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MOAB: Mesh Oriented datABase
(version 5.4.1)
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MOAB: Mesh Oriented datABase
(version 5.4.1)
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#include "moab/Core.hpp"#include "moab_mpi.h"#include "moab/ParallelComm.hpp"#include "MBParallelConventions.h"#include "moab/iMOAB.h"#include "TestUtil.hpp"#include "moab/CpuTimer.hpp"#include "moab/ProgOptions.hpp"#include <iostream>#include <sstream>#include "imoab_coupler_utils.hpp"
Include dependency graph for imoab_read_map.cpp:Go to the source code of this file.
Functions | |
| int | main (int argc, char *argv[]) |
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
Definition at line 36 of file imoab_read_map.cpp.
References ProgOptions::addOpt(), atmFilename, CHECKIERR, cmpatm, context, create_group_and_comm(), create_joint_comm_group(), DENSE_DOUBLE, DENSE_INTEGER, endG1, endG2, fileWriteOptions(), groupTasks, ierr, iMOAB_AppID, iMOAB_DefineTagStorage(), iMOAB_DeregisterApplication(), iMOAB_Finalize(), iMOAB_GetDoubleTagStorage(), iMOAB_GetIntTagStorage(), iMOAB_GetMeshInfo(), iMOAB_Initialize(), iMOAB_LoadMesh(), iMOAB_RegisterApplication(), iMOAB_SetDoubleTagStorage(), iMOAB_WriteLocalMesh(), iMOAB_WriteMesh(), jgroup, MPI_COMM_WORLD, nghlay, numProcesses, ProgOptions::parseCommandLine(), POP_TIMER, PUSH_TIMER, rankInAtmComm, rankInGlobalComm, readopts(), startG1, and startG2.
{
int ierr;
int rankInGlobalComm, numProcesses;
MPI_Group jgroup;
std::string readopts( "PARALLEL=READ_PART;PARTITION=PARALLEL_PARTITION;PARALLEL_RESOLVE_SHARED_ENTS" );
// Timer data
moab::CpuTimer timer;
double timer_ops;
std::string opName;
MPI_Init( &argc, &argv );
MPI_Comm_rank( MPI_COMM_WORLD, &rankInGlobalComm );
MPI_Comm_size( MPI_COMM_WORLD, &numProcesses );
MPI_Comm_group( MPI_COMM_WORLD, &jgroup ); // all processes in jgroup
std::string atmFilename = TestDir + "unittest/wholeATM_T.h5m";
// on a regular case, 5 ATM, 6 CPLATM (ATMX), 17 OCN , 18 CPLOCN (OCNX) ;
// intx atm/ocn is not in e3sm yet, give a number
// 6 * 100+ 18 = 618 : atmocnid
// 9 LND, 10 CPLLND
// 6 * 100 + 10 = 610 atmlndid:
// cmpatm is for atm on atm pes
// cmpocn is for ocean, on ocean pe
// cplatm is for atm on coupler pes
// cplocn is for ocean on coupelr pes
// atmocnid is for intx atm / ocn on coupler pes
//
int rankInAtmComm = -1;
int cmpatm = 5,
cplatm = 6; // component ids are unique over all pes, and established in advance;
std::string ocnFilename = TestDir + "unittest/recMeshOcn.h5m";
std::string mapFilename = TestDir + "unittest/atm_ocn_map.nc"; // this is a netcdf file!
std::string baseline = TestDir + "unittest/baseline1.txt";
int rankInOcnComm = -1;
int cmpocn = 17, cplocn = 18,
atmocnid = 618; // component ids are unique over all pes, and established in advance;
int rankInCouComm = -1;
int nghlay = 0; // number of ghost layers for loading the file
std::vector< int > groupTasks;
int startG1 = 0, startG2 = 0, endG1 = numProcesses - 1, endG2 = numProcesses - 1;
int startG4 = startG1, endG4 = endG1; // these are for coupler layout
int context_id = -1; // used now for freeing buffers
// default: load atm on 2 proc, ocean on 2,
// load map on 2 also, in parallel, distributed by rows (which is very bad actually for ocean mesh, because
// probably all source cells will be involved in coverage mesh on both tasks
ProgOptions opts;
opts.addOpt< std::string >( "atmosphere,t", "atm mesh filename (source)", &atmFilename );
opts.addOpt< std::string >( "ocean,m", "ocean mesh filename (target)", &ocnFilename );
opts.addOpt< std::string >( "map_file,w", "map file from source to target", &mapFilename );
opts.addOpt< int >( "startAtm,a", "start task for atmosphere layout", &startG1 );
opts.addOpt< int >( "endAtm,b", "end task for atmosphere layout", &endG1 );
opts.addOpt< int >( "startOcn,c", "start task for ocean layout", &startG2 );
opts.addOpt< int >( "endOcn,d", "end task for ocean layout", &endG2 );
opts.addOpt< int >( "startCoupler,g", "start task for coupler layout", &startG4 );
opts.addOpt< int >( "endCoupler,j", "end task for coupler layout", &endG4 );
int n = 1; // number of send/receive / project / send back cycles
opts.addOpt< int >( "iterations,n", "number of iterations for coupler", &n );
bool no_regression_test = false;
opts.addOpt< void >( "no_regression,r", "do not do regression test against baseline 1", &no_regression_test );
opts.parseCommandLine( argc, argv );
char fileWriteOptions[] = "PARALLEL=WRITE_PART";
if( !rankInGlobalComm )
{
std::cout << " atm file: " << atmFilename << "\n on tasks : " << startG1 << ":" << endG1
<< "\n ocn file: " << ocnFilename << "\n on tasks : " << startG2 << ":" << endG2
<< "\n map file:" << mapFilename << "\n on tasks : " << startG4 << ":" << endG4 << "\n";
if( !no_regression_test )
{
std::cout << " check projection against baseline: " << baseline << "\n";
}
}
// load files on 3 different communicators, groups
// first groups has task 0, second group tasks 0 and 1
// coupler will be on joint tasks, will be on a third group (0 and 1, again)
// first groups has task 0, second group tasks 0 and 1
// coupler will be on joint tasks, will be on a third group (0 and 1, again)
MPI_Group atmPEGroup;
MPI_Comm atmComm;
ierr = create_group_and_comm( startG1, endG1, jgroup, &atmPEGroup, &atmComm );
CHECKIERR( ierr, "Cannot create atm MPI group and communicator " )
MPI_Group ocnPEGroup;
MPI_Comm ocnComm;
ierr = create_group_and_comm( startG2, endG2, jgroup, &ocnPEGroup, &ocnComm );
CHECKIERR( ierr, "Cannot create ocn MPI group and communicator " )
// we will always have a coupler
MPI_Group couPEGroup;
MPI_Comm couComm;
ierr = create_group_and_comm( startG4, endG4, jgroup, &couPEGroup, &couComm );
CHECKIERR( ierr, "Cannot create cpl MPI group and communicator " )
// atm_coupler
MPI_Group joinAtmCouGroup;
MPI_Comm atmCouComm;
ierr = create_joint_comm_group( atmPEGroup, couPEGroup, &joinAtmCouGroup, &atmCouComm );
CHECKIERR( ierr, "Cannot create joint atm cou communicator" )
// ocn_coupler
MPI_Group joinOcnCouGroup;
MPI_Comm ocnCouComm;
ierr = create_joint_comm_group( ocnPEGroup, couPEGroup, &joinOcnCouGroup, &ocnCouComm );
CHECKIERR( ierr, "Cannot create joint ocn cou communicator" )
ierr = iMOAB_Initialize( argc, argv ); // not really needed anything from argc, argv, yet; maybe we should
CHECKIERR( ierr, "Cannot initialize iMOAB" )
int cmpAtmAppID = -1;
iMOAB_AppID cmpAtmPID = &cmpAtmAppID; // atm
int cplAtmAppID = -1; // -1 means it is not initialized
iMOAB_AppID cplAtmPID = &cplAtmAppID; // atm on coupler PEs
int cmpOcnAppID = -1;
iMOAB_AppID cmpOcnPID = &cmpOcnAppID; // ocn
int cplOcnAppID = -1, cplAtmOcnAppID = -1; // -1 means it is not initialized
iMOAB_AppID cplOcnPID = &cplOcnAppID; // ocn on coupler PEs
iMOAB_AppID cplAtmOcnPID = &cplAtmOcnAppID; // intx atm -ocn on coupler PEs
if( couComm != MPI_COMM_NULL )
{
MPI_Comm_rank( couComm, &rankInCouComm );
// Register all the applications on the coupler PEs
ierr = iMOAB_RegisterApplication( "ATMX", &couComm, &cplatm,
cplAtmPID ); // atm on coupler pes
CHECKIERR( ierr, "Cannot register ATM over coupler PEs" )
ierr = iMOAB_RegisterApplication( "OCNX", &couComm, &cplocn,
cplOcnPID ); // ocn on coupler pes
CHECKIERR( ierr, "Cannot register OCN over coupler PEs" )
}
if( atmComm != MPI_COMM_NULL )
{
MPI_Comm_rank( atmComm, &rankInAtmComm );
ierr = iMOAB_RegisterApplication( "ATM1", &atmComm, &cmpatm, cmpAtmPID );
CHECKIERR( ierr, "Cannot register ATM App" )
ierr = iMOAB_LoadMesh( cmpAtmPID, atmFilename.c_str(), readopts.c_str(), &nghlay );
CHECKIERR( ierr, "Cannot load atm mesh" )
}
MPI_Barrier( MPI_COMM_WORLD );
if( ocnComm != MPI_COMM_NULL )
{
MPI_Comm_rank( ocnComm, &rankInOcnComm );
ierr = iMOAB_RegisterApplication( "OCN1", &ocnComm, &cmpocn, cmpOcnPID );
CHECKIERR( ierr, "Cannot register OCN App" )
ierr = iMOAB_LoadMesh( cmpOcnPID, ocnFilename.c_str(), readopts.c_str(), &nghlay );
CHECKIERR( ierr, "Cannot load ocn mesh" )
}
MPI_Barrier( MPI_COMM_WORLD );
if( couComm != MPI_COMM_NULL )
{
// now load map between OCNx and ATMx on coupler PEs
ierr = iMOAB_RegisterApplication( "ATMOCN", &couComm, &atmocnid, cplAtmOcnPID );
CHECKIERR( ierr, "Cannot register ocn_atm map instance over coupler pes " )
}
int disc_orders[3] = { 4, 1, 1 };
const std::string intx_from_file_identifier = "map-from-file";
if( couComm != MPI_COMM_NULL )
{
int dummyCpl = -1;
int dummy_rowcol = -1;
int dummyType = 0;
ierr = iMOAB_LoadMappingWeightsFromFile( cplAtmOcnPID, &dummyCpl, &dummy_rowcol, &dummyType,
intx_from_file_identifier.c_str(), mapFilename.c_str() );
CHECKIERR( ierr, "failed to load map file from disk" );
}
if( atmCouComm != MPI_COMM_NULL )
{
int type = 1; // quads in source set
int direction = 1; // from source to coupler; will create a mesh on cplAtmPID
// because it is like "coverage", context will be cplocn
ierr = iMOAB_MigrateMapMesh( cmpAtmPID, cplAtmOcnPID, cplAtmPID, &atmCouComm, &atmPEGroup, &couPEGroup, &type,
&cmpatm, &cplocn, &direction );
CHECKIERR( ierr, "failed to migrate mesh for atm on coupler" );
#ifdef VERBOSE
if( *cplAtmPID >= 0 )
{
char prefix[] = "atmcov";
ierr = iMOAB_WriteLocalMesh( cplAtmPID, prefix );
CHECKIERR( ierr, "failed to write local mesh" );
}
#endif
}
MPI_Barrier( MPI_COMM_WORLD );
if( ocnCouComm != MPI_COMM_NULL )
{
int type = 3; // cells with GLOBAL_ID in ocean / target set
int direction = 2; // from coupler to target; will create a mesh on cplOcnPID
// it will be like initial migrate cmpocn <-> cplocn
ierr = iMOAB_MigrateMapMesh( cmpOcnPID, cplAtmOcnPID, cplOcnPID, &ocnCouComm, &ocnPEGroup, &couPEGroup, &type,
&cmpocn, &cplocn, &direction );
CHECKIERR( ierr, "failed to migrate mesh for ocn on coupler" );
#ifdef VERBOSE
if( *cplOcnPID >= 0 )
{
char prefix[] = "ocntgt";
ierr = iMOAB_WriteLocalMesh( cplOcnPID, prefix );
CHECKIERR( ierr, "failed to write local ocean mesh" );
char outputFileRec[] = "CoupOcn.h5m";
ierr = iMOAB_WriteMesh( cplOcnPID, outputFileRec, fileWriteOptions );
CHECKIERR( ierr, "failed to write ocean global mesh file" );
}
#endif
}
MPI_Barrier( MPI_COMM_WORLD );
int tagIndex[2];
int tagTypes[2] = { DENSE_DOUBLE, DENSE_DOUBLE };
int atmCompNDoFs = disc_orders[0] * disc_orders[0], ocnCompNDoFs = 1 /*FV*/;
const char* bottomFields = "a2oTbot:a2oUbot:a2oVbot";
const char* bottomProjectedFields = "a2oTbot_proj:a2oUbot_proj:a2oVbot_proj";
if( couComm != MPI_COMM_NULL )
{
ierr = iMOAB_DefineTagStorage( cplAtmPID, bottomFields, &tagTypes[0], &atmCompNDoFs, &tagIndex[0] );
CHECKIERR( ierr, "failed to define the field tags a2oTbot:a2oUbot:a2oVbot" );
ierr = iMOAB_DefineTagStorage( cplOcnPID, bottomProjectedFields, &tagTypes[1], &ocnCompNDoFs, &tagIndex[1] );
CHECKIERR( ierr, "failed to define the field tags a2oTbot_proj:a2oUbot_proj:a2oVbot_proj " );
}
// need to make sure that the coverage mesh (created during intx method) received the tag that
// need to be projected to target so far, the coverage mesh has only the ids and global dofs;
// need to change the migrate method to accommodate any GLL tag
// now send a tag from original atmosphere (cmpAtmPID) towards migrated coverage mesh
// (cplAtmPID), using the new coverage graph communicator
// make the tag 0, to check we are actually sending needed data
{
if( cplAtmAppID >= 0 )
{
int nverts[3], nelem[3], nblocks[3], nsbc[3], ndbc[3];
/*
* Each process in the communicator will have access to a local mesh instance, which
* will contain the original cells in the local partition and ghost entities. Number of
* vertices, primary cells, visible blocks, number of sidesets and nodesets boundary
* conditions will be returned in numProcesses 3 arrays, for local, ghost and total
* numbers.
*/
ierr = iMOAB_GetMeshInfo( cplAtmPID, nverts, nelem, nblocks, nsbc, ndbc );
CHECKIERR( ierr, "failed to get num primary elems" );
int numAllElem = nelem[2];
std::vector< double > vals;
int storLeng = atmCompNDoFs * numAllElem * 3; // 3 tags
int eetype = 1;
vals.resize( storLeng );
for( int k = 0; k < storLeng; k++ )
vals[k] = 0.;
ierr = iMOAB_SetDoubleTagStorage( cplAtmPID, bottomFields, &storLeng, &eetype, &vals[0] );
CHECKIERR( ierr, "cannot make tag nul" )
}
}
const char* concat_fieldname = "a2oTbot:a2oUbot:a2oVbot";
const char* concat_fieldnameT = "a2oTbot_proj:a2oUbot_proj:a2oVbot_proj";
// start a virtual loop for number of iterations
for( int iters = 0; iters < n; iters++ )
{
PUSH_TIMER( "Send/receive data from atm component to coupler in ocn context" )
if( atmComm != MPI_COMM_NULL )
{
// as always, use nonblocking sends
// this is for projection to ocean:
ierr = iMOAB_SendElementTag( cmpAtmPID, "a2oTbot:a2oUbot:a2oVbot", &atmCouComm, &cplocn );
CHECKIERR( ierr, "cannot send tag values" )
#ifdef GRAPH_INFO
int is_sender = 1;
int context = cplocn;
iMOAB_DumpCommGraph( cmpAtmPID, &context, &is_sender, "AtmCovOcnS" );
#endif
}
if( couComm != MPI_COMM_NULL )
{
// receive on atm on coupler pes, that was redistributed according to coverage
ierr = iMOAB_ReceiveElementTag( cplAtmPID, "a2oTbot:a2oUbot:a2oVbot", &atmCouComm, &cmpatm );
CHECKIERR( ierr, "cannot receive tag values" )
#ifdef GRAPH_INFO
int is_sender = 0;
int context = atmocnid; // the same context
iMOAB_DumpCommGraph( cmpAtmPID, &context, &is_sender, "AtmCovOcnR" );
#endif
}
// we can now free the sender buffers
if( atmComm != MPI_COMM_NULL )
{
ierr = iMOAB_FreeSenderBuffers( cmpAtmPID, &cplocn ); // context is for ocean
CHECKIERR( ierr, "cannot free buffers used to resend atm tag towards the coverage mesh" )
}
POP_TIMER( MPI_COMM_WORLD, rankInGlobalComm )
#ifdef VERBOSE
if( *cplAtmPID >= 0 && n == 1 )
{
char prefix[] = "atmcov_withdata";
ierr = iMOAB_WriteLocalMesh( cplAtmPID, prefix );
CHECKIERR( ierr, "failed to write local atm cov mesh with data" );
}
if( couComm != MPI_COMM_NULL && 1 == n )
{
// write only for n==1 case
char outputFileRecvd[] = "recvAtmCoupOcn.h5m";
ierr = iMOAB_WriteMesh( cplAtmPID, outputFileRecvd, fileWriteOptions );
CHECKIERR( ierr, "could not write recvAtmCoupOcn.h5m to disk" )
}
#endif
if( couComm != MPI_COMM_NULL )
{
/* We have the remapping weights now. Let us apply the weights onto the tag we defined
on the source mesh and get the projection on the target mesh */
PUSH_TIMER( "Apply Scalar projection weights" )
ierr = iMOAB_ApplyScalarProjectionWeights( cplAtmOcnPID, intx_from_file_identifier.c_str(),
concat_fieldname, concat_fieldnameT );
CHECKIERR( ierr, "failed to compute projection weight application" );
POP_TIMER( couComm, rankInCouComm )
if( 1 == n ) // write only for n==1 case
{
char outputFileTgt[] = "fOcnOnCpl8.h5m";
ierr = iMOAB_WriteMesh( cplOcnPID, outputFileTgt, fileWriteOptions );
CHECKIERR( ierr, "could not write fOcnOnCpl8.h5m to disk" )
}
}
// send the projected tag back to ocean pes, with send/receive tag
if( ocnComm != MPI_COMM_NULL )
{
int tagIndexIn2;
ierr =
iMOAB_DefineTagStorage( cmpOcnPID, bottomProjectedFields, &tagTypes[1], &ocnCompNDoFs, &tagIndexIn2 );
CHECKIERR( ierr, "failed to define the field tag for receiving back the tags "
"a2oTbot_proj:a2oUbot_proj:a2oVbot_proj on ocn pes" );
}
// send the tag to ocean pes, from ocean mesh on coupler pes
// from couComm, using common joint comm ocn_coupler
// as always, use nonblocking sends
// original graph (context is -1_
if( couComm != MPI_COMM_NULL )
{
// need to use ocean comp id for context
context_id = cmpocn; // id for ocean on comp
ierr =
iMOAB_SendElementTag( cplOcnPID, "a2oTbot_proj:a2oUbot_proj:a2oVbot_proj", &ocnCouComm, &context_id );
CHECKIERR( ierr, "cannot send tag values back to ocean pes" )
}
// receive on component 2, ocean
if( ocnComm != MPI_COMM_NULL )
{
context_id = cplocn; // id for ocean on coupler
ierr = iMOAB_ReceiveElementTag( cmpOcnPID, "a2oTbot_proj:a2oUbot_proj:a2oVbot_proj", &ocnCouComm,
&context_id );
CHECKIERR( ierr, "cannot receive tag values from ocean mesh on coupler pes" )
}
if( couComm != MPI_COMM_NULL )
{
context_id = cmpocn;
ierr = iMOAB_FreeSenderBuffers( cplOcnPID, &context_id );
}
MPI_Barrier( MPI_COMM_WORLD );
if( ocnComm != MPI_COMM_NULL && 1 == n ) // write only for n==1 case
{
#ifdef VERBOSE
char outputFileOcn[] = "OcnWithProj.h5m";
ierr = iMOAB_WriteMesh( cmpOcnPID, outputFileOcn, fileWriteOptions );
CHECKIERR( ierr, "could not write OcnWithProj.h5m to disk" )
#endif
// test results only for n == 1, for bottomTempProjectedField = "a2oTbot_proj"
if( !no_regression_test )
{
// the same as remap test
// get temp field on ocean, from conservative, the global ids, and dump to the baseline file
// first get GlobalIds from ocn, and fields:
int nverts[3], nelem[3];
ierr = iMOAB_GetMeshInfo( cmpOcnPID, nverts, nelem, 0, 0, 0 );
CHECKIERR( ierr, "failed to get ocn mesh info" );
std::vector< int > gidElems;
gidElems.resize( nelem[2] );
std::vector< double > tempElems;
tempElems.resize( nelem[2] );
// get global id storage
const std::string GidStr = "GLOBAL_ID"; // hard coded too
int tag_type = DENSE_INTEGER, ncomp = 1, tagInd = 0;
ierr = iMOAB_DefineTagStorage( cmpOcnPID, GidStr.c_str(), &tag_type, &ncomp, &tagInd );
CHECKIERR( ierr, "failed to define global id tag" );
int ent_type = 1;
ierr = iMOAB_GetIntTagStorage( cmpOcnPID, GidStr.c_str(), &nelem[2], &ent_type, &gidElems[0] );
CHECKIERR( ierr, "failed to get global ids" );
ierr = iMOAB_GetDoubleTagStorage( cmpOcnPID, "a2oTbot_proj", &nelem[2], &ent_type, &tempElems[0] );
CHECKIERR( ierr, "failed to get temperature field" );
int err_code = 1;
check_baseline_file( baseline, gidElems, tempElems, 1.e-9, err_code );
if( 0 == err_code )
std::cout << " passed baseline test atm2ocn on ocean task " << rankInOcnComm << "\n";
}
}
} // end loop iterations n
if( couComm != MPI_COMM_NULL )
{
ierr = iMOAB_DeregisterApplication( cplAtmOcnPID );
CHECKIERR( ierr, "cannot deregister app intx AO" )
}
if( ocnComm != MPI_COMM_NULL )
{
ierr = iMOAB_DeregisterApplication( cmpOcnPID );
CHECKIERR( ierr, "cannot deregister app OCN1" )
}
if( atmComm != MPI_COMM_NULL )
{
ierr = iMOAB_DeregisterApplication( cmpAtmPID );
CHECKIERR( ierr, "cannot deregister app ATM1" )
}
if( couComm != MPI_COMM_NULL )
{
ierr = iMOAB_DeregisterApplication( cplOcnPID );
CHECKIERR( ierr, "cannot deregister app OCNX" )
}
if( couComm != MPI_COMM_NULL )
{
ierr = iMOAB_DeregisterApplication( cplAtmPID );
CHECKIERR( ierr, "cannot deregister app ATMX" )
}
//#endif
ierr = iMOAB_Finalize();
CHECKIERR( ierr, "did not finalize iMOAB" )
// free atm coupler group and comm
if( MPI_COMM_NULL != atmCouComm ) MPI_Comm_free( &atmCouComm );
MPI_Group_free( &joinAtmCouGroup );
if( MPI_COMM_NULL != atmComm ) MPI_Comm_free( &atmComm );
if( MPI_COMM_NULL != ocnComm ) MPI_Comm_free( &ocnComm );
// free ocn - coupler group and comm
if( MPI_COMM_NULL != ocnCouComm ) MPI_Comm_free( &ocnCouComm );
MPI_Group_free( &joinOcnCouGroup );
if( MPI_COMM_NULL != couComm ) MPI_Comm_free( &couComm );
MPI_Group_free( &atmPEGroup );
MPI_Group_free( &ocnPEGroup );
MPI_Group_free( &couPEGroup );
MPI_Group_free( &jgroup );
MPI_Finalize();
return 0;
}
1.7.6.1