/*
* 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;
}
