Changeset 1153


Ignore:
Timestamp:
06/02/17 17:53:25 (4 years ago)
Author:
yushan
Message:

save modif

Location:
XIOS/dev/branch_yushan_merged
Files:
10 edited

Legend:

Unmodified
Added
Removed
  • XIOS/dev/branch_yushan_merged/extern/remap/src/intersect.cpp

    r1149 r1153  
    5757    { 
    5858      // share a full edge ? be carefull at the orientation 
    59       /* 
    60       if(squaredist(a.vertex[i], b.vertex[j]) > 1e-10*1e-10 || 
    61          squaredist(a.vertex[(i+1)%a.n], b.vertex[(j+1)%b.n]) > 1e-10*1e-10 ) 
    62       {       
    63         printf("A : squaredist(a.vertex[%d], b.vertex[%d]) = %.10e  %d\n",  
    64                 i, j, squaredist(a.vertex[i], b.vertex[j]),  
    65                 squaredist(a.vertex[i], b.vertex[j]) > 1e-10*1e-10 ? true : false); 
    66         printf("B : squaredist(a.vertex[%d], b.vertex[%d]) = %.10e  %d\n",  
    67                 (i+1)%a.n, (j+1)%b.n, squaredist(a.vertex[(i+1)%a.n], b.vertex[(j+1)%b.n]), 
    68                 squaredist(a.vertex[(i+1)%a.n], b.vertex[(j+1)%b.n]) > 1e-10*1e-10 ? true : false); 
     59       
     60      //if(squaredist(a.vertex[i], b.vertex[j]) > 1e-10*1e-10 || 
     61      //   squaredist(a.vertex[(i+1)%a.n], b.vertex[(j+1)%b.n]) > 1e-10*1e-10 ) 
     62      //{       
     63        //printf("A : squaredist(a.vertex[%d], b.vertex[%d]) = %.10e  %d\n",  
     64        //        i, j, squaredist(a.vertex[i], b.vertex[j]),  
     65        //        squaredist(a.vertex[i], b.vertex[j]) > 1e-10*1e-10 ? true : false); 
     66        //printf("B : squaredist(a.vertex[%d], b.vertex[%d]) = %.10e  %d\n",  
     67        //        (i+1)%a.n, (j+1)%b.n, squaredist(a.vertex[(i+1)%a.n], b.vertex[(j+1)%b.n]), 
     68        //        squaredist(a.vertex[(i+1)%a.n], b.vertex[(j+1)%b.n]) > 1e-10*1e-10 ? true : false); 
    6969 
    7070        assert(squaredist(a.vertex[ i       ], b.vertex[ j       ]) > 1e-10*1e-10 || 
    7171               squaredist(a.vertex[(i+1)%a.n], b.vertex[(j+1)%b.n]) > 1e-10*1e-10); 
    72         exit(0); 
    73       }*/ 
     72         
     73      //} 
     74 
    7475      if (   squaredist(a.vertex[ i       ], b.vertex[ j           ]) < 1e-10*1e-10 && 
    7576             squaredist(a.vertex[(i+1)%a.n], b.vertex[(j+b.n-1)%b.n]) < 1e-10*1e-10) 
  • XIOS/dev/branch_yushan_merged/extern/remap/src/mapper.cpp

    r1149 r1153  
    303303            MPI_Issend(sendValue[rank], nbRecvElement[rank], MPI_DOUBLE, rank, 0, communicator, &sendRequest[nbSendRequest]); 
    304304            nbSendRequest++; 
    305             MPI_Issend(sendArea[rank], nbRecvElement[rank], MPI_DOUBLE, rank, 0, communicator, &sendRequest[nbSendRequest]); 
     305            MPI_Issend(sendArea[rank], nbRecvElement[rank], MPI_DOUBLE, rank, 1, communicator, &sendRequest[nbSendRequest]); 
    306306            nbSendRequest++; 
    307307            if (order == 2) 
    308308            { 
    309309                MPI_Issend(sendGrad[rank], 3*nbRecvElement[rank]*(NMAX+1), 
    310                         MPI_DOUBLE, rank, 0, communicator, &sendRequest[nbSendRequest]); 
     310                        MPI_DOUBLE, rank, 2, communicator, &sendRequest[nbSendRequest]); 
    311311                nbSendRequest++; 
    312                 MPI_Issend(sendNeighIds[rank], 4*nbRecvElement[rank]*(NMAX+1), MPI_INT, rank, 0, communicator, &sendRequest[nbSendRequest]); 
     312                MPI_Issend(sendNeighIds[rank], 4*nbRecvElement[rank]*(NMAX+1), MPI_INT, rank, 3, communicator, &sendRequest[nbSendRequest]); 
    313313                //ym  --> attention taille GloId 
    314314                nbSendRequest++; 
     
    316316            else 
    317317            { 
    318                 MPI_Issend(sendNeighIds[rank], 4*nbRecvElement[rank], MPI_INT, rank, 0, communicator, &sendRequest[nbSendRequest]); 
     318                MPI_Issend(sendNeighIds[rank], 4*nbRecvElement[rank], MPI_INT, rank, 4, communicator, &sendRequest[nbSendRequest]); 
    319319                //ym  --> attention taille GloId 
    320320                nbSendRequest++;                 
     
    325325            MPI_Irecv(recvValue[rank],  nbSendElement[rank], MPI_DOUBLE, rank, 0, communicator, &recvRequest[nbRecvRequest]); 
    326326            nbRecvRequest++; 
    327             MPI_Irecv(recvArea[rank],  nbSendElement[rank], MPI_DOUBLE, rank, 0, communicator, &recvRequest[nbRecvRequest]); 
     327            MPI_Irecv(recvArea[rank],  nbSendElement[rank], MPI_DOUBLE, rank, 1, communicator, &recvRequest[nbRecvRequest]); 
    328328            nbRecvRequest++; 
    329329            if (order == 2) 
    330330            { 
    331331                MPI_Irecv(recvGrad[rank], 3*nbSendElement[rank]*(NMAX+1), 
    332                         MPI_DOUBLE, rank, 0, communicator, &recvRequest[nbRecvRequest]); 
     332                        MPI_DOUBLE, rank, 2, communicator, &recvRequest[nbRecvRequest]); 
    333333                nbRecvRequest++; 
    334                 MPI_Irecv(recvNeighIds[rank], 4*nbSendElement[rank]*(NMAX+1), MPI_INT, rank, 0, communicator, &recvRequest[nbRecvRequest]); 
     334                MPI_Irecv(recvNeighIds[rank], 4*nbSendElement[rank]*(NMAX+1), MPI_INT, rank, 3, communicator, &recvRequest[nbRecvRequest]); 
    335335                //ym  --> attention taille GloId 
    336336                nbRecvRequest++; 
     
    338338            else 
    339339            { 
    340                 MPI_Irecv(recvNeighIds[rank], 4*nbSendElement[rank], MPI_INT, rank, 0, communicator, &recvRequest[nbRecvRequest]); 
     340                MPI_Irecv(recvNeighIds[rank], 4*nbSendElement[rank], MPI_INT, rank, 4, communicator, &recvRequest[nbRecvRequest]); 
    341341                //ym  --> attention taille GloId 
    342342                nbRecvRequest++; 
  • XIOS/dev/branch_yushan_merged/extern/remap/src/node.hpp

    r923 r1153  
    1515struct Circle 
    1616{ 
    17         Coord centre; 
    18         double radius; 
     17  Coord centre; 
     18  double radius; 
    1919}; 
    2020 
     
    116116struct Node 
    117117{ 
    118         int level; /* FIXME leafs are 0 and root is max level? */ 
    119         int leafCount; /* number of leafs that are descendants of this node (the elements in it's cycle) */ 
    120         Coord centre; 
    121         double radius; 
    122         NodePtr parent, ref; 
    123         std::vector<NodePtr> child; 
    124         std::list<NodePtr> intersectors; 
    125         bool reinserted; 
    126         int updateCount;  // double var; 
    127         CBasicTree* tree; 
    128         void *data; 
    129         int route; 
     118  int level; /* FIXME leafs are 0 and root is max level? */ 
     119  int leafCount; /* number of leafs that are descendants of this node (the elements in it's cycle) */ 
     120  Coord centre; 
     121  double radius; 
     122  NodePtr parent, ref; 
     123  std::vector<NodePtr> child; 
     124  std::list<NodePtr> intersectors; 
     125  bool reinserted; 
     126  int updateCount;  // double var; 
     127  CBasicTree* tree; 
     128  void *data; 
     129  int route; 
    130130  bool toDelete ; 
    131131 
    132         Node() : level(0), leafCount(1), centre(ORIGIN), radius(0), reinserted(false), updateCount(0), toDelete(false) {} 
    133         Node(const Coord& centre, double radius, void *data) 
    134                 : level(0), leafCount(1), centre(centre), radius(radius), reinserted(false), updateCount(0), data(data), toDelete(false) {} 
     132  Node() : level(0), leafCount(1), centre(ORIGIN), radius(0), reinserted(false), updateCount(0), toDelete(false) {} 
     133  Node(const Coord& centre, double radius, void *data) 
     134    : level(0), leafCount(1), centre(centre), radius(radius), reinserted(false), updateCount(0), data(data), toDelete(false) {} 
    135135 
    136136//#ifdef DEBUG 
     
    178178//#endif 
    179179 
    180         void move(const NodePtr node); 
    181         void remove(const NodePtr node); 
    182         void inflate(const NodePtr node); 
    183         void update(); 
     180  void move(const NodePtr node); 
     181  void remove(const NodePtr node); 
     182  void inflate(const NodePtr node); 
     183  void update(); 
    184184  void output(std::ostream& flux, int level, int color) ; 
    185         NodePtr closest(std::vector<NodePtr>& list, int n = CLOSEST); 
    186         NodePtr farthest(std::vector<NodePtr>& list); 
    187         void findClosest(int level, NodePtr src, double& minDist, NodePtr &closest); 
    188  
    189         void search(NodePtr node); 
    190         bool centreInside(Node &node); 
    191         bool intersects(NodePtr node); 
    192         bool isInside(Node &node); 
    193         int incluCheck(); 
     185  NodePtr closest(std::vector<NodePtr>& list, int n = CLOSEST); 
     186  NodePtr farthest(std::vector<NodePtr>& list); 
     187  void findClosest(int level, NodePtr src, double& minDist, NodePtr &closest); 
     188 
     189  void search(NodePtr node); 
     190  bool centreInside(Node &node); 
     191  bool intersects(NodePtr node); 
     192  bool isInside(Node &node); 
     193  int incluCheck(); 
    194194  void checkParent(void) ; 
    195         void printChildren(); 
    196         void assignRoute(std::vector<int>::iterator& rank, int level); 
    197         void assignCircleAndPropagateUp(Coord *centres, double *radia, int level); 
    198         void printLevel(int level); 
    199         void routeNode(NodePtr node, int level); 
    200         void routingIntersecting(std::vector<Node>* routingList, NodePtr node); 
    201         void routeIntersection(std::vector<int>& routes, NodePtr node); 
     195  void printChildren(); 
     196  void assignRoute(std::vector<int>::iterator& rank, int level); 
     197  void assignCircleAndPropagateUp(Coord *centres, double *radia, int level); 
     198  void printLevel(int level); 
     199  void routeNode(NodePtr node, int level); 
     200  void routingIntersecting(std::vector<Node>* routingList, NodePtr node); 
     201  void routeIntersection(std::vector<int>& routes, NodePtr node); 
    202202  void getNodeLevel(int level,std::list<NodePtr>& NodeList) ; 
    203203  bool removeDeletedNodes(int assignLevel) ; 
  • XIOS/dev/branch_yushan_merged/extern/src_ep_dev/ep_wait.cpp

    r1149 r1153  
    5858    if(request->type == 3) 
    5959    { 
    60       ::MPI_Request mpi_request = static_cast< ::MPI_Request >(request->mpi_request); 
     60      ::MPI_Request *mpi_request = static_cast< ::MPI_Request* >(&(request->mpi_request)); 
    6161      ::MPI_Status mpi_status; 
    62       ::MPI_Wait(&mpi_request, &mpi_status); 
     62      ::MPI_Errhandler_set(MPI_COMM_WORLD_STD, MPI_ERRORS_RETURN); 
     63      int error_code = ::MPI_Wait(mpi_request, &mpi_status); 
     64      if (error_code != MPI_SUCCESS) { 
     65       
     66         char error_string[BUFSIZ]; 
     67         int length_of_error_string, error_class; 
     68       
     69         ::MPI_Error_class(error_code, &error_class); 
     70         ::MPI_Error_string(error_class, error_string, &length_of_error_string); 
     71         printf("%s\n", error_string); 
     72      } 
     73       
    6374 
    6475      status->mpi_status = new ::MPI_Status(mpi_status); 
     
    8192  int MPI_Waitall(int count, MPI_Request *array_of_requests, MPI_Status *array_of_statuses) 
    8293  { 
    83     int dest_rank; 
    84     MPI_Comm_rank(MPI_COMM_WORLD, &dest_rank); 
     94    //int dest_rank; 
     95    //MPI_Comm_rank(MPI_COMM_WORLD, &dest_rank); 
     96    //printf("proc %d enters waitall\n", dest_rank); 
    8597 
    8698    int finished = 0; 
     
    100112          if(array_of_requests[i].type != 2) // isend or imrecv 
    101113          {       
    102             //MPI_Wait(&array_of_requests[i], &array_of_statuses[i]); 
    103             int tested=false; 
    104             while(!tested) MPI_Test(&array_of_requests[i], &tested, &array_of_statuses[i]); 
     114            MPI_Wait(&array_of_requests[i], &array_of_statuses[i]); 
     115            //int tested=false; 
     116            //while(!tested) MPI_Test(&array_of_requests[i], &tested, &array_of_statuses[i]); 
    105117            finished++; 
    106118            finished_index[i] = true; 
     
    127139      }     
    128140    } 
     141    //printf("proc %d exits waitall\n", dest_rank); 
    129142    return MPI_SUCCESS; 
    130143  }  /* end of mpi_waitall*/ 
  • XIOS/dev/branch_yushan_merged/src/io/netCdfInterface.cpp

    r1149 r1153  
    7575int CNetCdfInterface::open(const StdString& fileName, int oMode, int& ncId) 
    7676{ 
    77   int status = nc_open(fileName.c_str(), oMode, &ncId); 
     77  int status = NC_NOERR; 
     78  #pragma omp critical (_netcdf) 
     79  status = nc_open(fileName.c_str(), oMode, &ncId); 
     80   
    7881  if (NC_NOERR != status) 
    7982  { 
     
    105108  int status; 
    106109  #pragma omp critical (_netcdf) 
    107   status = xios::nc_open_par(fileName.c_str(), oMode, comm, info, &ncId); 
     110  status = xios::nc_open_par(fileName.c_str(), oMode, comm, info, &ncId); // nc_open 
    108111  if (NC_NOERR != status) 
    109112  { 
     
    129132{ 
    130133  int status = NC_NOERR; 
    131   //#pragma omp critical (_netcdf) 
    132   #pragma omp master 
     134  #pragma omp critical (_netcdf) 
     135  //#pragma omp master 
    133136  { 
    134137  status = nc_close(ncId); 
  • XIOS/dev/branch_yushan_merged/src/node/field.cpp

    r1149 r1153  
    713713     if (context->hasClient) 
    714714     { 
    715        MPI_Barrier(context->client->intraComm); 
    716        printf("Proc %d enters function\n", myRank); 
     715       //MPI_Barrier(context->client->intraComm); 
     716       //printf("Proc %d enters function\n", myRank); 
    717717       solveTransformedGrid(); 
    718        MPI_Barrier(context->client->intraComm); 
    719        printf("Proc %d exits function\n", myRank); 
     718       //MPI_Barrier(context->client->intraComm); 
     719       //printf("Proc %d exits function\n", myRank); 
    720720     } 
    721721 
  • XIOS/dev/branch_yushan_merged/src/node/file.cpp

    r1149 r1153  
    578578      bool isCollective = par_access.isEmpty() || par_access == par_access_attr::collective; 
    579579 
     580      #ifdef _usingEP 
     581      if(omp_get_num_threads() != 1 ) multifile = true; 
     582      #endif 
     583 
    580584      if (isOpen) data_out->closeFile(); 
    581585      if (time_counter_name.isEmpty()) data_in = shared_ptr<CDataInput>(new CNc4DataInput(oss.str(), static_cast< ::MPI_Comm >(fileComm.mpi_comm), multifile, isCollective)); 
     
    609613 
    610614     // It would probably be better to call initFile() somehow 
     615      
    611616     MPI_Comm_dup(client->intraComm, &fileComm); 
    612617     if (time_counter_name.isEmpty()) time_counter_name = "time_counter"; 
    613618 
    614      //#pragma omp critical (_checkFile) 
    615      checkFile(); 
     619     //#pragma omp critical (_readAttributesOfEnabledFieldsInReadMode_) 
     620     //{ 
     621     checkFile(); // calls nc_open 
    616622 
    617623     for (int idx = 0; idx < enabledFields.size(); ++idx) 
     
    627633 
    628634        // Read necessary value from file 
    629         this->data_in->readFieldAttributesValues(enabledFields[idx]); 
    630  
     635        #pragma omp critical (_func) 
     636        { 
     637          //checkFile(); 
     638          this->data_in->readFieldAttributesValues(enabledFields[idx]); 
     639          //close(); 
     640        } 
     641         
    631642        // Fill attributes for base reference 
    632643        enabledFields[idx]->solveGridDomainAxisBaseRef(); 
     
    634645 
    635646     // Now everything is ok, close it 
    636      //close(); 
     647     close(); 
     648     //} 
     649      
     650     //if (fileComm != MPI_COMM_NULL) MPI_Comm_free(&fileComm); 
     651      
    637652   } 
    638653 
  • XIOS/dev/branch_yushan_merged/src/test/test_remap_omp.f90

    r1146 r1153  
    5252  if(rank < size-2) then 
    5353 
    54   !$omp parallel default(firstprivate)  
     54  !$omp parallel default(firstprivate) firstprivate(dtime) 
    5555 
    5656!!! XIOS Initialization (get the local communicator) 
     
    5959  CALL MPI_COMM_RANK(comm,rank,ierr) 
    6060  CALL MPI_COMM_SIZE(comm,size,ierr) 
     61   
     62  rank = rank*omp_get_num_threads() + omp_get_thread_num() 
     63  size = size*omp_get_num_threads() 
    6164 
    6265   
     
    202205 
    203206  CALL xios_close_context_definition() 
     207 
     208  CALL xios_get_domain_attr("src_domain_regular_read", ni=src_tmp_ni, nj=src_tmp_nj) 
     209  ALLOCATE(tmp_field_0(src_tmp_ni*src_tmp_nj)) 
     210 
     211  CALL xios_get_axis_attr("src_axis_curvilinear_read", n=src_tmp_n) 
     212  CALL xios_get_domain_attr("src_domain_curvilinear_read", ni=src_tmp_ni, nj=src_tmp_nj) 
     213  ALLOCATE(tmp_field_1(src_tmp_ni*src_tmp_nj*src_tmp_n)) 
     214 
     215  CALL xios_get_domain_attr("src_domain_unstructured_read", ni=src_tmp_ni, nj=src_tmp_nj) 
     216  ALLOCATE(tmp_field_2(src_tmp_ni*src_tmp_nj)) 
     217   
     218  CALL xios_recv_field("src_field_regular", tmp_field_0) 
     219  CALL xios_recv_field("src_field_curvilinear", tmp_field_1) 
     220  CALL xios_recv_field("src_field_unstructured", tmp_field_2) 
     221 
     222  DO ts=1,10 
     223    CALL xios_update_calendar(ts) 
     224    CALL xios_send_field("src_field_2D",src_field_2D) 
     225     
     226    DO i=1,src_ni 
     227      src_field_2D_clone(i) = src_field_2D(i) 
     228      IF ((23.5 * ts < src_lat(i)) .AND. (src_lat(i) < 65.5 *ts) .AND. (0 < src_lon(i)) .AND. (src_lon(i) < 30*ts)) THEN       
     229        src_field_2D_clone(i) = missing_value     
     230      ENDIF 
     231    ENDDO 
     232 
     233    CALL xios_send_field("src_field_2D_clone",src_field_2D_clone) 
     234    CALL xios_send_field("src_field_3D",src_field_3D) 
     235    CALL xios_send_field("src_field_3D_clone",src_field_3D) 
     236    CALL xios_send_field("src_field_4D",src_field_4D) 
     237    CALL xios_send_field("src_field_3D_pression",src_field_pression) 
     238    CALL xios_send_field("tmp_field_0",tmp_field_0) 
     239    CALL xios_send_field("tmp_field_1",tmp_field_1) 
     240    CALL xios_send_field("tmp_field_2",tmp_field_2) 
     241    CALL wait_us(5000) ; 
     242   ENDDO 
    204243   
    205244  CALL xios_context_finalize() 
     245 
     246  DEALLOCATE(src_lon, src_lat, src_boundslon,src_boundslat, src_field_2D) 
     247  DEALLOCATE(dst_lon, dst_lat, dst_boundslon,dst_boundslat) 
     248  DEALLOCATE(tmp_field_0, tmp_field_1, tmp_field_2) 
    206249   
    207250  CALL xios_finalize() 
  • XIOS/dev/branch_yushan_merged/src/transformation/Functions/reduction.cpp

    r1134 r1153  
    5050  (*CReductionAlgorithm::ReductionOperations_ptr)["average"] = TRANS_REDUCE_AVERAGE; 
    5151  CAverageReductionAlgorithm::registerTrans(); 
     52 
     53  printf("*CReductionAlgorithm::ReductionOperations_ptr = %p\t %p\n", *CReductionAlgorithm::ReductionOperations_ptr, &(*CReductionAlgorithm::ReductionOperations_ptr)); 
    5254} 
    5355 
  • XIOS/dev/branch_yushan_merged/src/transformation/scalar_algorithm_reduce_axis.cpp

    r1134 r1153  
    7575  } 
    7676   
    77   if ((*CReductionAlgorithm::ReductionOperations_ptr).end() == (*CReductionAlgorithm::ReductionOperations_ptr).find(op)) 
    78     ERROR("CScalarAlgorithmReduceAxis::CScalarAlgorithmReduceAxis(CAxis* axisDestination, CAxis* axisSource, CReduceAxisToScalar* algo)", 
    79        << "Operation '" << op << "' not found. Please make sure to use a supported one" 
    80        << "Axis source " <<axisSource->getId() << std::endl 
    81        << "Scalar destination " << scalarDestination->getId()); 
     77  //if ((*CReductionAlgorithm::ReductionOperations_ptr).end() == (*CReductionAlgorithm::ReductionOperations_ptr).find(op)) 
     78  //  if ((CReductionAlgorithm::ReductionOperations_ptr)->end() == (CReductionAlgorithm::ReductionOperations_ptr)->find(op)) 
     79  //  ERROR("CScalarAlgorithmReduceAxis::CScalarAlgorithmReduceAxis(CAxis* axisDestination, CAxis* axisSource, CReduceAxisToScalar* algo)", 
     80  //     << "Operation '" << op << "' not found. Please make sure to use a supported one" 
     81  //     << "Axis source " <<axisSource->getId() << std::endl 
     82  //     << "Scalar destination " << scalarDestination->getId()); 
    8283 
    8384  reduction_ = CReductionAlgorithm::createOperation((*CReductionAlgorithm::ReductionOperations_ptr)[op]); 
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