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update after pull request comments; addition of OUTPUTDIR variable to Damaris XML configuration

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This commit is contained in:
josh bowden 2024-05-17 17:36:18 +02:00
parent 3630177e3e
commit 2744614f9c
4 changed files with 53 additions and 38 deletions
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3
opm/simulators/flow/DamarisWriter.cpp
View File

@ -42,6 +42,7 @@ 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 only prints from rank 0
OpmLog::error(fmt::format("damariswriter::setPosition() : ( rank:{}) "
"damaris_set_position({}, ...), Damaris Error: {} ",
rank, field, damaris_error_string(dam_err)));
@ -54,6 +55,7 @@ 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 only prints from rank 0
OpmLog::error(fmt::format("damariswriter::setParameter() (rank:{}) "
"damaris_parameter_set(\"{}\",...)", rank, field));
}
@ -65,6 +67,7 @@ int write(const char* field, int rank, const void* data)
{
int dam_err = damaris_write(field, data);
if (dam_err != DAMARIS_OK) {
// OpmLog::error only prints from rank 0
OpmLog::error(fmt::format("damariswriter::write() : ( rank:{}) "
"damaris_write({}, ...), Damaris Error: {} ",
rank, field, damaris_error_string(dam_err)));

70
opm/simulators/flow/DamarisWriter.hpp
View File

@ -158,10 +158,10 @@ public:
"the same node/server as it is used for the Damaris shmem name and by "
"the Python Dask library to locate sections of variables.");
Parameters::registerParam<TypeTag, Properties::DamarisLimitVariables>
("A comma separated list of variable names that a user wants to pass"
("A comma separated list of variable names that a user wants to pass "
"through via DamarisOutput::DamarisWriter::writeOutput)() to the "
"damaris_write() call. This can be used to limit the number of"
"variables being passed to the Daamis plugins (Paraview, Python and HDF5)");
"damaris_write() call. This can be used to limit the number of "
"variables being passed to the Damaris plugins (Paraview, Python and HDF5)");
}
// The Simulator object should preferably have been const - the
@ -269,39 +269,26 @@ public:
this->damarisUpdate_ = false;
}
/*if (this->damarisOutputModule_->getPRESSURE_ptr() != nullptr)
{
dam_err_ = DamarisOutput::setPosition("PRESSURE", rank_,
this->elements_rank_offsets_[rank_]);
dam_err_ = DamarisOutput::write("PRESSURE", rank_,
this->damarisOutputModule_->getPRESSURE_ptr());
dam_err_ = DamarisOutput::endIteration(rank_);
}*/
// Call damaris_set_position() for all available variables
// There is an assumption that all variables are the same size, with the same offset.
// see initDamarisTemplateXmlFile.cpp for the Damaris XML descriptions.
for ( auto damVar : localCellData ) {
// std::map<std::string, data::CellData>
const std::string name = damVar.first ;
dam_err_ = DamarisOutput::setPosition(name.c_str(), rank_,
this->elements_rank_offsets_[rank_]);
}
int cell_data_written = 0 ;
// Call damaris_write() for all available variables
for ( auto damVar : localCellData )
for ( const auto& damVar : localCellData )
{
// std::map<std::string, data::CellData>
const std::string& name = damVar.first ;
std::unordered_set<std::string>::const_iterator is_in_set = wanted_vars_set_.find ( name );
if ((is_in_set != wanted_vars_set_.end() ) || (wanted_vars_set_.size() == 0)) {
data::CellData dataCol = damVar.second ;
// If the wanted_vars_set_ set is empty then we default to passing through
// all the variables/
if (wanted_vars_set_.count(name) || wanted_vars_set_.empty())
{
const data::CellData& dataCol = damVar.second ;
OpmLog::debug(fmt::format("Name of Damaris Variable : ( rank:{}) name: {} ", rank_, name));
// Call damaris_set_position() for all available variables
// There is an assumption that all variables are the same size, with the same offset.
// see initDamarisTemplateXmlFile.cpp for the Damaris XML descriptions.
dam_err_ = DamarisOutput::setPosition(name.c_str(), rank_,
this->elements_rank_offsets_[rank_]);
// It does not seem I can test for what type of data is present (double or int)
// in the std::variant within the data::CellData, so I will use a try catch block.
// Although, only MPI_RANK and GLOBAL_CELL_INDEX are set as integer types (in the
@ -312,6 +299,8 @@ public:
if (dataCol.data<double>().size() >= this->numElements_) {
dam_err_ = DamarisOutput::write(name.c_str(), rank_,
dataCol.data<double>().data()) ;
} else {
OpmLog::info(fmt::format("( rank:{}) The variable \"{}\" was found to be of a different size {} (not {}).", rank_, name, dataCol.data<double>().size(), this->numElements_ ));
}
}
catch (std::bad_variant_access const& ex) {
@ -319,13 +308,20 @@ public:
if (dataCol.data<int>().size() >= this->numElements_) {
dam_err_ = DamarisOutput::write(name.c_str(), rank_,
dataCol.data<int>().data()) ;
} else {
OpmLog::info(fmt::format("( rank:{}) The variable \"{}\" was found to be of a different size {} (not {}).", rank_, name, dataCol.data<int>().size(), this->numElements_ ));
}
}
++cell_data_written ;
}
}
if (!cell_data_written) {
OpmLog::info(fmt::format("( rank:{}) No simulation data written to the Damaris server - check --damaris-limit-variables command line option (if used) has valid variable name(s) and that the Damaris XML file contains variable names that are available in your simulation.", rank_));
} else {
OpmLog::debug(fmt::format("( rank:{}) {} Damaris Variables written to the Damaris servers", rank_, cell_data_written));
}
/*
Code for when we want to pass to Damaris the single cell 'block' data variables
auto mybloc = damarisOutputModule_->getBlockData() ;
@ -399,7 +395,13 @@ private:
// Fill the created memory area
std::fill(mpi_rank_var.data(), mpi_rank_var.data() + numElements_, rank_);
// Pass the output directory string through as a Damaris variable so that
// Python code (as an example) can use the path as required.
const auto& outputDir = simulator_.vanguard().eclState().cfg().io().getOutputDir();
if (outputDir.size() > 0) {
dam_err_ = DamarisOutput::setParameter("path_string_length", rank_, outputDir.size()) ;
dam_err_ = DamarisOutput::write("OUTPUTDIR", rank_, outputDir.c_str());
}
}
void writeDamarisGridOutput()

9
opm/simulators/utils/DamarisKeywords.hpp
View File

@ -85,6 +85,8 @@ struct DamarisSettings {
* Damaris and perform checks and logic so as to create a valid XML file.
* N.B. The created XML file can be overridden using an environment variable
* FLOW_DAMARIS_XML_FILE that points to a Damaris XML file.
*
* N.B. This needs to be called before damaris_init()
*/
template<class TypeTag>
std::map<std::string, std::string>
@ -116,6 +118,7 @@ getSetOfIncludedVariables(void)
{
std::unordered_set<std::string> resuset ;
std::string tstr;
// The --damaris-limit-variables command line option (defaults to empty string)
std::string damarisLimitVars = Parameters::get<TypeTag, Properties::DamarisLimitVariables>();
std::stringstream ss(damarisLimitVars);
@ -125,8 +128,10 @@ getSetOfIncludedVariables(void)
// tstr.erase(std::remove_if(tstr.begin(), tstr.end(), ::isspace), tstr.end());
std::string::iterator end_pos = std::remove(tstr.begin(), tstr.end(), ' ');
tstr.erase(end_pos, tstr.end());
// place in set (no duplicates possible in set)
resuset.insert(tstr) ;
// place in set (no duplicates possible in set and no empty string)
if (tstr != "") {
resuset.insert(tstr) ;
}
}
return (resuset) ;
}

9
opm/simulators/utils/initDamarisXmlFile.cpp
View File

@ -48,13 +48,18 @@ std::string initDamarisXmlFile()
<parameter name="n_elements_total" type="int" value="1" />
<parameter name="n_elements_local" type="int" value="1" />
<parameter name="n" type="int" value="1" />
<parameter name="path_string_length" type="int" value="1" />
<layout name="path_string_layout" type="char" dimensions="path_string_length" comment="The length of the output directory path string" />
<variable name="OUTPUTDIR" layout="path_string_layout" type="scalar" visualizable="false" mesh="#" unit="" time-varying="false" store="#" script="_MAKE_AVAILABLE_IN_PYTHON_" />
<layout name="zonal_layout_usmesh_integer" type="int" dimensions="n_elements_local" global="n_elements_total" comment="For the field data e.g. Pressure" />
<variable name="GLOBAL_CELL_INDEX" layout="zonal_layout_usmesh_integer" type="scalar" visualizable="false" time-varying="false" centering="zonal" store="_MYSTORE_OR_EMPTY_REGEX_" script="_MAKE_AVAILABLE_IN_PYTHON_" />
<layout name="zonal_layout_usmesh" type="double" dimensions="n_elements_local" global="n_elements_total" comment="For the field data e.g. Pressure" />
<variable name="PRESSURE" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="us_mesh" unit="_PRESSURE_UNIT_" centering="zonal" select-file="GLOBAL_CELL_INDEX" store="_MYSTORE_OR_EMPTY_REGEX_" script="_MAKE_AVAILABLE_IN_PYTHON_" />
<variable name="MY_TEST_VAR" layout="zonal_layout_usmesh" type="scalar" visualizable="true" mesh="us_mesh" unit="" centering="zonal" time-varying="true" select-file="GLOBAL_CELL_INDEX" store="_MYSTORE_OR_EMPTY_REGEX_" script="_MAKE_AVAILABLE_IN_PYTHON_" />
_MORE_VARIABLES_REGEX_
<variable name="MPI_RANK" layout="zonal_layout_usmesh_integer" type="scalar" visualizable="true" mesh="us_mesh" unit="rank" centering="zonal" store="_MYSTORE_MESH_OR_EMPTY_REGEX_" time-varying="false" select-file="GLOBAL_CELL_INDEX" script="_MAKE_AVAILABLE_IN_PYTHON_" comment="The MPI rank of each cell"/>