptr(&in), 1, type_to_mpi<T>(), to_void_ptr(out.data()), 1, type_to_mpi<T>(), comm, &request);
+
+    return {request};
+  }
+
+  template <class T, std::size_t N>
+  Request iall_gather(MPI_Comm comm, std::array<T,N> const& in, std::vector<T>& out)
+  {
+    int size = 1;
+    MPI_Comm_size(comm, &size);
+    out.resize(size * N);
+    MPI_Request request;
+    MPI_Iallgather(to_void_ptr(in.data()), N, type_to_mpi<T>(), to_void_ptr(out.data()), N, type_to_mpi<T>(), comm, &request);
+
+    return {request};
+  }
+
+}} // end namespace AMDiS::Mpi
+
+#endif // HAVE_MPI

src/amdis/common/parallel/Communicator.hpp

+#pragma once
+
+#if HAVE_MPI
+#include <array>
+#include <iostream>
+#include <list>
+#include <map>
+#include <memory>
+#include <string>
+#include <type_traits>
+#include <vector>
+
+#include <mpi.h>
+
+#include <amdis/Environment.hpp>
+#include <amdis/common/ConceptsBase.hpp>
+#include <amdis/common/TypeTraits.hpp>
+#include <amdis/common/parallel/Request.hpp>
+#include <amdis/common/parallel/RecvDynamicSize.hpp>
+#include <amdis/common/parallel/MpiTraits.hpp>
+
+namespace AMDiS {
+namespace Concepts {
+  template <class T>
+  constexpr bool RawPointer = std::is_pointer<std::decay_t<T>>::value;
+}
+
+namespace Mpi
+{
+  struct Tag
+  {
+    int value = 0;
+  };
+
+  class Communicator
+  {
+  public:
+
+    /// Constructor, stores an MPI communicator, e.g. MPI_COMM_WORLD
+    Communicator(MPI_Comm comm = Environment::comm())
+      : comm_(comm)
+    {
+      MPI_Comm_size(comm_, &size_);
+      MPI_Comm_rank(comm_, &rank_);
+    }
+
+
+  public:
+
+    operator MPI_Comm() const { return comm_; }
+
+    int size() const { return size_; }
+    int rank() const { return rank_; }
+
+  public:
+
+    // send mpi datatype
+    template <class Data, REQUIRES(not Concepts::RawPointer<Data>)>
+    void send(Data const& data, int to, Tag tag = {}) const;
+
+    // send array of mpi datatypes
+    template <class T>
+    void send(T const* data, std::size_t size, int to, Tag tag = {}) const;
+
+    template <class T, std::size_t N>
+    void send(T const (&data)[N], int to, Tag tag = {}) const
+    {
+      send(&data[0], N, to, tag);
+    }
+
+    template <class T, std::size_t N>
+    void send(std::array<T,N> const& array, int to, Tag tag = {}) const
+    {
+      send(array.data(), N, to, tag);
+    }
+
+    template <class T>
+    void send(std::vector<T> const& vec, int to, Tag tag = {}) const;
+
+    void send(std::string const& str, int to, Tag tag = {}) const
+    {
+      MPI_Send(to_void_ptr(str.data()), int(str.size()), MPI_CHAR, to, tag.value, comm_);
+    }
+
+
+    // -------------------------------------------------------------------------------------
+
+
+    // send mpi datatype (non-blocking)
+    template <class Data, REQUIRES(not Concepts::RawPointer<Data>)>
+    Request isend(Data const& data, int to, Tag tag = {}) const;
+
+    // send array of mpi datatypes (non-blocking)
+    template <class Data>
+    Request isend(Data const* data, std::size_t size, int to, Tag tag = {}) const;
+
+    template <class T, std::size_t N>
+    Request isend(T const (&data)[N], int to, Tag tag = {}) const
+    {
+      return isend(&data[0], N, to, tag);
+    }
+
+    template <class T, std::size_t N>
+    Request isend(std::array<T,N> const& array, int to, Tag tag = {}) const
+    {
+      return isend(array.data(), N, to, tag);
+    }
+
+    template <class T>
+    Request isend(std::vector<T> const& vec, int to, Tag tag = {}) const;
+
+    Request isend(std::string const& str, int to, Tag tag = {}) const
+    {
+      MPI_Request request;
+      MPI_Isend(to_void_ptr(str.data()), int(str.size()), MPI_CHAR, to, tag.value, comm_, &request);
+      return {request};
+    }
+
+    // -------------------------------------------------------------------------------------
+
+    // receive mpi datatype
+    template <class Data, REQUIRES(not Concepts::RawPointer<Data>)>
+    MPI_Status recv(Data& data, int from, Tag tag = {}) const;
+
+    // receive array of mpi datatypes
+    template <class T>
+    MPI_Status recv(T* data, std::size_t size, int from, Tag tag = {}) const;
+
+    template <class T, std::size_t N>
+    MPI_Status recv(T (&data)[N], int from, Tag tag = {}) const
+    {
+      return recv(data, N, from, tag);
+    }
+
+    template <class T, std::size_t N>
+    MPI_Status recv(std::array<T,N>& data, int from, Tag tag = {}) const
+    {
+      return recv(data.data(), N, from, tag);
+    }
+
+    template <class T>
+    MPI_Status recv(std::vector<T>& data, int from, Tag tag = {}) const;
+
+    MPI_Status recv(std::string& str, int from, Tag tag = {}) const
+    {
+      MPI_Status status;
+      MPI_Probe(from, tag.value, comm_, &status);
+
+      int size = 0;
+      MPI_Get_count(&status, MPI_CHAR, &size);
+
+      str.resize(size);
+      MPI_Recv(&str[0], size, MPI_CHAR, from, tag.value, comm_, MPI_STATUS_IGNORE);
+      return status;
+    }
+
+    // -------------------------------------------------------------------------------------
+
+    // receive mpi datatype
+    template <class Data, REQUIRES(not Concepts::RawPointer<Data>)>
+    Request irecv(Data& data, int from, Tag tag = {}) const;
+
+    // receive array of mpi datatypes
+    template <class Data>
+    Request irecv(Data* data, std::size_t size, int from, Tag tag = {}) const;
+
+    template <class T, std::size_t N>
+    Request irecv(T (&data)[N], int from, Tag tag = {}) const
+    {
+      return irecv(&data[0], N, from, tag);
+    }
+
+    template <class T, std::size_t N>
+    Request irecv(std::array<T,N>& data, int from, Tag tag = {}) const
+    {
+      return irecv(data.data(), N, from, tag);
+    }
+
+    template <class Receiver>
+      std::enable_if_t< Concepts::Callable<Receiver,MPI_Status>, Request>
+    irecv(Receiver&& recv, int from, Tag tag = {}) const
+    {
+      return Request{ RecvDynamicSize(from, tag.value, comm_, std::forward<Receiver>(recv)) };
+    }
+
+    // receive vector of mpi datatypes
+    // 1. until message received, call MPI_Iprobe to retrieve status and size of message
+    // 2. resize data-vector
+    // 3. receive data into vector
+    template <class T>
+    Request irecv(std::vector<T>& vec, int from, Tag tag = {}) const;
+
+    Request irecv(std::string& str, int from, Tag tag = {}) const
+    {
+      return Request{RecvDynamicSize(from,tag.value,comm_,
+        [comm=comm_,&str](MPI_Status status) -> MPI_Request
+        {
+          int size = 0;
+          MPI_Get_count(&status, MPI_CHAR, &size);
+
+          str.resize(size);
+          MPI_Request req;
+          MPI_Irecv(&str[0], size, MPI_CHAR, status.MPI_SOURCE, status.MPI_TAG, comm, &req);
+
+          return req;
+        }) };
+    }
+
+
+  protected:
+
+    // free unused buffers
+    void check_buffers() const
+    {
+      using Buffers = std::decay_t<decltype(buffers_)>;
+
+      std::list<typename Buffers::iterator> remove;
+      for (auto it = buffers_.begin(); it != buffers_.end(); ++it) {
+        int flag;
+        MPI_Request_get_status(it->first, &flag, MPI_STATUS_IGNORE);
+        if (flag != 0)
+          remove.push_back(it);
+      }
+
+      for (auto it : remove)
+        buffers_.erase(it);
+    }
+
+
+    std::pair<MPI_Request, std::string>& make_buffer(MPI_Status status, std::size_t len) const
+    {
+      auto it = buffers_.emplace(buffers_.end(), MPI_Request{}, std::string(len,' '));
+      buffers_iterators_[{status.MPI_SOURCE, status.MPI_TAG}] = it;
+      return buffers_.back();
+    }
+
+    std::pair<MPI_Request, std::string>& get_buffer(MPI_Status status) const
+    {
+      auto it = buffers_iterators_[{status.MPI_SOURCE, status.MPI_TAG}];
+      return *it;
+    }
+
+  protected:
+
+    MPI_Comm comm_;
+
+    int rank_ = 0;
+    int size_ = 1;
+
+    using BufferList = std::list< std::pair<MPI_Request, std::string> >;
+    mutable BufferList buffers_;
+
+    using BufferIter = BufferList::iterator;
+    mutable std::map<std::pair<int,int>, BufferIter> buffers_iterators_;
+  };
+
+}} // end namespace AMDiS::Mpi
+
+#endif // HAVE_MPI
+
+#include <amdis/common/parallel/Communicator.inc.hpp>

src/amdis/common/parallel/Communicator.inc.hpp

+#pragma once
+
+#if HAVE_MPI
+
+namespace AMDiS { namespace Mpi {
+
+// send mpi datatype
+template <class Data, REQUIRES_(not Concepts::RawPointer<Data>)>
+void Communicator::send(Data const& data, int to, Tag tag) const
+{
+  MPI_Send(to_void_ptr(&data), 1, type_to_mpi<Data>(), to, tag.value, comm_);
+}
+
+
+// send array of mpi datatypes
+template <class Data>
+void Communicator::send(Data const* data, std::size_t size, int to, Tag tag) const
+{
+  MPI_Send(to_void_ptr(data), int(size), type_to_mpi<Data>(), to, tag.value, comm_);
+}
+
+
+template <class T>
+void Communicator::send(std::vector<T> const& vec, int to, Tag tag) const
+{
+  MPI_Send(to_void_ptr(vec.data()), int(vec.size()), type_to_mpi<T>(), to, tag.value, comm_);
+}
+
+
+// -------------------------------------------------------------------------------------
+
+
+// send mpi datatype (non-blocking)
+template <class Data, REQUIRES_(not Concepts::RawPointer<Data>)>
+Request Communicator::isend(Data const& data, int to, Tag tag) const
+{
+  MPI_Request request;
+  MPI_Isend(to_void_ptr(&data), 1, type_to_mpi<Data>(), to, tag.value, comm_, &request);
+  return {request};
+}
+
+
+// send array of mpi datatypes (non-blocking)
+template <class Data>
+Request Communicator::isend(Data const* data, std::size_t size, int to, Tag tag) const
+{
+  MPI_Request request;
+  MPI_Isend(to_void_ptr(data), size, type_to_mpi<Data>(), to, tag.value, comm_, &request);
+  return {request};
+}
+
+
+template <class T>
+Request Communicator::isend(std::vector<T> const& vec, int to, Tag tag) const
+{
+  MPI_Request request;
+  MPI_Isend(to_void_ptr(vec.data()), int(vec.size()), type_to_mpi<T>(), to, tag.value, comm_, &request);
+  return {request};
+}
+
+// -------------------------------------------------------------------------------------
+
+// receive mpi datatype
+template <class Data, REQUIRES_(not Concepts::RawPointer<Data>)>
+MPI_Status Communicator::recv(Data& data, int from, Tag tag) const
+{
+  MPI_Status status;
+  MPI_Recv(&data, 1, type_to_mpi<Data>(), from, tag.value, comm_, &status);
+  return status;
+}
+
+
+// receive array of mpi datatypes
+template <class Data>
+MPI_Status Communicator::recv(Data* data, std::size_t size, int from, Tag tag) const
+{
+  MPI_Status status;
+  MPI_Recv(data, size, type_to_mpi<Data>(), from, tag.value, comm_, &status);
+  return status;
+}
+
+
+// receive array of mpi datatypes
+template <class T>
+MPI_Status Communicator::recv(std::vector<T>& vec, int from, Tag tag) const
+{
+  MPI_Status status;
+  MPI_Probe(from, tag.value, comm_, &status);
+
+  int size = 0;
+  MPI_Get_count(&status, type_to_mpi<T>(), &size);
+  int min_size = std::max(size,1);
+
+  vec.resize(min_size);
+  MPI_Recv(vec.data(), min_size, type_to_mpi<T>(), from, tag.value, comm_, MPI_STATUS_IGNORE);
+  if (size != min_size)
+    vec.resize(size);
+  return status;
+}
+
+
+// -------------------------------------------------------------------------------------
+
+// receive mpi datatype
+template <class Data, REQUIRES_(not Concepts::RawPointer<Data>)>
+Request Communicator::irecv(Data& data, int from, Tag tag) const
+{
+  MPI_Request request;
+  MPI_Irecv(&data, 1, type_to_mpi<Data>(), from, tag.value, comm_, &request);
+  return {request};
+}
+
+
+// receive array of mpi datatypes
+template <class Data>
+Request Communicator::irecv(Data* data, std::size_t size, int from, Tag tag) const
+{
+  MPI_Request request;
+  MPI_Irecv(data, size, type_to_mpi<Data>(), from, tag.value, comm_, &request);
+  return {request};
+}
+
+
+template <class T>
+Request Communicator::irecv(std::vector<T>& vec, int from, Tag tag) const
+{
+  return Request{ RecvDynamicSize(from,tag.value,comm_,
+    [comm=comm_,&vec](MPI_Status status) -> MPI_Request
+    {
+      int size = 0;
+      MPI_Get_count(&status, type_to_mpi<T>(), &size);
+      int min_size = std::max(size,1);
+
+      vec.resize(min_size);
+      MPI_Request req;
+      MPI_Irecv(vec.data(), min_size, type_to_mpi<T>(), status.MPI_SOURCE, status.MPI_TAG, comm, &req);
+      return req;
+    },
+    [&vec](MPI_Status status)
+    {
+      int size = 0;
+      MPI_Get_count(&status, type_to_mpi<T>(), &size);
+      vec.resize(size);
+    }) };
+}
+
+}} // end namespace AMDiS::Mpi
+
+#endif // HAVE_MPI

src/amdis/common/parallel/MpiTraits.hpp

+#pragma once
+
+#if HAVE_MPI
+
+#include <functional>
+#include <type_traits>
+
+#include <mpi.h>
+
+#include <dune/common/parallel/mpitraits.hh>
+
+namespace AMDiS {
+
+// forward declarations
+namespace Operation {
+  struct Plus;
+  struct Multiplies;
+  struct Max;
+  struct Min;
+}
+
+namespace Mpi
+{
+  namespace Impl2
+  {
+    template <class T>
+    struct is_mpi_type : std::false_type {};
+
+    template <> struct is_mpi_type<char> : std::true_type {};
+    template <> struct is_mpi_type<short> : std::true_type {};
+    template <> struct is_mpi_type<int> : std::true_type {};
+    template <> struct is_mpi_type<long> : std::true_type {};
+    template <> struct is_mpi_type<long long> : std::true_type {};
+    template <> struct is_mpi_type<signed char> : std::true_type {};
+    template <> struct is_mpi_type<unsigned char> : std::true_type {};
+    template <> struct is_mpi_type<unsigned short> : std::true_type {};
+    template <> struct is_mpi_type<unsigned int> : std::true_type {};
+    template <> struct is_mpi_type<unsigned long> : std::true_type {};
+    template <> struct is_mpi_type<unsigned long long> : std::true_type {};
+    template <> struct is_mpi_type<float> : std::true_type {};
+    template <> struct is_mpi_type<double> : std::true_type {};
+    template <> struct is_mpi_type<long double> : std::true_type {};
+
+    template <class T1, class T2>
+    struct is_mpi_type<std::pair<T1,T2>> : std::integral_constant<bool,
+      is_mpi_type<T1>::value &&
+      is_mpi_type<T2>::value &&
+      std::is_standard_layout<std::pair<T1,T2>>::value
+      >
+    {};
+
+  } // end namespace Impl2
+
+  template <class T>
+  using is_mpi_type = Impl2::is_mpi_type<T>;
+
+
+  template <class T>
+  MPI_Datatype type_to_mpi() { return Dune::MPITraits<T>::getType(); }
+
+  namespace Impl2
+  {
+    template <class T> using always_false = std::false_type;
+
+    template <class Op>
+    struct op_to_mpi;
+
+    template <> struct op_to_mpi<Operation::Min> { static MPI_Op value() { return MPI_MIN; } };
+    template <> struct op_to_mpi<Operation::Max> { static MPI_Op value() { return MPI_MAX; } };
+
+    template <> struct op_to_mpi<std::plus<>> { static MPI_Op value() { return MPI_SUM; } };
+    template <> struct op_to_mpi<Operation