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Refactored the Damaris command line functionality so that commandline arguments are accessed where they are needed in the DamarisKeywords() method

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This commit is contained in:
josh bowden
2023-09-24 22:23:31 +02:00
parent bb38c57b1b
commit c7c4bffa7c
6 changed files with 85 additions and 77 deletions
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34
opm/simulators/flow/Main.cpp
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@@ -240,40 +240,8 @@ void Main::setupDamaris(const std::string& outputDir )
ensureOutputDirExists(outputDir);
}
bool enableDamarisOutputCollective = true ;
bool saveToDamarisHDF5 = true ;
std::string damarisPythonFilename = "" ;
std::string damarisPythonParaviewFilename = "" ;
std::string damarisSimName = "" ; // empty defaults to opm-sim-<magic_number>
std::string damarisLogLevel = "info" ;
int nDamarisCores = 1 ;
int nDamarisNodes = 0 ;
long shmemSizeBytes = 536870912 ;
enableDamarisOutputCollective = EWOMS_GET_PARAM(PreTypeTag, bool, EnableDamarisOutputCollective) ;
saveToDamarisHDF5 = EWOMS_GET_PARAM(PreTypeTag, bool, DamarisSaveToHdf);
damarisPythonFilename = EWOMS_GET_PARAM(PreTypeTag, std::string, DamarisPythonScript);
damarisPythonParaviewFilename = EWOMS_GET_PARAM(PreTypeTag, std::string, DamarisPythonParaviewScript);
damarisSimName = EWOMS_GET_PARAM(PreTypeTag, std::string, DamarisSimName);
nDamarisCores = EWOMS_GET_PARAM(PreTypeTag, int, DamarisDedicatedCores);
nDamarisNodes = EWOMS_GET_PARAM(PreTypeTag, int, DamarisDedicatedNodes);
shmemSizeBytes = EWOMS_GET_PARAM(PreTypeTag, long, DamarisSharedMemeorySizeBytes);
damarisLogLevel = EWOMS_GET_PARAM(PreTypeTag, std::string, DamarisLogLevel);
std::map<std::string, std::string> find_replace_map ;
find_replace_map = Opm::DamarisOutput::DamarisKeywords(EclGenericVanguard::comm(),
outputDir,
enableDamarisOutputCollective,
saveToDamarisHDF5,
nDamarisCores,
nDamarisNodes,
shmemSizeBytes,
damarisPythonFilename,
damarisSimName,
damarisLogLevel,
damarisPythonParaviewFilename
);
find_replace_map = Opm::DamarisOutput::DamarisKeywords(EclGenericVanguard::comm(), outputDir);
// By default EnableDamarisOutputCollective is true so all simulation results will
// be written into one single file for each iteration using Parallel HDF5.

8
opm/simulators/flow/Main.hpp
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@@ -72,9 +72,7 @@
#include <opm/simulators/utils/ParallelEclipseState.hpp>
#endif
#if HAVE_DAMARIS
#include <opm/simulators/utils/DamarisKeywords.hpp>
#endif
#include <cassert>
#include <cstdlib>
@@ -98,6 +96,10 @@ struct FlowEarlyBird {
} // namespace Opm::Properties
#if HAVE_DAMARIS
#include <opm/simulators/utils/DamarisKeywords.hpp>
#endif
namespace Opm {
namespace Action { class State; }

81
opm/simulators/utils/DamarisKeywords.cpp
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@@ -17,22 +17,31 @@
along with OPM. If not, see <http://www.gnu.org/licenses/>.
*/
#include <config.h>
#include <opm/simulators/flow/Main.hpp>
#include <opm/models/utils/propertysystem.hh>
#include <opm/models/utils/parametersystem.hh>
#include <opm/simulators/utils/DamarisKeywords.hpp>
#include <damaris/env/Environment.hpp>
#include <string>
#include <map>
#include <random>
#include <fstream>
#include <Damaris.h>
#include <mpi.h>
/*
/**
Below are the Damaris Keywords supported by Damaris to be filled
in the built-in XML file.
The entries in the map below will be filled by the corresponding
Damaris Keywords. Yet, only output directory and FileMode are to
be chosen by the user
Damaris Keywords.
The command line arguments are defined in ebos/damariswriter.hh
and defaults are set in ebos/eclproblem_properties.hh
*/
namespace Opm::DamarisOutput
@@ -73,29 +82,43 @@ bool FileExists(const std::string filename_in, const MPI_Comm comm, const int ra
std::map<std::string, std::string>
DamarisKeywords(MPI_Comm comm, std::string OutputDir,
bool enableDamarisOutputCollective,
bool saveToHDF5,
int nDamarisCores,
int nDamarisNodes,
long shmemSizeBytes,
std::string pythonFilename,
std::string simName,
std::string logLevel,
std::string paraviewPythonFilename )
DamarisKeywords(MPI_Comm comm, std::string OutputDir)
{
typedef Properties::TTag::FlowEarlyBird PreTypeTag;
bool enableDamarisOutputCollective = true ;
bool saveToDamarisHDF5 = true ;
std::string pythonFilename = "" ;
std::string paraviewPythonFilename = "" ;
std::string damarisSimName = "" ; // empty defaults to opm-sim-<magic_number>
std::string damarisLogLevel = "info" ;
int nDamarisCores = 1 ;
int nDamarisNodes = 0 ;
long shmemSizeBytes = 536870912 ;
// Get all of the Damaris keywords (except for --enable-damaris, which is used in simulators/flow/Main.hpp)
// These command line arguments are defined in ebos/damariswriter.hh and defaults are set in ebos/eclproblem_properties.hh
enableDamarisOutputCollective = EWOMS_GET_PARAM(PreTypeTag, bool, EnableDamarisOutputCollective) ;
saveToDamarisHDF5 = EWOMS_GET_PARAM(PreTypeTag, bool, DamarisSaveToHdf);
pythonFilename = EWOMS_GET_PARAM(PreTypeTag, std::string, DamarisPythonScript);
paraviewPythonFilename = EWOMS_GET_PARAM(PreTypeTag, std::string, DamarisPythonParaviewScript);
damarisSimName = EWOMS_GET_PARAM(PreTypeTag, std::string, DamarisSimName);
nDamarisCores = EWOMS_GET_PARAM(PreTypeTag, int, DamarisDedicatedCores);
nDamarisNodes = EWOMS_GET_PARAM(PreTypeTag, int, DamarisDedicatedNodes);
shmemSizeBytes = EWOMS_GET_PARAM(PreTypeTag, long, DamarisSharedMemeorySizeBytes);
damarisLogLevel = EWOMS_GET_PARAM(PreTypeTag, std::string, DamarisLogLevel);
int rank ;
MPI_Comm_rank(comm, &rank) ;
std::string saveToHDF5_str("MyStore") ;
if (! saveToHDF5 ) saveToHDF5_str = "#" ;
if (! saveToDamarisHDF5 ) saveToHDF5_str = "#" ;
// These strings are used to comment out an XML element if it is not reqired
std::string disablePythonXMLstart("!--") ;
std::string disablePythonXMLfin("--") ;
std::string disableParaviewXMLstart("!--") ;
std::string disableParaviewXMLfin("--") ;
// Test if input Python file exists and set the name of the script for <variable ... script="" > )XML elements
std::string publishToPython_str("") ;
if (pythonFilename != ""){
@@ -139,14 +162,26 @@ DamarisKeywords(MPI_Comm comm, std::string OutputDir,
damarisOutputCollective_str="FilePerCore" ;
}
std::string simName_str ;
if (simName == "") {
std::string simName_str("") ;
if (damarisSimName == "") {
// Having a different simulation name is important if multiple simulations
// are running on the same node, as it is used to name the simulations shmem area
// and when one sim finishes it removes its shmem file.
simName_str = "opm-sim-" + damaris::Environment::GetMagicNumber() ;
// simName_str = damaris::Environment::GetMagicNumber(comm) ;
if (simName_str == "") {
// We will add a random value as GetMagicNumber(comm) requires latest Damaris
// Seed with a real random value, if available
std::random_device r;
// Choose a random number between 0 and MAX_INT
std::default_random_engine e1(r());
std::uniform_int_distribution<int> uniform_dist(0, std::numeric_limits<int>::max());
int rand_int = uniform_dist(e1);
simName_str = std::to_string(rand_int) ;
} else {
simName_str = "opm-flow-" + simName_str ;
}
} else {
simName_str = simName ;
simName_str = damarisSimName ;
}
if ((nDamarisCores > 0) && (nDamarisNodes > 0))
@@ -174,7 +209,7 @@ DamarisKeywords(MPI_Comm comm, std::string OutputDir,
shmemSizeBytes_str = "536870912" ;
}
std::string logLevel_str(logLevel) ;
std::string logLevel_str(damarisLogLevel) ;
// _MAKE_AVAILABLE_IN_PYTHON_
// _PYTHON_SCRIPT_

22
opm/simulators/utils/DamarisKeywords.hpp
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@@ -22,7 +22,9 @@
#include <string>
#include <map>
#include <mpi.h>
/*
Below is the std::map with the keywords that are supported by Damaris.
@@ -38,24 +40,22 @@ namespace Opm::DamarisOutput
* Returns true if the file exists.
* Tests to see if filename string is empty
* or the "#" character and if so returns false.
* Tests for file existance on ranl 0 and
* passes result via MPI to all other ranks.
*/
bool FileExists(const std::string filename_in, const MPI_Comm comm, const int rank) ;
/**
* Returns true if the file exists. Tests to see if filename string is empty or the "#" character and if so returns false.
* Creates the map of search strings and repacement strings that will be used to
* modify a templated Damaris XML file which will be used to intialize Damaris.
* This function will access all the OPM flow comand line arguments related to
* 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.
*/
std::map<std::string, std::string>
DamarisKeywords(MPI_Comm comm, std::string OutputDir,
bool enableDamarisOutputCollective,
bool saveToHDF5,
int nDamarisCores,
int nDamarisNodes,
long shmemSizeBytes,
std::string pythonFilename,
std::string simName,
std::string logLevel,
std::string paraviewPythonFilename ) ;
DamarisKeywords(MPI_Comm comm, std::string OutputDir) ;
} // namespace Opm::DamarisOutput

5
opm/simulators/utils/DamarisOutputModule.cpp
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@@ -36,7 +36,6 @@ 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::map<std::string, std::string>& find_replace_map )
@@ -56,7 +55,7 @@ initializeDamaris(MPI_Comm comm, int mpiRank, std::map<std::string, std::string>
mpiRank, cs_damaris_xml_file, damaris_error_string(dam_err_) ));
}
} else {
// Prepare the XML file
// 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)
@@ -80,6 +79,4 @@ initializeDamaris(MPI_Comm comm, int mpiRank, std::map<std::string, std::string>
}
}
} // namespace Opm::DamarisOutput

8
opm/simulators/utils/DamarisOutputModule.hpp
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@@ -41,7 +41,13 @@ namespace Opm::DamarisOutput
{
// Initialize an XML file
std::string initDamarisXmlFile();
// Initialize Damaris by filling in th XML file and storing it in the chosen directory
/**
* Initialize Damaris by either:
* 1/ Filling in a templated XML file and storing it in the chosen directory (output directory)
* 2/ Reading a file specified by the environment variable FLOW_DAMARIS_XML_FILE
*
*/
void initializeDamaris(MPI_Comm comm, int mpiRank, std::map<std::string, std::string>& find_replace_map );
} // namespace Opm::DamarisOutput