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damariswriter: properly encapsulate Damaris

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This commit is contained in:
Arne Morten Kvarving 2024-01-30 13:20:11 +01:00
parent 59d781c11b
commit 89880bfe2f
4 changed files with 118 additions and 73 deletions
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3
CMakeLists_files.cmake
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@ -623,7 +623,8 @@ if (Damaris_FOUND AND MPI_FOUND)
list (APPEND PUBLIC_HEADER_FILES opm/simulators/utils/DamarisVar.hpp)
list (APPEND PUBLIC_HEADER_FILES opm/simulators/utils/GridDataOutput.hpp
opm/simulators/utils/GridDataOutput_impl.hpp)
list(APPEND MAIN_SOURCE_FILES opm/simulators/utils/DamarisVar.cpp
list(APPEND MAIN_SOURCE_FILES ebos/damariswriter.cc
opm/simulators/utils/DamarisVar.cpp
opm/simulators/utils/GridDataOutput.cpp)
endif()

84
ebos/damariswriter.cc Normal file
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@ -0,0 +1,84 @@
// -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
// vi: set et ts=4 sw=4 sts=4:
/*
Copyright 2022 SINTEF Digital, Mathematics and Cybernetics.
Copyright 2023 Inria, Bretagne–Atlantique Research Center
This file is part of the Open Porous Media project (OPM).
OPM is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 2 of the License, or
(at your option) any later version.
OPM is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with OPM. If not, see <http://www.gnu.org/licenses/>.
Consult the COPYING file in the top-level source directory of this
module for the precise wording of the license and the list of
copyright holders.
*/
#include <config.h>
#include <ebos/damariswriter.hh>
#include <opm/common/OpmLog/OpmLog.hpp>
#include <Damaris.h>
#include <fmt/format.h>
namespace Opm::DamarisOutput {
int setPosition(const char* field, int rank, int64_t pos)
{
int dam_err = damaris_set_position(field, &pos);
if (dam_err != DAMARIS_OK) {
OpmLog::error(fmt::format("damariswriter::writeOutput() : ( rank:{})"
"damaris_set_position({}, ...), Damaris Error: {} ",
rank, field, damaris_error_string(dam_err)));
}
return dam_err;
}
int setParameter(const char* field, int rank, int value)
{
int dam_err = damaris_parameter_set(field, &value, sizeof(int));
if (dam_err != DAMARIS_OK) {
OpmLog::error(fmt::format("(rank:{}) Damaris library produced an error result for "
"damaris_parameter_set(\"{}\",...)", rank, field));
}
return dam_err;
}
int write(const char* field, int rank, const void* data)
{
int dam_err = damaris_write(field, data);
if (dam_err != DAMARIS_OK) {
OpmLog::error(fmt::format("damariswriter::writeOutput() : ( rank:{}) "
"damaris_write({}, ...), Damaris Error: {} ",
rank, field, damaris_error_string(dam_err)));
}
return dam_err;
}
int endIteration(int rank)
{
int dam_err = damaris_end_iteration();
if (dam_err != DAMARIS_OK) {
OpmLog::error(fmt::format("damariswriter::writeOutput() : ( rank:{}) "
"damaris_end_iteration(), Damaris Error: {} ",
rank, damaris_error_string(dam_err)));
}
return dam_err;
}
}

103
ebos/damariswriter.hh
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@ -47,15 +47,24 @@
#include <fmt/format.h>
#include <Damaris.h>
#include <algorithm>
#include <limits>
#include <memory>
#include <numeric>
#include <stdexcept>
#include <string>
namespace Opm {
namespace DamarisOutput {
int endIteration(int rank);
int setParameter(const char* field, int rank, int value);
int setPosition(const char* field, int rank, int64_t pos);
int write(const char* field, int rank, const void* data);
}
/*!
* \ingroup EclBlackOilSimulator
*
@ -211,28 +220,12 @@ public:
if (this->damarisOutputModule_->getPRESSURE_ptr() != nullptr)
{
int64_t temp_int64_t[1];
temp_int64_t[0] = static_cast<int64_t>(this->elements_rank_offsets_[rank_]);
dam_err_ = damaris_set_position("PRESSURE", temp_int64_t);
if (dam_err_ != DAMARIS_OK) {
OpmLog::error(fmt::format("damariswriter::writeOutput() : ( rank:{})"
"damaris_set_position(PRESSURE, ...), Damaris Error: {} ",
rank_, damaris_error_string(dam_err_) ));
}
dam_err_ = DamarisOutput::setPosition("PRESSURE", rank_,
this->elements_rank_offsets_[rank_]);
dam_err_ = DamarisOutput::write("PRESSURE", rank_,
this->damarisOutputModule_->getPRESSURE_ptr());
dam_err_ = damaris_write("PRESSURE", (void*)this->damarisOutputModule_->getPRESSURE_ptr());
if (dam_err_ != DAMARIS_OK) {
OpmLog::error(fmt::format("damariswriter::writeOutput() : ( rank:{}) "
"damaris_write(PRESSURE, ...), Damaris Error: {} ",
rank_, damaris_error_string(dam_err_) ));
}
dam_err_ = damaris_end_iteration();
if (dam_err_ != DAMARIS_OK) {
OpmLog::error(fmt::format("damariswriter::writeOutput() : ( rank:{}) "
"damaris_end_iteration(), Damaris Error: {} ",
rank_, damaris_error_string(dam_err_) ));
}
dam_err_ = DamarisOutput::endIteration(rank_);
}
} // end of ! isSubstep
}
@ -257,25 +250,16 @@ private:
{
// GLOBAL_CELL_INDEX is used to reorder variable data when writing to disk
// This is enabled using select-file="GLOBAL_CELL_INDEX" in the <variable> XML tag
if ( this->collectToIORank_.isParallel() ){
const std::vector<int>& local_to_global = this->collectToIORank_.localIdxToGlobalIdxMapping();
dam_err_ = damaris_write("GLOBAL_CELL_INDEX", local_to_global.data());
if (this->collectToIORank_.isParallel()) {
const std::vector<int>& local_to_global = this->collectToIORank_.localIdxToGlobalIdxMapping();
dam_err_ = DamarisOutput::write("GLOBAL_CELL_INDEX", rank_, local_to_global.data());
} else {
std::vector<int> local_to_global_filled ;
local_to_global_filled.resize(this->numElements_) ;
for (int i = 0 ; i < this->numElements_ ; i++)
{
local_to_global_filled[i] = i ;
}
dam_err_ = damaris_write("GLOBAL_CELL_INDEX", local_to_global_filled.data());
std::iota(local_to_global_filled.begin(), local_to_global_filled.end(), 0);
dam_err_ = DamarisOutput::write("GLOBAL_CELL_INDEX", rank_, local_to_global_filled.data());
}
if (dam_err_ != DAMARIS_OK) {
OpmLog::error(fmt::format("damariswriter::writeOutput() :"
"( rank:{}) damaris_write(GLOBAL_CELL_INDEX, ...), Damaris Error: {} ",
rank_, damaris_error_string(dam_err_) ));
}
// This is an example of writing to the Damaris shared memory directly (i.e. not using
// damaris_write() to copy data there)
// We will add the MPI rank value directly into shared memory using the DamarisVar
@ -284,14 +268,12 @@ private:
DamarisVarInt mpi_rank_var_test(1, {std::string("n_elements_local")}, std::string("MPI_RANK"), rank_);
mpi_rank_var_test.setDamarisParameterAndShmem( {this->numElements_ } ) ;
// Fill the created memory area
for (int i = 0 ; i < this->numElements_; i++ )
{
mpi_rank_var_test.data()[i] = rank_ ; // write the rank vaue to the shared memory area.
}
std::fill(mpi_rank_var_test.data(), mpi_rank_var_test.data() + numElements_, rank_);
}
void setupDamarisWritingPars(Parallel::Communication comm, const int n_elements_local_grid, std::vector<unsigned long long>& elements_rank_offsets)
void setupDamarisWritingPars(Parallel::Communication comm,
const int n_elements_local_grid,
std::vector<unsigned long long>& elements_rank_offsets)
{
// one for each rank -- to be gathered from each client rank
std::vector<unsigned long long> elements_rank_sizes(nranks_);
@ -319,21 +301,11 @@ private:
// Set the paramater so that the Damaris servers can allocate the correct amount of memory for the variabe
// Damaris parameters only support int data types. This will limit models to be under size of 2^32-1 elements
// ToDo: Do we need to check that local ranks are 0 based ?
int temp_int = static_cast<int>(elements_rank_sizes[rank_]);
dam_err_ = damaris_parameter_set("n_elements_local", &temp_int, sizeof(int));
if (dam_err_ != DAMARIS_OK) {
OpmLog::error("( rank:" + std::to_string(rank_)+") Damaris library produced an error result for "
"damaris_parameter_set(\"n_elements_local\", &temp_int, sizeof(int));");
}
dam_err_ = DamarisOutput::setParameter("n_elements_local", rank_, elements_rank_sizes[rank_]);
// Damaris parameters only support int data types. This will limit models to be under size of 2^32-1 elements
// ToDo: Do we need to check that n_elements_global_max will fit in a C int type (INT_MAX)
if( n_elements_global_max <= std::numeric_limits<int>::max() ) {
temp_int = static_cast<int>(n_elements_global_max);
dam_err_ = damaris_parameter_set("n_elements_total", &temp_int, sizeof(int));
if (dam_err_ != DAMARIS_OK) {
OpmLog::error("( rank:" + std::to_string(rank_)+") Damaris library produced an error result for "
"damaris_parameter_set(\"n_elements_total\", &temp_int, sizeof(int));");
}
dam_err_ = DamarisOutput::setParameter("n_elements_total", rank_, n_elements_global_max);
} else {
OpmLog::error(fmt::format("( rank:{} ) The size of the global array ({}) is"
"greater than what a Damaris paramater type supports ({}). ",
@ -344,28 +316,15 @@ private:
// Use damaris_set_position to set the offset in the global size of the array.
// This is used so that output functionality (e.g. HDF5Store) knows global offsets of the data of the ranks
int64_t temp_int64_t[1];
temp_int64_t[0] = static_cast<int64_t>(elements_rank_offsets[rank_]);
dam_err_ = damaris_set_position("PRESSURE", temp_int64_t);
if (dam_err_ != DAMARIS_OK) {
OpmLog::error("( rank:" + std::to_string(rank_)+") Damaris library produced an error result for "
"damaris_set_position(\"PRESSURE\", temp_int64_t);");
}
dam_err_ = damaris_set_position("GLOBAL_CELL_INDEX", temp_int64_t);
if (dam_err_ != DAMARIS_OK) {
OpmLog::error("( rank:" + std::to_string(rank_)+") Damaris library produced an error result for "
"damaris_set_position(\"GLOBAL_CELL_INDEX\", temp_int64_t);");
}
dam_err_ = DamarisOutput::setPosition("PRESSURE", rank_, elements_rank_offsets[rank_]);
dam_err_ = DamarisOutput::setPosition("GLOBAL_CELL_INDEX", rank_, elements_rank_offsets[rank_]);
// Set the size of the MPI variable
DamarisVarInt mpi_rank_var(1, {std::string("n_elements_local")}, std::string("MPI_RANK"), rank_) ;
mpi_rank_var.setDamarisPosition({*temp_int64_t}) ;
mpi_rank_var.setDamarisPosition({static_cast<int64_t>(elements_rank_offsets[rank_])});
}
void writeDamarisGridOutput( void )
void writeDamarisGridOutput()
{
const auto& gridView = simulator_.gridView();
Opm::GridDataOutput::SimMeshDataAccessor geomData(gridView, Dune::Partitions::interior) ;

1
opm/simulators/flow/Main.cpp
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@ -31,6 +31,7 @@
#include <opm/simulators/utils/readDeck.hpp>
#if HAVE_DAMARIS
#include <Damaris.h>
#include <opm/simulators/utils/DamarisOutputModule.hpp>
#endif