/usr/include/trilinos/Zoltan2_findUniqueGids.hpp is in libtrilinos-zoltan2-dev 12.12.1-5.
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//
// ***********************************************************************
//
// Zoltan2: A package of combinatorial algorithms for scientific computing
// Copyright 2012 Sandia Corporation
//
// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
// the U.S. Government retains certain rights in this software.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of the Corporation nor the names of the
// contributors may be used to endorse or promote products derived from
// this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
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//
// Questions? Contact Karen Devine (kddevin@sandia.gov)
// Erik Boman (egboman@sandia.gov)
// Siva Rajamanickam (srajama@sandia.gov)
//
// ***********************************************************************
//
// @HEADER
/*! \file Zoltan2_findUniqueGids.hpp
\brief Convert keys stored in std::vector to unique Gids stored in
std::vector.
*/
#ifndef _ZOLTAN2_FINDUNIQUEGIDS_HPP_
#define _ZOLTAN2_FINDUNIQUEGIDS_HPP_
#include <Zoltan2_Standards.hpp>
#include <vector>
#include <Tpetra_MultiVector.hpp>
#include <Tpetra_Vector.hpp>
#include <Zoltan2_TPLTraits.hpp>
#include <zoltan_dd.h>
#include <zoltan_dd_const.h>
namespace Zoltan2
{
template <typename gno_t>
size_t findUniqueGidsCommon(
size_t num_keys,
int num_gid,
ZOLTAN_ID_PTR ddkeys,
char *ddnewgids,
MPI_Comm mpicomm
)
{
int num_lid = 0; // Local IDs not needed
int debug_level = 0;
int num_user = sizeof(gno_t);
Zoltan_DD_Struct *dd = NULL;
Zoltan_DD_Create(&dd, mpicomm, num_gid, num_lid, num_user, num_keys,
debug_level);
ZOLTAN_ID_PTR ddnotneeded = NULL; // Local IDs not needed
Zoltan_DD_Update(dd, ddkeys, ddnotneeded, ddnewgids, NULL, int(num_keys));
//////////
// Insert unique GIDs for DD entries in User data here.
// Get value of first gid on this rank
ssize_t nDDEntries = (ssize_t)(dd->nodecnt);
ssize_t firstIdx;
MPI_Scan(&nDDEntries, &firstIdx, 1, MPI_LONG_LONG, MPI_SUM, mpicomm);
firstIdx -= nDDEntries; // do not include this rank's entries in prefix sum
// Loop over all directory entries, updating their userdata with updated gid
DD_NodeIdx cnt = 0;
for (DD_NodeIdx i = 0; i < dd->nodelistlen; i++) {
DD_Node *ptr = &(dd->nodelist[i]);
if (!(ptr->free)) {
char *userchar = (char*)(ptr->gid + (dd->gid_length + dd->lid_length));
gno_t *newgid = (gno_t*) userchar;
*newgid = gno_t(firstIdx + cnt);
cnt++;
}
}
///////////
// Retrieve the global numbers and put in the result gids vector
Zoltan_DD_Find(dd, ddkeys, ddnotneeded, ddnewgids, NULL, int(num_keys), NULL);
Zoltan_DD_Destroy(&dd);
ssize_t nUnique = 0;
MPI_Allreduce(&nDDEntries, &nUnique, 1, MPI_LONG_LONG, MPI_SUM, mpicomm);
return size_t(nUnique);
}
////////////////////////////////////////////////////////////////////////////
template <typename lno_t, typename gno_t>
size_t findUniqueGids(
Tpetra::MultiVector<gno_t, lno_t, gno_t> &keys,
Tpetra::Vector<gno_t, lno_t, gno_t> &gids
)
{
// Input: Tpetra MultiVector of keys; key length = numVectors()
// May contain duplicate keys within a processor.
// May contain duplicate keys across processors.
// Input: Empty Tpetra Vector with same map for holding the results
// Output: Filled gids vector, containing unique global numbers for
// each unique key. Global numbers are in range [0,#UniqueKeys).
size_t num_keys = keys.getLocalLength();
size_t num_entries = keys.getNumVectors();
#ifdef HAVE_ZOLTAN2_MPI
MPI_Comm mpicomm = Teuchos::getRawMpiComm(*(keys.getMap()->getComm()));
#else
// Zoltan's siMPI will be used here
{
int flag;
MPI_Initialized(&flag);
if (!flag) {
int narg = 0;
char **argv = NULL;
MPI_Init(&narg, &argv);
}
}
MPI_Comm mpicomm = MPI_COMM_WORLD; // Will get MPI_COMM_WORLD from siMPI
#endif
int num_gid = TPL_Traits<ZOLTAN_ID_PTR,gno_t>::NUM_ID * num_entries;
int num_user = sizeof(gno_t);
// Buffer the keys for Zoltan_DD
Teuchos::ArrayRCP<const gno_t> *tmpKeyVecs =
new Teuchos::ArrayRCP<const gno_t>[num_entries];
for (size_t v = 0; v < num_entries; v++) tmpKeyVecs[v] = keys.getData(v);
ZOLTAN_ID_PTR ddkeys = new ZOLTAN_ID_TYPE[num_gid * num_keys];
size_t idx = 0;
for (size_t i = 0; i < num_keys; i++) {
for (size_t v = 0; v < num_entries; v++) {
ZOLTAN_ID_PTR ddkey = &(ddkeys[idx]);
TPL_Traits<ZOLTAN_ID_PTR,gno_t>::ASSIGN(ddkey, tmpKeyVecs[v][i]);
idx += TPL_Traits<ZOLTAN_ID_PTR,gno_t>::NUM_ID;
}
}
delete [] tmpKeyVecs;
// Allocate memory for the result
char *ddnewgids = new char[num_user * num_keys];
// Compute the new GIDs
size_t nUnique = findUniqueGidsCommon<gno_t>(num_keys, num_gid,
ddkeys, ddnewgids, mpicomm);
// Copy the result into the output vector
gno_t *result = (gno_t *)ddnewgids;
for (size_t i = 0; i < num_keys; i++)
gids.replaceLocalValue(i, result[i]);
// Clean up
delete [] ddkeys;
delete [] ddnewgids;
return nUnique;
}
////////////////////////////////////////////////////////////////////////////
template <typename key_t, typename gno_t>
size_t findUniqueGids(
std::vector<key_t> &keys,
std::vector<gno_t> &gids,
const Teuchos::Comm<int> &comm
)
{
// Input: Vector of keys; key length = key_t.size()
// Each key must have the same size. std::array<gno_t, N> is
// an example of a good key_t.
// May contain duplicate keys within a processor.
// May contain duplicate keys across processors.
// Input: Empty vector for holding the results
// Output: Filled gids vector, containing unique global numbers for
// each unique key. Global numbers are in range [0,#UniqueKeys).
//
// Note: This code uses the Zoltan Distributed Directory to assign the
// unique global numbers. Right now, it hacks into the Zoltan_DD
// data structures. If we like this approach, we can add some
// elegance to the Zoltan_DD, allowing operations internal to the
// directory.
size_t num_keys = keys.size();
key_t dummy;
size_t num_entries = dummy.size();
#ifdef HAVE_ZOLTAN2_MPI
MPI_Comm mpicomm = Teuchos::getRawMpiComm(comm);
#else
// Zoltan's siMPI will be used here
{
int flag;
MPI_Initialized(&flag);
if (!flag) {
int narg = 0;
char **argv = NULL;
MPI_Init(&narg, &argv);
}
}
MPI_Comm mpicomm = MPI_COMM_WORLD; // Will get MPI_COMM_WORLD from siMPI
#endif
int num_gid = TPL_Traits<ZOLTAN_ID_PTR,gno_t>::NUM_ID * num_entries;
int num_user = sizeof(gno_t);
// Buffer the keys for Zoltan_DD
ZOLTAN_ID_PTR ddkeys = new ZOLTAN_ID_TYPE[num_gid * num_keys];
size_t idx = 0;
for (size_t i = 0; i < num_keys; i++) {
for (size_t v = 0; v < num_entries; v++) {
ZOLTAN_ID_PTR ddkey = &(ddkeys[idx]);
TPL_Traits<ZOLTAN_ID_PTR,gno_t>::ASSIGN(ddkey, keys[i][v]);
idx += TPL_Traits<ZOLTAN_ID_PTR,gno_t>::NUM_ID;
}
}
// Allocate memory for the result
char *ddnewgids = new char[num_user * num_keys];
// Compute the new GIDs
size_t nUnique = findUniqueGidsCommon<gno_t>(num_keys, num_gid,
ddkeys, ddnewgids, mpicomm);
// Copy the result into the output vector
gno_t *result = (gno_t *)ddnewgids;
for (size_t i = 0; i < num_keys; i++)
gids[i] = result[i];
// Clean up
delete [] ddkeys;
delete [] ddnewgids;
return nUnique;
}
} // namespace Zoltan2
#endif
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