/* * python bulkload class method */ static PyObject * python_sorted_btree_bulkload(PyObject *klass, PyObject *args) { int i, result; PyObject *item_list, *order, *iter, *item, *prev = NULL; if (!PyArg_ParseTuple(args, "OO!", &item_list, &PyInt_Type, &order)) return NULL; if ((iter = PyObject_GetIter(item_list)) == NULL) return NULL; for (i = 0, item = PyIter_Next(iter); item; ++i, item = PyIter_Next(iter)) { if (i) { result = PyObject_RichCompareBool(prev, item, Py_LT); if (result <= 0) { if (!result) PyErr_SetString(PyExc_ValueError, "the bulkloaded list must already be sorted"); Py_DECREF(prev); Py_DECREF(item); Py_DECREF(iter); return NULL; } Py_DECREF(prev); } prev = item; } if (prev) Py_DECREF(prev); Py_DECREF(iter); if ((iter = PyObject_GetIter(item_list)) == NULL) return NULL; btsort_pyobject *tree = PyObject_GC_New( btsort_pyobject, &btsort_pytypeobj); if (bulkload(tree, iter, (int)PyInt_AsLong(order))) return NULL; return (PyObject *)tree; }
int main(int argc, char **argv) { mesh_t *mesh; double double_message[5]; double x, y, z, factor = 0, vscut = 0; double elapsedtime; #ifndef NO_OUTPUT int32_t eindex; int32_t remains, batch, idx; mrecord_t *partTable; #endif MPI_Init(&argc, &argv); MPI_Comm_rank(MPI_COMM_WORLD, &myID); MPI_Comm_size(MPI_COMM_WORLD, &theGroupSize); /* Read commandline arguments */ if (argc != 5) { if (myID == 0) { fprintf(stderr, "usage: qmesh cvmdb physics.in numerical.in "); fprintf(stderr, "meshdb\n"); fprintf(stderr, "cvmdb: path to an etree database or a flat file.\n"); fprintf(stderr, "physics.in: path to physics.in.\n"); fprintf(stderr, "numerical.in: path to numerical.in.\n"); fprintf(stderr, "meshetree: path to the output mesh etree.\n"); fprintf(stderr, "\n"); } MPI_Finalize(); return -1; } /* Change the working directory to $LOCAL */ /* localpath = getenv("LOCAL"); if (localpath == NULL) { fprintf(stderr, "Thread %d: Cannot get $LOCAL value\n", myID); MPI_Abort(MPI_COMM_WORLD, ERROR); exit(1); } if (chdir(localpath) != 0) { fprintf(stderr, "Thread %d: Cannot chdir to %s\n", myID, localpath); MPI_Abort(MPI_COMM_WORLD, ERROR); exit(1); } */ /* Replicate the material database among the processors */ /* if ((theGroupSize - 1) / PROCPERNODE >= 1) { MPI_Comm replica_comm; if (myID % PROCPERNODE != 0) { MPI_Comm_split(MPI_COMM_WORLD, MPI_UNDEFINED, myID, &replica_comm); } else { int replica_id; off_t filesize, remains, batchsize; void *filebuf; int fd; MPI_Comm_split(MPI_COMM_WORLD, 0, myID, &replica_comm); MPI_Comm_rank(replica_comm, &replica_id); if (replica_id == 0) { struct stat statbuf; if (stat(argv[1], &statbuf) != 0) { fprintf(stderr, "Thread 0: Cannot get stat of %s\n", argv[1]); MPI_Abort(MPI_COMM_WORLD, ERROR); exit(1); } filesize = statbuf.st_size; } MPI_Bcast(&filesize, sizeof(off_t), MPI_CHAR, 0, replica_comm); if ((filebuf = malloc(FILEBUFSIZE)) == NULL) { fprintf(stderr, "Thread %d: run out of memory while ", myID); fprintf(stderr, "preparing to receive material database\n"); MPI_Abort(MPI_COMM_WORLD, ERROR); exit(1); } fd = (replica_id == 0) ? open(argv[1], O_RDONLY) : open(argv[1], O_CREAT|O_TRUNC|O_WRONLY, S_IRUSR|S_IWUSR); if (fd == -1) { fprintf(stderr, "Thread %d: Cannot create replica database\n", myID); perror("open"); MPI_Abort(MPI_COMM_WORLD, ERROR); exit(1); } remains = filesize; while (remains > 0) { batchsize = (remains > FILEBUFSIZE) ? FILEBUFSIZE : remains; if (replica_id == 0) { if (read(fd, filebuf, batchsize) != batchsize) { fprintf(stderr, "Thread 0: Cannot read database\n"); perror("read"); MPI_Abort(MPI_COMM_WORLD, ERROR); exit(1); } } MPI_Bcast(filebuf, batchsize, MPI_CHAR, 0, replica_comm); if (replica_id != 0) { if (write(fd, filebuf, batchsize) != batchsize) { fprintf(stderr, "Thread %d: Cannot write replica ", myID); fprintf(stderr, "database\n"); MPI_Abort(MPI_COMM_WORLD, ERROR); exit(1); } } remains -= batchsize; } if (close(fd) != 0) { fprintf(stderr, "Thread %d: cannot close replica database\n", myID); perror("close"); MPI_Abort(MPI_COMM_WORLD, ERROR); exit(1); } } MPI_Barrier(MPI_COMM_WORLD); } */ /* Initialize static global varialbes */ if (myID == 0) { /* Processor 0 reads the parameters */ if (initparameters(argv[2], argv[3], &x, &y, &z) != 0) { fprintf(stderr, "Thread %d: Cannot init parameters\n", myID); MPI_Abort(MPI_COMM_WORLD, ERROR); exit(1); } factor = theFactor; vscut = theVsCut; double_message[0] = x; double_message[1] = y; double_message[2] = z; double_message[3] = factor; double_message[4] = vscut; /* fprintf(stderr, "&double_message[0] = %p\n", &double_message[0]); fprintf(stderr, "&double_message[4] = %p\n", &double_message[4]); fprintf(stderr, "Thread 0: %f %f %f %f %f\n", x, y, z, factor, vscut); */ } MPI_Bcast(double_message, 5, MPI_DOUBLE, 0, MPI_COMM_WORLD); x = double_message[0]; y = double_message[1]; z = double_message[2]; factor = double_message[3]; vscut = double_message[4]; theNorth_m = x; theEast_m = y; theDepth_m = z; /* printf("Thread %d: %f %f %f %f %f\n", myID, x, y, z, factor, vscut); */ theFactor = factor; theVsCut = vscut; MPI_Barrier(MPI_COMM_WORLD); elapsedtime = -MPI_Wtime(); if (myID == 0) { fprintf(stdout, "PE = %d, Freq = %.2f\n", theGroupSize, theFreq); fprintf(stdout, "-----------------------------------------------\n"); } /*---- Generate and partition an unstructured octree mesh ----*/ if (myID == 0) { fprintf(stdout, "octor_newtree ... "); } /* * RICARDO: Carful with new_octree parameters (cutoff_depth) */ myOctree = octor_newtree(x, y, z, sizeof(edata_t), myID, theGroupSize, MPI_COMM_WORLD, 0); if (myOctree == NULL) { fprintf(stderr, "Thread %d: fail to create octree\n", myID); MPI_Abort(MPI_COMM_WORLD, ERROR); exit(1); } MPI_Barrier(MPI_COMM_WORLD); elapsedtime += MPI_Wtime(); if (myID == 0) { fprintf(stdout, "done.... %.2f seconds\n", elapsedtime); } #ifdef USECVMDB /* Open my copy of the material database */ theCVMEp = etree_open(argv[1], O_RDONLY, CVMBUFSIZE, 0, 0); if (!theCVMEp) { fprintf(stderr, "Thread %d: Cannot open CVM etree database %s\n", myID, argv[1]); MPI_Abort(MPI_COMM_WORLD, ERROR); exit(1); } #else /* Use flat data record file and distibute the data in memories */ elapsedtime = -MPI_Wtime(); if (myID == 0) { fprintf(stdout, "slicing CVM database ..."); } theCVMRecord = sliceCVM(argv[1]); MPI_Barrier(MPI_COMM_WORLD); elapsedtime += MPI_Wtime(); if (theCVMRecord == NULL) { fprintf(stderr, "Thread %d: Error obtaining the CVM records from %s\n", myID, argv[1]); MPI_Abort(MPI_COMM_WORLD, ERROR); exit(1); }; if (myID == 0) { fprintf(stdout, "done.... %.2f seconds\n", elapsedtime); } #endif elapsedtime = -MPI_Wtime(); if (myID == 0) { fprintf(stdout, "octor_refinetree ..."); } if (octor_refinetree(myOctree, toexpand, setrec) != 0) { fprintf(stderr, "Thread %d: fail to refine octree\n", myID); MPI_Abort(MPI_COMM_WORLD, ERROR); exit(1); } MPI_Barrier(MPI_COMM_WORLD); elapsedtime += MPI_Wtime(); if (myID == 0) { fprintf(stdout, "done.... %.2f seconds\n", elapsedtime); } elapsedtime = -MPI_Wtime(); if (myID == 0) { fprintf(stdout, "octor_balancetree ... "); } if (octor_balancetree(myOctree, setrec, 0) != 0) { /* no progressive meshing (ricardo) */ fprintf(stderr, "Thread %d: fail to balance octree\n", myID); MPI_Abort(MPI_COMM_WORLD, ERROR); exit(1); } MPI_Barrier(MPI_COMM_WORLD); elapsedtime += MPI_Wtime(); if (myID == 0) { fprintf(stdout, "done.... %.2f seconds\n", elapsedtime); } #ifdef USECVMDB /* Close the material database */ etree_close(theCVMEp); #else free(theCVMRecord); #endif /* USECVMDB */ elapsedtime = -MPI_Wtime(); if (myID == 0) { fprintf(stdout, "octor_partitiontree ..."); } if (octor_partitiontree(myOctree, NULL) != 0) { fprintf(stderr, "Thread %d: fail to balance load\n", myID); MPI_Abort(MPI_COMM_WORLD, ERROR); exit(1); } MPI_Barrier(MPI_COMM_WORLD); elapsedtime += MPI_Wtime(); if (myID == 0) { fprintf(stdout, "done.... %.2f seconds\n", elapsedtime); } elapsedtime = - MPI_Wtime(); if (myID == 0) { fprintf(stdout, "octor_extractmesh ... "); } mesh = octor_extractmesh(myOctree, NULL); if (mesh == NULL) { fprintf(stderr, "Thread %d: fail to extract mesh\n", myID); MPI_Abort(MPI_COMM_WORLD, ERROR); exit(1); } MPI_Barrier(MPI_COMM_WORLD); elapsedtime += MPI_Wtime(); if (myID == 0) { fprintf(stdout, "done.... %.2f seconds\n", elapsedtime); } /* We can do without the octree now */ octor_deletetree(myOctree); /*---- Obtain and print the statistics of the mesh ----*/ if (myID == 0) { int64_t etotal, ntotal, dntotal; int32_t received, procid; int32_t *enumTable, *nnumTable, *dnnumTable; int32_t rcvtrio[3]; /* Allocate the arrays to hold the statistics */ enumTable = (int32_t *)malloc(sizeof(int32_t) * theGroupSize); nnumTable = (int32_t *)malloc(sizeof(int32_t) * theGroupSize); dnnumTable = (int32_t *)malloc(sizeof(int32_t) * theGroupSize); if ((enumTable == NULL) || (nnumTable == NULL) || (dnnumTable == NULL)) { fprintf(stderr, "Thread 0: out of memory\n"); MPI_Abort(MPI_COMM_WORLD, ERROR); exit(1); } /* Fill in my counts */ enumTable[0] = mesh->lenum; nnumTable[0] = mesh->lnnum; dnnumTable[0] = mesh->ldnnum; /* Initialize sums */ etotal = mesh->lenum; ntotal = mesh->lnnum; dntotal = mesh->ldnnum; /* Fill in the rest of the tables */ received = 0; while (received < theGroupSize - 1) { int32_t fromwhom; MPI_Status status; MPI_Probe(MPI_ANY_SOURCE, STAT_MSG, MPI_COMM_WORLD, &status); fromwhom = status.MPI_SOURCE; MPI_Recv(rcvtrio, 3, MPI_INT, fromwhom, STAT_MSG, MPI_COMM_WORLD, &status); enumTable[fromwhom] = rcvtrio[0]; nnumTable[fromwhom] = rcvtrio[1]; dnnumTable[fromwhom] = rcvtrio[2]; etotal += rcvtrio[0]; ntotal += rcvtrio[1]; dntotal += rcvtrio[2]; received++; } fprintf(stdout, "Mesh statistics:\n"); fprintf(stdout, " Elements Nodes Danglings\n"); #ifdef ALPHA_TRU64UNIX_CC fprintf(stdout, "Total : %10ld%10ld %10ld\n\n", etotal, ntotal, dntotal); for (procid = 0; procid < theGroupSize; procid++) { fprintf(stdout, "Proc %5d: %10d%10d %10d\n", procid, enumTable[procid], nnumTable[procid], dnnumTable[procid]); } #else fprintf(stdout, "Total : %10qd%10qd %10qd\n\n", etotal, ntotal, dntotal); for (procid = 0; procid < theGroupSize; procid++) { fprintf(stdout, "Proc %5d: %10d%10d %10d\n", procid, enumTable[procid], nnumTable[procid], dnnumTable[procid]); } #endif free(enumTable); free(nnumTable); free(dnnumTable); } else { int32_t sndtrio[3]; sndtrio[0] = mesh->lenum; sndtrio[1] = mesh->lnnum; sndtrio[2] = mesh->ldnnum; MPI_Send(sndtrio, 3, MPI_INT, 0, STAT_MSG, MPI_COMM_WORLD); } #ifndef NO_OUTPUT /*---- Join elements and nodes, and send to Thread 0 for output */ /* Allocate a fixed size buffer space to store the join results */ partTable = (mrecord_t *)calloc(BATCH, sizeof(mrecord_t)); if (partTable == NULL) { fprintf(stderr, "Thread %d: out of memory\n", myID); MPI_Abort(MPI_COMM_WORLD, ERROR); exit(1); } if (myID == 0) { char *mEtree; etree_t *mep; int32_t procid; mEtree = argv[4]; mep = etree_open(mEtree, O_CREAT|O_RDWR|O_TRUNC, 0, sizeof(mdata_t),3); if (mep == NULL) { fprintf(stderr, "Thread 0: cannot create mesh etree\n"); MPI_Abort(MPI_COMM_WORLD, ERROR); exit(1); } /* Begin an appending operation */ if (etree_beginappend(mep, 1) != 0) { fprintf(stderr, "Thread 0: cannot begin an append operation\n"); MPI_Abort(MPI_COMM_WORLD, ERROR); exit(1); } eindex = 0; while (eindex < mesh->lenum) { remains = mesh->lenum - eindex; batch = (remains < BATCH) ? remains : BATCH; for (idx = 0; idx < batch; idx++) { mrecord_t *mrecord; int32_t whichnode; int32_t localnid0; mrecord = &partTable[idx]; /* Fill the address field */ localnid0 = mesh->elemTable[eindex].lnid[0]; mrecord->addr.x = mesh->nodeTable[localnid0].x; mrecord->addr.y = mesh->nodeTable[localnid0].y; mrecord->addr.z = mesh->nodeTable[localnid0].z; mrecord->addr.level = mesh->elemTable[eindex].level; mrecord->addr.type = ETREE_LEAF; /* Find the global node ids for the vertices */ for (whichnode = 0; whichnode < 8; whichnode++) { int32_t localnid; int64_t globalnid; localnid = mesh->elemTable[eindex].lnid[whichnode]; globalnid = mesh->nodeTable[localnid].gnid; mrecord->mdata.nid[whichnode] = globalnid; } memcpy(&mrecord->mdata.edgesize, mesh->elemTable[eindex].data, sizeof(edata_t)); eindex++; } /* for a batch */ if (bulkload(mep, partTable, batch) != 0) { fprintf(stderr, "Thread 0: Error bulk-loading data\n"); MPI_Abort(MPI_COMM_WORLD, ERROR); exit(1); } } /* for all the elements Thread 0 has */ /* Receive data from other processors */ for (procid = 1; procid < theGroupSize; procid++) { MPI_Status status; int32_t rcvbytecount; /* Signal the next processor to go ahead */ MPI_Send(NULL, 0, MPI_CHAR, procid, GOAHEAD_MSG, MPI_COMM_WORLD); while (1) { MPI_Probe(procid, MESH_MSG, MPI_COMM_WORLD, &status); MPI_Get_count(&status, MPI_CHAR, &rcvbytecount); batch = rcvbytecount / sizeof(mrecord_t); if (batch == 0) { /* Done */ break; } MPI_Recv(partTable, rcvbytecount, MPI_CHAR, procid, MESH_MSG, MPI_COMM_WORLD, &status); if (bulkload(mep, partTable, batch) != 0) { fprintf(stderr, "Thread 0: Cannot bulk-load data from "); fprintf(stderr, "Thread %d\n", procid); MPI_Abort(MPI_COMM_WORLD, ERROR); exit(1); } } /* while there is more data to be received from procid */ } /* for all the processors */ /* End the appending operation */ etree_endappend(mep); /* Close the mep to ensure the data is on disk */ if (etree_close(mep) != 0) { fprintf(stderr, "Thread 0: Cannot close the etree database\n"); MPI_Abort(MPI_COMM_WORLD, ERROR); exit(1); } } else { /* Processors other than 0 needs to send data to 0 */ int32_t sndbytecount; MPI_Status status; /* Wait for my turn */ MPI_Recv(NULL, 0, MPI_CHAR, 0, GOAHEAD_MSG, MPI_COMM_WORLD, &status); eindex = 0; while (eindex < mesh->lenum) { remains = mesh->lenum - eindex; batch = (remains < BATCH) ? remains : BATCH; for (idx = 0; idx < batch; idx++) { mrecord_t *mrecord; int32_t whichnode; int32_t localnid0; mrecord = &partTable[idx]; /* Fill the address field */ localnid0 = mesh->elemTable[eindex].lnid[0]; mrecord->addr.x = mesh->nodeTable[localnid0].x; mrecord->addr.y = mesh->nodeTable[localnid0].y; mrecord->addr.z = mesh->nodeTable[localnid0].z; mrecord->addr.level = mesh->elemTable[eindex].level; mrecord->addr.type = ETREE_LEAF; /* Find the global node ids for the vertices */ for (whichnode = 0; whichnode < 8; whichnode++) { int32_t localnid; int64_t globalnid; localnid = mesh->elemTable[eindex].lnid[whichnode]; globalnid = mesh->nodeTable[localnid].gnid; mrecord->mdata.nid[whichnode] = globalnid; } memcpy(&mrecord->mdata.edgesize, mesh->elemTable[eindex].data, sizeof(edata_t)); eindex++; } /* for a batch */ /* Send data to proc 0 */ sndbytecount = batch * sizeof(mrecord_t); MPI_Send(partTable, sndbytecount, MPI_CHAR, 0, MESH_MSG, MPI_COMM_WORLD); } /* While there is data left to be sent */ /* Send an empty message to indicate the end of my transfer */ MPI_Send(NULL, 0, MPI_CHAR, 0, MESH_MSG, MPI_COMM_WORLD); } /* Free the memory for the partial join results */ free(partTable); #endif octor_deletemesh(mesh); MPI_Finalize(); return 0; }