Utilities::MPI::create_mpi_data_type_n_bytes

part of dealii#12752

doc/news/changes/minor/20211117tjhei

@@ -0,0 +1,3 @@
+New: Utilities::MPI::create_mpi_data_type_n_bytes() helps with large MPI communication and IO.
+<br>
+(Timo Heister, 2021/11/17)

include/deal.II/base/mpi.h

@@ -498,6 +498,39 @@ namespace Utilities
                                 const MPI_Comm &comm);
 #endif
 
+
+    /**
+     * Create an MPI_Datatype that consists of @p n_bytes bytes.
+     *
+     * The resulting data type can be used in MPI send/recv or MPI IO to process
+     * messages of sizes larger than 2 GB with MPI_Byte as the underlying data
+     * type. This helper is required for MPI versions before 4.0 because
+     * routines like MPI_Send
+     * use a signed interger for the @p count variable. Instead, you can use this
+     * data type with the appropriate size set to the size of your message and
+     * by passing
+     * 1 as the @p count.
+     *
+     * @note You need to free this data type after you are done using it by calling
+     * <code>MPI_Type_free(&result)</code>.
+     *
+     * Usage example:
+     * <code>
+     * std::vector<char> buffer;
+     * if (buffer.size()<(1U<<31))
+     *   MPI_Send(buffer.data(), buffer.size(), MPI_BYTE, dest, tag, comm);
+     * else
+     * {
+     *   MPI_Datatype bigtype;
+     *   Utilities::MPI::create_mpi_data_type_n_bytes(bigtype, buffer.size());
+     *   MPI_Send(buffer.data(), 1, bigtype, dest, tag, comm);
+     *   MPI_Type_free(&bigtype);
+     * }
+     * </code>
+     */
+    void
+    create_mpi_data_type_n_bytes(MPI_Datatype &result, std::size_t n_bytes);
+
     /**
      * Return the sum over all processors of the value @p t. This function is
      * collective over all processors given in the

source/base/mpi.cc

@@ -281,6 +281,8 @@ namespace Utilities
       return res;
     }
 
+
+
     IndexSet
     create_evenly_distributed_partitioning(const MPI_Comm &          comm,
                                            const IndexSet::size_type total_size)
@@ -295,6 +297,81 @@ namespace Utilities
 
 
 
+    void
+    create_mpi_data_type_n_bytes(MPI_Datatype &result, std::size_t n_bytes)
+    {
+#  ifdef DEAL_II_WITH_MPI
+      // Simplified version from BigMPI repository, see
+      // https://github.com/jeffhammond/BigMPI/blob/5300b18cc8ec1b2431bf269ee494054ee7bd9f72/src/type_contiguous_x.c#L74
+      // (code is MIT licensed)
+
+      // We create an MPI datatype that has the layout A*nB where A is
+      // max_signed_int bytes repeated n times and B is the remainder.
+
+      const MPI_Count max_signed_int = (1U << 31) - 1;
+
+      const MPI_Count n_chunks          = n_bytes / max_signed_int;
+      const MPI_Count n_bytes_remainder = n_bytes % max_signed_int;
+
+      Assert(static_cast<std::size_t>(max_signed_int * n_chunks +
+                                      n_bytes_remainder) == n_bytes,
+             ExcInternalError());
+
+      MPI_Datatype chunks;
+
+      int ierr = MPI_Type_vector(
+        n_chunks, max_signed_int, max_signed_int, MPI_BYTE, &chunks);
+      AssertThrowMPI(ierr);
+
+      MPI_Datatype remainder;
+      ierr = MPI_Type_contiguous(n_bytes_remainder, MPI_BYTE, &remainder);
+      AssertThrowMPI(ierr);
+
+      const int      blocklengths[2]  = {1, 1};
+      const MPI_Aint displacements[2] = {0,
+                                         static_cast<MPI_Aint>(n_chunks) *
+                                           max_signed_int};
+
+      // This fails if Aint happens to be 32 bits (maybe on some 32bit
+      // systems as it has type "long" which is usually 64bits) or the
+      // message is very, very big.
+      AssertThrow(
+        displacements[1] == n_chunks * max_signed_int,
+        ExcMessage(
+          "ERROR in create_mpi_data_type_n_bytes(), size too big to support."));
+
+      const MPI_Datatype types[2] = {chunks, remainder};
+      ierr =
+        MPI_Type_create_struct(2, blocklengths, displacements, types, &result);
+      AssertThrowMPI(ierr);
+
+      ierr = MPI_Type_commit(&result);
+      AssertThrowMPI(ierr);
+
+      ierr = MPI_Type_free(&chunks);
+      AssertThrowMPI(ierr);
+      ierr = MPI_Type_free(&remainder);
+      AssertThrowMPI(ierr);
+
+#    ifdef DEBUG
+#      if DEAL_II_MPI_VERSION_GTE(3, 0)
+      MPI_Count size64;
+      // this function is only available starting MPI 3.0:
+      ierr = MPI_Type_size_x(result, &size64);
+      AssertThrowMPI(ierr);
+
+      Assert(size64 == static_cast<MPI_Count>(n_bytes), ExcInternalError());
+#      endif
+#    endif
+
+#  else
+      (void)result;
+      (void)n_bytes;
+#  endif
+    }
+
+
+
     std::vector<unsigned int>
     compute_point_to_point_communication_pattern(
       const MPI_Comm &                 mpi_comm,

tests/mpi/create_mpi_datatype_01.cc

@@ -0,0 +1,116 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2021 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.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+
+// Test Utilities::MPI::create_mpi_data_type_n_bytes
+
+// To not require a lot of memory, we run this test with smaller
+// size. Change this bool to test the real 64bit size communication:
+const bool run_big = false;
+
+#include <deal.II/base/mpi.h>
+
+#include "../tests.h"
+
+using namespace dealii;
+
+void
+test_data_type(long long n_bytes)
+{
+  MPI_Datatype bigtype;
+  Utilities::MPI::create_mpi_data_type_n_bytes(bigtype, n_bytes);
+
+  deallog << "checking size " << n_bytes << ":";
+
+  int size32;
+  int ierr = MPI_Type_size(bigtype, &size32);
+  AssertThrowMPI(ierr);
+
+  if (size32 == MPI_UNDEFINED)
+    deallog << " size32="
+            << "UNDEFINED (too big)";
+  else
+    deallog << " size32=" << size32;
+
+#if DEAL_II_MPI_VERSION_GTE(3, 0)
+  MPI_Count size64;
+  ierr = MPI_Type_size_x(bigtype, &size64);
+  AssertThrowMPI(ierr);
+
+  deallog << " size64=" << size64;
+#endif
+
+  deallog << std::endl;
+
+  MPI_Type_free(&bigtype);
+}
+
+void
+test_send_recv(MPI_Comm comm)
+{
+  unsigned int    myid    = Utilities::MPI::this_mpi_process(comm);
+  const long long n_bytes = (run_big) ? ((1ULL << 31) + 37) : (37ULL);
+
+  if (myid == 0)
+    {
+      std::vector<char> buffer(n_bytes, 'A');
+      buffer[n_bytes - 1] = 'B';
+      MPI_Datatype bigtype;
+      Utilities::MPI::create_mpi_data_type_n_bytes(bigtype, buffer.size());
+      int ierr =
+        MPI_Send(buffer.data(), 1, bigtype, 1 /* dest */, 0 /* tag */, comm);
+      AssertThrowMPI(ierr);
+      ierr = MPI_Type_free(&bigtype);
+      AssertThrowMPI(ierr);
+    }
+  else if (myid == 1)
+    {
+      std::vector<char> buffer(n_bytes, '?');
+      MPI_Datatype      bigtype;
+      Utilities::MPI::create_mpi_data_type_n_bytes(bigtype, buffer.size());
+      int ierr = MPI_Recv(buffer.data(),
+                          1,
+                          bigtype,
+                          0 /* src */,
+                          0 /* tag */,
+                          comm,
+                          MPI_STATUS_IGNORE);
+      AssertThrowMPI(ierr);
+      ierr = MPI_Type_free(&bigtype);
+      AssertThrowMPI(ierr);
+
+      AssertThrow(buffer[0] == 'A', ExcInternalError());
+      AssertThrow(buffer[n_bytes - 1] == 'B', ExcInternalError());
+    }
+  deallog << "send_recv: OK" << std::endl;
+}
+
+int
+main(int argc, char *argv[])
+{
+  Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
+  MPILogInitAll                    all;
+
+  test_data_type(0);
+  test_data_type(1);
+  test_data_type(1ULL << 30);
+  test_data_type(1ULL << 31);
+  test_data_type(1ULL << 32);
+  test_data_type(1ULL << 33);
+  test_data_type(1ULL << 55);
+  test_data_type(58493729485ULL);
+
+  test_send_recv(MPI_COMM_WORLD);
+}

tests/mpi/create_mpi_datatype_01.mpirun=2.output

@@ -0,0 +1,21 @@
+
+DEAL:0::checking size 0: size32=0 size64=0
+DEAL:0::checking size 1: size32=1 size64=1
+DEAL:0::checking size 1073741824: size32=1073741824 size64=1073741824
+DEAL:0::checking size 2147483648: size32=UNDEFINED (too big) size64=2147483648
+DEAL:0::checking size 4294967296: size32=UNDEFINED (too big) size64=4294967296
+DEAL:0::checking size 8589934592: size32=UNDEFINED (too big) size64=8589934592
+DEAL:0::checking size 36028797018963968: size32=UNDEFINED (too big) size64=36028797018963968
+DEAL:0::checking size 58493729485: size32=UNDEFINED (too big) size64=58493729485
+DEAL:0::send_recv: OK
+
+DEAL:1::checking size 0: size32=0 size64=0
+DEAL:1::checking size 1: size32=1 size64=1
+DEAL:1::checking size 1073741824: size32=1073741824 size64=1073741824
+DEAL:1::checking size 2147483648: size32=UNDEFINED (too big) size64=2147483648
+DEAL:1::checking size 4294967296: size32=UNDEFINED (too big) size64=4294967296
+DEAL:1::checking size 8589934592: size32=UNDEFINED (too big) size64=8589934592
+DEAL:1::checking size 36028797018963968: size32=UNDEFINED (too big) size64=36028797018963968
+DEAL:1::checking size 58493729485: size32=UNDEFINED (too big) size64=58493729485
+DEAL:1::send_recv: OK
+