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Geometric mesh data added for in-situ visualisation

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added access to DUNE mesh geometry and passing through data to Damaris;
Updated command line so users can specifiy Python or Paraview script names and other paramaters that control Damaris
- Simulation name
- Number of dedicated cores or dedicated nodes
- Shared memory region size
- switch to turn off HDF5 output.
- Damaris logging level
This commit is contained in:
josh bowden
2023-09-22 23:23:29 +02:00
parent 18f0d8fd27
commit 8095eb0c48
13 changed files with 1522 additions and 132 deletions
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opm/simulators/utils/DamarisOutputModule.cpp
+34 -28
View File
@@ -30,50 +30,56 @@
#include <fmt/format.h>
namespace Opm::DamarisOutput
{
std::string initDamarisXmlFile(); // Defined in initDamarisXMLFile.cpp, to avoid messing up this file.
// Initialize Damaris by filling in th XML file and storing it in the chosen directory
void
initializeDamaris(MPI_Comm comm, int mpiRank, std::string outputDir, bool enableDamarisOutputCollective)
initializeDamaris(MPI_Comm comm, int mpiRank, std::map<std::string, std::string>& find_replace_map )
{
if (outputDir.empty()) {
outputDir = ".";
}
// Prepare the XML file
std::string damaris_config_xml = initDamarisXmlFile();
damaris::model::ModifyModel myMod = damaris::model::ModifyModel(damaris_config_xml);
// The map will make it precise the output directory and FileMode (either FilePerCore or Collective storage)
// The map file find all occurences of the string in position 1 and repalce it/them with string in position 2
std::map<std::string, std::string> find_replace_map = DamarisKeywords(outputDir, enableDamarisOutputCollective);
myMod.RepalceWithRegEx(find_replace_map);
std::string damaris_xml_filename_str = outputDir + "/damaris_config.xml";
if (mpiRank == 0) {
myMod.SaveXMLStringToFile(damaris_xml_filename_str);
}
int damaris_err;
int dam_err_;
/* Get the name of the Damaris input file from an environment variable if available */
const char* cs_damaris_xml_file = getenv("FLOW_DAMARIS_XML_FILE");
if (cs_damaris_xml_file != NULL) {
std::cout << "INFO: initializing Damaris from environment variable FLOW_DAMARIS_XML_FILE: "
if (cs_damaris_xml_file != NULL)
{
std::cout << "INFO: Initializing Damaris from environment variable FLOW_DAMARIS_XML_FILE: "
<< cs_damaris_xml_file << std::endl;
damaris_err = damaris_initialize(cs_damaris_xml_file, MPI_COMM_WORLD);
if (damaris_err != DAMARIS_OK) {
std::cerr << "ERROR: damaris_initialize() error via FLOW_DAMARIS_XML_FILE=" << cs_damaris_xml_file
<< std::endl;
dam_err_ = damaris_initialize(cs_damaris_xml_file, MPI_COMM_WORLD);
if (dam_err_ != DAMARIS_OK) {
OpmLog::error(fmt::format("ERORR: damariswriter::initializeDamaris() : ( rank:{}) "
"damaris_initialize({}, MPI_COMM_WORLD), Damaris Error: {} ",
mpiRank, cs_damaris_xml_file, damaris_error_string(dam_err_) ));
}
} else {
std::cout << "INFO: initializing Damaris using internally built file:" << damaris_xml_filename_str << std::endl;
damaris_err = damaris_initialize(damaris_xml_filename_str.c_str(), comm);
if (damaris_err != DAMARIS_OK) {
std::cerr << "ERROR: damaris_initialize() error via built file:" << std::endl << myMod.GetConfigString();
// Prepare the XML file
std::string damaris_config_xml = initDamarisXmlFile(); // This is the template for a Damaris XML file
damaris::model::ModifyModel myMod = damaris::model::ModifyModel(damaris_config_xml);
// The map will make it precise the output directory and FileMode (either FilePerCore or Collective storage)
// The map file find all occurences of the string in position 1 and replace it/them with string in position 2
// std::map<std::string, std::string> find_replace_map = DamarisKeywords(outputDir, enableDamarisOutputCollective);
myMod.RepalceWithRegEx(find_replace_map);
std::string outputDir = find_replace_map["_PATH_REGEX_"] ;
std::string damaris_xml_filename_str = outputDir + "/damaris_config.xml";
if (mpiRank == 0) {
myMod.SaveXMLStringToFile(damaris_xml_filename_str);
}
std::cout << "INFO: Initializing Damaris using internally built file:" << damaris_xml_filename_str << " (N.B. use FLOW_DAMARIS_XML_FILE to override)" << std::endl;
dam_err_ = damaris_initialize(damaris_xml_filename_str.c_str(), comm);
if (dam_err_ != DAMARIS_OK) {
OpmLog::error(fmt::format("ERORR: damariswriter::initializeDamaris() : ( rank:{}) "
"damaris_initialize({}, MPI_COMM_WORLD), Damaris Error: {}. Error via OPM internally built file:",
mpiRank, cs_damaris_xml_file, damaris_error_string(dam_err_) ));
}
}
}
} // namespace Opm::DamarisOutput